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{ Component, OnInit } from '@angular/core';\n\n@Component({\n  selector: 'app-benchmark',\n  templateUrl: './benchmark.component.html',\n  styleUrls: ['./benchmark.component.scss']\n})\nexport class BenchmarkComponent implements OnInit {\n\n  constructor() { }\n\n  ngOnInit(): void {\n  }\n\n}\n","<div class=\"container\">\n  <div class=\"d-flex flex-column\">\n    <h3 class=\"p-3 text-info\"> Benchmarks</h3>\n\n    <div class=\"p-3 mb-2 bg-white\">\n      <select class=\"m-3 form-control form-control-lg text-info\">\n        <option>T Cell - Class I</option>\n        <option>B Cell - Class I</option>\n        <option>Epitope Clustering and Homology</option>\n        <option>MHC Allele Frequency</option>\n      </select>\n\n      <table class=\"table table-bordered m-3\">\n        <thead>\n        <tr>\n          <th scope=\"col\">Server</th>\n          <th scope=\"col\">2021-03-05</th>\n          <th scope=\"col\">2021-02-19</th>\n          <th scope=\"col\">2021-01-29</th>\n          <th scope=\"col\">2021-01-15</th>\n          <th scope=\"col\">2021-01-01</th>\n          <th scope=\"col\">2020-12-25</th>\n          <th scope=\"col\">2020-12-18</th>\n          <th scope=\"col\">2020-12-11</th>\n          <th scope=\"col\">2020-11-13</th>\n          <th scope=\"col\">2020-10-02</th>\n          <th scope=\"col\">2020-09-11</th>\n        </tr>\n        </thead>\n        <tbody>\n        <tr>\n          <th scope=\"row\">\n            <a routerLink=\"/\">ARB</a>\n          </th>\n          <td>78</td>\n          <td>63</td>\n          <td>62</td>\n          <td>37</td>\n          <td>38</td>\n          <td>68</td>\n          <td>51</td>\n          <td>36</td>\n          <td>50</td>\n          <td>45</td>\n          <td>51</td>\n        </tr>\n        <tr>\n          <th scope=\"row\">\n            <a routerLink=\"/\">SMMPMBEC</a>\n          </th>\n          <td>74</td>\n          <td>62</td>\n          <td>63</td>\n          <td>41</td>\n          <td>31</td>\n          <td>63</td>\n          <td>80</td>\n          <td>68</td>\n          <td>65</td>\n          <td>45</td>\n          <td>51</td>\n        </tr>\n        <tr>\n          <th scope=\"row\">\n            <a routerLink=\"/\">NetMHCSPan 4.0</a>\n          </th>\n          <td>74</td>\n          <td>62</td>\n          <td>63</td>\n          <td>41</td>\n          <td>31</td>\n          <td>63</td>\n          <td>80</td>\n          <td>68</td>\n          <td>65</td>\n          <td>45</td>\n          <td>51</td>\n        </tr>\n        <tr>\n          <th scope=\"row\">\n            <a routerLink=\"/\">NetMHCcons</a>\n          </th>\n          <td>74</td>\n          <td>62</td>\n          <td>63</td>\n          <td>41</td>\n          <td>31</td>\n          <td>63</td>\n          <td>80</td>\n          <td>68</td>\n          <td>65</td>\n          <td>45</td>\n          <td>51</td>\n        </tr>\n        <tr>\n          <th scope=\"row\">\n            <a routerLink=\"/\">DeepSeqPa</a>\n          </th>\n          <td>74</td>\n          <td>62</td>\n          <td>63</td>\n          <td>41</td>\n          <td>31</td>\n          <td>63</td>\n          <td>80</td>\n          <td>68</td>\n          <td>65</td>\n          <td>45</td>\n          <td>51</td>\n        </tr>\n\n        <tr>\n          <th scope=\"row\">\n            <a routerLink=\"/\">NetMHCpan 2.8</a>\n          </th>\n          <td>74</td>\n          <td>62</td>\n          <td>63</td>\n          <td>41</td>\n          <td>31</td>\n          <td>63</td>\n          <td>80</td>\n          <td>68</td>\n          <td>65</td>\n          <td>45</td>\n          <td>51</td>\n        </tr>\n\n        <tr>\n          <th scope=\"row\">\n            <a routerLink=\"/\">SMM</a>\n          </th>\n          <td>56</td>\n          <td>55</td>\n          <td>61</td>\n          <td>62</td>\n          <td>31</td>\n          <td>63</td>\n          <td>80</td>\n          <td>68</td>\n          <td>65</td>\n          <td>45</td>\n          <td>51</td>\n        </tr>\n\n        <tr>\n          <th scope=\"row\">\n            <a routerLink=\"/\">ANN 4.0</a>\n          </th>\n          <td>56</td>\n          <td>55</td>\n          <td>61</td>\n          <td>62</td>\n          <td>31</td>\n          <td>63</td>\n          <td>80</td>\n          <td>68</td>\n          <td>65</td>\n          <td>45</td>\n          <td>51</td>\n        </tr>\n\n        <tr>\n          <th scope=\"row\">\n            <a routerLink=\"/\">mhcflurry 1.2.0</a>\n          </th>\n          <td>43</td>\n          <td>44</td>\n          <td>44</td>\n          <td>70</td>\n          <td>31</td>\n          <td>63</td>\n          <td>80</td>\n          <td>68</td>\n          <td>65</td>\n          <td>45</td>\n          <td>51</td>\n        </tr>\n        <tr>\n          <th scope=\"row\">\n            <a routerLink=\"/\">Pickpocket</a>\n          </th>\n          <td>25</td>\n          <td>23</td>\n          <td>35</td>\n          <td>23</td>\n          <td>31</td>\n          <td>63</td>\n          <td>30</td>\n          <td>18</td>\n          <td>57</td>\n          <td>54</td>\n          <td>41</td>\n        </tr>\n\n        <tr>\n          <th scope=\"row\">\n            <a routerLink=\"/\">NetMHCpan 3.0</a>\n          </th>\n          <td></td>\n          <td></td>\n          <td></td>\n          <td></td>\n          <td></td>\n          <td></td>\n          <td></td>\n          <td></td>\n          <td>66</td>\n          <td>65</td>\n          <td>61</td>\n        </tr>\n\n        <tr>\n          <th scope=\"row\">\n            <a routerLink=\"/\">Ann 3.4</a>\n          </th>\n          <td></td>\n          <td></td>\n          <td></td>\n          <td></td>\n          <td></td>\n          <td></td>\n          <td></td>\n          <td></td>\n          <td>66</td>\n          <td>66</td>\n          <td>66</td>\n        </tr>\n\n        </tbody>\n      </table>\n    </div>\n\n  </div>\n</div>\n","import { NgxGoogleAnalyticsModule, NgxGoogleAnalyticsRouterModule } from 'ngx-google-analytics';\n\nexport const environment = {\n  name: 'PROD',\n  production: true,\n  api_url: 'https://api-nextgen-tools.iedb.org',\n  api_port: '443',\n  auth_endpoint: '/token/',\n  auth_refresh_endpoint: '/token/refresh/',\n  upload_endpoint: '/import/',\n  optionalModules: [\n    NgxGoogleAnalyticsModule.forRoot('G-MFNL7MJ8EV'),\n    NgxGoogleAnalyticsRouterModule\n  ],\n};\n","<!--<div class=\"container\" id=\"citation-component\">-->\n<!--  <div class=\"d-flex flex-column\">-->\n<!--    <h3 class=\"p-3 text-info\"> CITATION</h3>-->\n<!--    <div class=\"p-3 mb-2 bg-light\">-->\n<!--      <h4> MHC Class I Prediction </h4>-->\n<!--      <p>-->\n<!--        ANN Method - -->\n<!--        <a-->\n<!--          href=\"http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&amp;db=pubmed&amp;dopt=AbstractPlus&amp;list_uids=12717023\"-->\n<!--          target=\"_blank\">-->\n<!--          Nielsen M, Lundegaard C, Worning P, Lauemoller SL, Lamberth K, Buus S, Brunak S, Lund O. 2003. Reliable-->\n<!--          prediction of T-cell epitopes using-->\n<!--          neural networks with novel sequence representations. <i>Protein Sci</i> <b>12</b>:1007-1017.</a>-->\n<!--      </p>-->\n<!--      <p>-->\n<!--        ARB Method - -->\n<!--        <a-->\n<!--          href=\"http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&amp;db=pubmed&amp;dopt=AbstractPlus&amp;list_uids=15868141\"-->\n<!--          target=\"_blank\">-->\n<!--          Bui HH, Sidney J, Peters B, Sathiamurthy M, Sinichi A, Purton KA, Mothe BR, Chisari FV, Watkins DI, Sette A.-->\n<!--          2005.-->\n<!--          Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications. <i>Immunogenetics</i>-->\n<!--          <b>57</b>:304-314.</a>-->\n<!--      </p>-->\n\n<!--      <p>-->\n<!--        SMM Method - -->\n<!--        <a-->\n<!--          href=\"http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&amp;db=pubmed&amp;dopt=AbstractPlus&amp;list_uids=15927070\"-->\n<!--          target=\"_blank\">-->\n<!--          Peters B, Sette A. 2005. Generating quantitative models describing the sequence specificity of-->\n<!--          biological processes with the stabilized matrix method. <i>BMC Bioinformatics</i> <b>6</b>:132.</a>-->\n<!--      </p>-->\n\n<!--      <p>-->\n<!--        NetMHCcons Method - -->\n<!--        <a-->\n<!--          href=\"http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&amp;db=pubmed&amp;dopt=AbstractPlus&amp;list_uids=22009319\"-->\n<!--          target=\"_blank\">-->\n<!--          Karosiene E, Lundegaard C, Lund O and Nielsen M. 2012. NetMHCcons: a consensus method for the major-->\n<!--          histocompatibility complex class I predictions. <i>Immunogenetics</i> <b>64(3)</b>:177-186</a>-->\n<!--      </p>-->\n\n\n<!--      <p>-->\n<!--        Pickpocket Method - -->\n<!--        <a-->\n<!--          href=\"http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&amp;db=pubmed&amp;dopt=AbstractPlus&amp;list_uids=19297351\"-->\n<!--          target=\"_blank\">-->\n<!--          Zhang H, Lund O and Nielsen M. 2009. The PickPocket method for predicting binding specificities for receptors-->\n<!--          based on receptor pocket similarities: application to MHC–peptide binding.-->\n<!--          <i>Bioinformatics</i> <b>25(10)</b>:1293–1299.</a>-->\n<!--      </p>-->\n<!--    </div>-->\n<!--    <div class=\"p-3 mb-2 bg-light\">-->\n<!--      <h4> MHC Class II Prediction </h4>-->\n<!--      <p>-->\n<!--        <a-->\n<!--          href=\"http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&amp;db=pubmed&amp;dopt=AbstractPlus&amp;list_uids=15868141\"-->\n<!--          target=\"_blank\">-->\n<!--          Bui HH, Sidney J, Peters B, Sathiamurthy M, Sinichi A, Purton KA, Mothe BR, Chisari FV, Watkins-->\n<!--          DI, Sette A. 2005. Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix-->\n<!--          applications. <i>Immunogenetics</i> <b>57</b>:304-314.</a>-->\n<!--      </p>-->\n<!--      <p>-->\n<!--        <a-->\n<!--          href=\"http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=17608956\"-->\n<!--          target=\"_blank\">-->\n<!--          Nielsen M, Lundegaard C, Lund O. 2007. Prediction of MHC class II binding affinity using-->\n<!--          SMM-align, a novel stabilization matrix alignment method. <i>BMC Bioinformatics</i> <b>8</b>:238.</a>-->\n<!--      </p>-->\n\n<!--      <p>-->\n<!--        <a-->\n<!--          href=\"http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=10385319\"-->\n<!--          target=\"_blank\">-->\n<!--          Sturniolo T, Bono E, Ding J, Raddrizzani L, Tuereci O, Sahin U, Braxenthaler M, Gallazzi F,-->\n<!--          Protti MP, Sinigaglia F, Hammer J. 1999. Generation of tissue-specific and promiscuous HLA ligand databases-->\n<!--          using DNA microarrays and virtual HLA class II matrices. <i>Nat Biotechnol</i> <b>17</b>:555-561.</a>-->\n<!--      </p>-->\n<!--    </div>-->\n<!--    <div class=\"p-3 mb-2 bg-light\">-->\n<!--      <h4> Combined Proteasomal Cleavage/TAP Transport/MHC Class I Predictor </h4>-->\n<!--      <p>-->\n<!--        <a-->\n<!--          href=\"http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&amp;db=pubmed&amp;dopt=AbstractPlus&amp;list_uids=15868101\"-->\n<!--          target=\"_blank\">-->\n<!--          Tenzer S, Peters B, Bulik S, Schoor O, Lemmel C, Schatz MM, Kloetzel PM, Rammensee HG, Schild-->\n<!--          H, Holzhutter HG. 2005. Modeling the MHC class I pathway by combining predictions of proteasomal cleavage, TAP-->\n<!--          transport and MHC class I binding. <i>Cell Mol Life Sci</i> <b>62</b>:1025-1037.</a>-->\n<!--      </p>-->\n<!--      <p>-->\n<!--        <a-->\n<!--          href=\"http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&amp;db=pubmed&amp;dopt=AbstractPlus&amp;list_uids=12902473\"-->\n<!--          target=\"_blank\">-->\n<!--          Peters B, Bulik S, Tampe R, Van Endert PM, Holzhutter HG. 2003. Identifying MHC class I epitopes by predicting-->\n<!--          the TAP transport efficiency-->\n<!--          of epitope precursors. <i>J Immunol</i><b>171</b>:1741-1749.</a>-->\n<!--      </p>-->\n\n<!--    </div>-->\n<!--    <div class=\"p-3 mb-2 bg-light\">-->\n<!--      <h4> NetChop, NetCTL and NetCTLpan </h4>-->\n<!--      <p>-->\n<!--        <a-->\n<!--          href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=15744535\"-->\n<!--          target=\"_blank\">-->\n<!--          Nielsen M, Lundegaard C, Lund O, Kesmir C. 2005. The role of the proteasome in generating-->\n<!--          cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage.-->\n<!--          <i>Immunogenetics</i> <b>57</b>:33-41.</a>-->\n<!--      </p>-->\n<!--      <p>-->\n<!--        <a-->\n<!--          href=\"http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=11983929\"-->\n<!--          target=\"_blank\">-->\n<!--          Kesmir C, Nussbaum AK, Schild H, Detours V, Brunak S. 2002. Prediction of proteasome cleavage-->\n<!--          motifs by neural networks. <i>Protein Eng</i> <b>15</b>:287-296.</a>-->\n<!--      </p>-->\n\n<!--      <p>-->\n<!--        <a-->\n<!--          href=\"http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=15997466\"-->\n<!--          target=\"_blank\">-->\n<!--          Larsen MV, Lundegaard C, Lamberth K, Buus S, Brunak S, Lund O, Nielsen M. 2005. An integrative-->\n<!--          approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport-->\n<!--          efficiency, and proteasomal cleavage predictions. <i>Eur J Immunol</i><b>35</b>:2295-2303.</a>-->\n<!--      </p>-->\n<!--      <p>-->\n<!--        <a-->\n<!--          href=\"http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&amp;db=pubmed&amp;dopt=AbstractPlus&amp;list_uids=12717023\"-->\n<!--          target=\"_blank\">-->\n<!--          Nielsen M, Lundegaard C, Worning P, Lauemoller SL, Lamberth K, Buus S, Brunak S, Lund O. 2003.-->\n<!--          Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. <i>Protein-->\n<!--          Sci</i> <b>12</b>:1007-1017.</a>-->\n<!--      </p>-->\n<!--      <p>-->\n<!--        <a-->\n<!--          href=\"http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=14617044\"-->\n<!--          target=\"_blank\">-->\n<!--          Buus S, Lauemoller SL, Worning P, Kesmir C, Frimurer T, Corbet S, Fomsgaard A, Hilden J, Holm-->\n<!--          A, Brunak S. 2003. Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee'-->\n<!--          artificial neural network approach. <i>Tissue Antigens</i> <b>62</b>:378-384.</a>1-->\n<!--      </p>-->\n<!--      <p>-->\n<!--        <a-->\n<!--          href=\"http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&amp;db=pubmed&amp;dopt=AbstractPlus&amp;list_uids=20379710\"-->\n<!--          target=\"_blank\">-->\n<!--          Stranzl T, Larsen MV, Lundegaard C, Nielsen M. NetCTLpan: pan-specific MHC class I pathway epitope-->\n<!--          predictions. <i>Immunogenetics</i> <b>62</b>:357-68.</a>-->\n<!--      </p>-->\n<!--    </div>-->\n<!--    <div class=\"p-3 mb-2 bg-light\">-->\n<!--      <h4> Scale-Based B Cell Epitope Prediction </h4>-->\n<!--      <p>-->\n<!--        <a-->\n<!--          href=\"http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&amp;db=pubmed&amp;dopt=AbstractPlus&amp;list_uids=364941\"-->\n<!--          target=\"_blank\">-->\n<!--          Chou PY, Fasman GD. 1978. Prediction of the secondary structure of proteins from their amino-->\n<!--          acid sequence. <i>Adv Enzymol Relat Areas Mol Biol</i> <b>47</b>:45-148.</a>-->\n<!--      </p>-->\n<!--      <p>-->\n<!--        <a-->\n<!--          href=\"http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&amp;db=pubmed&amp;dopt=AbstractPlus&amp;list_uids=2991600\"-->\n<!--          target=\"_blank\">-->\n<!--          Emini EA, Hughes JV, Perlow DS, Boger J. 1985. Induction of hepatitis A virus-neutralizing-->\n<!--          antibody by a virus-specific synthetic peptide. <i>J Virol</i> <b>55</b>:836-839.</a>-->\n<!--      </p>-->\n<!--      <p>-->\n<!--        <a href=\"http://www.springerlink.com/content/q1224q1555013j53/\" target=\"_blank\">-->\n<!--          Karplus PA, Schulz GE. 1985. Prediction of chain flexibility in proteins. <i>Naturwissenschaften</i><b>72</b>:212-213.</a>-->\n<!--      </p>-->\n<!--      <p>-->\n<!--        <a-->\n<!--          href=\"http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&amp;db=pubmed&amp;dopt=AbstractPlus&amp;list_uids=1702393\"-->\n<!--          target=\"_blank\">-->\n<!--          Kolaskar AS, Tongaonkar PC. 1990. A semi-empirical method for prediction of antigenic-->\n<!--          determinants on protein antigens. <i>FEBS Lett</i> <b>276</b>:172-174.</a>-->\n<!--      </p>-->\n<!--      <p>-->\n<!--        <a-->\n<!--          href=\"http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&amp;db=pubmed&amp;dopt=AbstractPlus&amp;list_uids=2430611\"-->\n<!--          target=\"_blank\">-->\n<!--          Parker JM, Guo D, Hodges RS. 1986. New hydrophilicity scale derived from high-performance-->\n<!--          liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and-->\n<!--          X-ray-derived accessible sites. <i>Biochemistry</i> <b>25</b>:5425-5432.</a>-->\n<!--      </p>-->\n<!--      <p>-->\n<!--        <a-->\n<!--          href=\"http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&amp;db=pubmed&amp;dopt=AbstractPlus&amp;list_uids=16635264\"-->\n<!--          target=\"_blank\">-->\n<!--          Larsen JE, Lund O, Nielsen M. 2006. Improved method for predicting linear B-cell epitopes.<i>Immunome Res</i>-->\n<!--          <b>2</b>:2.</a>-->\n<!--      </p>-->\n<!--      <p>-->\n<!--        <a-->\n<!--          href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=17910770\"-->\n<!--          target=\"_blank\">-->\n<!--          Ponomarenko JV, Bourne PE. 2007. Antibody-protein interactions: benchmark datasets and-->\n<!--          prediction tools evaluation. <i>BMC Struct Biol</i> <b>7</b>:64.</a>-->\n<!--      </p>-->\n<!--    </div>-->\n<!--    <div class=\"p-3 mb-2 bg-light\">-->\n<!--      <h4> Discotope </h4>-->\n<!--      <p>-->\n<!--        <a-->\n<!--          href=\"http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=17001032\"-->\n<!--          target=\"_blank\">-->\n<!--          Haste Andersen P, Nielsen M, Lund O. 2006. Prediction of residues in discontinuous B-cell-->\n<!--          epitopes using protein 3D structures. <i>Protein Sci</i> <b>15</b>:2558-2567.</a>-->\n<!--      </p>-->\n\n<!--    </div>-->\n<!--    <div class=\"p-3 mb-2 bg-light\">-->\n<!--      <h4> Ellipro </h4>-->\n<!--      <p>-->\n<!--        <a href=\"http://www.biomedcentral.com/1471-2105/9/514\" target=\"_blank\">-->\n<!--          Ponomarenko JV, Bui H, Li W, Fusseder N, Bourne PE, Sette A, Peters B. 2008. ElliPro: a new structure-based-->\n<!--          tool for the prediction of antibody epitopes.-->\n<!--          <span style=\"font-style: italic;\">BMC Bioinformatics</span> <span style=\"font-weight: bold;\">9</span>:514</a>-->\n<!--      </p>-->\n<!--    </div>-->\n<!--    <div class=\"p-3 mb-2 bg-light\">-->\n<!--      <h4> Population Coverage </h4>-->\n<!--      <p>-->\n<!--        <a-->\n<!--          href=\"http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=16545123\"-->\n<!--          target=\"_blank\">-->\n<!--          Bui HH, Sidney J, Dinh K, Southwood S, Newman MJ, Sette A. 2006. Predicting population coverage-->\n<!--          of T-cell epitope-based diagnostics and vaccines. <i>BMC Bioinformatics</i> <b>7</b>:153.</a>-->\n<!--      </p>-->\n<!--    </div>-->\n<!--    <div class=\"p-3 mb-2 bg-light\">-->\n<!--      <h4> Epitope Conservancy Analysis </h4>-->\n<!--      <p>-->\n<!--        <a-->\n<!--          href=\"http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=17897458\"-->\n<!--          target=\"_blank\">-->\n<!--          Bui HH, Sidney J, Li W, Fusseder N, Sette A. 2007. Development of an epitope conservancy-->\n<!--          analysis tool to facilitate the design of epitope-based diagnostics and vaccines. <i>BMC Bioinformatics</i>-->\n<!--          <b>8</b>:361.</a>-->\n<!--      </p>-->\n<!--    </div>-->\n<!--    <div class=\"p-3 mb-2 bg-light\">-->\n<!--      <h4> Homology Mapping </h4>-->\n<!--      <p>-->\n<!--        <a-->\n<!--          href=\"http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&amp;cmd=Retrieve&amp;dopt=AbstractPlus&amp;list_uids=17313688\"-->\n<!--          target=\"_blank\">-->\n<!--          Beaver JE, Bourne PE, Ponomarenko JV. 2007. EpitopeViewer: a Java application for the-->\n<!--          visualization and analysis of immune epitopes in the Immune Epitope Database and Analysis Resource (IEDB).-->\n<!--          <i>Immunome Res</i> <b>3</b>:3.</a>-->\n<!--      </p>-->\n<!--    </div>-->\n<!--  </div>-->\n<!--</div>-->\n\n\n<!--<div class=\"container\" id=\"citation-component\">-->\n<!--  <div class=\"d-flex flex-column\">-->\n<!--    <h3 class=\"p-3 text-info\"> CITATION</h3>-->\n<!--    <p *ngFor=\"let citation of citations\">-->\n<!--      {{citation.method_name}} ({{citation.key}}) - -->\n<!--      <a-->\n<!--        [href]=\"'https://pubmed.ncbi.nlm.nih.gov/'.concat(citation.pubmed_id)\"-->\n<!--        target=\"_blank\">-->\n<!--        {{citation.citation_html}}</a>-->\n<!--    </p>-->\n<!--  </div>-->\n<!--</div>-->\n\n<div class=\"container\" id=\"citation-component\">\n  <div *ngIf=\"loading\" class=\"p-2 d-flex justify-content-center col\">\n    <div class=\"spinner-border text-primary align-self-center p-3 mb-3\" role=\"status\">\n      <span class=\"visually-hidden sr-only\" >Loading...</span>\n    </div>\n  </div>\n  <div *ngIf=\"!loading\" class=\"d-flex flex-column\">\n    <h3 class=\"p-3 text-primary-new text-center\"> Cite Us</h3>\n    <p class=\"px-3 fst-italic\">Publications for each of the individual methods that have been implemented on this site\n      are listed below, as well as publications describing the IEDB Analysis Resource in general. Please cite\n      accordingly in any works published that make use of this resource.</p>\n    <hr>\n    <div *ngFor=\"let name of uniq\" class=\"p-3 mb-3 bg-secondary-new\">\n      <ng-container *ngFor=\"let citation of groupedCitations | keyvalue\">\n        <ng-container *ngIf=\"name && name===citation.key\">\n          <h4> {{citation.key}} </h4>\n          <p *ngFor=\"let article of citation.value\">\n            {{article.display_name}} ({{article.method_version}})\n            <a\n              [href]=\"'https://pubmed.ncbi.nlm.nih.gov/'.concat(article.pubmed_id)\"\n              target=\"_blank\">\n              {{article.citation_html}}</a>\n          </p>\n        </ng-container>\n      </ng-container>\n    </div>\n\n  </div>\n</div>\n","import { Component, OnInit } from '@angular/core';\nimport {HttpClient} from \"@angular/common/http\";\nimport _ from 'lodash';\nimport {environment} from \"../../environments/environment\";\n\nimport Citation from \"../_global/Citation\"\n\n@Component({\n  selector: 'app-citation',\n  templateUrl: './citation.component.html',\n  styleUrls: ['./citation.component.scss']\n})\nexport class CitationComponent implements OnInit {\n\n  loading: boolean = false;\n  citations: any[] = [];\n  uniq: string[] = []\n  groupedCitations: {\"T cell - class I\": Citation[]} = {\"T cell - class I\": []}\n\n  constructor(\n    private http: HttpClient\n  ) { }\n\n  ngOnInit(): void {\n    this.loading = true;\n    const CITATIONS_API_URL = `${environment['api_url']}/api/v1/citations`;\n    this.http.get<any>(CITATIONS_API_URL).subscribe(value => {\n      this.citations = value.data;\n      // this.citations =  _.orderBy(value.data, ['grouping_title', 'key']) /** uncomment later */\n      this.uniq = []\n      _.forEach(this.citations, (c) => {\n        if (!this.uniq.includes(c.grouping_title)) {\n          this.uniq.push(c.grouping_title)\n          console.log(c.grouping_title)\n          // @ts-ignore\n          this.groupedCitations[c.grouping_title] = [c]\n        } else {\n          // @ts-ignore\n          this.groupedCitations[c.grouping_title].push(c)\n        }\n      })\n      console.log(this.uniq)\n      console.log(this.groupedCitations)\n      this.loading = false;\n    })\n  }\n\n\n\n}\n","import { Pipe, PipeTransform } from '@angular/core';\n\n@Pipe({ name: 'keys' })\nexport class KeysPipe implements PipeTransform {\n  transform(value: {}): any {\n    if (!value) return null;\n    return Object.keys(value);\n  }\n}\n","import { Pipe, PipeTransform } from '@angular/core';\n\n@Pipe({ name: 'tag' })\nexport class tagPipe implements PipeTransform {\n  transform(value: string): any {\n    if(value) {\n      if(value==='mhcI') {\n        return 'MHC I';\n      }\n      else if(value==='allele7') {\n        return '7-Allele';\n      }\n      else if(value==='mhcII') {\n        return 'MHC II';\n      }\n      else if(value==='hlaAssociation') {\n        return 'HLA Association';\n      }\n      else if(value==='structure3D') {\n        return '3D Structure';\n      }\n      else if(value==='nonPeptidic') {\n        return 'Non-Peptidic';\n      }\n      else if(value==='mhcProcessing') {\n        return 'MHC Processing';\n      }\n      else if(value==='tapProcessing') {\n        return 'TAP Processing';\n      }\n      else if(['TCR', 'BCR', 'PDB', 'CD4', 'CD8', 'VCF'].includes(value)) {\n        return value;\n      }\n      else {\n        return value\n          // insert a space before all caps\n          .replace(/([A-Z])/g, ' $1')\n          // uppercase the first character\n          .replace(/^./, function(str){ return str.toUpperCase(); });\n      }\n    }\n    return null;\n  }\n}\n","<div class=\"container\" id=\"tools-list-component\">\n  <div class=\"row mx-auto\">\n    <div class=\"col-3 p-3 bg-light\">\n      <div class=\"d-flex justify-content-between\">\n        <b>Tags</b>\n        <button class=\"btn btn-sm btn-secondary\" [disabled]=\"!selectedTags.length\" (click)=\"deSelectAllTags($event)\">\n          Reset\n        </button>\n      </div>\n      <form [formGroup]=\"toolsListForm\">\n        <div class=\"form-check\" *ngFor=\"let key of initialTags | keys;\">\n          <input type=\"checkbox\" class=\"form-check-input\" [id]=\"key\" [formControlName]=\"key\" [value]=\"initialTags[key]\">\n          <label class=\"form-check-label\" [for]=\"key\">{{ key | tag }}</label>\n        </div>\n      </form>\n    </div>\n\n    <div class=\"col-9 p-3 bg-secondary-new bg-opacity-50\">\n      <div class=\"container bg-warning-new m-3\" *ngIf=\"selectedTools.length\">\n        <p class=\"text-center fw-bold\"> Tools Matching Any Selected Tags: {{ selectedTools.length }} | Tools Matching All Selected\n          Tags: {{ selectedTags.length === sortedTools[0].count ? countsForSelectedTools[0].length : 0 }}</p>\n      </div>\n\n      <div *ngFor=\"let tool of sortedTools;\" class=\"container p-3\">\n        <hr *ngIf=\"horizontalDivider.includes(tool.name)\"/>\n        <h5 *ngIf=\"horizontalDivider.includes(tool.name)\">\n          {{ countsForSelectedTools[horizontalDivider.indexOf(tool.name)].length }} {{countsForSelectedTools[horizontalDivider.indexOf(tool.name)].length === 1 ? 'Tool' : 'Tools'}} Matching {{ tool.count }} {{tool.count === 1 ? 'Tag' : 'Tags' }}\n\n        </h5>\n\n        <!--        Tool Name   -->\n        <h5>\n          <a *ngIf=\"tool.queryParams; else windowOnClick\" [routerLink]=\"'/pipeline'\" [queryParams]=\"tool.queryParams\">\n            {{ tool.name }}\n          </a>\n          <ng-template #windowOnClick>\n            <a [href]=\"tool.url\" target=\"_blank\">\n              {{ tool.name }}\n            </a>\n          </ng-template>\n        </h5>\n        <div>\n          <span *ngFor=\"let tag of tool.tags\"\n                [style.font-weight]=\" toolsListForm.controls[tag].value ? 'bold' : 'normal'\"\n                [className]=\"toolsListForm.controls[tag].value ? 'p-2 badge rounded-pill bg-danger-new' : 'p-2 badge rounded-pill bg-info-new'\"> <!--bg-info-new -->\n            {{ tag | tag }}\n          </span>\n        </div>\n      </div>\n\n      <hr>\n\n      <p> * - Redirect to legacy site.</p>\n    </div>\n\n  </div>\n</div>\n","import { Component, OnInit } from '@angular/core';\nimport {UntypedFormBuilder, UntypedFormGroup} from \"@angular/forms\";\nimport _ from 'lodash';\n\n@Component({\n  selector: 'app-tools-list',\n  templateUrl: './tools-list.component.html',\n  styleUrls: ['./tools-list.component.scss']\n})\nexport class ToolsListComponent implements OnInit {\n\n  initialTags: any = {\n    structure3D: false,\n    allele7: false,\n    alleleFrequency: false,\n    antibody: false,\n    bCell: false,\n    BCR: false,\n    bindingAffinity: false,\n    cancer: false,\n    CD4: false,\n    CD8: false,\n    conservation: false,\n    dataVisualization: false,\n    deimmunization: false,\n    elutedLigand: false,\n    epitope: false,\n    geneExpression: false,\n    hlaAssociation: false,\n    humoralImmunity: false,\n    immunogenicity: false,\n    mhcI: false,\n    mhcII: false,\n    modeling: false,\n    molecularDocking: false,\n    neoepitope: false,\n    nonPeptidic: false,\n    PDB: false,\n    peptideSimilarity: false,\n    population: false,\n    proteinStructure: false,\n    proteomeSearch: false,\n    protrusion: false,\n    responseFrequency: false,\n    rnaExpression: false,\n    smallMolecule: false,\n    synthesis: false,\n    tCell: false,\n    tapProcessing: false,\n    TCR: false,\n    transcription: false,\n    unwantedImmuneResponse: false,\n    VCF: false\n  }\n\n  tools = [\n    {queryParams: {tool: 'tc1'}, name: 'T Cell Prediction - Class I', tags: [\"CD8\", \"bindingAffinity\", \"elutedLigand\", \"epitope\", \"hlaAssociation\", \"immunogenicity\", \"mhcI\", \"tCell\", \"tapProcessing\"], count: 0, routerLink: 't-cell-prediction'},\n    {queryParams: {tool: 'cluster'}, name: 'Cluster', tags: [\"conservation\", \"dataVisualization\", \"hlaAssociation\", \"peptideSimilarity\"], count: 0, routerLink: 'cluster'},\n    {queryParams: {tool: 'pepmatch'}, name: 'PEPMatch', tags: ['conservation', 'peptideSimilarity', 'proteomeSearch'], count: 0, routerLink: 'pepmatch'},\n    {queryParams: {tool: 'pepx'}, name: 'PepX', tags: ['geneExpression', 'rnaExpression', 'transcription', 'cancer'], count: 0, routerLink: '_blank'},\n    {queryParams: {tool: 'pepvcomp'}, name: 'Peptide Variant Comparison', tags: ['bindingAffinity', 'cancer', 'CD8', 'dataVisualization', 'elutedLigand', 'epitope', 'hlaAssociation', 'immunogenicity', 'mhcI', 'neoepitope', 'tCell'], count: 0, routerLink: 'pepcomp'},\n    {queryParams: {tool: 'mutpepgen'}, name: 'Mutated Peptide Generator', tags: ['cancer','neoepitope', 'VCF'], count: 0, routerLink: 'pepcomp'},\n    {url: 'http://tools.iedb.org/mhcii/', name: 'MHC-II Binding Predictions*', tags: [\"allele7\", \"bindingAffinity\", \"CD4\", \"elutedLigand\", \"epitope\", \"immunogenicity\", \"mhcII\", \"tCell\"], count: 0, routerLink: '_blank'},\n    {url: 'http://tools.iedb.org/bcell/', name: 'B Cell Linear Epitope Prediction*', tags: ['antibody', 'bCell', 'epitope', 'humoralImmunity','immunogenicity'], count: 0, routerLink: '_blank'},\n    {url: 'http://tools.iedb.org/conservancy/', name: 'Epitope Conservancy Analysis*', tags: ['conservation'], count: 0, routerLink: '_blank'},\n    {url: 'http://tools.iedb.org/discotope/', name: 'Discotope*', tags: [ \"structure3D\", \"antibody\", \"bCell\", \"dataVisualization\", \"epitope\", \"humoralImmunity\", \"immunogenicity\", \"PDB\",], count: 0, routerLink: '_blank'},\n    {url: 'http://tools.iedb.org/population/', name: 'Population Coverage*', tags:  [\"alleleFrequency\", \"hlaAssociation\", \"population\", \"responseFrequency\"], count: 0, routerLink: '_blank'},\n    {url: 'http://tools.iedb.org/ellipro/', name: 'Ellipro*', tags: [ \"structure3D\", \"antibody\", \"bCell\", \"dataVisualization\", \"epitope\", \"humoralImmunity\", \"immunogenicity\", \"PDB\"], count: 0, routerLink: '_blank'},\n    {url: 'http://tools.iedb.org/tepitool/', name: 'TepiTool*', tags: [ 'bindingAffinity', 'CD4', 'CD8', 'epitope', 'hlaAssociation', 'mhcI', 'mhcII', 'protrusion', 'tCell'], count: 0, routerLink: '_blank'},\n    {url: 'http://tools.iedb.org/deimmunization/', name: 'Deimmunization*', tags: ['bindingAffinity', 'deimmunization',  'immunogenicity', 'mhcI', 'mhcII', 'tCell',  'unwantedImmuneResponse'], count: 0, routerLink: '_blank'},\n    {url: 'http://tools.iedb.org/docktope/', name: 'Docktope*', tags: [\"structure3D\", \"hlaAssociation\", \"mhcI\", \"modeling\", \"molecularDocking\", \"proteinStructure\",\"PDB\", \"TCR\", \"tCell\"], count: 0, routerLink: '_blank'},\n    {url: 'http://tools.iedb.org/lyra/', name: 'LYRA*', tags: [\"structure3D\", \"antibody\", \"BCR\", \"bCell\", \"dataVisualization\", \"modeling\", \"PDB\", \"TCR\",\"tCell\"], count: 0, routerLink: '_blank'},\n    {url: 'http://tools.iedb.org/immunomebrowser/', name: 'ImmunomeBrowser*', tags: [ 'dataVisualization', 'epitope', 'immunogenicity', 'modeling', 'responseFrequency'], count: 0, routerLink: '_blank'},\n    {url: 'http://tools.iedb.org/rate/', name: 'RATE*', tags: ['antibody', 'hlaAssociation', 'mhcI', 'mhcII', 'responseFrequency', 'tCell'], count: 0, routerLink: '_blank'},\n    {url: 'http://tools.iedb.org/axelf/', name: 'Axel-F*', tags: ['cancer', 'CD8', 'epitope', 'mhcI', 'tCell', 'rnaExpression', 'TCR', 'transcription'], count: 0, routerLink: '_blank'},\n    {url: 'http://tools.iedb.org/tcrmatch/', name: 'TCRMatch*', tags: ['CD4', 'CD8', 'tCell', 'TCR'], count: 0, routerLink: '_blank'},\n    {url: 'http://tools.iedb.org/np_epitope_predictor/', name: 'NP Epitope Predictor*', tags: ['bCell', 'dataVisualization', 'epitope', 'nonPeptidic', 'smallMolecule', 'tCell'], count: 0, routerLink: '_blank'},\n    {url: 'http://tools.iedb.org/sceptre/', name: 'SCEptRe*', tags: ['structure3D','bCell', 'BCR', 'mhcI', 'mhcII', 'PDB', 'tCell', 'TCR'], count: 0, routerLink: '_blank'},\n    {url: 'http://tools.iedb.org/pepsysco/', name: 'PepSySco* (Peptide Synthesis)', tags: ['synthesis'], count: 0, routerLink: '_blank'},\n  ]\n\n  sortedTools: any = []\n\n  selectedTools: any[] = [] // used for counts\n  selectedTags: string[] = [] // used for counts\n  horizontalDivider: string[] = [];\n  countsForSelectedTools: any[] = [];\n\n  toolsListForm!: UntypedFormGroup;\n\n  constructor(\n    private formBuilder: UntypedFormBuilder,\n  ) { }\n\n  ngOnInit(): void {\n    this.toolsListForm = this.formBuilder.group(this.initialTags);\n\n    const firstTools = this.tools.slice(0, 6)\n    const legacyTools = this.tools.slice(6, )\n\n    this.sortedTools = firstTools.concat(_.orderBy(legacyTools, 'name'));\n\n    this.countsForSelectedTools = _.reverse(_.values(_.groupBy(this.sortedTools, 'name')));\n    console.log(this.countsForSelectedTools);\n    this.onChange();\n  }\n\n  onChange(): void {\n    /**\n     *\n     * */\n    this.toolsListForm.valueChanges.subscribe(val => {\n      console.log(val);\n\n      this.selectedTools = [];\n      this.sortedTools = [];\n      this.horizontalDivider = [];\n\n      this.selectedTags = _.keys(_.pickBy(val, (v: any, k:string) => {\n        if (v === true) {\n          return k\n        }\n        return null\n      }));\n      console.log(this.selectedTags);\n\n      if(this.selectedTags.length === 0) {\n        const firstTools = this.tools.slice(0, 3)\n        const legacyTools = this.tools.slice(3, 21)\n\n        this.sortedTools = firstTools.concat(_.orderBy(legacyTools, 'name'));\n        return\n      }\n\n      const tempSelectedTools: string[] = [];\n\n      _.forEach(this.selectedTags, (tag) => {\n        console.log(tag);\n        _.forEach(this.tools, (tool) => {\n          if (tool.tags.includes(tag)) {\n            tempSelectedTools.push(tool.name);\n          }\n        })\n      })\n\n      console.log(tempSelectedTools);\n\n      this.selectedTools = _.values(_.groupBy(tempSelectedTools)).map(d => ({name: d[0], count: d.length}));\n\n      _.forEach(this.tools, (tool) => {\n        _.forEach(this.selectedTools, (fool) => {\n          if (tool.name === fool.name) {\n            tool.count = fool.count;\n            this.sortedTools.push(tool);\n          }\n        })\n      })\n      this.sortedTools = _.orderBy(this.sortedTools, 'count', 'desc');\n      let mostcount = this.sortedTools[0].count - 1;\n      this.horizontalDivider.push(this.sortedTools[0].name);\n       _.forEach(this.sortedTools, (tool) => {\n        if(tool.count === mostcount) {\n          mostcount -= 1;\n          this.horizontalDivider.push(tool.name);\n        }\n      });\n\n      this.countsForSelectedTools = _.reverse(_.values(_.groupBy(this.sortedTools, 'count')));\n\n      /** DEBUGGER */\n      // console.log(this.selectedTools);\n      // console.log(this.sortedTools);\n      // console.log(this.selectedTags);\n      // console.log(this.horizontalDivider);\n      // console.log(this.countsForSelectedTools);\n    })\n  }\n\n  deSelectAllTags(e: any) {\n    /**\n     *\n     * */\n    this.toolsListForm.reset();\n    this.selectedTags = [];\n    this.horizontalDivider = [];\n    this.selectedTools = [];\n\n    const firstTools = this.tools.slice(0, 3)\n    const legacyTools = this.tools.slice(3, 21)\n    this.sortedTools = firstTools.concat(_.orderBy(legacyTools, 'name'));\n  }\n}\n","import { Component, OnInit } from '@angular/core';\n\n@Component({\n  selector: 'app-tool-contribution',\n  templateUrl: './tool-contribution.component.html',\n  styleUrls: ['./tool-contribution.component.scss']\n})\nexport class ToolContributionComponent implements OnInit {\n\n  constructor() { }\n\n  ngOnInit(): void {\n  }\n\n}\n","<div class=\"container\" id=\"tool-contribution-component\">\n  <div class=\"d-flex flex-column\">\n    <h3 class=\"p-3 text-primary-new text-center\"> Contribution To The IEDB NextGen Tools</h3>\n    <div class=\"p-3 mb-2 bg-secondary-new\">\n      <p>\n        An overarching goal of the IEDB is to be the central repository for tools that are of general use to the\n        immunology and immunoinformatics community.\n        We encourage developers of such tools to contact us to inquire about hosting your tool at the IEDB.\n        The IEDB team would work with developers to create a web portal and keep it up and running indefinitely.\n        We believe this arrangement benefits all parties involved and the immunology community as a whole.\n        The process for submitting your tool for inclusion at the IEDB NG Tools is outlined below.\n      </p>\n    </div>\n    <h3 class=\"p-3 text-primary-new text-center\"> Tool Contribution Process</h3>\n    <div class=\"p-3 mb-2 bg-secondary-new\">\n      <div class=\"d-flex flex-row\">\n        <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"32\" height=\"32\" fill=\"currentColor\" class=\"bi bi-envelope\"\n             viewBox=\"0 0 16 16\">\n          <path\n            d=\"M0 4a2 2 0 0 1 2-2h12a2 2 0 0 1 2 2v8a2 2 0 0 1-2 2H2a2 2 0 0 1-2-2V4zm2-1a1 1 0 0 0-1 1v.217l7 4.2 7-4.2V4a1 1 0 0 0-1-1H2zm13 2.383l-4.758 2.855L15 11.114v-5.73zm-.034 6.878L9.271 8.82 8 9.583 6.728 8.82l-5.694 3.44A1 1 0 0 0 2 13h12a1 1 0 0 0 .966-.739zM1 11.114l4.758-2.876L1 5.383v5.73z\"/>\n        </svg>\n        <h4 class=\"mx-3\">\n          1. Submission\n        </h4>\n      </div>\n      Email help@iedb.org and include:\n      <ul>\n        <li>\n          A summary of the problem that your tool addresses and what it is of general interest\n        </li>\n        <li>\n          The publication status of your tool\n        </li>\n        <li>\n          If there’s a web server that hosts the tool, please provide URL\n        </li>\n        <li>\n          Time frame in which you will be ready to hand off your tool to IEDB developers\n        </li>\n      </ul>\n    </div>\n\n    <div class=\"p-3 mb-2 bg-secondary-new\">\n      <div class=\"d-flex flex-row\">\n        <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"32\" height=\"32\" fill=\"currentColor\" class=\"bi bi-search\" viewBox=\"0 0 16 16\">\n          <path d=\"M11.742 10.344a6.5 6.5 0 1 0-1.397 1.398h-.001c.03.04.062.078.098.115l3.85 3.85a1 1 0 0 0 1.415-1.414l-3.85-3.85a1.007 1.007 0 0 0-.115-.1zM12 6.5a5.5 5.5 0 1 1-11 0 5.5 5.5 0 0 1 11 0z\"/>\n        </svg>\n        <h4 class=\"mx-3\">\n          2. Evaluation\n        </h4>\n      </div>\n      Submissions will be evaluated by IEDB staff to determine whether the tool fits within the scope of the IEDB and we\n      have the capability (hardware, personnel, etc) to implement it.\n    </div>\n\n    <div class=\"p-3 mb-2 bg-secondary-new\">\n      <div class=\"d-flex flex-row\">\n        <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"32\" height=\"32\" fill=\"currentColor\"\n             class=\"bi bi-arrow-90deg-left\" viewBox=\"0 0 16 16\">\n          <path fill-rule=\"evenodd\"\n                d=\"M1.146 4.854a.5.5 0 0 1 0-.708l4-4a.5.5 0 1 1 .708.708L2.707 4H12.5A2.5 2.5 0 0 1 15 6.5v8a.5.5 0 0 1-1 0v-8A1.5 1.5 0 0 0 12.5 5H2.707l3.147 3.146a.5.5 0 1 1-.708.708l-4-4z\"/>\n        </svg>\n        <h4 class=\"mx-3\">\n          3. Decision\n        </h4>\n      </div>\n      You will receive a reply within 4 weeks with either a decision or a request for further information. If your tool\n      is approved for inclusion, you will work with IEDB developers to hand off code and create a web portal at the\n      IEDB.\n    </div>\n\n    <div class=\"p-3 mb-2 bg-secondary-new\">\n      <div class=\"d-flex flex-row\">\n        <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"32\" height=\"32\" fill=\"currentColor\" class=\"bi bi-bug-fill\"\n             viewBox=\"0 0 16 16\">\n          <path\n            d=\"M4.978.855a.5.5 0 1 0-.956.29l.41 1.352A4.985 4.985 0 0 0 3 6h10a4.985 4.985 0 0 0-1.432-3.503l.41-1.352a.5.5 0 1 0-.956-.29l-.291.956A4.978 4.978 0 0 0 8 1a4.979 4.979 0 0 0-2.731.811l-.29-.956z\"/>\n          <path\n            d=\"M13 6v1H8.5v8.975A5 5 0 0 0 13 11h.5a.5.5 0 0 1 .5.5v.5a.5.5 0 1 0 1 0v-.5a1.5 1.5 0 0 0-1.5-1.5H13V9h1.5a.5.5 0 0 0 0-1H13V7h.5A1.5 1.5 0 0 0 15 5.5V5a.5.5 0 0 0-1 0v.5a.5.5 0 0 1-.5.5H13zm-5.5 9.975V7H3V6h-.5a.5.5 0 0 1-.5-.5V5a.5.5 0 0 0-1 0v.5A1.5 1.5 0 0 0 2.5 7H3v1H1.5a.5.5 0 0 0 0 1H3v1h-.5A1.5 1.5 0 0 0 1 11.5v.5a.5.5 0 1 0 1 0v-.5a.5.5 0 0 1 .5-.5H3a5 5 0 0 0 4.5 4.975z\"/>\n        </svg>\n        <h4 class=\"mx-3\">\n          4. Testing\n        </h4>\n      </div>\n      The tool will be thoroughly tested for bugs and the load it exerts on the IEDB servers.\n    </div>\n\n    <div class=\"p-3 mb-2 bg-secondary-new\">\n      <div class=\"d-flex flex-row\">\n        <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"32\" height=\"32\" fill=\"currentColor\" class=\"bi bi-upload\"\n             viewBox=\"0 0 16 16\">\n          <path\n            d=\"M.5 9.9a.5.5 0 0 1 .5.5v2.5a1 1 0 0 0 1 1h12a1 1 0 0 0 1-1v-2.5a.5.5 0 0 1 1 0v2.5a2 2 0 0 1-2 2H2a2 2 0 0 1-2-2v-2.5a.5.5 0 0 1 .5-.5z\"/>\n          <path\n            d=\"M7.646 1.146a.5.5 0 0 1 .708 0l3 3a.5.5 0 0 1-.708.708L8.5 2.707V11.5a.5.5 0 0 1-1 0V2.707L5.354 4.854a.5.5 0 1 1-.708-.708l3-3z\"/>\n        </svg>\n        <h4 class=\"mx-3\">\n          5. Tools Go Live\n        </h4>\n      </div>\n      After you give the go-ahead, links will be made public and it will be officially announced under 'New and Noteworthy'\n      and the 'Release Notes' on the IEDB support pages, and incorporated into the IEDB's next submission to the annual NAR webserver issue.\n    </div>\n\n    <div class=\"p-3 mb-2 bg-secondary-new\">\n      <div class=\"d-flex flex-row\">\n        <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"32\" height=\"32\" fill=\"currentColor\" class=\"bi bi-clock\"\n             viewBox=\"0 0 16 16\">\n          <path d=\"M8 3.5a.5.5 0 0 0-1 0V9a.5.5 0 0 0 .252.434l3.5 2a.5.5 0 0 0 .496-.868L8 8.71V3.5z\"/>\n          <path d=\"M8 16A8 8 0 1 0 8 0a8 8 0 0 0 0 16zm7-8A7 7 0 1 1 1 8a7 7 0 0 1 14 0z\"/>\n        </svg>\n        <h4 class=\"mx-3\">\n          6. Updates\n        </h4>\n      </div>\n      Any updates you make to the tool can be applied, tested, and released in our 6-month development cycle.\n    </div>\n  </div>\n</div>\n","import Stage from \"../../_global/Stage\";\nimport Tool from \"../../_global/Tool\";\n\nexport const initTCellPredictionState: Stage = {\n  stage_number: 1,\n  stage_type: 'prediction',\n  tool_group: 'mhci',\n  stage_display_name: 'T Cell Prediction - Class I',\n  input_parameters: {},\n  // table_state: {columns: {}},\n  table_state: [{table: 'peptide_table', columns: {}}],\n  stage_messages: {errors: [], warnings: []}\n}\n\nexport const initClusterState: Stage = {\n  stage_number: 1,\n  stage_type: 'prediction',\n  tool_group: 'cluster',\n  stage_display_name: 'Cluster',\n  input_parameters: {},\n  // table_state: {columns: {}},\n  table_state: [{table: 'peptide_table', columns: {}}],\n  stage_messages: {errors: [], warnings: []}\n}\n\nexport const initPepMatchState: Stage = {\n  stage_number: 1,\n  stage_type: 'prediction',\n  tool_group: 'pepmatch',\n  stage_display_name: 'Pepmatch',\n  input_parameters: {},\n  // table_state: {columns: {}},\n  table_state: [{table: 'peptide_table', columns: {}}],\n  stage_messages: {errors: [], warnings: []}\n}\n\nexport const initPepXState: Stage = {\n  stage_number: 1,\n  stage_type: 'prediction',\n  tool_group: 'pepx',\n  stage_display_name: 'PepX',\n  input_parameters: {},\n  // table_state: {columns: {}},\n  table_state: [{table: 'peptide_table', columns: {}}, {table: 'peptide_gene_summary_table', columns: {}}],\n  stage_messages: {errors: [], warnings: []}\n}\n\nexport const initPeptideBindingComparisonState: Stage = {\n  stage_number: 1,\n  stage_type: 'prediction',\n  tool_group: 'peptide_variant_comparison',\n  stage_display_name: 'Peptide Variant Comparison',\n  input_parameters: {},\n  table_state: [{table: 'peptide_table', columns: {}}],\n  // table_state: {columns: {}},\n  stage_messages: {errors: [], warnings: []}\n}\n\nexport const initMutatedPeptideGeneratorState: Stage = {\n  stage_number: 1,\n  stage_type: 'prediction',\n  tool_group: 'mutgen',\n  stage_display_name: 'Mutated Peptide Generator',\n  input_parameters: {},\n  table_state: [{table: 'unique_peptide', columns: {}}, {table: 'peptide', columns: {}}],\n  stage_messages: {errors: [], warnings: []}\n}\n\n/////////////\n\nexport const initTCellPredictionTool: Tool = {\n  name: 'T-Cell Prediction',\n  toolGroup: 'mhci',\n  loading: false,\n  submitted: false,\n  appliedFilters: undefined,\n  disabled: false\n}\n\nexport const initClusterTool: Tool = {\n  name: 'Cluster',\n  toolGroup: 'cluster',\n  loading: false,\n  submitted: false,\n  appliedFilters: undefined,\n  disabled: false\n}\n\nexport const initPepmatchTool: Tool = {\n  name: 'Pepmatch',\n  toolGroup: 'pepmatch',\n  loading: false,\n  submitted: false,\n  appliedFilters: undefined,\n  disabled: false\n}\n\nexport const initPepxTool: Tool = {\n  name: 'Pepx',\n  toolGroup: 'pepx',\n  loading: false,\n  submitted: false,\n  appliedFilters: undefined,\n  disabled: false\n}\n\nexport const initPeptideBindingComparisonTool: Tool = {\n  name: 'Peptide Variant Comparison',\n  toolGroup: 'peptide_variant_comparison',\n  loading: false,\n  submitted: false,\n  appliedFilters: undefined,\n  disabled: false\n}\n\nexport const initMutatedPeptideGeneratorTool: Tool = {\n  name: 'Mutated Peptide Generator',\n  toolGroup: 'mutgen',\n  loading: false,\n  submitted: false,\n  appliedFilters: undefined,\n  disabled: false\n}\n\n/////////// Params //////////\n\nexport const initParams = {\n  \"pipeline_id\": '',\n  \"run_stage_range\": [1, 1],\n  \"stages\": []\n}\n","export function isASCII(str: string)\n{\n  return /^[\\x00-\\x7F]*$/.test(str);\n}\n\nexport function IsJsonString(str: string) {\n  try {\n    JSON.parse(str);\n  } catch (e) {\n    return false;\n  }\n  return true;\n}\n\nexport function ltrim(str:string) {\n  /**\n   * https://stackoverflow.com/a/24282245/8794234\n   * */\n  if(!str) return str;\n  return str.replace(/^\\s+/g, '');\n}\n","export function isMaxLength(str: string, maxCharacters: number)\n{\n  return str.length <= maxCharacters;\n}\n","import { BehaviorSubject, Observable } from 'rxjs';\nimport { distinctUntilChanged, map } from 'rxjs/operators';\n\nexport class StateService<T> {\n\n  private state$: BehaviorSubject<T>;\n  protected get state(): T {\n    return this.state$.getValue();\n  }\n\n  constructor(initialState: T) {\n    this.state$ = new BehaviorSubject<T>(initialState);\n  }\n\n  protected select<K>(mapFn: (state: T) => K): Observable<K> {\n    return this.state$.asObservable().pipe(\n      map((state: T) => mapFn(state)),\n      distinctUntilChanged()\n    );\n  }\n\n  protected setState(newState: Partial<T>) {\n    this.state$.next({\n      ...this.state,\n      ...newState,\n    });\n  }\n}\n","import {Injectable} from '@angular/core';\nimport {HttpClient, HttpParams} from '@angular/common/http';\nimport {UntypedFormGroup} from \"@angular/forms\";\nimport {Observable, BehaviorSubject} from 'rxjs';\nimport {debounce, catchError, debounceTime, distinctUntilChanged, map, tap, switchMap} from 'rxjs/operators';\n\nimport {environment} from '../../../environments/environment';\nimport * as _ from \"lodash\";\n\nconst API_URL = `${environment['api_url']}/api/v1/pipeline`;\nconst PIPELINE_SPEC_API_URL = `${environment['api_url']}/api/v1/pipeline_spec`;\nconst RESULT_API_URL = `${environment['api_url']}/results`;\nconst PARAMS = new HttpParams();\nimport Allele from \"../../_global/Allele\";\n@Injectable({\n  providedIn: 'root'\n})\nexport class PipelineService {\n\n  public _currentPipelineId  = new BehaviorSubject('');\n\n  public get currentPipelineId(): Observable<string> {\n    return this._currentPipelineId.asObservable();\n  }\n  runSetInterval: any;\n\n  constructor(private http: HttpClient) {\n  }\n\n  postPipeline(data: object): Observable<any> {\n    /**\n     /api/v1/pipeline\n     * */\n    console.log(JSON.stringify(data, null, 2));\n    return this.http.post(API_URL, data)\n      .pipe(\n        tap((resp: any) => {\n          // console.log(resp); // debugger\n        })\n      )\n  }\n\n  putPipeline(pipelineId: string, data: object): Observable<any> {\n    /**\n     /api/v1/pipeline\n     * */\n    console.log(JSON.stringify(data, null, 2));\n    return this.http.put(`${API_URL}/${pipelineId}`, data)\n      .pipe(\n        tap((resp: any) => {\n          // console.log(resp); // debugger\n        })\n      )\n  }\n\n  getPipeline(pipelineId: string) {\n    /**\n     /api/v1/pipeline/{pipeline_id}\n     {\n  \"pipeline_id\": \"b5bec4c9-d657-483f-9cab-5113d62c6c2e\",\n  \"pipeline_title\": \"\",\n  \"pipeline_date\": \"2022-01-17\",\n  \"pipeline_spec_id\": \"631f3a1c-4fbd-4968-9266-b56019f0a5e4\",\n  \"email\": \"\",\n  \"title\": \"\",\n  \"stages\": [\n    {\n      \"stage_id\": \"dd20849b-642a-4c00-9b71-8b799c6c8e57\",\n      \"stage_url\": \"https://api-iedb-ar-prototype-dev.lji.org/api/v1/stage/dd20849b-642a-4c00-9b71-8b799c6c8e57\",\n      \"stage_number\": 1,\n      \"input_stage_number\": null,\n      \"input_stage_id\": null,\n      \"stage_type\": \"prediction\",\n      \"tool_group\": \"mhci\",\n      \"stage_messages\": {},\n      \"stage_status\": \"done\",\n      \"stage_result_id\": \"1642448438.4946783-crBK5D3C\",\n      \"stage_result_uri\": \"https://api-iedb-ar-prototype-dev.lji.org/api/v1/results/1642448438.4946783-crBK5D3C\",\n      \"input_data\": {\n        \"input_parameters_id\": \"1642448437.0379062-7KNyAzhE\",\n        \"input_parameters_uri\": \"https://api-iedb-ar-prototype-dev.lji.org/api/v1/get_object/1642448437.0379062-7KNyAzhE\",\n        \"input_sequence_text_id\": \"1642448437.0429754-blM9DgMu\",\n        \"input_sequence_text_uri\": \"https://api-iedb-ar-prototype-dev.lji.org/api/v1/get_object/1642448437.0429754-blM9DgMu\"\n      }\n    }\n  ]\n}\n     */\n\n    return this.http.get(`${API_URL}/${pipelineId}?return_input_URIs=True`)\n      .pipe(\n        tap((resp: any) => {\n          console.log(resp);\n        })\n      )\n  }\n\n  getPipelineSpec(pipelineSpecId: string) {\n    /**\n     {\n  \"pipeline_spec_id\": \"8acffb74-f561-433e-b1f4-082e616ef287\",\n  \"description\": \"\",\n  \"pipeline_params\": {\n    \"stages\": [\n      {\n        \"stage_type\": \"prediction\",\n        \"tool_group\": \"cluster\",\n        \"table_state\": {\n          \"columns\": {}\n        },\n        \"stage_number\": 1,\n        \"input_datasets\": [\n          {}\n        ],\n        \"input_parameters\": {\n          \"predictors\": [\n            {\n              \"type\": \"cluster\",\n              \"method\": \"cliques\"\n            }\n          ],\n          \"cluster_pct_identity\": 0.4,\n          \"peptide_length_range\": [\n            0,\n            0\n          ]\n        }\n      },\n      {\n        \"stage_type\": \"prediction\",\n        \"tool_group\": \"mhci\",\n        \"table_state\": {\n          \"columns\": {}\n        },\n        \"stage_number\": 2,\n        \"input_datasets\": [\n          {\n            \"data_to_pipe\": \"peptide\",\n            \"input_stage_number\": 1\n          }\n        ],\n        \"input_parameters\": {\n          \"alleles\": \"H2-Kb,H2-Db\",\n          \"predictors\": [\n            {\n              \"type\": \"binding\",\n              \"method\": \"netmhcpan_el\"\n            }\n          ],\n          \"peptide_length_range\": [\n            9,\n            10\n          ]\n        }\n      }\n    ],\n    \"api_version\": \"0.1.0\"\n  }\n}\n     */\n\n    return this.http.get(`${PIPELINE_SPEC_API_URL}/${pipelineSpecId}`)\n      .pipe(\n        tap((resp: any) => {\n          console.log(resp);\n        })\n      )\n  }\n\n  getResults(result_url: string) {\n    console.log(result_url);\n    return this.http.get<any>(result_url);\n  }\n\n  /** formgroup -> params convert functions */\n  convertTCellForm (tCellForm: UntypedFormGroup) {\n    /** Alleles */\n    const selectedAlleles = _.map(tCellForm.get('alleles')?.value, allele => allele.label).join(',').replace(/\\s/g, '')\n    const break_peptides = tCellForm.get('breakPeptides')?.value;\n\n    /** predictors */\n    const predictors = tCellForm.value.predictionModels;\n    /** peptide length range */\n    const peptide_length_range = tCellForm.value.peptideLength;\n\n    return {\n      alleles: selectedAlleles,\n      // break_peptides: !break_peptides,\n      peptide_length_range: break_peptides ? null : peptide_length_range,\n      predictors,\n    };\n  }\n\n  convertClusterForm (clusterForm: UntypedFormGroup) {\n    /** threshold */\n    const threshold = clusterForm.getRawValue().threshold;\n    /** minimum_len */\n    let minimum_len = clusterForm.getRawValue().peptideLength[0];\n    minimum_len = minimum_len === 4 ? 0 : minimum_len;\n    /** maximum_len */\n    let maximum_len = clusterForm.getRawValue().peptideLength[1];\n    maximum_len = maximum_len === 26 ? 0 : maximum_len;\n    /** method */\n    let method = clusterForm.getRawValue().method;\n\n    return {\n      \"cluster_pct_identity\": threshold,\n      \"peptide_length_range\": [minimum_len,maximum_len],\n      \"predictors\": [\n        {\n          \"type\": \"cluster\",\n          \"method\": method\n        }\n      ]\n    }\n  }\n\n  convertPepmatchForm (form: UntypedFormGroup) {\n    /** mismatch */\n    const mismatch = form.getRawValue().mismatch;\n    /** one_match */\n    let best_match = form.getRawValue().bestMatch;\n    /** proteome */\n    let proteome = form.getRawValue().proteome;\n    /** include_unmatched_peptides */\n    let include_unmatched_peptides = form.getRawValue().include_unmatched_peptides;\n\n    return {\n      mismatch,\n      proteome,\n      best_match,\n      include_unmatched_peptides\n    }\n  }\n\n  convertPepxForm (form: UntypedFormGroup) {\n    /** qLevel */\n    const qlevel = form.getRawValue().qlevel;\n    /** datasource - optional */\n    let datasource = form.getRawValue().datasource;\n    /** datasets */\n    let dataset_id = form.getRawValue().dataset_id;\n\n    return {\n      qlevel,\n      datasource,\n      dataset_id\n    }\n  }\n\n  convertPepcompForm(form: UntypedFormGroup) {\n    /** alleles */\n    const selectedAlleles = _.map(form.get('alleles')?.value, allele => allele.label).join(',').replace(/\\s/g, '')\n    /** predictors */\n    const predictors = form.value.predictionModels;\n\n    return {\n      alleles: selectedAlleles,\n      predictors,\n    }\n  }\n\n  convertMutgenForm(form: UntypedFormGroup) {\n    /** peptideLength */\n    const peptide_length = form.getRawValue().peptideLength;\n    /** peptideMutationPosition1 */\n    let peptide_mutation_position1 = form.getRawValue().peptideMutationPosition1;\n    /** peptideMutationPosition1 */\n    let peptide_mutation_position2 = form.getRawValue().peptideMutationPosition2;\n    /** frameshiftOverlap */\n    let frameshift_overlap = form.getRawValue().frameshiftOverlap;\n    // /** maximum_peptide_length */\n    let maximum_peptide_length = form.getRawValue().maximumPeptideLength;\n    /** min_len_near_start_stop */\n    let min_len_near_start_stop = form.getRawValue().minLengthNearStartStop;\n    return {\n      peptide_length,\n      peptide_mutation_position1,\n      peptide_mutation_position2,\n      frameshift_overlap,\n      maximum_peptide_length,\n      min_len_near_start_stop: 16,\n      \"reference_genome\": \"GRCh38\",\n    }\n  }\n}\n","import {Injectable} from '@angular/core';\nimport {HttpClient} from \"@angular/common/http\";\nimport {Observable} from \"rxjs\";\n// import {tap} from \"rxjs/operators\";\n\nimport Stage from \"../../../_global/Stage\";\nimport Tool from \"../../../_global/Tool\";\nimport PipelineParams from \"../../../_global/PipelineParams\";\nimport {StateService} from \"../state.service\";\nimport {PipelineService} from \"../../pipeline-service/pipeline.service\";\nimport {\n  initTCellPredictionState, initTCellPredictionTool,\n  initClusterState, initClusterTool, initPepmatchTool, initPepMatchState\n} from \"../default-stage-states\";\n\n\n/**\n {\n  \"pipeline_id\": \"\",\n  \"run_stage_range\": [\n    1,\n    1\n  ],\n  \"stages\": [\n    {\n      \"stage_number\": 1,\n      \"stage_type\": \"prediction\",\n      \"tool_group\": \"mhci\",\n      \"input_sequence_text\": \">LCMV Armstrong, Protein GP\\nMGQIVTMFEALPHIIDEVINI\\n\",\n      \"input_parameters\": {\n        \"alleles\": \"H2-Kb,H2-Db\",\n        \"peptide_length_range\": [\n          9,\n          10\n        ],\n        \"predictors\": [\n          {\n            \"type\": \"binding\",\n            \"method\": \"netmhcpan_el\"\n          }\n        ]\n      }\n    }\n  ]\n * */\n\ninterface PipelineState {\n  pipeline_id: string,\n  pipeline_spec_id: string,\n  run_stage_range: [number, number],\n  inputSequenceText?: string,\n  inputVcfText?: string,\n  stages: Stage[],\n  tools: Tool[],\n  // table_states: TableState[],\n  params: PipelineParams\n}\n\nconst initialState: PipelineState = {\n  pipeline_id: '',\n  pipeline_spec_id: '',\n  inputSequenceText: '',\n  // inputVcfText: '',\n  run_stage_range: [1, 1],\n  stages: [],\n  tools: [],\n  params: {\n    pipeline_id: '',\n    run_stage_range: [1, 1],\n    stages: []\n  } // last parameter sent to api\n};\n\n@Injectable({\n  providedIn: 'root'\n})\nexport class PipelineStateService extends StateService<PipelineState> {\n\n  stages$: Observable<Stage[]> = this.select(state => state.stages);\n  tools$: Observable<Tool[]> = this.select(state => state.tools);\n  pipelineId$: Observable<string> = this.select(state => state.pipeline_id);\n  pipelineSpecId$: Observable<string> = this.select(state => state.pipeline_spec_id);\n  inputSequenceText$: Observable<string | undefined> = this.select(state => state.inputSequenceText);\n  inputVcfText$: Observable<string | undefined> = this.select(state => state.inputVcfText);\n  params$: Observable<PipelineParams> = this.select(state => state.params);\n\n  constructor(\n    private _pipelineService: PipelineService\n  ) {\n    super(initialState); // now need to set stages\n    this.stages$.subscribe(value => {\n      // Default initial state - set to initTCellPredictionState\n      console.log(value);\n      if (value.length === 0) {\n        this.setState({\n          stages: [\n            initTCellPredictionState\n          ]\n        })\n      }\n    })\n    this.tools$.subscribe(value => {\n      // Default initial state - set to initTCellPredictionState\n      console.log(value);\n      if (value.length === 0) {\n        this.setState({\n          tools: [\n            initTCellPredictionTool\n          ]\n        })\n      }\n    })\n  }\n\n  /** Params */\n  setParams(params: any) {\n    this.setState({params})\n  }\n\n  setPipelineId(pipelineId: string) {\n    this.setState({pipeline_id: pipelineId});\n  }\n\n  setPipelineSpecId(pipelineSpecId: string) {\n    this.setState({pipeline_spec_id: pipelineSpecId});\n  }\n\n  setPipelineIdToParams(pipelineId: string) {\n    const params = {...this.state.params} // hard copy\n    console.log(params);\n    params.pipeline_id = pipelineId\n    this.setState({params})\n  }\n\n  setStagesToParams(stages: Stage[]) {\n    /**\n     Used in GET Pipeline to set all stages at once.\n     * */\n    const params = {...this.state.params} // hard copy\n    console.log(params);\n    params.stages = stages;\n    this.setState({params})\n  }\n\n\n  addStageToParams(stage: Stage) {\n    const params = {...this.state.params} // hard copy\n    console.log(params);\n    params.stages.push(stage);\n    this.setState({params})\n  }\n\n  insertStageToParams(stage: Stage, index: number) {\n    const params = {...this.state.params} // hard copy\n    let stages = params.stages;\n    stages[index] = stage;\n    params.stages = stages;\n    // console.log(params);\n    this.setState({params})\n  }\n\n  applyFiltersToParams(stageIndex: number, columns: any) {\n    /**\n     * Adds columns object as table_state.columns in params\n     *\n     * */\n    const params = {...this.state.params} // hard copy\n    const stages = params.stages;\n    console.log(stages);\n    const stageTemp = stages[stageIndex];\n    stageTemp.table_state.columns = columns;\n    stages[stageIndex] = stageTemp\n    params.stages = stages;\n    this.setState({params})\n  }\n\n  popStageFromParams() {\n    const params = {...this.state.params} // hard copy\n    let stages = params.stages;\n\n    stages.pop();\n\n    params.stages = stages;\n    this.setState({params})\n  }\n\n  /**\n   * Stage\n   * */\n\n  addStage(stage: Stage) {\n    /**\n     Add T-cell or Cluster (no results)\n     * */\n    this.setState({\n      stages: [...this.state.stages, stage]\n    })\n  }\n\n  setStages(stages: Stage[]) {\n    /**\n     Used in GET Pipeline to set all stages at once.\n     * */\n    this.setState({\n      stages: stages\n    })\n  }\n\n  changeResultUrl(url: string, index: number) {\n    let stages = [...this.state.stages]\n    stages[index].result_url = url\n    stages[index].stage_messages!.warnings = []\n    stages[index].stage_messages!.errors = []\n    this.setState({\n      stages: stages\n    })\n  }\n\n  setInitialStage(stage: Stage) {\n    /**\n     Used in navbar component\n     * */\n    this.setState({\n      stages: [stage]\n    })\n  }\n\n  insertStage(stage: Stage, index: number) {\n    let stages = [...this.state.stages]\n    stages[index] = stage;\n    this.setState({stages})\n  }\n\n  insertTableStateToStage(table_state: any, index: number) {\n    let stages = [...this.state.stages]\n    stages[index].table_state = table_state;\n    this.setState({stages})\n  }\n\n  insertInputParametersToStage(input_parameters: any, index: number) {\n    let stages = [...this.state.stages]\n    stages[index].input_parameters = input_parameters;\n    this.setState({stages})\n  }\n\n  popStage() {\n    let stages = [...this.state.stages]\n    stages.pop();\n    this.setState({stages});\n  }\n\n  /**\n   * Tool\n   * */\n  setTools(tools: Tool[]) {\n    this.setState({\n      tools\n    })\n  }\n\n\n  setInitialTool(tool: Tool) {\n    const copy = Object.assign({}, tool)\n    /**\n     Used in navbar component\n     * */\n    this.setState({\n      tools: [copy]\n    })\n  }\n\n  insertTool(tool: Tool, index: number) {\n    let tools = [...this.state.tools]\n    tools[index] = tool;\n    this.setState({tools})\n  }\n\n  popTool() {\n    let tools = [...this.state.tools]\n    tools.pop();\n    this.setState({tools})\n  }\n\n  setToolDisabled(disabled: boolean, index: number) {\n    let tools = [...this.state.tools]\n    const tempTool = tools[index];\n    tempTool.disabled = disabled;\n    tools[index] = tempTool;\n    this.setState({tools})\n  }\n\n  setToolLoading(loading: boolean, submitted: boolean, index: number) {\n    let tools = [...this.state.tools]\n    const tempTool = tools[index];\n    tempTool.loading = loading;\n    tempTool.submitted = submitted;\n    tools[index] = tempTool;\n    this.setState({tools})\n  }\n\n  setToolAppliedFilters(appliedFilters: boolean, index: number) {\n    let tools = [...this.state.tools]\n    const tempTool = tools[index];\n    tempTool.appliedFilters = appliedFilters;\n    tools[index] = tempTool;\n    this.setState({tools})\n  }\n\n  insertInputDataUriToTool(input_data_uri: any, index: number) {\n    let tools = [...this.state.tools]\n    tools[index].input_data_uri = input_data_uri;\n    this.setState({tools})\n  }\n\n  setInputSequenceText(value: string) {\n    /**\n     updates inputSequenceText: string\n     * */\n    this.setState({inputSequenceText: value});\n  }\n  setInputVcfText(value: string) {\n    /**\n     updates InputVcfText: string\n     * */\n    this.setState({inputVcfText: value});\n  }\n}\n\n/**\n * state.service.ts\n export class StateService<T> {\n\n  private state$: BehaviorSubject<T>;\n  protected get state(): T {\n    return this.state$.getValue();\n  }\n\n  constructor(initialState: T) {\n    this.state$ = new BehaviorSubject<T>(initialState);\n  }\n\n  protected select<K>(mapFn: (state: T) => K): Observable<K> {\n    return this.state$.asObservable().pipe(\n      map((state: T) => mapFn(state)),\n      distinctUntilChanged()\n    );\n  }\n\n  protected setState(newState: Partial<T>) {\n    this.state$.next({\n      ...this.state,\n      ...newState,\n    });\n  }\n}\n */\n","import { Injectable } from '@angular/core';\nimport {HttpClient, HttpParams} from '@angular/common/http';\nimport {Observable, timer, of} from \"rxjs\";\nimport {debounce, catchError, debounceTime, distinctUntilChanged, map, tap, switchMap} from 'rxjs/operators';\n\nimport {environment} from '../../../environments/environment';\n\nconst ALLELE_SEARCH_API_URL = `${environment['api_url']}/api/v1/alleles/search`;\n\nconst PARAMS = new HttpParams();\n\n@Injectable({\n  providedIn: 'root'\n})\nexport class AlleleSearchService {\n\n  constructor(private http: HttpClient) { }\n\n  search(term: string) {\n    if (term === '') {\n      return of([]);\n    }\n    PARAMS.set('query', term)\n    let new_search_api_url = `${ALLELE_SEARCH_API_URL}?query=${term}&method=mhci`\n    console.log(new_search_api_url);\n    return this.http\n      .get(new_search_api_url).pipe(\n        map(response => {\n          // @ts-ignore\n          console.log(response['alleles']);\n          // @ts-ignore\n          return response['alleles']\n        })\n      );\n  }\n}\n","import { Injectable } from '@angular/core';\nimport {HttpClient, HttpHeaders} from \"@angular/common/http\";\n\nimport {environment} from '../../../environments/environment';\n// import * as _ from \"lodash\";\nconst API_URL = `${environment['api_url']}/api/v1/announcements`;\n\n@Injectable({\n  providedIn: 'root'\n})\n\nexport class AnnouncementService {\n\n  constructor(private http: HttpClient) { }\n\n  getAnnouncements() : any {\n    return this.http.get(API_URL)\n  }\n}\n","import { Injectable } from '@angular/core';\n\n@Injectable({\n  providedIn: 'root'\n})\nexport class AlertServiceService {\n\n  public messages: string[] = []; // used only for conditional rendering\n  public message = '';\n  public colors = 'alert-danger';\n\n  add(message: string, alertType: string) {\n    this.messages.push(message);\n    this.message = message;\n    this.colors = alertType;\n  }\n  clear() {\n    this.message = '';\n    this.messages = [];\n  }\n\n  displayMessage() {\n    if (this.messages.length > 0) {\n      return true;\n    }\n    return null;\n  }\n}\n","<div *ngIf=\"alertService.displayMessage()\" class=\"d-flex flex-row\">\n  <div [ngClass]=\"[alertService.colors, 'alert', 'p-2']\" role=\"alert\" style=\"width:100%\">\n<!--    <button type=\"button\" class=\"close\" aria-label=\"Close\"-->\n<!--            (click)=\"alertService.clear()\" [ngStyle]=\"{float: 'right'}\">-->\n<!--      <span aria-hidden=\"true\">&times;</span>-->\n<!--    </button>-->\n<!--    <h5> Validation Error(s) </h5>-->\n    <pre>{{alertService.message}}</pre>\n  </div>\n</div>\n\n","import { Component, OnInit } from '@angular/core';\nimport { AlertServiceService } from '../services/alert-service/alert-service.service';\n@Component({\n  selector: 'app-alert-component',\n  templateUrl: './alert-component.component.html',\n  styleUrls: ['./alert-component.component.scss']\n})\nexport class AlertComponentComponent implements OnInit {\n\n  constructor(public alertService: AlertServiceService) { }\n\n  ngOnInit(): void {\n  }\n\n}\n","import {\n  Directive,\n  Output,\n  Input,\n  EventEmitter,\n  HostBinding,\n  HostListener\n} from '@angular/core';\n\n@Directive({\n  selector: '[appDnd]'\n})\nexport class DndDirectiveDirective {\n\n  @HostBinding('class.fileover') private _fileOver: boolean | undefined;\n  @Output() fileDropped = new EventEmitter<any>();\n\n  // Dragover listener\n  @HostListener('dragover', ['$event']) onDragOver(evt: { preventDefault: () => void; stopPropagation: () => void; }) {\n    evt.preventDefault();\n    evt.stopPropagation();\n    this._fileOver = true;\n  }\n\n  // Dragleave listener\n  @HostListener('dragleave', ['$event']) public onDragLeave(evt: { preventDefault: () => void; stopPropagation: () => void; }) {\n    evt.preventDefault();\n    evt.stopPropagation();\n    this._fileOver = false;\n  }\n\n  // Drop listener\n  @HostListener('drop', ['$event']) public ondrop(evt: { preventDefault: () => void; stopPropagation: () => void; dataTransfer: { files: any; }; }) {\n    evt.preventDefault();\n    evt.stopPropagation();\n    this._fileOver = false;\n    let files = evt.dataTransfer.files;\n    if (files.length > 0) {\n      this.fileDropped.emit(files);\n    }\n  }\n}\n","<div class=\"container p-3\" id=\"home-component\">\n  <div class=\"row\">\n    <!--    Side Bar -->\n    <div class=\"col-3 d-flex flex-column\">\n\n      <div class=\"bg-secondary-new bg-opacity-50 my-3 p-3\">\n        <h5 class=\"text-primary-new\"> Announcements</h5>\n        <ul class=\"nav\">\n          <li class=\"nav-item\" *ngFor=\"let i of releases\">\n            <!-- use 'releases' instead of 'announcements'-->\n            <a class=\"nav-link\" [href]=\"i.url\" target=\"_blank\">\n              {{i.title}}\n            </a>\n          </li>\n        </ul>\n      </div>\n\n      <div class=\"bg-secondary-new bg-opacity-50 my-3 p-3\">\n        <h5 class=\"text-primary-new\"> Appearances & Events</h5>\n\n        <table>\n          <tbody style=\"font-size: 0.75rem\">\n          <tr>\n            <td>\n              <a href=\"http://workshop.iedb.org/\" target=\"_blank\">\n                Virtual User Workshop\n              </a>\n            </td>\n            <td class=\"date-cell\">Nov 5-7, 2024</td>\n          </tr>\n          <tr>\n            <td>\n              * Register\n              <a href=\"https://www.surveymonkey.com/r/IEDBUW2024\" target=\"_blank\">\n                Here\n              </a>\n            </td>\n          </tr>\n\n<!--          <tr>-->\n<!--            <td>IEDB Virtual User Workshop</td>-->\n<!--            <td class=\"date-cell\">Nov 5-7, 2024</td>-->\n<!--          </tr>-->\n\n          <tr>\n            <td>Festival of Biologics</td>\n            <td class=\"date-cell\">April 23-25, 2025</td>\n          </tr>\n          <tr>\n            <td>AACR 2025</td>\n            <td class=\"date-cell\">April 25-30, 2025</td>\n          </tr>\n          <tr>\n            <td>Immunology 2025 </td>\n            <td class=\"date-cell\">May 3-7, 2025</td>\n          </tr>\n          </tbody>\n        </table>\n\n\n<!--        <ul class=\"nav\">-->\n<!--        <li class=\"nav-item\" *ngFor=\"let i of events\">-->\n\n<!--&lt;!&ndash;            <a class=\"nav-link\" [href]=\"'https://discuss.iedb.org/t/'.concat(i.id)\" target=\"_blank\">&ndash;&gt;-->\n<!--&lt;!&ndash;            {{i.title}}&ndash;&gt;-->\n<!--&lt;!&ndash;            </a>&ndash;&gt;-->\n<!--          <a [attr.href]=\"i.href\" [className]=\"i.class\" target=\"_blank\">-->\n<!--            {{i.name}}-->\n<!--          </a>-->\n<!--          <a class=\"disabled\">* HEllo world</a>-->\n<!--        </li>-->\n<!--        </ul>-->\n\n<!--        <div class=\"d-flex flex-row\">-->\n<!--          <div class=\"flex-column mr-auto\">-->\n<!--            Antibody Society-->\n<!--          </div>-->\n<!--          <div class=\"flex-column\">-->\n<!--            Dec 9-13-->\n<!--          </div>-->\n<!--        </div>-->\n\n<!--        <div class=\"d-flex flex-row\">-->\n<!--          <div class=\"flex-column mr-auto\">-->\n<!--            AAAAI 2020-->\n<!--          </div>-->\n<!--          <div class=\"flex-column\">-->\n<!--            Mar 11-15-->\n<!--          </div>-->\n<!--        </div>-->\n\n<!--        <div class=\"d-flex flex-row\">-->\n<!--          <div class=\"flex-column mr-auto\">-->\n<!--            AAI 2020-->\n<!--          </div>-->\n<!--          <div class=\"flex-column\">-->\n<!--            May 13-16-->\n<!--          </div>-->\n<!--        </div>-->\n\n      </div>\n\n      <div class=\"bg-secondary-new bg-opacity-50 d-flex flex-column my-3 p-3\">\n        <h5 class=\"text-primary-new align-self-center\">Additional Resources</h5>\n        <div class=\"d-flex flex-column\">\n          <a type='button' class=\"btn btn-sky-blue text-white my-1\" [href]=\"swaggerUrl\"\n             target=\"_blank\">\n            API\n          </a>\n<!--          <button type='button' class=\"btn btn-outline-primary bg-white m-3 text-black-50\" routerLink=\"/benchmark\">-->\n<!--            Benchmarking-->\n<!--          </button>-->\n          <a type='button' class=\"btn btn-sky-blue text-white my-1\" routerLink=\"/download-all\">\n            Downloads\n          </a>\n        </div>\n      </div>\n    </div>\n\n    <!-- Main Component -->\n    <div class=\"col-9 d-flex flex-column\">\n      <h3 class=\"align-self-center text-primary-new\">Welcome to the Next-Generation IEDB Tools site!</h3>\n      <p class=\"align-self-center\">As a companion site to the Immune Epitope Database (IEDB), this site provides a\n        collection of tools for the prediction and analysis of immune epitopes.</p>\n\n      <a class=\"btn btn-sky-blue text-white align-self-center mx-auto mb-5\" style=\"width: 100%\" routerLink=\"/docs\" target=\"_blank\"><b>New User?</b> Learn to\n        use the website here!\n      </a>\n\n      <!--      T Cell Form -->\n      <div class=\"bg-secondary-new bg-opacity-50 d-flex flex-column p-3\" appDnd (fileDropped)=\"onFileDropped($event)\">\n      <h5>\n          <!--   href=\"javascript:void(0)\" used to make it look like a hyperlink -->\n          <a [routerLink]=\"'/pipeline'\" [queryParams]=\"{tool: 'tc1'}\"><u>T Cell Prediction - Class I</u></a>\n        </h5>\n        <div class=\"row\">\n          <div class=\"col-sm-12\">\n            <label class=\"fst-italic\">MHC class I binding affinity, TAP processing, and Immunogenicity predictions</label>\n<!--            <div class=\"btn-group btn-group-sm float-end class-option-btn-group\">-->\n<!--              <button [ngClass]=\"classI ? 'btn btn-primary' : 'btn btn-outline-primary'\" type='button'-->\n<!--                      (click)=\"classI=true\">I-->\n<!--              </button>-->\n<!--              <button [ngClass]=\"classI ? 'btn btn-outline-secondary disabled' : 'btn btn-primary disabled'\" type='button'-->\n<!--                      (click)=\"classI=false\">II-->\n<!--              </button>-->\n<!--            </div>-->\n\n          </div>\n        </div>\n        <form [formGroup]=\"tCellForm\">\n          <div class=\"d-flex form-group row\">\n            <div class=\"mt-2 col-sm-12\">\n              <textarea class=\"form-control\"\n                        id=\"sequenceFormControlTextArea\"\n                        rows=\"5\"\n                        formControlName=\"sequences\"\n                        [placeholder]=\"'Type/paste/drag sequences (max: 1,000,000 characters) into this box or click \\'Run\\' to use the example sequence:\\n >SARS2 spike glycoprotein\\nMFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT'\"></textarea>\n\n            </div>\n            <div class=\"col-sm-3 d-flex flex-column justify-content-start p-2\">\n              <div class=\"p-2 d-flex flex-column justify-content-start\">\n              </div>\n\n            </div>\n          </div>\n        </form>\n\n        <div class=\"form-group row\" id=\"alleleRow\">\n          <div class=\"col-sm-2 col-form-label\">\n            <label class=\"text-left\">MHC Allele(s)</label>\n          </div>\n          <div class=\"col-sm-10 d-flex flex-row\">\n            <input #alleleSearch id=\"allAlleles\" type=\"text\" class=\"form-control\"\n                   [ngbTypeahead]=\"search\"\n                   [inputFormatter]=\"inputFormatter\"\n                   [resultFormatter]=\"resultFormatter\"\n                   [editable]=\"false\"\n                   (selectItem)=\"onAlleleSelect($event, alleleSearch)\"\n                   placement=\"bottom-left\"\n                   (blur)=\"onBlurAlleleSelect($event, alleleSearch);\"\n                   (focus)=\"alleleSearch.value=''; alleleSearch.placeholder='';\"\n                   [defaultValue]=\"selectedAlleles.length ? selectedAlleleLabels : ''\"\n                   [placeholder]=\"'Ex: HLA-A*02:01'\"\n            />\n            <div class=\"button-container\">\n              <button *ngIf=\"selectedAlleles.length\" id=\"allele-clear-button\" type=\"button\"\n                      class=\"rounded-circle rounded-sm\"\n                      (click)=\"onAlleleClear(alleleSearch);\"\n                      ngbTooltip='Clear allele(s)'\n                      placement=\"right\"\n                      triggers=\"hover\">\n                <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n                     class=\"bi bi-x-circle\" viewBox=\"0 0 16 16\"\n                >\n                  <path d=\"M8 15A7 7 0 1 1 8 1a7 7 0 0 1 0 14zm0 1A8 8 0 1 0 8 0a8 8 0 0 0 0 16z\"/>\n                  <path\n                    d=\"M4.646 4.646a.5.5 0 0 1 .708 0L8 7.293l2.646-2.647a.5.5 0 0 1 .708.708L8.707 8l2.647 2.646a.5.5 0 0 1-.708.708L8 8.707l-2.646 2.647a.5.5 0 0 1-.708-.708L7.293 8 4.646 5.354a.5.5 0 0 1 0-.708z\"/>\n                </svg>\n              </button>\n              <button type=\"button\" id=\"allele-modal-button\" class=\"btn btn-dark-blue-grey text-white mr-2\" placement=\"right\"\n                      (click)=\"onOpenAlleleModal()\"\n                      [ngbTooltip]=\"tipContent\"\n                      [autoClose]=\"false\"\n                      #t=\"ngbTooltip\">\n                {{selectedAlleles.length}}\n              </button>\n            </div>\n<!--          </div>-->\n          <ng-template #tipContent>\n              <div>\n                Click to open Allele Selector\n              </div>\n              <ol *ngIf=\"selectedAlleles.length\">\n                <li *ngFor=\"let allele of selectedAlleles;\" [ngStyle]=\"{width: '100%'}\">\n                  {{allele?.label}}\n                </li>\n              </ol>\n          </ng-template>\n          <div class=\"col-sm-2\">\n            <div *ngIf=\"searching\" class=\"d-flex justify-content-center col\">\n              <div class=\"spinner-border text-primary align-self-center\" role=\"status\">\n                <span class=\"visually-hidden sr-only\">Loading...</span>\n              </div>\n            </div>\n          </div>\n          <div class=\"col-sm-3 text-right\">\n            <ng-template #runTipContent>\n                <span [style]=\"{whiteSpace: 'nowrap'}\">\n                  Click to run tool\n                </span>\n            </ng-template>\n            <!--            [disabled]=\"!(tCellForm.value['sequences'] && selectedAlleles.length>0)\"-->\n            <button type=\"button\" class=\"btn btn-dark-blue-grey text-white float-end\" (click)=\"runTCellPrediction()\"\n                    routerLink=\"/pipeline\"\n                    [state]=\"{run: true}\"\n                    [ngbTooltip]=\"runTipContent\"\n                    placement=\"top\">\n              <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n                   class=\"bi bi-play-fill\" viewBox=\"0 0 16 16\">\n                <path\n                  d=\"m11.596 8.697-6.363 3.692c-.54.313-1.233-.066-1.233-.697V4.308c0-.63.692-1.01 1.233-.696l6.363 3.692a.802.802 0 0 1 0 1.393z\"/>\n              </svg>\n            </button>\n          </div>\n        </div>\n      </div>\n    </div>\n\n      <a class=\"btn btn-sky-blue align-self-center text-white mx-auto mt-4 mb-3\" style=\"width: 100%\" routerLink=\"/all-tools-list\" target=\"_blank\">\n        <b>Additional Tools</b>\n      </a>\n      <!--      Tools List -->\n      <div class=\"bg-secondary-new bg-opacity-50 d-flex flex-column p-3\" appDnd (fileDropped)=\"onFileDropped($event)\">\n\n\n        <div class=\"row my-2\">\n          <div class=\"col-sm-6\">\n            <h5>\n              <!--   href=\"javascript:void(0)\" used to make it look like a hyperlink -->\n              <a [routerLink]=\"'/pipeline'\" [queryParams]=\"{tool: 'cluster'}\"><u>Cluster</u></a>\n            </h5>\n          </div>\n          <div class=\"col-sm-6\">\n            <label class=\"fst-italic\">Group peptides by sequence identity</label>\n          </div>\n        </div>\n        <div class=\"row my-2\">\n          <div class=\"col-sm-6\">\n            <h5>\n              <!--   href=\"javascript:void(0)\" used to make it look like a hyperlink -->\n              <a [routerLink]=\"'/pipeline'\" [queryParams]=\"{tool: 'mutpepgen'}\"><u>Mutated Peptide Generator</u></a>\n            </h5>\n          </div>\n          <div class=\"col-sm-6\">\n            <label class=\"fst-italic\">Generate neoepitopes from a VCF</label>\n          </div>\n        </div>\n        <div class=\"row my-2\">\n          <div class=\"col-sm-6\">\n            <h5>\n              <!--   href=\"javascript:void(0)\" used to make it look like a hyperlink -->\n              <a [routerLink]=\"'/pipeline'\" [queryParams]=\"{tool: 'pepvcomp'}\"><u>Peptide Variant Comparison</u></a>\n            </h5>\n          </div>\n          <div class=\"col-sm-6\">\n            <label class=\"fst-italic\"> Compare MHC binding / elution / immunogenicity\n              metrics between wild-type and mutant peptides\n            </label>\n          </div>\n        </div>\n        <div class=\"row my-2\">\n          <div class=\"col-sm-6\">\n            <h5>\n              <!--   href=\"javascript:void(0)\" used to make it look like a hyperlink -->\n              <a [routerLink]=\"'/pipeline'\" [queryParams]=\"{tool: 'pepmatch'}\"><u>PEPMatch</u></a>\n            </h5>\n          </div>\n          <div class=\"col-sm-6\">\n            <label class=\"fst-italic\">Search for closely related peptides in a reference proteome</label>\n          </div>\n        </div>\n        <div class=\"row my-2\">\n          <div class=\"col-sm-6\">\n            <h5>\n              <!--   href=\"javascript:void(0)\" used to make it look like a hyperlink -->\n              <a [routerLink]=\"'/pipeline'\" [queryParams]=\"{tool: 'pepx'}\"><u>PepX</u></a>\n            </h5>\n          </div>\n          <div class=\"col-sm-6\">\n            <label class=\"fst-italic\">Estimate peptide abundance from RNA-Seq expression datasets</label>\n          </div>\n        </div>\n\n      </div>\n\n      <!--      Coming Soon Banner - commented out when adding Tools List up top (7/25/2024)-->\n<!--      <div class=\"bg-warning bg-opacity-50 d-flex flex-column p-3 my-3\">-->\n<!--        <label class=\"fst-italic\">More tools coming soon.</label>-->\n<!--      </div>-->\n\n      <!--      B Cell Form -->\n<!--      <div class=\"bg-warning bg-opacity-50 d-flex flex-column p-3 mt-3 mb-3\" [style]=\"{opacity: 1}\">-->\n<!--        <h5><u>B Cell Prediction</u></h5>-->\n<!--        <p class=\"fst-italic\">Predicts antibody epitopes from protein sequences</p>-->\n<!--        <form [formGroup]=\"bCellForm\">-->\n<!--          <div class=\"d-flex form-group row\">-->\n<!--            <div class=\"mt-2 col-sm-12\">-->\n<!--              <textarea class=\"form-control\"-->\n<!--                        id=\"bCellSequenceFormControlTextArea\"-->\n<!--                        rows=\"5\"-->\n<!--                        formControlName=\"sequences\"></textarea>-->\n\n<!--            </div>-->\n<!--            <div class=\"col-sm-3 d-flex flex-column justify-content-start p-2\">-->\n<!--              <div class=\"p-2 d-flex flex-column justify-content-start\">-->\n<!--              </div>-->\n\n<!--            </div>-->\n<!--          </div>-->\n<!--        </form>-->\n<!--        <div class=\"row\" id=\"alleleRow-2\">-->\n\n<!--          <div class=\"col-sm-10 d-flex flex-row\">-->\n<!--              <p class=\"fst-italic text-danger\">-->\n<!--                Coming Soon-->\n<!--              </p>-->\n<!--          </div>-->\n<!--          <div class=\"col-sm-2 text-right\">-->\n<!--            <button type=\"button\" class=\"btn btn-primary text-white float-end\" (click)=\"null\"-->\n<!--                    routerLink=\"/pipeline\"-->\n<!--                    [state]=\"{run: true}\"-->\n<!--                    [ngbTooltip]=\"runTipContent\"-->\n<!--                    placement=\"top\"-->\n<!--                    disabled>-->\n<!--              <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"-->\n<!--                   class=\"bi bi-play-fill\" viewBox=\"0 0 16 16\">-->\n<!--                <path-->\n<!--                  d=\"m11.596 8.697-6.363 3.692c-.54.313-1.233-.066-1.233-.697V4.308c0-.63.692-1.01 1.233-.696l6.363 3.692a.802.802 0 0 1 0 1.393z\"/>-->\n<!--              </svg>-->\n<!--            </button>-->\n<!--          </div>-->\n<!--        </div>-->\n<!--        &lt;!&ndash;        <div class=\"d-flex form-group row\">&ndash;&gt;-->\n<!--        &lt;!&ndash;          <div class=\"mt-2 col-sm-12\">&ndash;&gt;-->\n<!--        &lt;!&ndash;            <label>Enter antingen </label>&ndash;&gt;-->\n<!--        &lt;!&ndash;          <textarea class=\"form-control\"&ndash;&gt;-->\n<!--        &lt;!&ndash;                    id=\"sequenceFormControlTextArea\"&ndash;&gt;-->\n<!--        &lt;!&ndash;                    rows=\"10\"&ndash;&gt;-->\n<!--        &lt;!&ndash;                    formControlName=\"sequences\"></textarea>&ndash;&gt;-->\n\n<!--        &lt;!&ndash;          </div>&ndash;&gt;-->\n<!--        &lt;!&ndash;          <div class=\"col-sm-3 d-flex flex-column justify-content-start p-2\">&ndash;&gt;-->\n<!--        &lt;!&ndash;            <div class=\"p-2 d-flex flex-column justify-content-start\">&ndash;&gt;-->\n<!--        &lt;!&ndash;            </div>&ndash;&gt;-->\n\n<!--        &lt;!&ndash;          </div>&ndash;&gt;-->\n<!--        &lt;!&ndash;        </div>&ndash;&gt;-->\n<!--      </div>-->\n  </div>\n</div>\n</div>\n\n<!--Allele Select Modal -->\n<ng-template #selectedAlleleModal let-modal2>\n  <div class=\"modal-header\">\n    <h4 class=\"modal-title\" id=\"modal-allele-title\">\n      Number of Selected Alleles: {{selectedAlleles.length}}\n    </h4>\n    <button type=\"button\" class=\"btn-close\" aria-label=\"Close\"\n            (click)=\"dismissAlleleModal();\"\n    >\n    </button>\n  </div>\n\n  <div class=\"modal-body\">\n    <div class=\"form-group row p-2\">\n      <div class=\"col-sm-3 col-form-label\">\n        <label [className]=\"'fw-bold'\">\n          <!--        <span *ngIf=\"inputChange.alleles\">(Edited) </span>-->\n          MHC Allele(s)\n        </label>\n      </div>\n      <div class=\"col-sm-7 d-flex flex-row\">\n        <!--        <input class=\"form-control\" formControlName=\"allele\" type=\"text\" placeholder=\"HLA-A*02:01,HLA-A*01:01\">-->\n        <input #alleleSearchModal type=\"text\" class=\"form-control\"\n               [ngbTypeahead]=\"search\"\n               [inputFormatter]=\"inputFormatter\"\n               [resultFormatter]=\"resultFormatter\"\n               [editable]=\"false\"\n               (selectItem)=\"onAlleleSelectModal({e : $event, input : alleleSearchModal})\"\n               placement=\"bottom-left\"\n               (blur)=\"onBlurAlleleSelect($event, alleleSearchModal)\"\n               (focus)=\"alleleSearchModal.value=''; alleleSearchModal.placeholder=''\"\n               [defaultValue]=\"selectedAlleles.length ? selectedModalAlleleLabels : ''\"\n               [placeholder]=\"'Ex: HLA-A*02:01'\"\n        />\n      </div>\n      <div class=\"col-sm-2\">\n        <div *ngIf=\"searching\" class=\"d-flex justify-content-center col\">\n          <div class=\"spinner-border text-primary align-self-center\" role=\"status\">\n            <span class=\"visually-hidden sr-only\">Loading...</span>\n          </div>\n        </div>\n      </div>\n    </div>\n\n    <div *ngIf=\"modalAlleles.length > 0\" class=\"p-2 d-flex flex-column justify-content-start\">\n\n      <!--            <app-alert-component></app-alert-component>-->\n\n      <ul class=\"list-group\">\n        <!--<li *ngFor=\"let i of selectedAssayProtocols;\" class=\"list-group-item list-group-item-success\">{{i['allele']['allele']}} {{i['assayCondition'] && '+'}} {{i['assayCondition']}}</li>-->\n        <li *ngFor=\"let i of modalAlleles; let j=index;\" class=\"list-group-item list-group-item-primary list-group-item-action\">{{i['label']}}\n          <button class=\"btn-close float-end\" type=\"button\" (click)=\"onAlleleDeselectModal(j, alleleSearchModal)\"\n                  [disabled]=\"searching\">\n          </button>\n        </li>\n      </ul>\n    </div>\n    <div class=\"modal-footer\">\n      <fieldset class=\"w-100\">\n        <button type=\"button\" class=\"btn btn-secondary\" (click)=\"generate27Alleles(alleleSearchModal)\"\n                ngbTooltip=\"Covers ~97% of the human population\"\n                placement=\"bottom\">27 Allele Panel\n        </button>\n        <button type=\"button\" class=\"btn btn-sm\" placement=\"right\"\n                [ngbPopover]=\"popOverContent\"\n                popoverTitle=\"27 Allele Panel Source\">\n          <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\" class=\"bi bi-info-circle\"\n               viewBox=\"0 0 16 16\">\n            <path d=\"M8 15A7 7 0 1 1 8 1a7 7 0 0 1 0 14zm0 1A8 8 0 1 0 8 0a8 8 0 0 0 0 16z\"/>\n            <path\n              d=\"m8.93 6.588-2.29.287-.082.38.45.083c.294.07.352.176.288.469l-.738 3.468c-.194.897.105 1.319.808 1.319.545 0 1.178-.252 1.465-.598l.088-.416c-.2.176-.492.246-.686.246-.275 0-.375-.193-.304-.533L8.93 6.588zM9 4.5a1 1 0 1 1-2 0 1 1 0 0 1 2 0z\"/>\n          </svg>\n        </button>\n        <ng-template #popOverContent>\n          <a target=\"_blank\"\n             href=\"https://help.iedb.org/hc/en-us/articles/114094151851-HLA-allele-frequencies-and-reference-sets-with-maximal-population-coverage\">\n            HLA allele frequencies and reference sets with maximal population coverage\n          </a>\n        </ng-template>\n        <div class=\"float-end\">\n          <button type=\"button\" class=\"btn btn-secondary mx-1\" (click)=\"onAlleleClearModal(alleleSearchModal);\">\n            Clear Selected Allele(s)\n          </button>\n          <button type=\"button\" class=\"btn btn-sky-blue mx-1\" (click)=\"onSubmitModalAlleles(); alleleSearch.focus()\">\n            Submit\n          </button>\n        </div>\n      </fieldset>\n    </div>\n<!--    <div class=\"modal-footer\">-->\n<!--      <fieldset class=\"w-100\">-->\n<!--        <button type=\"button\" class=\"btn btn-outline-dark\" (click)=\"generate27Alleles(alleleSearchModal)\"-->\n<!--                ngbTooltip=\"Covers ~97% of the human population\"-->\n<!--                placement=\"bottom\">27 Allele Panel</button>-->\n<!--        <button type=\"button\" class=\"btn btn-sm\" placement=\"right\"-->\n<!--                [ngbPopover]=\"popOverContent\"-->\n<!--                popoverTitle=\"27 Allele Panel Source\">-->\n<!--          <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\" class=\"bi bi-info-circle\" viewBox=\"0 0 16 16\">-->\n<!--            <path d=\"M8 15A7 7 0 1 1 8 1a7 7 0 0 1 0 14zm0 1A8 8 0 1 0 8 0a8 8 0 0 0 0 16z\"/>-->\n<!--            <path d=\"m8.93 6.588-2.29.287-.082.38.45.083c.294.07.352.176.288.469l-.738 3.468c-.194.897.105 1.319.808 1.319.545 0 1.178-.252 1.465-.598l.088-.416c-.2.176-.492.246-.686.246-.275 0-.375-.193-.304-.533L8.93 6.588zM9 4.5a1 1 0 1 1-2 0 1 1 0 0 1 2 0z\"/>-->\n<!--          </svg>-->\n<!--        </button>-->\n<!--        <ng-template #popOverContent>-->\n<!--          <a target=\"_blank\" href=\"https://help.iedb.org/hc/en-us/articles/114094151851-HLA-allele-frequencies-and-reference-sets-with-maximal-population-coverage\">-->\n<!--            HLA allele frequencies and reference sets with maximal population coverage-->\n<!--          </a>-->\n<!--        </ng-template>-->\n<!--&lt;!&ndash;        ngbAutoFocus&ndash;&gt;-->\n<!--        <button type=\"button\" class=\"btn btn-outline-dark float-end\"-->\n<!--                (click)=\"onAlleleClear(alleleSearchModal)\">Clear Selected Allele(s)</button>-->\n<!--      </fieldset>-->\n<!--    </div>-->\n\n\n  </div>\n\n</ng-template>\n\n<!--Alert Modal -->\n<ng-template #alertModal let-modal4>\n  <div class=\"modal-header\">\n    <h4 class=\"modal-title\" id=\"alert-modal-title\">Validation Error(s)</h4>\n    <button type=\"button\" class=\"btn-close\" aria-label=\"Close\" (click)=\"modal4.dismiss('Cross click');\">\n    </button>\n  </div>\n  <div class=\"modal-body\">\n    <app-alert-component></app-alert-component>\n  </div>\n  <div class=\"modal-footer\">\n    <!--    <button type=\"button\" class=\"btn btn-secondary\" (click)=\"null\">Reset</button>-->\n    <!--    <button type=\"button\" class=\"btn btn-primary\" (click)=\"null\">Display</button>-->\n  </div>\n</ng-template>\n","import {Component, ElementRef, OnInit, ViewChild} from '@angular/core';\nimport {UntypedFormBuilder, UntypedFormGroup} from \"@angular/forms\";\nimport {Router} from '@angular/router';\n\nimport _ from 'lodash';\nimport {NgbModal} from \"@ng-bootstrap/ng-bootstrap\";\n\nimport {Observable, of} from \"rxjs\";\nimport {catchError, debounceTime, distinctUntilChanged, switchMap, tap} from \"rxjs/operators\";\n\nimport Allele from \"../_global/Allele\";\nimport {AlleleSearchService} from \"../services/allele-search/allele-search.service\";\nimport {PipelineStateService} from \"../services/state-services/pipeline-state-service/pipeline-state.service\";\nimport {\n  initTCellPredictionState\n} from \"../services/state-services/default-stage-states\";\nimport {environment} from \"../../environments/environment\";\nimport * as alleleData from \"../services/data/27-alleles.json\";\nimport {isASCII} from \"../util/string-helpers\";\nimport {Location} from \"@angular/common\";\nimport {isMaxLength} from \"../util/is-max-length\";\nimport {AlertServiceService} from \"../services/alert-service/alert-service.service\";\nimport {AnnouncementService} from \"../services/announcement-service/announcement-service.service\";\n\n@Component({\n  selector: 'app-home',\n  templateUrl: './home.component.html',\n  styleUrls: ['./home.component.scss']\n})\nexport class HomeComponent implements OnInit {\n\n  swaggerUrl = `${environment['api_url']}/apidocs`\n\n  maxCharacters = 1000000\n\n  classI = true;\n  tCellForm!: UntypedFormGroup;\n  searching = false;\n  searchFailed = false;\n\n  bCellForm = new UntypedFormGroup({});\n\n  /** Allele Variables */\n  selectedAlleles: Allele[] = [];\n  modalAlleles: Allele[] = [];\n\n  // topics: any[] = []; // events\n  announcements: any[] = [\n    \"Next-Generation IEDB Tools site released to public\"\n  ]; // topics\n\n  releases:{title: string, url: string}[] = [\n    {title: 'Next-Generation IEDB Tools Website and API - Release 2.0', url: 'https://help.iedb.org/hc/en-us/articles/27040672746907'},\n    {title: 'Next-Generation IEDB Tools Website and API - Release 1.2', url: 'https://help.iedb.org/hc/en-us/articles/23989174535707'},\n    {title: 'Next-Generation IEDB Tools Website and API - Release 1.1', url: 'https://help.iedb.org/hc/en-us/articles/19688305823515'},\n    {title: 'Next-Generation IEDB Tools Website and API - Release 1.0', url: 'https://help.iedb.org/hc/en-us/articles/12422998636955'}\n  ]\n\n  tools = [\n    // {queryParams: {tool: 'tc1'}, name: 'T Cell Prediction - Class I', tags: [\"CD8\", \"bindingAffinity\", \"elutedLigand\", \"epitope\", \"hlaAssociation\", \"immunogenicity\", \"mhcI\", \"tCell\", \"tapProcessing\"], count: 0, routerLink: 't-cell-prediction'},\n    {queryParams: {tool: 'cluster'}, name: 'Cluster', tags: [\"conservation\", \"dataVisualization\", \"hlaAssociation\", \"peptideSimilarity\"], count: 0, routerLink: 'cluster'},\n    {queryParams: {tool: 'pepmatch'}, name: 'PEPMatch', tags: ['conservation', 'peptideSimilarity', 'proteomeSearch'], count: 0, routerLink: 'pepmatch'},\n    {queryParams: {tool: 'pepx'}, name: 'PepX', tags: ['geneExpression', 'rnaExpression', 'transcription'], count: 0, routerLink: '_blank'},\n    {queryParams: {tool: 'pepvcomp'}, name: 'Peptide Variant Comparison', tags: ['bindingAffinity', 'cancer', 'CD8', 'dataVisualization', 'elutedLigand', 'epitope', 'hlaAssociation', 'immunogenicity', 'mhcI', 'neoepitope', 'tCell'], count: 0, routerLink: 'pepcomp'},\n    {queryParams: {tool: 'mutpepgen'}, name: 'Mutated Peptide Generator', tags: ['cancer','neoepitope', 'VCF'], count: 0, routerLink: 'pepcomp'},\n  ]\n\n  @ViewChild('selectedAlleleModal') alleleModal!: ElementRef;\n  @ViewChild('alertModal') alertModal!: ElementRef;\n\n  constructor(\n    private formBuilder: UntypedFormBuilder,\n    private route: Router,\n    private location: Location,\n    private modalService: NgbModal,\n    private _stateService: PipelineStateService,\n    private _service: AlleleSearchService,\n    private _announcementService: AnnouncementService,\n    public alertService: AlertServiceService,\n  ) { }\n\n  ngOnInit(): void {\n    this.tCellForm = this.formBuilder.group({\n      sequences: '',\n    });\n    this.bCellForm = this.formBuilder.group({\n      sequences: '',\n    });\n\n    this._stateService.setPipelineId('');\n    this._stateService.setPipelineSpecId('');\n\n    // this._announcementService.getAnnouncements().subscribe((resp: { [x: string]: any[]; }) => {\n    //   console.log(resp)\n    //   // this.topics = resp['topics'];\n    //   // this.events = resp['topics'].filter(o=>o['tags'][0] === 'event').slice(-3)\n    //   // this.announcements = resp['topics'].filter(o=>o['tags'][0] === 'announcement').slice(-3)\n    // })\n  }\n\n\n  onFileDropped($event: any[]) {\n    console.log($event);\n    const file = $event[0];\n    const fileSize = file.size / 1024; // in kB\n    console.log(file.type);\n    if (fileSize > 20000) {\n      this.alertService.add('File Size is too big! (20mB max)', 'alert-danger');\n      this.open(this.alertModal);\n    }\n    else {\n      this.prepareSequenceFileList($event);\n    }\n  }\n\n  prepareSequenceFileList(files: Array<any>) {\n    console.log(files);\n    // this.fileName = files[0].name;\n    const reader = new FileReader();\n    const myForm = this.tCellForm;\n    for (const item of files) {\n      // console.log(item);\n      reader.readAsText(item);\n      reader.onload = () => {\n        const val = reader.result?.toString() || '';\n        console.log(val);\n        const v = isASCII(val);\n        console.log(v);\n        if (v) {\n          // myForm.patchValue({inputSequenceText: val.substring(0, this.maxCharacters)});\n          const w = isMaxLength(val, this.maxCharacters)\n          if (w) {\n            myForm.patchValue({sequences: val});\n          } else {\n            this.alertService.add(`Sequence is too long - max Sequence length is ${this.maxCharacters.toLocaleString(\"en-US\")} characters`, 'alert-danger');\n            this.open(this.alertModal);\n          }\n          // this.sequenceParser(val);  // auto parser\n        } else {\n          this.alertService.add('Invalid file type.\\nValid file types are .txt, .fa, .fasta, .json, .faa,', 'alert-danger');\n          this.open(this.alertModal);\n        }\n      };\n\n      reader.onerror = () => {\n        console.log(reader.error);\n      };\n      item.progress = 0;\n    }\n  }\n\n  runTCellPrediction() {\n    const initTCellPredictionTool2 = {\n      name: 'T-Cell Prediction',\n      toolGroup: 'mhci',\n      loading: false,\n      submitted: false,\n      appliedFilters: undefined,\n      disabled: false\n    }\n\n    sessionStorage.setItem('sequences', this.tCellForm.get('sequences')?.value);\n    sessionStorage.setItem('selectedAlleles', JSON.stringify(this.selectedAlleles));\n\n    // const source = {\n    //   input_parameters: {\n    //     inputSequenceText: this.tCellForm.get('sequences')?.value,\n    //     alleles: this.selectedAlleles\n    //   }\n    // }\n    // const initState = Object.assign(initTCellPredictionState, source)\n    //\n    // console.log(initState)\n    this._stateService.setInitialStage(initTCellPredictionState)\n    this._stateService.setInitialTool(initTCellPredictionTool2)\n    // this._stateService.setParams(initParams)\n    this._stateService.setPipelineId('')\n    this._stateService.setPipelineSpecId('')\n  }\n\n\n  /** T Cell Prediction Functions */\n  get selectedAlleleLabels() {\n    return this.selectedAlleles.map((o => o.label)).join(', ');\n  }\n\n  get selectedModalAlleleLabels() {\n    return this.modalAlleles.map(((o: { label: string; }) => o.label)).join(', ');\n  }\n\n  search = (text$: Observable<string>) =>\n    text$.pipe(\n      debounceTime(300),\n      distinctUntilChanged(),\n      tap(() => this.searching = true),\n      switchMap(term => {\n          console.log(term);\n          return this._service.search(term).pipe(\n            tap(() => this.searchFailed = false),\n            catchError(() => {\n              this.searchFailed = true;\n              return of([]);\n            }))\n        }\n      ),\n      tap(() => this.searching = false)\n    )\n\n  resultFormatter = (result: any) => {\n    /**\n     *  The function that converts an item from the result list to a string to display in the popup.\n     * */\n    return result.synonyms.length > 0 ? `${result.label} - ${result.synonyms}` : result.label;\n  }\n\n\n  inputFormatter(value: any) {\n    /**\n     * The function that converts an item from the result list to a string to display in the <input> field.\n     * */\n    if (value.label) {\n      return `${value.label}`;\n    }\n    return '';\n  }\n\n  /** Allele Search Functions */\n  onAlleleSelect(e: any, input: any) {\n    // this.inputEl.nativeElement.value = '';\n    e.preventDefault();\n    const selectedAllele = e.item;\n    console.log(selectedAllele);\n    let labels = _.map(this.selectedAlleles, (allele) => allele.label)\n    if (!labels.includes(selectedAllele.label)) {\n      this.selectedAlleles.push(selectedAllele);\n    }\n    // sessionStorage.setItem('selectedAlleles', JSON.stringify(this.selectedAlleles));\n    input.value = '';\n  }\n\n  onAlleleSelectModal({e, input}: { e: any, input: any }) {\n    e.preventDefault();\n    const selectedAllele = e.item;\n    let labels = _.map(this.modalAlleles, (allele) => allele.label)\n    if (!labels.includes(selectedAllele.label)) {\n      this.modalAlleles.push(selectedAllele);\n    }\n    input.value = '';\n  }\n\n  onBlurAlleleSelect(e: any, input: any) {\n    /**\n     * Displays alleles in the text box when out of focus.\n     * */\n    e.preventDefault();\n    input.value = '';\n    input.placeholder = 'Ex. HLA-A*02:01'\n    if(this.selectedAlleles.length) {\n      const labels = _.map(this.selectedAlleles, (o) => {\n        return o.label;\n      });\n      input.value = labels.join(', ');\n    }\n  }\n\n  open(content: any) {\n    this.modalService.open(content, {\n      ariaLabelledBy: 'modal-basic-title',\n      size: 'lg',\n      animation: true,\n      backdrop: 'static'\n    }).result.then((result) => {\n      // this.closeResult = `Closed with: ${result}`;\n      // this.saveState = false;\n      // this.modalOpen = false;\n    }, (reason) => {\n      // this.closeResult = `Dismissed ${HomeComponentComponent.getDismissReason(reason)}`;\n    });\n  }\n\n  onOpenAlleleModal() {\n    this.open(this.alleleModal)\n    this.modalAlleles = [...this.selectedAlleles]\n    console.log(this.modalAlleles)\n  }\n\n\n  dismissAlleleModal() {\n    this.modalService.dismissAll()\n  }\n\n\n  onAlleleClear(input: any) {\n    this.selectedAlleles = []\n    input.value = '';\n    input.placeholder = 'Ex. HLA-A*02:01'\n  }\n\n  onAlleleDeselect(selectedAllele: Allele, input: any) {\n    this.selectedAlleles = _.filter(this.selectedAlleles, (a) => a.label !== selectedAllele.label);\n    if(this.selectedAlleles.length) {\n      const labels = _.map(this.selectedAlleles, (o) => {\n        return o.label;\n      });\n      input.value = labels.join(', ');\n    }\n  }\n\n  onAlleleDeselectModal(index: number, input: { value: string }) {\n    _.pullAt(this.modalAlleles, [index])\n    const labels = this.modalAlleles.map(((o: { label: string; }) => o.label)).join(', ')\n    input.value = this.modalAlleles.length ? labels : ''\n  }\n\n  generate27Alleles(input: any) {\n    const { alleles } = alleleData;\n    this.modalAlleles = _.map(alleles.split(','), (allele) => {return{label: allele, synonym: null, score: null}})\n    input.value = this.selectedAlleleLabels;\n  }\n\n  onSubmitModalAlleles() {\n    this.selectedAlleles = []\n    _.forEach(this.modalAlleles, (selectedAllele) => {\n      this.selectedAlleles.push(selectedAllele);\n    })\n    this.modalService.dismissAll()\n  }\n\n  onAlleleClearModal(input: { value: string; }) {\n    this.modalAlleles = []\n    input.value = ''\n  }\n}\n","<div class=\"container\" id=\"download-all-component\">\n  <div class=\"d-flex flex-column\">\n    <h3 class=\"py-3 text-primary-new mt-2\"> IEDB Tools: Website Usage</h3>\n    <div class=\"p-3 mb-2 bg-secondary-new\">\n<!--      <h5 class=\"text-primary\">Complete Download: Entire IEDB Analysis Resource</h5>-->\n      <p>\n        Data and tools within the IEDB are presented as a public resource and are free to access for all users, including commercial users.\n      </p>\n    </div>\n\n    <h3 class=\"py-3 text-primary-new\"> IEDB Tools: Download</h3>\n    <div class=\"p-3 mb-2 bg-secondary-new\">\n      <h5 class=\"text-primary-new\">Complete Download: Entire IEDB Analysis Resource</h5>\n      <p>\n        For users that would like to run the entire analysis resource locally, a virtual machine image file is available\n        with a paid commercial license. The image is kept in sync with the current version of the IEDB Analysis Resource\n        and is updated on a six month cycle. Please <a href=\"mailto: license@iedb.org\">contact us</a> for details on\n        licensing options.\n      </p>\n    </div>\n\n    <div class=\"p-3 mb-2 bg-secondary-new\">\n      <h5 class=\"text-primary-new\">Standalone Download</h5>\n      <p>\n        Several of the tools hosted on the IEDB NG Tools website are available as command-line tools, freely available\n        to academic users through an open source license. For complete list of all versions of standalone tools used on\n        the Legacy or NG Tools websites, click <a href=\"https://downloads.iedb.org/tools/\" target=\"_blank\">here</a>.\n      </p>\n    </div>\n\n    <div class=\"py-3 mb-2 bg-white\">\n\n      <h3 class=\"py-3 text-primary-new\"> IEDB Tools: License Agreement</h3>\n      <select class=\"mb-3 form-select form-control-lg text-primary-new\" [(ngModel)]=\"selectedTool\">\n        <option value=\"mhc-class-i-binding\">\n          T Cell Prediction - Class I\n        </option>\n        <option value=\"pepmatch\">\n          Pepmatch\n        </option>\n        <option value=\"cluster\">\n          Cluster\n        </option>\n        <option value=\"pepx\">\n          PepX\n        </option>\n        <option value=\"pepcomp\">\n          Peptide Binding Comparison\n        </option>\n        <option value=\"mutgen\">\n          Mutated Peptide Generator\n        </option>\n      </select>\n      <div class=\"p-3 mb-2 bg-secondary-new\">\n        <h5 class=\"text-primary-new\">Description</h5>\n        <p class=\"py-3\" *ngIf=\"selectedTool==='mhc-class-i-binding'\">\n          This tool wraps up several methods to support the prediction of class I peptide: MHC binding, elution, immunogenicity, and antigen processing\n        </p>\n        <p class=\"py-3\" *ngIf=\"selectedTool==='cluster'\">\n          This tool groups epitopes into clusters based on sequence identity using one of 3 different algorithms\n        </p>\n        <p class=\"py-3\" *ngIf=\"selectedTool==='pepmatch'\">\n          The PepMatch standalone includes all functionality to scan a list of peptides for closely related sequences in\n          custom proteome databases using an ultra-efficient, deterministic algorithm.\n        </p>\n        <p class=\"py-3\" *ngIf=\"selectedTool==='pepx'\">\n          The Peptide eXpression annotator (pepX) takes a peptide as input,\n          identifies from which proteins the peptide can be derived, and returns\n          an estimate of the expression level of those source proteins from selected\n          public databases.\n        </p>\n        <p class=\"py-3\" *ngIf=\"selectedTool==='pepcomp'\">\n          This package is a wrapper around T Cell Class I tool and will run predictors\n          from that tool (binding, elution, immunogenicity) on a set of paired peptides\n          and compare the results.\n        </p>\n        <p class=\"py-3\" *ngIf=\"selectedTool==='mutgen'\">\n          The Mutant Peptide Generator tool will take a two-sample, SNPEff-annotated VCF as\n          input and generate predicted neo-peptides and the reference / WT peptides\n          with which they pair.\n        </p>\n\n        <h5 class=\"text-primary-new\">License Agreements </h5>\n        <p class=\"py-3\">\n          All standalone tools are distributed under the <a href=\"javascript:void(0);\" (click)=\"downloadNonProfit()\">Non-Profit Open Software License (Non-Profit OSL) version 3.0.</a>\n          Some tools, developed in coordination with the Technical University of Denmark, are distributed with <a href=\"javascript:void(0);\" (click)=\"downloadDTU()\"> additional\n          terms and conditions</a>. By downloading the tools, you are implicitly agreeing to the terms of all applicable\n          licenses.\n        </p>\n      </div>\n\n      <a type=\"button\" class=\"mt-2 btn btn-sky-blue btn-lg text-white\" (click)=\"onAgreeAndDownload()\">\n        Agree and Download\n      </a>\n    </div>\n\n  </div>\n</div>\n","import { Component, OnInit } from '@angular/core';\nimport {NgModel} from \"@angular/forms\";\nimport onCsvDownloadAllClickedNew from \"../util/on-csv-download\";\nimport {HttpClient, HttpHeaders} from \"@angular/common/http\";\nimport {ActivatedRoute, Router} from \"@angular/router\";\nimport {Location} from \"@angular/common\";\n// import * as data from \"./\"\n\n@Component({\n  selector: 'app-download-all',\n  templateUrl: './download-all.component.html',\n  styleUrls: ['./download-all.component.scss']\n})\nexport class DownloadAllComponent implements OnInit {\n\n  selectedTool = 'mhc-class-i-binding'\n\n  constructor(\n    private http: HttpClient,\n    private router: Router, private activatedRoute: ActivatedRoute, private location: Location,\n  ) {\n    this.selectedTool = this.router.getCurrentNavigation()?.extras?.state ? this.router.getCurrentNavigation()!.extras.state?.tool : 'mhc-class-i-binding'\n  }\n\n  ngOnInit(): void {}\n\n  onAgreeAndDownload() {\n    /**\n     T Cell, Class I\n     http://downloads.iedb.org/nextgen-tools/retrieve_package.php?tool=tcell_mhci\n\n     Cluster\n     http://downloads.iedb.org/nextgen-tools/retrieve_package.php?tool=cluster\n\n     PepMatch (will be uploaded soon)\n     http://downloads.iedb.org/nextgen-tools/retrieve_package.php?tool=pepmatch\n     * */\n    switch (this.selectedTool){\n      case 'mhc-class-i-binding':\n        window.open('https://downloads.iedb.org/nextgen-tools/retrieve_package.php?tool=tcell_mhci', '_self')\n        return\n      case 'pepmatch':\n        // window.open('https://github.com/IEDB/PEPMatch', \"_blank\")\n        window.open('https://downloads.iedb.org/nextgen-tools/retrieve_package.php?tool=pepmatch', \"_self\")\n        return\n      case 'cluster':\n        window.open('https://downloads.iedb.org/nextgen-tools/retrieve_package.php?tool=cluster', '_self')\n        return\n      case 'pepx':\n        window.open('https://downloads.iedb.org/nextgen-tools/retrieve_package.php?tool=pepx', '_self')\n        return\n      case 'pepcomp':\n        window.open('https://downloads.iedb.org/nextgen-tools/retrieve_package.php?tool=peptide_variant_comparison', '_self')\n        return\n      case 'mutgen':\n        window.open('https://downloads.iedb.org/nextgen-tools/retrieve_package.php?tool=mutated_peptide_generator', '_self')\n        return\n      default:\n        return\n    }\n  }\n\n  downloadNonProfit() {\n    const name = 'LICENSE-NonProfitOSL3'\n\n    function downLoadFile(data: any, type: string) {\n      const blob = new Blob([data], {type: type}); // thx: http://stackoverflow.com/a/18925211\n      const a = document.createElement('a');\n      a.setAttribute('style', 'display:none;');\n      document.body.appendChild(a);\n      const contentType = 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet;charset=UTF-16';\n      // var blob = new Blob([csvData], { type: contentType });\n      a.href = window.URL.createObjectURL(blob);\n      a.download = `${name}`\n      a.click();\n    }\n\n    this.http.get(`assets/LICENSES/${name}`, { responseType: 'text' })\n      .subscribe(data => {\n        downLoadFile(data, 'txt')\n        // console.log(data)\n      });\n  }\n\n  downloadDTU() {\n    const name = 'LICENSE-DTU'\n\n    function downLoadFile(data: any, type: string) {\n      const blob = new Blob([data], {type: type}); // thx: http://stackoverflow.com/a/18925211\n      const a = document.createElement('a');\n      a.setAttribute('style', 'display:none;');\n      document.body.appendChild(a);\n      const contentType = 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet;charset=UTF-16';\n      // var blob = new Blob([csvData], { type: contentType });\n      a.href = window.URL.createObjectURL(blob);\n      a.download = `${name}`\n      a.click();\n    }\n\n    this.http.get(`assets/LICENSES/${name}`, { responseType: 'text' })\n      .subscribe(data => {\n        downLoadFile(data, 'txt')\n        // console.log(data)\n      });\n  }\n\n}\n","import {HttpClient, HttpHeaders} from '@angular/common/http';\n\nexport default function onCsvDownloadAllClickedNew(API_URL: string, http: HttpClient, extension = 'txt') {\n  /**\n   * Creates a csv file of all the query_set in the backend.\n   * */\n  // console.log(API_URL);\n  const tableType = API_URL.split('/')[API_URL.split('/').length - 1];\n\n  const headers = new HttpHeaders();\n  headers.append('Accept', 'application/vnd.openxmlformatsofficedocument.spreadsheetml.sheet');\n\n  /**\n   * Method is use to download file.\n   * @param data - Array Buffer data\n   * @param type - type of the document.\n   */\n  function downLoadFile(data: any, type: string) {\n    const blob = new Blob([data], {type: type}); // thx: http://stackoverflow.com/a/18925211\n    const a = document.createElement('a');\n    a.setAttribute('style', 'display:none;');\n    document.body.appendChild(a);\n    const contentType = 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet;charset=UTF-16';\n    // var blob = new Blob([csvData], { type: contentType });\n    a.href = window.URL.createObjectURL(blob);\n    a.download = `${tableType}.${extension}`;\n    a.click();\n  }\n\n\n  const resp = http.get<any>(API_URL, {responseType: 'arraybuffer' as 'json', headers: headers,});\n\n  resp.subscribe((response) => {\n    downLoadFile(response, 'application/ms-excel');\n  });\n}\n","import * as _ from \"lodash\";\n\nexport function columnListToObject(columns: any[], tool_group: string)\n{\n  /**\n   * Creates column object that contains\n\n   * */\n  let colObj = {}\n\n  _.forEach(columns, (col, i) => {\n    const {type, value_limits} = col\n    // console.log(col.filterKey)\n    // console.log(value_limits)\n    if(type==='text' && col.value_limits.selectedValues.length) {\n      /** Text filter */\n      const key = col.filterKey;\n      const { selectedValues } = col.value_limits\n      const searchString = selectedValues.length == 1 ? selectedValues[0] : selectedValues.join('|')\n\n      // @ts-ignore\n      colObj[key] = {\n        search: {\n          search: searchString\n        },\n        tool_group: tool_group,\n        source: columns[i]['source'],\n        name: columns[i]['name']\n      }\n    }\n    //@ts-ignore\n    else if ((type==='int'|| type==='float') &&\n      (value_limits.minValue || value_limits.maxValue || value_limits.minValue === 0 || value_limits.maxValue === 0)) {\n      /** Number filter */\n        // this._stateService.applyFiltersToParams()\n      const key = col.filterKey;\n      // @ts-ignore\n      colObj[key] = {\n        search: {\n          min: col.value_limits.minValue,\n          max: col.value_limits.maxValue\n        },\n        tool_group: tool_group,\n        source: columns[i]['source'],\n        name: columns[i]['name']\n      };\n    }\n  })\n\n  return colObj\n}\n\nexport function columnObjectToList(str: string) {\n  try {\n    JSON.parse(str);\n  } catch (e) {\n    return false;\n  }\n  return true;\n}\n","import { Injectable } from '@angular/core';\nimport _ from 'lodash';\nimport {isASCII} from \"../../util/string-helpers\";\n\n@Injectable({\n  providedIn: 'root'\n})\nexport class SequenceParserService {\n  /**\n   * contains functions to parse string and structure them in filteredSequence.\n   * Also counts number of amino acids -> numOfAA\n\n   * */\n  public filteredSequences: { name: string, sequences: string }[] = [];\n  public numOfAA!: number;\n  public seqFormat: string = '';\n\n  fastaParser(fastaTexts: string): void {\n    this.filteredSequences = [];\n    const sequenceArray = fastaTexts.split('>');\n    sequenceArray.shift();\n    this.numOfAA = 0;\n    _.forEach(sequenceArray, (seq, i) => {\n      const newObj = {\n        name: getFirstLine(seq),\n        sequences: getSequence(seq)\n      };\n      this.filteredSequences.push(newObj);\n      this.numOfAA += newObj.sequences.length;\n    });\n    this.seqFormat = 'FASTA'\n  }\n\n  fastaValidate(fastaTexts: string): boolean {\n    /**\n     Validates the first 20 raw string lines\n     *\n     * */\n    let sequenceArray = fastaTexts.split('\\n').slice(0, 20);\n\n    let invalid = false;\n\n    // let nameRegexp = new RegExp('^[a-zA-Z0-9.\\\\-_>]+$')\n    let alphabetRegexp = new RegExp('^[a-zA-Z ]+$')\n\n    _.forEach(sequenceArray, (val, i): any => {\n      // console.log(i)\n      // console.log(val)\n      // console.log(typeof val)\n\n      if (val === ''){\n        // console.log('break0')\n        return false;\n      }\n      if (val[0] === '>' && !isASCII(val)) { // name\n        // console.log('break1');\n        invalid=true; return false;\n      }\n      else if (val[0] !== '>' && !alphabetRegexp.test(val)) {\n        // console.log('break2');\n        invalid=true; return false;\n      }\n    });\n    this.seqFormat = 'FASTA'\n    return !invalid;\n  }\n\n  jsonParser(jsonTexts: string): void {\n    this.filteredSequences = [];\n    const parseObj = JSON.parse(jsonTexts);\n    this.numOfAA = 0;\n    if (Array.isArray(parseObj)) {\n      this.filteredSequences = parseObj;\n      this.numOfAA = 1;\n    } else {\n      this.filteredSequences.push(parseObj);\n      this.numOfAA += parseObj.sequence.length;\n    }\n    this.seqFormat = 'JSON'\n  }\n\n  namedWhiteSpaceParser2(inputString: string): void {\n    /**\n     Two columns separated by ' ' or '\\t'\n     *\n     EX:\n     \"seq1 DDEDSKQNIFH\n     my_favorite_seq ADPGPHLMG\n     denv4.3 KAVELGVKLLHA\n     this-is-a_validName2 QLQNLGINP\"\n\n     TODO: As a first pass, I think the valid characters for names should be:\n\n     a-z (case insensitive)\n     0-9\n     - (hyphen)\n     . (period)\n     _ (underscore)\n\n     * */\n    this.filteredSequences = [];\n\n    // console.log(inputString);\n    let sequenceArray = inputString.split('\\n');\n    sequenceArray = _.filter(sequenceArray, (o) => o !== '');\n    // console.log(sequenceArray);\n    this.numOfAA = 0;\n    _.forEach(sequenceArray, (line) => {\n      const arr = line.includes(' ') ? line.split(' ') : line.split('\\t')\n      // console.log(arr);\n      const newObj = {\n        name: arr[0],\n        sequences: arr[1]\n      };\n      this.filteredSequences.push(newObj);\n      this.numOfAA += newObj.sequences.length;\n    });\n    this.seqFormat = 'Named White Space'\n  }\n\n  namedWhiteSpaceValidate(inputString: string, split: string): boolean {\n    /**\n     Two columns separated by ' ' or '\\t'\n     *\n     EX:\n     \"seq1 DDEDSKQNIFH\n     my_favorite_seq ADPGPHLMG\n     denv4.3 KAVELGVKLLHA\n     this-is-a_validName2 QLQNLGINP\"\n\n     TODO: As a first pass, I think the valid characters for names should be:\n\n     a-z (case insensitive)\n     0-9\n     - (hyphen)\n     . (period)\n     _ (underscore)\n\n\n     ^[\\w\\_\\-\\.]+$\n\n     [ACDEFGHIKLMNPQRSTVWYacdefghiklmnpqrstvwy]+\n\n     TODO: Document\n     regexp1\n     regexp2\n      general function\n\n     also take out this.filteredSequence\n\n     * */\n    this.filteredSequences = [];\n\n    // console.log(inputString);\n\n    let sequenceArray = inputString.split('\\n').slice(0, 10);\n    sequenceArray = _.filter(sequenceArray, (o) => o !== '');\n    // console.log(sequenceArray);\n    this.numOfAA = 0;\n    let arr: string[] = [];\n    let invalid = false;\n    /**\n     do\n     statement\n     while (condition);\n     * */\n    let separator = 'Space'\n    let regexp1 = new RegExp('^[a-zA-Z0-9.\\\\-_]+$')\n    let regexp2 = new RegExp('^[a-zA-Z]+$')\n    _.forEach(sequenceArray, (line, i): any => {\n      // console.log(i)\n      // split by it's separator\n      arr = line.split(split)\n      // console.log(arr)\n      if(\n        arr.length !== 2 || !regexp1.test(arr[0]) || !regexp2.test(arr[1])\n      ){console.log('break'); invalid=true; return false}\n\n      if(line.includes(' ')){\n        // arr = line.split(' ')\n        separator = 'Space'\n      } else if (line.includes('\\t')){\n        // console.log('inside tab if statement')\n        // arr = line.split('\\t')\n        separator = 'Tab'\n      } else if (line.includes('\\s')){\n        // arr = line.split('\\s')\n        separator = 'Space'\n      }\n      // console.log(separator)\n\n    });\n    this.seqFormat = `Named White Space (${separator})`\n    // console.log(sequenceArray)\n    // console.log(this.filteredSequences)\n    return !invalid;\n\n    // return this.filteredSequences.length <= 10\n  }\n\n  // namedWhiteSpaceParser(inputString: string): void {\n  //   this.filteredSequences = [];\n  //\n  //   console.log(inputString);\n  //   let sequenceArray = inputString.split('\\n');\n  //   sequenceArray = _.filter(sequenceArray, (o) => o !== '');\n  //   this.numOfAA = 0;\n  //   _.forEach(sequenceArray, (seq) => {\n  //     const newObj = {\n  //       name: getFirstLine(seq),\n  //       sequences: getSequence(seq)\n  //     };\n  //     this.filteredSequences.push(newObj);\n  //     this.numOfAA += newObj.sequences.length;\n  //   });\n  // }\n\n  unnamedWhiteSpaceValidate(inputString: string): boolean {\n    this.filteredSequences = [];\n\n    console.log(inputString);\n    let sequenceArray = [];\n    if (inputString.includes(' ')) {\n      sequenceArray = inputString.split(' ').slice(0, 10);\n    } else {\n      sequenceArray = inputString.split('\\n').slice(0, 10);\n    }\n    sequenceArray = _.filter(sequenceArray, (o) => o !== '');\n    this.numOfAA = 0;\n    let arr: string[] = [];\n    let invalid = false;\n\n    let regexp = new RegExp('^[a-zA-Z\\s\\t]+$')\n    _.forEach(sequenceArray, (line, i) : any=> {\n      // console.log(i)\n      // split by it's separator\n      // console.log(arr)\n      if(\n        !regexp.test(line)\n      ){console.log('break'); invalid=true; return false}\n    });\n    this.seqFormat = 'Un-named White Space'\n    // console.log(sequenceArray)\n    // console.log(this.filteredSequences)\n    if(invalid) {\n      return false\n    }\n    return this.filteredSequences.length <= 10\n  }\n\n  // unnamedWhiteSpaceParser(inputString: string): void {\n  //   this.filteredSequences = [];\n  //\n  //   console.log(inputString);\n  //   let sequenceArray = [];\n  //   if (inputString.includes(' ')) {\n  //     sequenceArray = inputString.split(' ');\n  //   } else {\n  //     sequenceArray = inputString.split('\\n');\n  //   }\n  //   sequenceArray = _.filter(sequenceArray, (o) => o !== '');\n  //   this.numOfAA = 0;\n  //   _.forEach(sequenceArray, (seq) => {\n  //     const newObj = {\n  //       name: getFirstLine(seq),\n  //       sequences: getSequence(seq)\n  //     };\n  //     this.filteredSequences.push(newObj);\n  //     this.numOfAA += newObj.sequences.length;\n  //   });\n  //   this.seqFormat = 'Un-named White Space'\n  // }\n\n}\n\n\n\nfunction getFirstLine(text: string) {\n  let index = text.indexOf('\\n');\n  if (index === -1) {\n    index = NaN;\n  }\n  return text.substring(0, index);\n}\n\nfunction getSequence(text: string) {\n  let index = text.indexOf('\\n');\n  if (index === -1) {\n    index = NaN;\n  }\n  return text.substring(index).replace(/\\n/g, '');\n}\n","<ng-container [formGroup]=\"ogFormGroup\">\n  <div class=\"form-group p-3 \">\n    <div class=\"d-flex flex-row\">\n      <!--MHC Binding-->\n      <label class=\"justify-content-center align-self-center mr-auto p-3\"> MHC-I Binding/Elution </label>\n      <div class=\"justify-content-center align-content-center flex-fill p-3\">\n        <label for=\"predictionMethodSelect\">Prediction Method</label>\n        <select *ngIf=\"predictionOption.length\" id=\"predictionMethodSelect\" formControlName=\"method\"\n                class=\"form-select form-control w-100\" [attr.disabled]=\"disabled ? '' : null\">\n          <option [value]=\"option['short_name']\"\n                  *ngFor=\"let option of predictionOption\">{{option['display_name']}}</option>\n        </select>\n        <div *ngIf=\"!predictionOption.length\" class=\"d-flex justify-content-center col\">\n          <div class=\"spinner-border text-primary align-self-center p-3 mb-3\" role=\"status\">\n            <span class=\"sr-only visually-hidden\">Loading...</span>\n          </div>\n        </div>\n      </div>\n      <div class=\"justify-content-end align-self-center align-content-center p-3\">\n        <button type=\"button\" class=\"btn-close\" aria-label=\"Close\" (click)=\"onCancelClick()\" [disabled]=\"disabled\">\n        </button>\n      </div>\n    </div>\n  </div>\n</ng-container>\n","import {Component, EventEmitter, OnInit, Output, Input} from '@angular/core';\nimport {ControlContainer, UntypedFormBuilder} from '@angular/forms'\n\n@Component({\n  selector: 'app-mhc-binding-formgroup',\n  templateUrl: './mhc-binding-formgroup.component.html',\n  styleUrls: ['./mhc-binding-formgroup.component.scss']\n})\nexport class MhcBindingFormgroupComponent implements OnInit {\n\n  @Input() modelIndex: number | any;\n  @Input() disabled: boolean | any;\n  @Input() predictionOption: {\n    display_name: string,\n    short_name: string,\n    group: string,\n    source: string,\n    has_ic50: boolean\n  }[] = [];\n\n  @Output() emitPredictionModelIndex = new EventEmitter<number>();\n  addProcessing: boolean = false;\n  public ogFormGroup: any = null;\n\n  constructor(\n    public controlContainer: ControlContainer,\n    private fb: UntypedFormBuilder\n  ) {\n  }\n\n  ngOnInit(): void {\n    this.ogFormGroup = this.controlContainer.control;\n  }\n\n  onCancelClick() {\n    this.emitPredictionModelIndex.emit(this.modelIndex);\n  }\n\n  addProcessingFormGroup(proteasome = 'immuno', tap_precursor = 1, tap_alpha = 0.2) {\n    this.ogFormGroup.addControl(\n      'processing',\n      this.fb.group({\n        proteasome: this.fb.control(proteasome),\n        tap_precursor: this.fb.control(tap_precursor),\n        tap_alpha: this.fb.control(tap_alpha)\n      })\n    )\n  }\n\n  removeProcessingFormGroup() {\n    this.ogFormGroup.removeControl('processing')\n  }\n\n  onAddProcessingChange() {\n    this.addProcessing = !this.addProcessing\n    this.addProcessing ? this.addProcessingFormGroup() : this.removeProcessingFormGroup()\n  }\n}\n","<ng-container [formGroup]=\"ogFormGroup\">\n  <div class=\"form-group p-3 d-flex flex-row\">\n    <label class=\"justify-content-center align-self-center p-3\">\n      Class I pMHC Immunogenicity\n    </label>\n    <div class=\"justify-content-center align-self-stretch align-content-center flex-fill p-3\">\n\n      <label for=\"position-input\">Positions To Mask</label>\n      <!--      Select -->\n      <select id=\"position-input\" formControlName=\"mask_choice\" class=\"form-select form-control w-100\"\n              [attr.disabled]=\"disabled ? '' : null\">\n        <option [value]=\"'default'\">1,2,C Terminal (Default)</option>\n        <option [value]=\"'by_allele'\">Allele Specific</option>\n        <option [value]=\"'custom'\">Custom</option>\n      </select>\n      <input id=\"custom-position\" class=\"form-control\" formControlName=\"position_to_mask\" type=\"text\"\n             *ngIf=\"mask_choice === 'custom'\">\n    </div>\n    <!--    Cancel Button -->\n    <div class=\"justify-content-end align-self-center align-content-center p-3\">\n      <button type=\"button\" class=\"btn-close\" aria-label=\"Close\" (click)=\"onCancelClick()\" [disabled]=\"disabled\">\n      </button>\n    </div>\n  </div>\n</ng-container>\n","import {Component, EventEmitter, Input, OnInit, Output} from '@angular/core';\nimport {ControlContainer} from '@angular/forms'\n\n@Component({\n  selector: 'app-pmhc-immunogenicity-formgroup',\n  templateUrl: './pmhc-immunogenicity-formgroup.component.html',\n  styleUrls: ['./pmhc-immunogenicity-formgroup.component.scss']\n})\nexport class PmhcImmunogenicityFormgroupComponent implements OnInit {\n  @Input() modelIndex: number | any;\n  @Input() disabled: boolean | any;\n\n  @Output() emitPredictionModelIndex = new EventEmitter<number>();\n  public ogFormGroup: any = null;\n\n  constructor(public controlContainer: ControlContainer) {\n  }\n\n  ngOnInit(): void {\n    this.ogFormGroup = this.controlContainer.control;\n  }\n\n  get mask_choice() {\n    return this.ogFormGroup.controls['mask_choice'].value\n  }\n\n  onCancelClick() {\n    this.emitPredictionModelIndex.emit(this.modelIndex);\n  }\n\n}\n","<div class=\"container-fluid p-2 mb-5 d-flex flex-column\">\n  <!--  Table buttons -->\n  <div class=\"d-flex flex-row p-2 align-self-center\" role=\"group\" aria-label=\"button-groups\">\n\n    <button class=\"btn btn-link text-dark d-flex flex-column justify-content-center align-items-center\"\n            type=\"button\"\n            aria-haspopup=\"true\" aria-expanded=\"false\" [matMenuTriggerFor]=\"animals\">\n      <svg width=\"1em\" height=\"1em\" viewBox=\"0 0 16 16\" class=\"bi bi-download\" fill=\"currentColor\"\n           xmlns=\"http://www.w3.org/2000/svg\">\n        <path fill-rule=\"evenodd\"\n              d=\"M.5 8a.5.5 0 0 1 .5.5V12a1 1 0 0 0 1 1h12a1 1 0 0 0 1-1V8.5a.5.5 0 0 1 1 0V12a2 2 0 0 1-2 2H2a2 2 0 0 1-2-2V8.5A.5.5 0 0 1 .5 8z\"/>\n        <path fill-rule=\"evenodd\"\n              d=\"M5 7.5a.5.5 0 0 1 .707 0L8 9.793 10.293 7.5a.5.5 0 1 1 .707.707l-2.646 2.647a.5.5 0 0 1-.708 0L5 8.207A.5.5 0 0 1 5 7.5z\"/>\n        <path fill-rule=\"evenodd\" d=\"M8 1a.5.5 0 0 1 .5.5v8a.5.5 0 0 1-1 0v-8A.5.5 0 0 1 8 1z\"/>\n      </svg>\n      Download\n    </button>\n    <mat-menu #animals=\"matMenu\">\n      <button mat-menu-item [matMenuTriggerFor]=\"vertebrates\">All rows</button>\n      <button mat-menu-item [matMenuTriggerFor]=\"invertebrates\">Displayed rows</button>\n    </mat-menu>\n\n    <mat-menu #vertebrates=\"matMenu\">\n      <button mat-menu-item (click)=\"downloadAllTsv()\">TSV</button>\n      <button mat-menu-item (click)=\"downloadAllCsv()\">CSV</button>\n      <button mat-menu-item (click)=\"downloadAllJSON()\">JSON</button>\n    </mat-menu>\n    <mat-menu #invertebrates=\"matMenu\">\n      <button mat-menu-item (click)=\"downloadTSV()\">TSV</button>\n      <button mat-menu-item (click)=\"downloadCSV()\">CSV</button>\n      <button mat-menu-item (click)=\"downloadJSON()\">JSON</button>\n    </mat-menu>\n\n<!--    <button type=\"button\"-->\n<!--            class=\"btn btn-link text-dark d-flex flex-column justify-content-center align-items-center\"-->\n<!--            (click)=\"getTableState()\">-->\n<!--      <svg width=\"1em\" height=\"1em\" viewBox=\"0 0 16 16\" class=\"bi bi-share\" fill=\"currentColor\"-->\n<!--           xmlns=\"http://www.w3.org/2000/svg\">-->\n<!--        <path fill-rule=\"evenodd\"-->\n<!--              d=\"M11.724 3.947l-7 3.5-.448-.894 7-3.5.448.894zm-.448 9l-7-3.5.448-.894 7 3.5-.448.894z\"/>-->\n<!--        <path fill-rule=\"evenodd\"-->\n<!--              d=\"M13.5 4a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3zm0 1a2.5 2.5 0 1 0 0-5 2.5 2.5 0 0 0 0 5zm0 10a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3zm0 1a2.5 2.5 0 1 0 0-5 2.5 2.5 0 0 0 0 5zm-11-6.5a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3zm0 1a2.5 2.5 0 1 0 0-5 2.5 2.5 0 0 0 0 5z\"/>-->\n<!--      </svg>-->\n<!--      Share-->\n<!--    </button>-->\n    <button type=\"button\"\n            class=\"btn btn-link text-dark d-flex flex-column justify-content-center align-items-center\"\n            (click)=clearTableState()>\n      <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n           class=\"bi bi-arrow-clockwise\" viewBox=\"0 0 16 16\">\n        <path fill-rule=\"evenodd\" d=\"M8 3a5 5 0 1 0 4.546 2.914.5.5 0 0 1 .908-.417A6 6 0 1 1 8 2v1z\"/>\n        <path\n          d=\"M8 4.466V.534a.25.25 0 0 1 .41-.192l2.36 1.966c.12.1.12.284 0 .384L8.41 4.658A.25.25 0 0 1 8 4.466z\"/>\n      </svg>\n      Reset Table\n    </button>\n    <button type=\"button\"\n            class=\"btn btn-link text-dark d-flex flex-column justify-content-center align-items-center\"\n            (click)=\"onOpenDisplayColumnModal()\">\n      <svg width=\"1em\" height=\"1em\" viewBox=\"0 0 16 16\" class=\"bi bi-table\" fill=\"currentColor\"\n           xmlns=\"http://www.w3.org/2000/svg\">\n        <path fill-rule=\"evenodd\"\n              d=\"M0 2a2 2 0 0 1 2-2h12a2 2 0 0 1 2 2v12a2 2 0 0 1-2 2H2a2 2 0 0 1-2-2V2zm15 2h-4v3h4V4zm0 4h-4v3h4V8zm0 4h-4v3h3a1 1 0 0 0 1-1v-2zm-5 3v-3H6v3h4zm-5 0v-3H1v2a1 1 0 0 0 1 1h3zm-4-4h4V8H1v3zm0-4h4V4H1v3zm5-3v3h4V4H6zm4 4H6v3h4V8z\"/>\n      </svg>\n      Display Columns\n    </button>\n    <button *ngIf=\"!tableStateSaving; else savingButton\"\n            type=\"button\"\n            [ngbTooltip]=\"inputChange ? saveTableStateTipContent : null\"\n            [disabled]=\"!inputChange\"\n            [ngClass]=\"inputChange ? 'btn btn-warning-new d-flex flex-column justify-content-center align-items-center' : 'btn btn-link text-dark d-flex flex-column justify-content-center align-items-center'\"\n            (click)=\"onSaveTableState()\">\n      <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"1em\" height=\"1em\" fill=\"currentColor\" class=\"bi bi-save\"\n           viewBox=\"0 0 16 16\">\n        <path\n          d=\"M2 1a1 1 0 0 0-1 1v12a1 1 0 0 0 1 1h12a1 1 0 0 0 1-1V2a1 1 0 0 0-1-1H9.5a1 1 0 0 0-1 1v7.293l2.646-2.647a.5.5 0 0 1 .708.708l-3.5 3.5a.5.5 0 0 1-.708 0l-3.5-3.5a.5.5 0 1 1 .708-.708L7.5 9.293V2a2 2 0 0 1 2-2H14a2 2 0 0 1 2 2v12a2 2 0 0 1-2 2H2a2 2 0 0 1-2-2V2a2 2 0 0 1 2-2h2.5a.5.5 0 0 1 0 1H2z\"/>\n      </svg>\n      Save Table State\n    </button>\n    <ng-template #saveTableStateTipContent>\n      Please save table state in order to pipe to the next tool.\n    </ng-template>\n    <ng-template #savingButton>\n      <button type=\"button\"\n              [style.background-color]=\"'#E8D491'\"\n              class=\"btn btn-link text-dark d-flex flex-column justify-content-center align-items-center\">\n        <div class=\"spinner-border spinner-border-sm\" role=\"status\">\n          <span class=\"visually-hidden sr-only\">Loading...</span>\n        </div>\n        Saving...\n      </button>\n    </ng-template>\n\n  </div>\n  <!--   Table -->\n  <div class=\"row justify-content-center\">\n    <div class=\"col-auto\">\n      <table datatable [dtOptions]=\"dtOptions\" [dtTrigger]=\"dtTrigger\"\n             [style.border-color]=\"inputChange ? '#E8D491' : null\"\n             class='table table-responsive table-fit table-hover table-bordered px-2 sticky-header'\n             [id]=\"'DataTables_'.concat(tool_group).concat(table_name)\">\n        <colgroup>\n          <col\n            *ngFor=\"let column of visibleColumns;\" [id]=\"'column'.concat(column.name)\"\n            [ngStyle]=\"{'background-color': (dataToPipe === 'peptide_table'.concat('.', column.name) && table_name==='peptide_table') ||\n                                            (dataToPipe === 'peptide_gene_summary_table'.concat('.', column.name) && table_name==='peptide_gene_summary_table') ||\n                                            ([dataToPipe, dataToPipe2].includes( 'unique_peptide'.concat('.', column.name)) && table_name==='unique_peptide') ||\n                                            ([dataToPipe, dataToPipe2].includes( 'peptide'.concat('.', column.name)) && table_name==='peptide') ? '#759dc3' : null,}\"\n          />\n        </colgroup>\n\n        <thead>\n        <tr>\n          <th *ngFor=\"let column of columns; index as i;\" class=\"header\">\n            {{column.display_name}}\n\n              <div ngbDropdown\n                   #filterDropdown=\"ngbDropdown\"\n                   (openChange)=\"checkClosedDropdown($event)\"\n                   *ngIf=\"column['value_limits']\"\n                   class=\"d-inline-block\"\n                   container=\"body\"\n                   display=\"dynamic\">\n                <button [className]=\"column['value_limits']!['applied'] ? 'btn btn-sm btn-dark-blue-grey' : 'btn btn-sm btn-white-blue'\"\n                        ngbDropdownToggle\n                        (click)=\"stopProp($event); checkOpenedDropdown(i)\">\n                  <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\" class=\"bi bi-funnel\"\n                       viewBox=\"0 0 16 16\">\n                    <path\n                      d=\"M1.5 1.5A.5.5 0 0 1 2 1h12a.5.5 0 0 1 .5.5v2a.5.5 0 0 1-.128.334L10 8.692V13.5a.5.5 0 0 1-.342.474l-3 1A.5.5 0 0 1 6 14.5V8.692L1.628 3.834A.5.5 0 0 1 1.5 3.5v-2zm1 .5v1.308l4.372 4.858A.5.5 0 0 1 7 8.5v5.306l2-.666V8.5a.5.5 0 0 1 .128-.334L13.5 3.308V2h-11z\"/>\n                  </svg>\n                </button>\n                <div ngbDropdownMenu (click)=\"stopProp($event)\">\n                  <button ngbDropdownItem (click)=\"onSortColumns(i, 'asc')\">Sort A&rarr;Z</button>\n                  <button ngbDropdownItem (click)=\"onSortColumns(i, 'desc')\">Sort Z&rarr;A</button>\n                  <div class=\"dropdown-divider\"></div>\n                  <!--      text filter, number filter  form      -->\n                  <div>\n                    <!--                  <div class=\"px-1 py-3\">-->\n                    <ng-container *ngIf=\"['int', 'float'].includes(column['type']); else stringFilterTemplate;\">\n                      <form class=\"number-filter-form p-2\">\n                        <div class=\"form-group\">\n                          <label>Min:</label>\n                          <input type=\"number\"\n                                 [className]=\"'min'.concat(i.toString()).concat(tool_group).concat(table_name).concat(' form-control')\"\n                                 [placeholder]=\"columns[i]['value_limits']!['min']\"\n                                 [value]=\"columns[i]['value_limits']!['minValue']\">\n                        </div>\n\n                        <div class=\"form-group\">\n                          <label>Max: </label>\n                          <input type=\"number\" class=\"form-control\"\n                                 [className]=\"'max'.concat(i.toString()).concat(tool_group).concat(table_name).concat(' form-control')\"\n                                 [placeholder]=\"columns[i]['value_limits']!['max']\"\n                                 [value]=\"columns[i]['value_limits']!['maxValue']\">\n                        </div>\n\n                        <div class=\"flex-row d-flex\">\n                          <button type=\"button\" class=\"btn btn-secondary\"\n                                  (click)=\"onClearNumberFilter(i); filterDropdown.close()\">Clear\n                          </button>\n                          <button type=\"button\" class=\"btn btn-dark-blue-grey text-white\"\n                                  (click)=\"onNumberFilter(i); filterDropdown.close();\">\n                            OK\n                          </button>\n                        </div>\n                      </form>\n                    </ng-container>\n                    <ng-template #stringFilterTemplate>\n\n                      <form class=\"string-filter-form\">\n                        <div class=\"form-group row p-2\">\n                          <label [for]=\"'textFilter'.concat(i.toString())\">Filter by value: </label>\n                          <div class=\"input-group input-group-sm\">\n                            <input type=\"text\" class=\"form-control\"\n                                   [id]=\"'textFilter'.concat(i.toString())\"\n                                   (keyup)=\"onFilterPossibleValues($event, i)\">\n                            <div class=\"input-group-append\">\n                          <span class=\"input-group-text\">\n                            <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n                                 class=\"bi bi-search\" viewBox=\"0 0 16 16\">\n                              <path\n                                d=\"M11.742 10.344a6.5 6.5 0 1 0-1.397 1.398h-.001c.03.04.062.078.098.115l3.85 3.85a1 1 0 0 0 1.415-1.414l-3.85-3.85a1.007 1.007 0 0 0-.115-.1zM12 6.5a5.5 5.5 0 1 1-11 0 5.5 5.5 0 0 1 11 0z\"/>\n                            </svg>\n                          </span>\n                            </div>\n                          </div>\n                        </div>\n                        <ul class=\"list-group\" id=\"text-filter-list-group\">\n                          <li *ngIf=\"column['value_limits']!['possibleValues']?.length\" class=\"list-group-item\">\n                            <!--                          [className]=\"'form-check-input select-all-checkbox'\"-->\n                            <input type=\"checkbox\"\n                                   class=\"form-check-input me-1 select-all-checkbox\"\n                                   (change)=\"onCheckSelectAllTextValue($event, i)\"\n                                   [checked]=\"columns[i]['value_limits']!['selectedValues'].length === columns[i]['value_limits']!['possibleValues']?.length\">\n                            (Select All)\n                          </li>\n                          <li *ngFor=\"let value of column['value_limits']!['possibleValues'];\" class=\"list-group-item\"\n                              [ngStyle]=\"column['name'] === 'peptide' ? {fontFamily: 'courier'} : null\">\n                            <input type=\"checkbox\"\n                                   [className]=\"'form-check-input me-1 column-checkbox-'.concat(i.toString())\"\n                                   [id]=\"value.concat('-column-'.concat(i.toString()))\"\n                                   [checked]=\"column['value_limits']!['selectedValues'].includes(createRegexSafe(value))\"\n                                   [value]=\"value\" (change)=\"onTextValueSelect($event, i)\">\n                            {{value}}\n                          </li>\n                        </ul>\n\n\n                        <div class=\"flex-row d-flex\">\n                          <button type=\"button\" class=\"btn btn-secondary\"\n                                  (click)=\"onClearTextFilter(i); filterDropdown.close()\">\n                            Clear\n                          </button>\n                          <button type=\"button\" class=\"btn btn-primary\"\n                                  (click)=\"onTextFilter(i); filterDropdown.close();\">OK\n                          </button>\n                        </div>\n                      </form>\n                    </ng-template>\n                  </div>\n                </div>\n              </div>\n\n            <span *ngFor=\"let o of currentOrder; index as priority\" class=\"badge rounded-pill text-bg-secondary mx-1\" ngbTooltip=\"number indicates sort order\" placement=\"bottom-right\">\n            <span *ngIf=\"currentOrder.length > 1 && o[0] === i\">{{priority + 1}}</span>\n          </span>\n          </th>\n        </tr>\n        </thead>\n\n      </table>\n    </div>\n  </div>\n\n</div>\n\n<!--Display Column Modal-->\n<ng-template #displayColumnModal let-modal>\n  <div class=\"modal-header\">\n    <h4 class=\"modal-title\" id=\"modal-column-display-title\">Select Columns to Display</h4>\n    <button type=\"button\" class=\"btn-close\" aria-label=\"Close\" (click)=\"dismissModal()\"></button>\n  </div>\n  <div class=\"modal-body\">\n    <form [formGroup]=\"columnDisplayForm\">\n      <div class=\"d-flex flex-column\" *ngFor=\"let uniqSrc of uniqSources\">\n        <h5 class=\"d-flex justify-content-center\">\n          {{uniqSrc.split('.')[1] || uniqSrc.split('.')[0] | titlecase}}\n          <!-- NOTE: commented out code https://gitlab.lji.org/iedb/tools/tools-redesign/ar-redesign-prototype/-/issues/592-->\n          <!--          {{uniqSrc.split('.')[1] | titlecase}} -->\n        </h5>\n        <ng-container *ngFor=\"let o of columns\" class=\"form-check\">\n          <div *ngIf=\"uniqSrc===o['source']\"\n               [ngbTooltip]=\"columnDisplayForm.controls[o.filterKey].disabled ? tipContent : ''\"\n               placement=\"bottom-left\">\n            <input type=\"checkbox\" class=\"form-check-input\" [id]=\"o.filterKey\"\n                   [formControlName]=o.filterKey>\n            <label class=\"form-check-label fw-bold px-2\"\n                   [for]=\"o.filterKey\">{{o.display_name}}</label>\n            <small>\n              {{o.description}}\n            </small>\n          </div>\n        </ng-container>\n      </div>\n    </form>\n  </div>\n  <div class=\"modal-footer\">\n    <button type=\"button\" class=\"btn btn-secondary\" (click)=\"onDefaultColumns()\">Reset</button>\n    <button type=\"button\" class=\"btn btn-dark-blue-grey text-white\" (click)=\"onSetDisplayColumns()\">Display</button>\n  </div>\n</ng-template>\n<ng-template #tipContent>\n  <p [style]=\"{whiteSpace: 'pre-line'}\">\n  Sorted column and columns that can be used as inputs downstream cannot be hidden.\n  </p>\n</ng-template>\n","import {\n  Component,\n  OnInit,\n  AfterViewInit,\n  ViewChild,\n  ViewChildren,\n  Input,\n  OnDestroy,\n  Output,\n  EventEmitter, ElementRef,\n  QueryList\n} from '@angular/core';\nimport {UntypedFormBuilder, UntypedFormGroup} from \"@angular/forms\";\n\nimport {NgbModal, NgbDropdown} from '@ng-bootstrap/ng-bootstrap';\nimport _ from 'lodash';\nimport {Observable, Subject} from 'rxjs';\nimport {takeUntil} from \"rxjs/operators\";\nimport { Papa } from 'ngx-papaparse';\n\nimport {DataTableDirective} from 'angular-datatables';\nimport {ADTSettings} from 'angular-datatables/src/models/settings';\n\nimport {PipelineStateService} from \"../services/state-services/pipeline-state-service/pipeline-state.service\";\nimport Columns from '../_global/Columns';\nimport Tool from \"../_global/Tool\";\nimport Stage from \"../_global/Stage\";\n\n@Component({\n  selector: 'app-result-table',\n  templateUrl: './result-table.component.html',\n  styleUrls: ['./result-table.component.scss']\n})\nexport class ResultTableComponent implements OnInit, AfterViewInit, OnDestroy {\n\n  @ViewChild(DataTableDirective, {static: false}) dtElement!: DataTableDirective;\n  dtOptions: ADTSettings = {};\n\n  @ViewChild('displayColumnModal') displayColumnModal!: ElementRef;\n\n  /** NgbDropdowns */\n  @ViewChildren(NgbDropdown) dropdowns!: QueryList<NgbDropdown>;\n  private dropdown!: NgbDropdown;\n\n  @Input() inputChange: boolean = false;\n  /** API Call Variables */\n  @Input() table_data: [(number | string)[]] = [[]]; // peptide_table\n  @Input() order: [][] | any = [];\n  @Input() columns: Columns[] | any; // peptide_table\n  defaultColumnConfig: object = {};\n  @Input() warnings: [] = []\n  @Input() tool_group!: string;\n  @Input() index!: number;\n  @Input() tableStateSaving = false;\n  @Input() table_name!: string;\n\n  @Output() emitSaveTableState = new EventEmitter<any>();\n  @Output() emitFilterApplied = new EventEmitter<any>();\n  @Output() emitResetTableState = new EventEmitter<any>();\n\n  prevColumnDisplayFormValue!: object\n  columnDisplayForm!: UntypedFormGroup\n  uniqSources: string[] = [];\n  /** We use this trigger because fetching the list of persons can be quite long,\n   thus we ensure the data is fetched before rendering */\n  dtTrigger: Subject<ADTSettings> = new Subject<ADTSettings>();\n\n  unsubscribe$ = new Subject();\n  // params$: Observable<PipelineParams> = this._stateService.params$;\n\n  tools$: Observable<Tool[]> = this._stateService.tools$;\n  tools: Tool[] = [];\n\n  stages$: Observable<Stage[]> = this._stateService.stages$;\n  stages: Stage[] = [];\n\n  pipelineId$: Observable<string> = this._stateService.pipelineId$;\n  pipelineId = '';\n\n  dataToPipe: string = '';\n  dataToPipe2: string = '';\n\n  currentOrder: [][] | any;\n\n  table_state: any; // used in GET Pipeline\n  searchCols: any[] = [] // used in GET Pipeline\n\n  loading = false;\n  constructor(\n    private formBuilder: UntypedFormBuilder,\n    private modalService: NgbModal,\n    private papa: Papa,\n    private _stateService: PipelineStateService\n  ) {\n  }\n\n  ngOnInit() {\n    this.currentOrder = [...this.order];\n\n    this.dtOptions = {\n      dom:\n        '<\"\" ' +\n        '<\"row p-1\" ' +\n        '<\"col-3 pt-3\" l>' +\n        '<\"col-4 px-5\" i>' +\n        '<\"col-5\" p>>> t' +\n        '<\"\" ' +\n        '<\"row p-1\" ' +\n        '<\"col-3 pt-3\" l>' +\n        '<\"col-4 px-5\" i>' +\n        '<\"col-5\" p>>>', // https://datatables.net/examples/basic_init/dom.html\n      autoWidth: false,\n      pagingType: 'simple_numbers',\n      paging: true,\n      pageLength: 50,\n      ordering: true,\n      orderMulti: true,\n      stateSave: false,\n      language: {\n        lengthMenu: \"Show _MENU_ rows\",\n        info: \"_START_ to _END_ of _TOTAL_ rows\",\n        infoFiltered: \"(filtered from _MAX_ total rows)\"\n      },\n      data: this.table_data,\n      order: this.currentOrder,\n      columnDefs: _.map(this.columns, (column, i) => {\n        return {\n          targets: [i],\n          createdCell: (td, cellData, rowData, row, col) => {\n            let textAlign = ['int', 'float'].includes(column.type) ? 'right' : 'left';\n            $(td).css('text-align', textAlign);\n          },\n          visible: !column.hidden, // set default visible columns\n          render: (data, type) => {\n            // console.log(i, data, type);\n            if (column.type === 'int' && isNaN(data)) return parseInt(data);\n            else if (column.type === 'float' && !isNaN(data) &&\n              type === 'display' && column.number_of_digits) return parseFloat(data).toFixed(column.number_of_digits);\n            else if (column.type === 'float' && !isNaN(data)) return parseFloat(data);\n            else if (column.type === 'float' && isNaN(data)) return null;\n            // if (column.name === 'protein_name' && data.length>=column.display_length) return `${data.substring(0, column.display_length)}...`;\n            return data;\n          }\n        }\n      }),\n      destroy: true,\n      deferRender: true,\n      orderClasses: false,\n      searchCols: []\n    };\n\n  //   get tools\n    this.tools$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n      // console.log('tools$');\n      // console.log(value);\n      this.tools = value;\n    })\n\n    this.stages$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n      this.stages = value;\n\n      /** set dataToPipe */\n      if(this.stages.length>=2) {\n        const stage = this.stages[this.index+1]; // get the last stage\n        // this.dataToPipe = stage?.piped_input && stage.piped_input[0].piped_fields[0];\n\n        this.dataToPipe = stage?.piped_data && stage!.piped_data?.piped_input && stage.piped_data.piped_input[0]?.piped_fields![0] || '';\n        this.dataToPipe2 = stage?.piped_data && stage!.piped_data?.piped_input && stage.piped_data.piped_input[0]?.piped_fields![1] || '';\n        console.log(`dataToPipe = ${this.dataToPipe}`)\n        console.log(`dataToPipe2 = ${this.dataToPipe2}`)\n      } else {\n        this.dataToPipe = '';\n        this.dataToPipe2 = '';\n      }\n      // console.log(this.dataToPipe);\n\n      /** set filters from GET Pipeline */\n      this.table_state = this.stages[this.index]?.table_state;\n      this.searchCols = Array.from({length: this.columns.length}, ()=> {})\n\n      /**\n       * Added 'this.table_state' in if statement and\n       *\n       * this.table_state[0] = peptide_table\n       * this.table_state[1] = peptide_gene_summary_table (pepx)\n       * */\n      let tableIndex: number\n      switch (this.table_name) {\n        case 'peptide_gene_summary_table':\n          tableIndex = 1\n          break;\n        case 'peptide':\n          tableIndex = 1\n          break;\n        case 'unique_peptide':\n          tableIndex = 0\n          break;\n        default: // peptide_table\n          tableIndex = 0\n      }\n\n      if(this.table_state && this.table_state[tableIndex] && !_.isEmpty(this.table_state[tableIndex]?.columns)) {\n        // console.log(`tableIndex=${tableIndex}`);\n        // console.log(this.table_state[tableIndex].columns);\n        // console.log(this.columns);\n        for (const col in this.table_state[tableIndex].columns) {\n          let column = this.table_state[tableIndex].columns[col]\n          const{ name, source } = column\n          const { min, max, search } = column.search;\n          let i = _.findIndex(this.columns, {name, source})\n\n          // console.log(i)\n          // console.log({name, source})\n\n          this.columns[i].value_limits.minValue = min || min === 0 ? min : NaN\n          this.columns[i].value_limits.maxValue = max || max === 0 ? max : NaN\n\n          this.searchCols[i] = {search: search, regex: true, smart: false}\n          this.columns[i].value_limits.selectedValues = search ? search.split('|') : []\n          this.columns[i].value_limits.applied = true\n        }\n\n      }\n      // this.dtOptionsArr[this.index].searchCols = this.searchCols;\n      this.dtOptions.searchCols = this.searchCols;\n    })\n\n    this.pipelineId$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n      console.log(`pipelineId=${value}`);\n      this.pipelineId = value;\n    })\n\n  }\n\n  ngAfterViewInit() {\n    this.setColumnDisplayForm();\n    this.dtTrigger.next();\n    // this.setMinAndMax();\n\n    // console.log(this.filterDropdown.isOpen())\n  }\n\n  ngOnDestroy(): void {\n    // $.fn.dataTable.ext.search = [];\n    this.dtTrigger.unsubscribe();\n    this.unsubscribe$.next();\n    this.unsubscribe$.complete();\n  }\n\n  get visibleColumns() {\n    return _.filter(this.columns, c => !c.hidden) as Columns[]\n  }\n\n  onOpenDisplayColumnModal() {\n    this.prevColumnDisplayFormValue = this.columnDisplayForm.value;\n    console.log(this.columnDisplayForm.value)\n    this.disableSortedColumnInputs()\n    this.disableInputColumns()\n    this.open(this.displayColumnModal)\n  }\n\n  disableSortedColumnInputs() {\n    /**\n     * Prior to opening modal,\n     * disable controls from columnDisplayForm that have sorted columns.\n     * */\n    this.columnDisplayForm.enable();\n    this.dtElement.dtInstance.then((dtInstance: DataTables.Api) => {\n      const colIndex = [];\n      const order = dtInstance.state().order;\n      _.forEach(order, (o) => {\n        console.log(o);\n        colIndex.push(o[0]);\n        const formControlName = this.columns[o[0]].filterKey;\n        console.log(formControlName);\n        this.columnDisplayForm.controls[`${formControlName}`].disable();\n      })\n    });\n  }\n\n  disableInputColumns() {\n    /**\n     * Prior to opening modal,\n     * disable controls from columnDisplayForm that have columns that can be used downstream (i.e. peptide and cluster_concensus).\n     * */\n    this.columnDisplayForm.controls['core.peptide']?.value && this.columnDisplayForm.controls['core.peptide'].disable()\n    this.columnDisplayForm.controls['cluster.peptide']?.value && this.columnDisplayForm.controls['cluster.peptide'].disable()\n    this.columnDisplayForm.controls['cluster.cluster_consensus']?.value && this.columnDisplayForm.controls['cluster.cluster_consensus'].disable()\n\n  }\n\n  /** Column Display Modal Functions*/\n\n  open(content: any) {\n    /**\n     * Open Modal\n     * */\n    this.modalService.open(content, {\n      ariaLabelledBy: 'modal-basic-title',\n      size: 'lg',\n      animation: true,\n      backdrop: 'static'\n    }).result.then((result) => {\n      console.log(result)\n      // this.closeResult = `Closed with: ${result}`;\n    }, (reason) => {\n      console.log(reason)\n    });\n  }\n\n  dismissModal() {\n    this.columnDisplayForm.patchValue(this.prevColumnDisplayFormValue)\n\n    this.modalService.dismissAll()\n  }\n\n  onSetDisplayColumns() {\n    /**\n     * Display onClick\n     * */\n    let visibleColumns: number[] = []; // let visibleColumns: string[] = [];\n    let invisibleColumns: number[] = []; // let invisibleColumns: string[] = [];\n\n    this.dtElement.dtInstance.then((dtInstance: DataTables.Api) => {\n      console.log(dtInstance);\n      _.forEach(this.columns, (o, i: number) => {\n        if (this.columnDisplayForm.controls[`${o.filterKey}`].value) {\n          visibleColumns.push(i)\n          this.columns[i].hidden = false\n        }\n        else {\n          invisibleColumns.push(i);\n          this.columns[i].hidden = true\n        }\n      })\n      dtInstance.columns(visibleColumns).visible(true);\n      dtInstance.columns(invisibleColumns).visible(false);\n      this.modalService.dismissAll();\n    });\n  }\n\n  setColumnDisplayForm() {\n    /**\n     * 1) set's this.selectedColumn w/ recommendedColumns, smmColumns, consensusColumns\n     * 2) set's this.columnDisplayForm with the proper inputs.\n     * 3) Also sets $.fn.dataTable.ext which allows number filtering\n     * */\n    let controlConfig: any = {}\n    this.uniqSources = [];\n    _.forEach(this.columns, (col, i: number) => {\n      controlConfig[`${col.filterKey}`] = !col.hidden;\n      if (!this.uniqSources.includes(col.source)) {\n        this.uniqSources.push(col.source);\n      }\n      // datatables adding min/max filters for each of the table\n      $.fn['dataTable'].ext.search.push((settings: any, data: string[], dataIndex: any) => {\n\n        // const table = settings.table()\n        if (settings.nTable.id !== `DataTables_${this.tool_group}${this.table_name}`){\n          return true;\n        }\n\n        // const id = parseFloat(data[i]) || i; // use data for the id column - can't use this because '0' does not get\n        const val = parseFloat(data[i]); // 0 does get set properly\n        /**\n         1. Both min and max are numbers\n         * */\n        if ((isNaN(this.columns[i].value_limits?.minValue) && isNaN(this.columns[i].value_limits?.maxValue)) ||\n          (isNaN(this.columns[i].value_limits?.minValue) && val <= this.columns[i].value_limits?.maxValue) ||\n          (this.columns[i].value_limits?.minValue <= val && isNaN(this.columns[i].value_limits?.maxValue)) ||\n          (this.columns[i].value_limits?.minValue <= val && val <= this.columns[i].value_limits?.maxValue)) {\n          return true;\n        }\n        return false;\n\n      })\n    })\n    this.columnDisplayForm = this.formBuilder.group(controlConfig);\n    this.defaultColumnConfig = controlConfig\n  }\n\n  onDefaultColumns() {\n    /**\n     uses this.defaultColumnConfig that gets set in this.setColumnDisplayForm()\n     * */\n    this.columnDisplayForm = this.formBuilder.group(this.defaultColumnConfig);\n  }\n\n  stopProp(e: { stopPropagation: () => void; }) {\n    /** used in column filters */\n    e.stopPropagation();\n  }\n\n  onSortColumns(colIndex: number, order: string) {\n    /** used in column filters */\n    this.dtElement.dtInstance.then((dtInstance: DataTables.Api) => {\n      dtInstance.order([colIndex, order]).draw();\n    });\n  }\n\n  /** General filter functions */\n  onFilterDropdownOpen() {\n    $('.mat-drawer-content').removeClass(\"fixed-position\");\n    $('.reset-button').prop(\"disabled\", false);\n    $('.run-button').prop(\"disabled\", false);\n  }\n\n  onFilterDropdownClose() {\n    $('.mat-drawer-content').addClass(\"fixed-position\");\n    $('.reset-button').prop(\"disabled\", true);\n    $('.run-button').prop(\"disabled\", true);\n  }\n\n  checkClosedDropdown(e: boolean) {\n    if(!e) {this.onFilterDropdownOpen();}\n  }\n\n  checkOpenedDropdown(i: number) {\n    /**\n     * used in ngbDropdown - disable scroll when dropdown filter is applied.\n     * */\n    // Check which dropdown was clicked\n    this.dropdown = this.dropdowns.get(i) as NgbDropdown;\n    // Check if the clicked dropdown is open\n    if(this.dropdown.isOpen()) {this.onFilterDropdownClose();}\n  }\n\n\n  /** Number Filter Functions*/\n  setMinAndMax() {\n    let that = this;\n    this.dtElement.dtInstance.then((dtInstance: DataTables.Api) => {\n      const newColumns = dtInstance.columns()\n      newColumns.every(function(i) {\n        let column = this;\n        const columnValue = column.dataSrc();\n\n        let sortFunc;\n        if (columnValue !== 'core_peptide') {\n          sortFunc = (a: number, b: number) => a - b\n        }\n        /** Text Filter */\n        let distinctArray: any[] = [];\n        column.data().sort(sortFunc).each(function (d, j) {\n          if (distinctArray.indexOf(d) == -1) {\n            distinctArray.push(d);\n          }\n        });\n        /** Set Text/Number Filter Values */\n        // console.log(that.columns[i]['type']);\n        if (that.columns[i]['type'] === 'text') {\n          that.columns[i]['value_limits']['possibleValues'] = distinctArray\n        } else {\n          that.columns[i]['value_limits']['min'] = distinctArray[0]\n          that.columns[i]['value_limits']['max'] = distinctArray[distinctArray.length - 1]\n        }\n      })\n    })\n  }\n\n  onClearNumberFilter(i: number) {\n    $(`.min${i}${this.tool_group}${this.table_name}, .max${i}${this.tool_group}${this.table_name}`).val(NaN);\n    this.columns[i]['value_limits']['applied'] = false;\n    this.columns[i]['value_limits']['minValue'] = NaN;\n    this.columns[i]['value_limits']['maxValue'] = NaN;\n    this.dtElement.dtInstance.then((dtInstance: DataTables.Api) => {\n      dtInstance.column(i).search(\n        '',\n        true, false\n      ).draw();\n      this.emitFilterApplied.emit()\n    });\n  }\n  onNumberFilter(i: number) {\n\n    this.columns[i]['value_limits']['minValue'] = parseFloat(<string>$(`.min${i}${this.tool_group}${this.table_name}`).val());\n    this.columns[i]['value_limits']['maxValue'] = parseFloat(<string>$(`.max${i}${this.tool_group}${this.table_name}`).val());\n\n    const {minValue, maxValue} = this.columns[i]['value_limits'];\n\n    const filterApplied = !!(minValue || maxValue || minValue === 0 || maxValue === 0);\n    this.columns[i]['value_limits']['applied'] = filterApplied\n\n    console.log(`index=${i}`)\n    console.log(minValue)\n    console.log(maxValue)\n\n    this.dtElement.dtInstance.then((dtInstance: DataTables.Api) => {\n      dtInstance.draw();\n      this.emitFilterApplied.emit()\n    });\n  }\n\n  /** Text Filter Functions*/\n  onFilterPossibleValues(e: any, i: number) {\n    /**\n     * .toUpperCase() make it case insensitive\n     * */\n\n    let value = e.target.value;\n    this.dtElement.dtInstance.then((dtInstance: DataTables.Api) => {\n      let column = dtInstance.column(i);\n      let distinctArray: any[] = [];\n      column.data().sort().each(function (d, j) {\n        if (distinctArray.indexOf(d) == -1) {\n          distinctArray.push(d);\n        }\n      });\n      this.columns[i]['value_limits']['possibleValues'] = value ?\n        _.filter(distinctArray, (item) => _.startsWith(item.toUpperCase(), value.toUpperCase())) :\n        distinctArray\n    });\n\n  }\n\n  onClearTextFilter(i: number) {\n    this.columns[i]['value_limits']['applied'] = false;\n    $('.column-checkbox-'.concat(i.toString())).prop('checked', false);\n    this.columns[i]['value_limits'].selectedValues = []\n    this.dtElement.dtInstance.then((dtInstance: DataTables.Api) => {\n      dtInstance.column(i).search(\n        '',\n        true, false\n      ).draw();\n      this.emitFilterApplied.emit()\n      // this.checkFilterApplied(dtInstance);\n    });\n  }\n\n  onTextFilter(i: number) {\n    /**\n     *\n     * TODO: Edit this for params\n     {\n      \"search\": {\n        \"search\": \"^MGQIVTMFE$|^GQIVTMFEA$|^QIVTMFEAL$\"\n      },\n        \"tool_group\": \"mhci\",\n        \"name\": \"peptide\",\n        \"source\": \"core\"\n    },\n     * */\n    const { name, filters, value_limits, source } = this.columns[i];\n    const {selectedValues} = value_limits;\n    let searchString = selectedValues.length == 1 ? selectedValues[0] : selectedValues.join('|')\n    this.columns[i]['value_limits']['applied'] = !!(selectedValues.length);\n    /** create searchObject */\n\n    console.log(searchString)\n\n    this.dtElement.dtInstance.then((dtInstance: DataTables.Api) => {\n        dtInstance.column(i).search(\n          searchString,\n          true, false\n        ).draw();\n        this.emitFilterApplied.emit()\n      }\n    );\n  }\n\n  createRegexSafe(searchString: string) {\n    /**\n     * Helper function - used in onTextValueSelect\n     * */\n    return '^' + searchString.toString().split('+').join('\\\\+').split('-').join('\\\\-').split('[').join('\\\\[').split(']').join('\\\\]').split('*').join('\\\\*') + '$';\n  }\n\n  onCheckSelectAllTextValue(e: any, i: number) {\n    /**\n     * e: $event\n     * i: column index\n     * */\n    const checked = e.target.checked;\n    this.columns[i]['value_limits'].selectedValues = [];\n    if (checked) { // select all\n      _.forEach(this.columns[i]['value_limits']['possibleValues'], (value) => {\n        this.columns[i]['value_limits'].selectedValues.push(\n          this.createRegexSafe(value)\n        );\n      });\n    }\n  }\n\n  onTextValueSelect(e: any, i: number) {\n    const checked = e.target.checked, value = e.target.value;\n    // console.log(`checked=${checked} || value=${value}`)\n    if (checked) {\n      this.columns[i]['value_limits'].selectedValues.push(\n        this.createRegexSafe(value)\n      );\n    } else {\n      _.remove(this.columns[i]['value_limits'].selectedValues, (possibleValue) => this.createRegexSafe(value) === possibleValue)\n    }\n    // console.log(this.columns[i]['value_limits']);\n  }\n\n  clearTableState(): void {\n\n    this.emitResetTableState.emit()\n\n    this.currentOrder = [...this.order]\n    this.dtOptions.order = this.currentOrder\n\n    this.dtTrigger.next(this.dtOptions);\n\n    const initTool = this.tools[this.index];\n    const unSubmittedTool = {\n      ...initTool,\n      appliedFilters: undefined\n    }\n    this._stateService.insertTool(unSubmittedTool, this.index);\n    const table_state = [{table: 'peptide_table', columns: {}}]\n    this._stateService.insertTableStateToStage(table_state, this.index);\n    this._stateService.applyFiltersToParams(this.index, {});\n    this.setColumnDisplayForm();\n    this.setMinAndMax();\n  }\n\n  onSaveTableState() {\n    // Create colObj\n    // console.log(this.columns)\n    // console.log(this.tool_group)\n    // let colObj = columnListToObject(this.columns, this.tool_group)\n    //\n    // const table_state = [{table: 'peptide_table', columns: colObj}]\n    // this._stateService.insertTableStateToStage(table_state, this.index)\n    // this._stateService.insertTableStateToStage({columns: colObj}, this.index)\n\n    this.emitSaveTableState.emit()\n  }\n\n  downloadResultFiles(data: string, format: string, fileName='result') {\n    const a = document.createElement('a');\n    a.setAttribute('style', 'display:none;');\n    document.body.appendChild(a);\n    // const contentType = 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet;charset=UTF-16';\n    // var blob = new Blob([csvData], { type: contentType });\n    const blob = new Blob([data]); // thx: http://stackoverflow.com/a/18925211\n\n    // const blob = new Blob([data]); // thx: http://stackoverflow.com/a/18925211\n    a.href = window.URL.createObjectURL(blob);\n    switch (format) {\n      case 'csv':\n        a.download = `${fileName}.csv`;\n        break;\n      case 'tsv':\n        a.download = `${fileName}.tsv`;\n        break;\n      case 'json':\n        a.download = `${fileName}.json`;\n        break;\n      default:\n        a.download = `${fileName}.txt`;\n        break;\n    }\n\n    a.click();\n  }\n\n  // convertCurrentResultToTsv() : string {\n  //   // currently csv instead of tsv\n  //   let str = '';\n  //   let header = ''\n  //   _.forEach(this.columns, (col) => {\n  //     // header+= `${col.name}\\t`\n  //     header+= `${col.name},`\n  //   })\n  //   str += `${header}\\n`\n  //   _.forEach(this.table_data, (row) => {\n  //     console.log(row)\n  //     // let newRow = row.toString().replace(/,/g, '\\t')\n  //     let newRow = row.toString()\n  //     console.log(newRow)\n  //     str += `${newRow}\\n`\n  //   })\n  //   str += '\\n'\n  //   return str\n  // }\n\n  // convertCurrentResultToTSV2(data: any, visible_columns: any) : any {\n  //   // currently csv instead of tsv\n  //   let str = '';\n  //   let header = ''\n  //   _.forEach(this.columns, (col, i) => {\n  //     if(visible_columns[i]) {\n  //       header+= `${col.name},` // header+= `${col.name}\\t`\n  //     }\n  //   })\n  //   str += `${header}\\n`\n  //   _.forEach(data, (row) => {\n  //     const tempRow: any = []\n  //     _.forEach(row, (val, i) => {\n  //       if(visible_columns[i]) {\n  //         // let newRow = row.toString().replace(/,/g, '\\t')\n  //         tempRow.push(val)\n  //       }\n  //     })\n  //     let newRow = tempRow.toString()\n  //     str += `${newRow}\\n`\n  //   })\n  //   str += '\\n'\n  //   return str\n  // }\n\n  convertCurrentResultToJSON() : any {\n    return _.map(this.table_data, (row) => {\n      let obj: any = {}\n      _.forEach(row, (value, i) => {\n        obj[this.columns[i].display_name] = value\n      })\n      return obj\n    })\n  }\n\n  convertCurrentResultToJSON2(data: any, visible_columns: any) : any {\n    return _.map(data, (row) => {\n      let obj: any = {}\n      _.forEach(row, (value, i) => {\n        if(visible_columns[i]) {\n          obj[this.columns[i].display_name] = value\n        }\n      })\n      return obj\n    })\n  }\n\n  downloadAllTsv() {\n    /**\n     * JSON -> TSV -> File\n     * */\n    const fileName = `${this.table_name}_${this.pipelineId.substring(0, 8)}`\n\n    this.dtElement.dtInstance.then((dtInstance: DataTables.Api) => {\n      /** dtInstance.order() -> lodash order */\n      const order = dtInstance.order()\n\n      const lodashOrder = this.convertDTOrderToLodash(order)\n\n      /** get and sort data */\n      const data = this.convertCurrentResultToJSON();\n\n      const sortedData = _.orderBy(data, ...lodashOrder)\n\n      console.log(sortedData)\n\n      const config = {\n        delimiter: \"\\t\",\n      }\n      /** convert to tsv and download result */\n      const csvData = this.papa.unparse(sortedData, config)\n      console.log(csvData)\n      this.downloadResultFiles(csvData, 'tsv', fileName)\n    })\n  }\n\n  downloadAllCsv() {\n    /**\n     * JSON -> CSV -> File\n     * */\n    const fileName = `${this.table_name}_${this.pipelineId.substring(0, 8)}`\n\n    this.dtElement.dtInstance.then((dtInstance: DataTables.Api) => {\n      /** dtInstance.order() -> lodash order */\n      const order = dtInstance.order()\n\n      const lodashOrder = this.convertDTOrderToLodash(order)\n\n      /** get and sort data */\n      const data = this.convertCurrentResultToJSON();\n\n      const sortedData = _.orderBy(data, ...lodashOrder)\n      /** download sorted data */\n      const csvData = this.papa.unparse(sortedData)\n      console.log(csvData)\n      this.downloadResultFiles(csvData, 'csv', fileName)\n    })\n  }\n\n  downloadAllJSON() {\n    /**\n     * JSON -> File\n     * */\n    const fileName = `${this.table_name}_${this.pipelineId.substring(0, 8)}`\n\n    this.dtElement.dtInstance.then((dtInstance: DataTables.Api) => {\n      /** dtInstance.order() -> lodash order */\n      const order = dtInstance.order()\n\n      const lodashOrder = this.convertDTOrderToLodash(order)\n\n      /** get and sort data */\n      const data = this.convertCurrentResultToJSON();\n\n      const sortedData = _.orderBy(data, ...lodashOrder)\n\n      /** download sorted data */\n      this.downloadResultFiles(JSON.stringify(sortedData, null, 2), 'json', fileName)\n    })\n\n  }\n\n  downloadTSV() {\n    const fileName = `${this.table_name}_${this.pipelineId.substring(0, 8)}_displayed`\n\n    this.dtElement.dtInstance.then((dtInstance: DataTables.Api) => {\n        const peptide_table = dtInstance.rows({page: 'current', search: 'applied'}).data();\n        console.log(peptide_table)\n        const d = dtInstance.columns().visible();\n        console.log(d)\n        // const data = this.convertCurrentResultToTSV2(peptide_table, d)\n        const data = this.convertCurrentResultToJSON2(peptide_table, d)\n        const config = {\n          delimiter: \"\\t\",\n        }\n        const csvData = this.papa.unparse(data, config)\n        console.log(csvData)\n        this.downloadResultFiles(csvData, 'tsv', fileName)\n      }\n    );\n  }\n\n  downloadCSV() {\n    const fileName = `${this.table_name}_${this.pipelineId.substring(0, 8)}_displayed`\n\n    this.dtElement.dtInstance.then((dtInstance: DataTables.Api) => {\n        const peptide_table = dtInstance.rows({page: 'current', search: 'applied'}).data();\n        console.log(peptide_table)\n        const d = dtInstance.columns().visible();\n        console.log(d)\n        // const data = this.convertCurrentResultToTSV2(peptide_table, d)\n        const data = this.convertCurrentResultToJSON2(peptide_table, d)\n        const csvData = this.papa.unparse(data)\n        console.log(csvData)\n        this.downloadResultFiles(csvData, 'csv', fileName)\n      }\n    );\n  }\n\n  downloadJSON() {\n    const fileName = `${this.table_name}_${this.pipelineId.substring(0, 8)}_displayed`\n\n    this.dtElement.dtInstance.then((dtInstance: DataTables.Api) => {\n      const peptide_table = dtInstance.rows( {page:'current', search: 'applied'} ).data();\n      console.log(peptide_table)\n      const d = dtInstance.columns().visible();\n      console.log(d)\n      const data = this.convertCurrentResultToJSON2(peptide_table, d)\n      console.log(data)\n      this.downloadResultFiles(JSON.stringify(data, null, 2), 'json', fileName)\n      }\n    );\n  }\n\n  convertDTOrderToLodash(order: (string | number)[][]) {\n    /**\n     Helper function for download all\n     convert dt table order -> lodash orderBy\n\n     * https://datatables.net/reference/api/order()\n     * https://lodash.com/docs/4.17.15#orderBy\n\n     * */\n    // console.log(this.columns)\n    const tempVal = _.map(order, (o) => {\n      const a = this.columns[o[0]]\n      // console.log(a)\n      return [a['display_name'], o[1]]\n    })\n\n    const temp1: string[] = []\n    const temp2: string[] = []\n    _.forEach(tempVal, (o) => {\n      temp1.push(o[0])\n      temp2.push(o[1])\n    })\n\n    return [temp1, temp2]\n  }\n}\n","<ng-container [formGroup]=\"ogFormGroup\">\n  <div class=\"form-group p-3 \">\n    <div class=\"d-flex flex-row\">\n      <!--MHC Binding-->\n      <label class=\"justify-content-center align-self-center mr-auto p-3\"> MHC-I Processing </label>\n      <div class=\"justify-content-center align-content-center flex-fill p-3\">\n        <label for=\"predictionMethodSelect\">Prediction Method</label>\n        <select *ngIf=\"processingOptions.length\" id=\"predictionMethodSelect\" formControlName=\"method\"\n                class=\"form-select form-control w-100\" (change)=\"onMethodChange($event)\" [attr.disabled]=\"disabled ? '' : null\">\n          <option [value]=\"option['short_name']\"\n                  *ngFor=\"let option of processingOptions\">{{option['display_name']}}</option>\n        </select>\n        <div *ngIf=\"!processingOptions.length\" class=\"d-flex justify-content-center col\">\n          <div class=\"spinner-border text-primary align-self-center p-3 mb-3\" role=\"status\">\n            <span class=\"sr-only visually-hidden\">Loading...</span>\n          </div>\n        </div>\n      </div>\n      <div class=\"justify-content-end align-self-center align-content-center p-3\">\n        <button type=\"button\" class=\"btn-close\" aria-label=\"Close\" (click)=\"onCancelClick()\" [disabled]=\"disabled\">\n        </button>\n      </div>\n    </div>\n    <!--    Basic Processing -->\n    <ng-container *ngIf=\"processingMethod==='basic_processing'\">\n      <hr style=\"border-color: #759dc3\"/>\n      <div class=\"d-flex flex-row flex-fill p-3\">\n        <label class=\"justify-content-center align-self-center p-3\"> MHC-I Binding Methods </label>\n        <div class=\"justify-content-center align-content-center flex-fill p-3\">\n          <select class=\"form-control form-select\" formControlName=\"mhc_binding_method\" [attr.disabled]=\"disabled ? '' : null\">\n            <option [value]=\"option['short_name']\"\n                    *ngFor=\"let option of basicProcessingPredictionOption\">{{option['display_name']}}</option>\n          </select>\n        </div>\n      </div>\n      <div class=\"d-flex flex-row flex-fill justify-content-center p-3\">\n        <div class=\"justify-content-center align-content-center\">\n          <label for=\"proteasomeSelect\">Proteasome Cleavage</label>\n          <select id=\"proteasomeSelect\"\n                  class=\"form-control form-select\" formControlName=\"proteasome\" [attr.disabled]=\"disabled ? '' : null\">\n            <option [value]=\"'immuno'\">immuno</option>\n            <option [value]=\"'constitutive'\">constitutive</option>\n          </select>\n        </div>\n        <div class=\"justify-content-center align-content-center d-flex flex-column p-2\">\n          <h6 class=\"text-center align-self-center\">Transporter associated with antigen processing</h6>\n          <div class=\"bd-highlight m-1 align-self-center d-flex flex-row justify-content-center\">\n            <!--Max Precursor form group-->\n            <div class=\"px-2 mb-3 col-sm-5\">\n              <div class=\"form-group row\">\n                <label for=\"maxPrecursorInput\" class=\"col-sm-8 col-form-label col-form-label-sm\"\n                       id=\"max-precursor-label\">Max Precursor Extension</label>\n                <div class=\"col-sm-4\">\n                  <input type=\"text\"\n                         id=\"maxPrecursorInput\"\n                         formControlName=\"tap_precursor\"\n                         class=\"form-control form-control-sm\"\n                         aria-label=\"Small\"\n                         aria-describedby=\"inputGroup-sizing-sm\"\n                         [attr.disabled]=\"disabled ? '' : null\">\n                </div>\n              </div>\n            </div>\n            <!--Alpha Factor form group-->\n            <div class=\"px-2 mb-3 col-sm-5\">\n              <div class=\"form-group row\">\n                <label for=\"alphaFactorInput\" class=\"col-sm-7 col-form-label col-form-label-sm\"\n                       id=\"alpha-factor-label\">Alpha Factor</label>\n                <div class=\"col-sm-5\">\n                  <input type=\"text\"\n                         formControlName=\"tap_alpha\"\n                         id=\"alphaFactorInput\"\n                         class=\"form-control form-control-sm\"\n                         aria-label=\"Small\"\n                         [attr.disabled]=\"disabled ? '' : null\">\n                </div>\n              </div>\n            </div>\n\n          </div>\n        </div>\n      </div>\n\n    </ng-container>\n    <!--    NetCTL -->\n    <ng-container *ngIf=\"processingMethod==='netctl'\">\n      <hr style=\"border-color: #759dc3\"/>\n      <div class=\"row p-3 align-items-end\">\n        <label class=\"col-4\"> Weight on C terminal cleavage </label>\n        <div class=\"col-8 custom-ngx-slider\">\n            <ngx-slider\n              formControlName=\"cleavage_weight\"\n              [options]=\"options\"\n            ></ngx-slider>\n        </div>\n      </div>\n      <div class=\"row p-3 align-items-end\">\n        <label class=\"col-4\"> Weight on TAP transport efficiency </label>\n        <div class=\"col-8 custom-ngx-slider\">\n          <ngx-slider\n            formControlName=\"tap_weight\"\n            [value]=\"0.05\"\n            [options]=\"options\"></ngx-slider>\n        </div>\n      </div>\n      <div class=\"row p-3 align-items-end\">\n        <label class=\"col-4\"> Threshold </label>\n        <div class=\"col-8 custom-ngx-slider\">\n          <ngx-slider\n            formControlName='threshold'\n            [value]=\"netCtlThreshold\"\n            [options]=\"options\"></ngx-slider>\n        </div>\n      </div>\n    </ng-container>\n    <!--    Netchop -->\n    <ng-container *ngIf=\"processingMethod==='netchop'\">\n      <hr style=\"border-color: #759dc3\"/>\n      <div class=\"row p-3 align-items-end\">\n        <label class=\"col-2\"> Network Method </label>\n        <div class=\"col-10\">\n          <select class=\"form-control form-select\" formControlName=\"network_method\" [attr.disabled]=\"disabled ? '' : null\">\n            <option [value]=\"'c_term'\">C term 3.0</option>\n            <option [value]=\"'20S'\">20s 30</option>\n          </select>\n        </div>\n      </div>\n      <div class=\"row p-3 align-items-end\">\n        <label class=\"col-2\"> Threshold </label>\n        <div class=\"col-10 custom-ngx-slider\">\n          <ngx-slider\n            [attr.disabled]=\"disabled ? '' : null\"\n            formControlName=\"threshold\"\n            [value]=\"netChopThreshold\"\n            [options]=\"options\"></ngx-slider>\n        </div>\n      </div>\n    </ng-container>\n    <!--    NetCTLpan -->\n    <ng-container *ngIf=\"processingMethod==='netctlpan'\">\n      <hr style=\"border-color: #759dc3\"/>\n      <div class=\"row p-3 align-items-end\">\n        <label class=\"col-4\"> Weight on C terminal cleavage </label>\n        <div class=\"col-8 custom-ngx-slider\">\n          <!--             todo - add formControlName    -->\n          <ngx-slider\n            id=\"weightOnCTerminalCleavage\"\n            formControlName=\"cleavage_weight\"\n            [value]=\"0.225\"\n            [options]=\"options2\"></ngx-slider>\n        </div>\n      </div>\n      <div class=\"row p-3 align-items-end\">\n        <label class=\"col-4\"> Weight on TAP transport efficiency</label>\n        <div class=\"col-8 custom-ngx-slider\">\n          <ngx-slider\n            formControlName=\"tap_weight\"\n            id=\"weightOnTAPtransport\"\n            [value]=\"0.025\"\n            [options]=\"options2\"></ngx-slider>\n        </div>\n      </div>\n\n      <div class=\"row p-3 align-items-end\">\n        <label class=\"col-4\"> Percentile Rank Threshold </label>\n        <div class=\"col-8 custom-ngx-slider\">\n          <ngx-slider\n            formControlName=\"epitope_threshold\"\n            id=\"thresholdForEpitopeID\"\n            [value]=\"1\"\n            [options]=\"options3\"></ngx-slider>\n        </div>\n      </div>\n    </ng-container>\n\n  </div>\n</ng-container>\n","import {Component, EventEmitter, Input, OnChanges, OnInit, Output, SimpleChanges} from '@angular/core';\nimport {ControlContainer, UntypedFormBuilder, FormGroup} from \"@angular/forms\";\nimport * as _ from \"lodash\";\n// import {Options} from \"@angular-slider/ngx-slider\";\nimport {Options} from 'ngx-slider-v2'\n\n@Component({\n  selector: 'app-mhc-i-processing-formgroup-new',\n  templateUrl: './mhc-i-processing-formgroup-new.component.html',\n  styleUrls: ['./mhc-i-processing-formgroup-new.component.scss']\n})\nexport class MhcIProcessingFormgroupNewComponent implements OnInit, OnChanges {\n\n  @Input() modelIndex: number | any;\n  @Input() disabled: boolean = false;\n  @Input() processingOptions: { display_name: string, short_name: string, group: string, source: string, has_ic50: boolean }[] = [];\n  @Input() basicProcessingPredictionOption: { display_name: string, short_name: string, group: string, source: string, has_ic50: boolean }[] = [];\n\n  @Output() emitPredictionModelIndex = new EventEmitter<number>();\n  addProcessing: boolean = false;\n  public ogFormGroup: any = null;\n\n  // Netchop\n  netChopThreshold = 0.5\n  netCtlThreshold = 0.75\n  options: Options = {\n    disabled: false,\n    floor: 0,\n    ceil: 1,\n    step: 0.01,\n    ticksArray: [0, 0.5, 1],\n    showTicksValues: true,\n    translate: (value: number): string => {\n      return value.toFixed(2);\n    }\n  };\n\n  options2: Options = {\n    disabled: true,\n    floor: 0,\n    ceil: 1,\n    step: 0.005,\n    ticksArray: [0, 0.5, 1],\n    showTicksValues: true,\n    translate: (value: number): string => {\n      return value.toFixed(3);\n    }\n  };\n\n  options3: Options = {\n    disabled: false,\n    floor: 0,\n    ceil: 100,\n    step: 0.5,\n    ticksArray: [0, 50, 100],\n    showTicksValues: true,\n    translate: (value: number): string => {\n      return value.toFixed(1);\n    }\n  };\n\n  constructor(\n    public controlContainer: ControlContainer,\n    private fb: UntypedFormBuilder,\n  ) { }\n\n  ngOnInit(): void {\n    this.ogFormGroup = this.controlContainer.control;\n    // this.options = Object.assign({}, this.options, {disabled: this.disabled});\n    // this.options2 = Object.assign({}, this.options2, {disabled: this.disabled});\n    // this.options3 = Object.assign({}, this.options3, {disabled: this.disabled});\n\n    // this.ogFormGroup.controls['method'].valueChanges.subscribe((val: any) => {\n    //   console.log(val);\n    // })\n  }\n  ngOnChanges(changes: SimpleChanges) {\n    if (changes['disabled']){\n      const disabled = changes['disabled'].currentValue;\n      console.log(`disabled=${disabled}`)\n      this.options = Object.assign({}, this.options, {disabled});\n      this.options2 = Object.assign({}, this.options2, {disabled});\n      this.options3 = Object.assign({}, this.options3, {disabled});\n    }\n  }\n\n\n  get has_ice50() {\n    return _.find(this.processingOptions, {short_name: this.ogFormGroup.controls['method'].value})?.has_ic50\n  }\n\n  get processingMethod() {\n    return this.ogFormGroup.controls['method'].value\n  }\n\n  onCancelClick() {\n    this.emitPredictionModelIndex.emit(this.modelIndex);\n  }\n\n  onMethodChange(e: any) {\n    /**\n     * Note MHC-NP only requires 'type' and 'method'\n     * */\n\n    const value = e.target.value\n    _.forOwn(this.ogFormGroup.value, (v, k) => {this.ogFormGroup.removeControl(k)}) // clear ogFormGroup\n\n    this.ogFormGroup.setControl('type', this.fb.control('processing'))\n    this.ogFormGroup.setControl('method', this.fb.control(value))\n\n    switch (value) {\n      case 'basic_processing': {\n        this.ogFormGroup.setControl('mhc_binding_method', this.fb.control('netmhcpan_ba'))\n        this.ogFormGroup.setControl('proteasome', this.fb.control('immuno'))\n        this.ogFormGroup.setControl('tap_precursor', this.fb.control(1))\n        this.ogFormGroup.setControl('tap_alpha', this.fb.control(0.2))\n        break;\n      }\n      case 'netchop': {\n        this.ogFormGroup.setControl('network_method', this.fb.control('c_term'))\n        this.ogFormGroup.setControl('threshold', this.fb.control(0.7))\n        break;\n      }\n      case 'netctl': {\n        this.ogFormGroup.setControl('cleavage_weight', this.fb.control(0.15))\n        this.ogFormGroup.setControl('tap_weight', this.fb.control(0.05))\n        this.ogFormGroup.setControl('threshold', this.fb.control(0.75))\n        break;\n      }\n      case 'netctlpan': {\n        this.ogFormGroup.setControl('cleavage_weight', this.fb.control(0.225))\n        this.ogFormGroup.setControl('tap_weight', this.fb.control(0.025))\n        this.ogFormGroup.setControl('epitope_threshold', this.fb.control(1.0))\n        break;\n      }\n      default:\n        break\n    }\n\n  }\n}\n","<!--[ngClass]=\"{disabled: componentDisabled}\"-->\n<form [formGroup]=\"tCellForm\" (ngSubmit)=\"onRunMain()\" class=\"container\">\n  <div class=\"d-flex flex-row p-2\">\n    <h2 class=\"pe-2 display-5\">{{index + 1}}</h2>\n    <hr class=\"mt-4 flex-grow-1 divider\"/>\n  </div>\n  <div class=\"d-flex pb-3\">\n    <h4 class=\"p-2 tool-name\" id=\"mhci-label\">T Cell Prediction - Class I</h4>\n    <div class=\"d-flex flex-row tool-links\" role=\"group\" aria-label=\"tool-links\">\n      <button type=\"button\" class=\"btn btn-link text-dark d-flex flex-column justify-content-center align-items-center\">\n          <a target=\"_blank\" routerLink=\"/docs/tools/tcell/index.html\" class=\"text-dark d-flex flex-column justify-content-center align-items-center\">\n          <svg width=\"1em\" height=\"1em\" viewBox=\"0 0 16 16\" class=\"bi bi-file-earmark-text\" fill=\"currentColor\"\n               xmlns=\"http://www.w3.org/2000/svg\">\n            <path\n              d=\"M4 1h5v1H4a1 1 0 0 0-1 1v10a1 1 0 0 0 1 1h8a1 1 0 0 0 1-1V6h1v7a2 2 0 0 1-2 2H4a2 2 0 0 1-2-2V3a2 2 0 0 1 2-2z\"/>\n            <path d=\"M9 4.5V1l5 5h-3.5A1.5 1.5 0 0 1 9 4.5z\"/>\n            <path fill-rule=\"evenodd\"\n                  d=\"M5 11.5a.5.5 0 0 1 .5-.5h2a.5.5 0 0 1 0 1h-2a.5.5 0 0 1-.5-.5zm0-2a.5.5 0 0 1 .5-.5h5a.5.5 0 0 1 0 1h-5a.5.5 0 0 1-.5-.5zm0-2a.5.5 0 0 1 .5-.5h5a.5.5 0 0 1 0 1h-5a.5.5 0 0 1-.5-.5z\"/>\n          </svg>\n        Docs\n        </a>\n      </button>\n      <button type=\"button\" class=\"btn btn-link\">\n        <a target=\"_blank\" [href]=\"swaggerUrl\" class=\"text-dark d-flex flex-column justify-content-center align-items-center\">\n          <svg width=\"1em\" height=\"1em\" viewBox=\"0 0 16 16\" class=\"bi bi-gear\" fill=\"currentColor\"\n               xmlns=\"http://www.w3.org/2000/svg\">\n            <path fill-rule=\"evenodd\"\n                  d=\"M8.837 1.626c-.246-.835-1.428-.835-1.674 0l-.094.319A1.873 1.873 0 0 1 4.377 3.06l-.292-.16c-.764-.415-1.6.42-1.184 1.185l.159.292a1.873 1.873 0 0 1-1.115 2.692l-.319.094c-.835.246-.835 1.428 0 1.674l.319.094a1.873 1.873 0 0 1 1.115 2.693l-.16.291c-.415.764.42 1.6 1.185 1.184l.292-.159a1.873 1.873 0 0 1 2.692 1.116l.094.318c.246.835 1.428.835 1.674 0l.094-.319a1.873 1.873 0 0 1 2.693-1.115l.291.16c.764.415 1.6-.42 1.184-1.185l-.159-.291a1.873 1.873 0 0 1 1.116-2.693l.318-.094c.835-.246.835-1.428 0-1.674l-.319-.094a1.873 1.873 0 0 1-1.115-2.692l.16-.292c.415-.764-.42-1.6-1.185-1.184l-.291.159A1.873 1.873 0 0 1 8.93 1.945l-.094-.319zm-2.633-.283c.527-1.79 3.065-1.79 3.592 0l.094.319a.873.873 0 0 0 1.255.52l.292-.16c1.64-.892 3.434.901 2.54 2.541l-.159.292a.873.873 0 0 0 .52 1.255l.319.094c1.79.527 1.79 3.065 0 3.592l-.319.094a.873.873 0 0 0-.52 1.255l.16.292c.893 1.64-.902 3.434-2.541 2.54l-.292-.159a.873.873 0 0 0-1.255.52l-.094.319c-.527 1.79-3.065 1.79-3.592 0l-.094-.319a.873.873 0 0 0-1.255-.52l-.292.16c-1.64.893-3.433-.902-2.54-2.541l.159-.292a.873.873 0 0 0-.52-1.255l-.319-.094c-1.79-.527-1.79-3.065 0-3.592l.319-.094a.873.873 0 0 0 .52-1.255l-.16-.292c-.892-1.64.902-3.433 2.541-2.54l.292.159a.873.873 0 0 0 1.255-.52l.094-.319z\"/>\n            <path fill-rule=\"evenodd\"\n                  d=\"M8 5.754a2.246 2.246 0 1 0 0 4.492 2.246 2.246 0 0 0 0-4.492zM4.754 8a3.246 3.246 0 1 1 6.492 0 3.246 3.246 0 0 1-6.492 0z\"/>\n          </svg>\n          API\n        </a>\n      </button>\n      <button type=\"button\" class=\"btn btn-link text-dark d-flex flex-column justify-content-center align-items-center\"\n              routerLink=\"/download-all\"\n              [state]=\"{tool: 'mhc-class-i-binding'}\">\n        <svg width=\"1em\" height=\"1em\" viewBox=\"0 0 16 16\" class=\"bi bi-cloud-arrow-down\" fill=\"currentColor\"\n             xmlns=\"http://www.w3.org/2000/svg\">\n          <path fill-rule=\"evenodd\"\n                d=\"M4.406 3.342A5.53 5.53 0 0 1 8 2c2.69 0 4.923 2 5.166 4.579C14.758 6.804 16 8.137 16 9.773 16 11.569 14.502 13 12.687 13H3.781C1.708 13 0 11.366 0 9.318c0-1.763 1.266-3.223 2.942-3.593.143-.863.698-1.723 1.464-2.383zm.653.757c-.757.653-1.153 1.44-1.153 2.056v.448l-.445.049C2.064 6.805 1 7.952 1 9.318 1 10.785 2.23 12 3.781 12h8.906C13.98 12 15 10.988 15 9.773c0-1.216-1.02-2.228-2.313-2.228h-.5v-.5C12.188 4.825 10.328 3 8 3a4.53 4.53 0 0 0-2.941 1.1z\"/>\n          <path fill-rule=\"evenodd\"\n                d=\"M7.646 10.854a.5.5 0 0 0 .708 0l2-2a.5.5 0 0 0-.708-.708L8.5 9.293V5.5a.5.5 0 0 0-1 0v3.793L6.354 8.146a.5.5 0 1 0-.708.708l2 2z\"/>\n        </svg>\n        Download\n      </button>\n      <button type=\"button\" class=\"btn btn-link text-dark d-flex flex-column justify-content-center align-items-center\"\n              routerLink=\"/citation\">\n        <svg width=\"1em\" height=\"1em\" viewBox=\"0 0 16 16\" class=\"bi bi-chat-square-quote\" fill=\"currentColor\"\n             xmlns=\"http://www.w3.org/2000/svg\">\n          <path fill-rule=\"evenodd\"\n                d=\"M14 1H2a1 1 0 0 0-1 1v8a1 1 0 0 0 1 1h2.5a2 2 0 0 1 1.6.8L8 14.333 9.9 11.8a2 2 0 0 1 1.6-.8H14a1 1 0 0 0 1-1V2a1 1 0 0 0-1-1zM2 0a2 2 0 0 0-2 2v8a2 2 0 0 0 2 2h2.5a1 1 0 0 1 .8.4l1.9 2.533a1 1 0 0 0 1.6 0l1.9-2.533a1 1 0 0 1 .8-.4H14a2 2 0 0 0 2-2V2a2 2 0 0 0-2-2H2z\"/>\n          <path fill-rule=\"evenodd\"\n                d=\"M7.066 4.76A1.665 1.665 0 0 0 4 5.668a1.667 1.667 0 0 0 2.561 1.406c-.131.389-.375.804-.777 1.22a.417.417 0 1 0 .6.58c1.486-1.54 1.293-3.214.682-4.112zm4 0A1.665 1.665 0 0 0 8 5.668a1.667 1.667 0 0 0 2.561 1.406c-.131.389-.375.804-.777 1.22a.417.417 0 1 0 .6.58c1.486-1.54 1.293-3.214.682-4.112z\"/>\n        </svg>\n        Cite\n      </button>\n    </div>\n  </div>\n  <!--  Sequence Input-->\n  <ng-container *ngIf=\"index===0\">\n    <div class=\"row p-2\">\n      <h5 class=\"col-3 text-left\">Input Sequence(s)</h5>\n\n      <div class=\"col-9\">\n        <!--          <div class=\"btn-group btn-group-sm ml-auto\">-->\n        <button type=\"button\" class=\"btn btn-sm btn-dark-blue-grey text-white\" (click)=\"null\"\n                [disabled]=\"!submitted\"\n                data-toggle=\"dropdown\"\n                data-bs-toggle=\"dropdown\" aria-haspopup=\"true\" aria-expanded=\"false\">\n          <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n               class=\"bi bi-download\" viewBox=\"0 0 16 16\">\n            <path\n              d=\"M.5 9.9a.5.5 0 0 1 .5.5v2.5a1 1 0 0 0 1 1h12a1 1 0 0 0 1-1v-2.5a.5.5 0 0 1 1 0v2.5a2 2 0 0 1-2 2H2a2 2 0 0 1-2-2v-2.5a.5.5 0 0 1 .5-.5z\"/>\n            <path\n              d=\"M7.646 11.854a.5.5 0 0 0 .708 0l3-3a.5.5 0 0 0-.708-.708L8.5 10.293V1.5a.5.5 0 0 0-1 0v8.793L5.354 8.146a.5.5 0 1 0-.708.708l3 3z\"/>\n          </svg>\n        </button>\n        <div class=\"dropdown-menu\" aria-labelledby=\"dropdownMenuButton\">\n          <div class=\"dropdown-item\">\n            <label>Download as: </label>\n            &nbsp;\n            <div class=\"btn-group\">\n              <button\n                [className]=\"submitted ? 'btn btn-sky-blue text-white' : 'btn btn-outline-secondary'\"\n                type=\"button\" (click)=\"onDownloadJson()\">\n                JSON\n              </button>\n              <button\n                [className]=\"submitted ? 'btn btn-sky-blue text-white' : 'btn btn-outline-secondary'\"\n                type=\"button\" (click)=\"onDownloadFasta()\"\n              >FASTA\n              </button>\n              <button\n                [className]=\"submitted ? 'btn btn-sky-blue text-white' : 'btn btn-outline-secondary'\"\n                type=\"button\" (click)=\"onDownloadOriginal()\"\n              >Original\n              </button>\n            </div>\n          </div>\n        </div>\n        &nbsp;\n        <input type=\"file\"\n               #uploader\n               style=\"display: none\"\n               id=\"file\"\n               (change)=\"uploadSequenceFile($event)\">\n\n        <ng-template #uploadSequencesTipContent>\n          <div>\n            Upload sequence file <br> (.txt, .json, .fasta)\n          </div>\n\n        </ng-template>\n        <button type=\"button\" class=\"btn btn-dark-blue-grey btn-sm text-white\" (click)=\"uploader.click()\" [disabled]=\"loading\"\n                ngbTooltip='Clear allele(s)'\n                [ngbTooltip]=\"uploadSequencesTipContent\" placement=\"right\">\n          <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\" class=\"bi bi-upload\"\n               viewBox=\"0 0 16 16\">\n            <path\n              d=\"M.5 9.9a.5.5 0 0 1 .5.5v2.5a1 1 0 0 0 1 1h12a1 1 0 0 0 1-1v-2.5a.5.5 0 0 1 1 0v2.5a2 2 0 0 1-2 2H2a2 2 0 0 1-2-2v-2.5a.5.5 0 0 1 .5-.5z\"/>\n            <path\n              d=\"M7.646 1.146a.5.5 0 0 1 .708 0l3 3a.5.5 0 0 1-.708.708L8.5 2.707V11.5a.5.5 0 0 1-1 0V2.707L5.354 4.854a.5.5 0 1 1-.708-.708l3-3z\"/>\n          </svg>\n        </button>\n        &nbsp;\n      </div>\n    </div>\n    <div class=\"d-flex flex-column p-2\" appDnd (fileDropped)=\"onFileDropped($event)\">\n      <!--      [style.border-color]=\"inputChange.input_sequence_text ? '#E8D491' : null\"    -->\n      <textarea class='form-control'\n                [style.border-color]=\"inputChange.input_sequence_text ? '#E8D491' : null\"\n                id=\"sequenceFormControlTextArea\"\n                rows=\"10\"\n                formControlName=\"inputSequenceText\"\n                [maxlength]=\"maxCharacters\"\n                [readOnly]=\"loading\"\n                [placeholder]=\"'Type/paste/drag sequences (max: 1,000,000 characters) into this box or click \\'Run\\' to use the example sequence:\\n >SARS2 spike glycoprotein\\nMFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT'\"></textarea>\n\n      <div class=\"d-flex flex-row-reverse justify-content-between p-2\">\n        <small *ngIf=\"inputSequenceText.length >= maxCharacters; else sequenceCounter\" class=\"text-danger-new\">\n          Sequence text is too long -  {{maxCharacters | number}} characters allowed\n        </small>\n        <ng-template #sequenceCounter>\n          <small class=\"text-muted\">\n            Format: {{seqFormat}} | {{numOfCharacters | number}} characters\n          </small>\n        </ng-template>\n        <small *ngIf=\"inputChange.input_sequence_text\" class=\"help-block form-text text-warning-new\">\n          Parameter changed since prediction.\n        </small>\n      </div>\n    </div>\n  </ng-container>\n\n  <!--  Prediction parameter -->\n  <div class=\"row p-2\">\n    <h5 class=\"col-3 text-left\">Prediction Parameters</h5>\n    <div class=\"col-9\">\n\n      <ng-template #downloadParametersTipContent>\n        Download parameters\n      </ng-template>\n\n      <button class='btn btn-dark-blue-grey btn-sm text-white' type=\"button\" (click)=\"onDownloadParameter()\"\n              [ngbTooltip]=\"downloadParametersTipContent\" placement=\"right\">\n        <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-download\" viewBox=\"0 0 16 16\">\n          <path\n            d=\"M.5 9.9a.5.5 0 0 1 .5.5v2.5a1 1 0 0 0 1 1h12a1 1 0 0 0 1-1v-2.5a.5.5 0 0 1 1 0v2.5a2 2 0 0 1-2 2H2a2 2 0 0 1-2-2v-2.5a.5.5 0 0 1 .5-.5z\"/>\n          <path\n            d=\"M7.646 11.854a.5.5 0 0 0 .708 0l3-3a.5.5 0 0 0-.708-.708L8.5 10.293V1.5a.5.5 0 0 0-1 0v8.793L5.354 8.146a.5.5 0 1 0-.708.708l3 3z\"/>\n        </svg>\n      </button>\n    </div>\n  </div>\n  <!--  Peptide Length -->\n  <div class=\"form-group row p-2\" id=\"peptideLengthRow\">\n    <div class=\"col-sm-3 col-form-label\">\n      <label class=\"text-left\">Peptide Length(s)</label>\n    </div>\n\n    <div class=\"col-sm-8\">\n      <div [className]=\"inputChange.lengths ? 'input-change-slider' : 'custom-ngx-slider'\">\n        <ngx-slider\n          formControlName=\"peptideLength\"\n          (userChangeEnd)=\"onLengthChange($event)\"\n          [options]=\"peptideLengthSliderOptions\"></ngx-slider>\n        <small *ngIf=\"inputChange.lengths\" class=\"help-block form-text text-warning-new\">\n          Parameter changed since prediction.\n        </small>\n      </div>\n\n    </div>\n    <div class=\"col-sm-1\">\n      <div class=\"form-check pt-4\">\n        <input class=\"form-check-input\"\n               type=\"checkbox\"\n               id=\"asIsCheckbox\"\n               formControlName=\"breakPeptides\"\n               [attr.disabled]=\"loading ? true : null\"\n        >\n        <label class=\"form-check-label\" for=\"asIsCheckbox\" ngbTooltip='as-is defintion' placement=\"right\">\n          as-is\n        </label>\n      </div>\n    </div>\n  </div>\n\n  <div class=\"form-group row p-2\" id=\"alleleRow\">\n    <div class=\"col-sm-3 col-form-label\">\n      <label class=\"text-left\">\n        MHC Allele(s)\n      </label>\n    </div>\n    <div class=\"col-sm-4\">\n      <div class=\"d-flex flex-row\">\n        <ng-template #rt let-r=\"result\" let-t=\"term\">\n          <ngb-highlight [result]=\"resultFormatter(r)\" [term]=\"t\"></ngb-highlight>\n        </ng-template>\n        <input #alleleSearch id=\"allAlleles\" type=\"text\" class=\"form-control\"\n               [style.border-color]=\"inputChange.alleles ? '#E8D491' : null\"\n               [ngbTypeahead]=\"search\"\n               [inputFormatter]=\"inputFormatter\"\n               [resultTemplate]=\"rt\"\n               [editable]=\"false\"\n               [disabled]=\"loading\"\n               (selectItem)=\"onAlleleSelect({e : $event, input : alleleSearch})\"\n               [placeholder]=\"'Ex: HLA-A*02:01'\"\n        />\n      </div>\n    </div>\n    <div class=\"col-sm-1\">\n      <div *ngIf=\"searching && !modalOpen\" class=\"d-flex justify-content-center col\">\n        <div class=\"spinner-border text-primary align-self-center\" role=\"status\">\n          <span class=\"visually-hidden sr-only\">Loading...</span>\n        </div>\n      </div>\n    </div>\n    <div class=\"col-sm-4 text-start\">\n    <button type=\"button\" class=\"btn btn-dark-blue-grey text-white\"\n            (click)=\"onOpenAlleleModal()\"\n            [style]=\"{'whiteSpace': 'nowrap', 'textAlign': 'center'}\"\n            [disabled]=\"loading\">\n      Allele Finder\n    </button>\n    </div>\n  </div>\n  <div class=\"row p-2\">\n  <div class=\"offset-sm-3 col-sm-9\" style=\"min-height: 40px\">\n    <div [className]=\"inputChange.alleles ? 'p-2 input-change' : 'p-2 border'\">\n    <mat-chip-list>\n      <mat-chip *ngFor=\"let allele of alleles.value; let j=index;\">\n        {{allele.label}}\n        <button matChipRemove (click)=\"onAlleleDeselect(j)\" [disabled]=\"loading\">\n          <mat-icon>cancel</mat-icon>\n        </button>\n      </mat-chip>\n    </mat-chip-list>\n    </div>\n    <small *ngIf=\"inputChange.alleles\" class=\"help-block form-text text-warning-new\">\n      Parameter changed since prediction.\n    </small>\n  </div>\n  </div>\n\n  <div class=\"d-flex flex-row-reverse justify-content-between p-2\">\n    <small class=\"text-muted\">\n    {{alleles.length}} allele(s)\n    </small>\n  </div>\n\n\n  <div class=\"row p-2\">\n    <label class=\"col-sm-12 pb-2 text-left\">\n      Prediction Model(s)\n    </label>\n  </div>\n\n  <div cdkDropList id=\"prediction-model-list\" (cdkDropListDropped)=\"dropPredictionModel($event)\"\n       class=\"d-flex flex-column p-2\">\n    <!--    [className]=\"inputChange.predictors ? 'input-change' : null\"-->\n    <div [className]=\"inputChange.predictors ? 'input-change' : null\">\n      <div class=\"d-flex flex-row bg-secondary-new border\" *ngFor=\"let pm of predictionModels.controls; let i=index;\" cdkDrag [cdkDragDisabled]=\"loading\">\n        <!--Prediction Models-->\n        <div cdkDragHandle class=\"p-3 justify-content-start align-self-center align-content-center drag-handle\">\n          <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"24\" height=\"24\" fill=\"currentColor\" class=\"bi bi-justify\"\n               viewBox=\"0 0 16 16\">\n            <path fill-rule=\"evenodd\"\n                  d=\"M2 12.5a.5.5 0 0 1 .5-.5h11a.5.5 0 0 1 0 1h-11a.5.5 0 0 1-.5-.5zm0-3a.5.5 0 0 1 .5-.5h11a.5.5 0 0 1 0 1h-11a.5.5 0 0 1-.5-.5zm0-3a.5.5 0 0 1 .5-.5h11a.5.5 0 0 1 0 1h-11a.5.5 0 0 1-.5-.5zm0-3a.5.5 0 0 1 .5-.5h11a.5.5 0 0 1 0 1h-11a.5.5 0 0 1-.5-.5z\"/>\n          </svg>\n        </div>\n        <app-mhc-binding-formgroup *ngIf=\"pm.get('type')?.value === 'binding'\" [formGroup]=\"$any(pm)\"\n                                   style=\"width:100%\"\n                                   [modelIndex]=\"i\" [disabled]=\"loading\"\n                                   [predictionOption]=\"predictionOptions\"\n                                   (emitPredictionModelIndex)=\"removePredictorByIndex(i)\"></app-mhc-binding-formgroup>\n        <app-pmhc-immunogenicity-formgroup *ngIf=\"pm.get('type')?.value === 'immunogenicity'\" [formGroup]=\"$any(pm)\"\n                                           style=\"width:100%\"\n                                           [modelIndex]=\"i\" [disabled]=\"loading\"\n                                           (emitPredictionModelIndex)=\"removePredictorByIndex(i)\"></app-pmhc-immunogenicity-formgroup>\n        <app-mhc-i-processing-formgroup-new *ngIf=\"pm.get('type')?.value === 'processing'\" [formGroup]=\"$any(pm)\"\n                                            style=\"width:100%\"\n                                            [modelIndex]=\"i\" [disabled]=\"loading\"\n                                            [processingOptions]=\"processingOptions\"\n                                            [basicProcessingPredictionOption]=\"basicProcessingPredictionOption\"\n                                            (emitPredictionModelIndex)=\"removePredictorByIndex(i)\"></app-mhc-i-processing-formgroup-new>\n<!--        <app-mhc-np-formgroup *ngIf=\"pm.get('type')?.value === 'mhcnp'\" [formGroup]=\"$any(pm)\"-->\n<!--                              style=\"width:100%\"-->\n<!--                              [modelIndex]=\"i\" [disabled]=\"loading\"-->\n<!--                              [predictionOption]=\"predictionOptions\"-->\n<!--                              (emitPredictionModelIndex)=\"removePredictorByIndex(i)\"></app-mhc-np-formgroup>-->\n      </div>\n    </div>\n  </div>\n  <small *ngIf=\"inputChange.predictors\" class=\"help-block form-text text-warning-new\">\n    Parameter changed since prediction.\n  </small>\n\n\n  <div class=\"d-flex flex-row-reverse p-2\">\n    <div class=\"p-2\">\n      <div class=\"dropdown\">\n        <button class=\"btn btn-dark-blue-grey text-white dropdown-toggle\" type=\"button\" id=\"predictionModelDropdownMenu\"\n                data-bs-toggle=\"dropdown\"\n                data-toggle=\"dropdown\"\n                aria-haspopup=\"true\" aria-expanded=\"false\" [disabled]=\"loading\">\n          Add Another Prediction\n        </button>\n        <div class=\"dropdown-menu\" aria-labelledby=\"dropdownMenu2\">\n          <button class=\"dropdown-item\" type=\"button\" (click)=\"addpredictionModel()\">MHC Binding/Elution</button>\n          <button class=\"dropdown-item\" type=\"button\" (click)=\"addPmhcImmungencityFormGroup()\">Class I pMHC\n            Immunogenicity\n          </button>\n          <button class=\"dropdown-item\" type=\"button\" (click)=\"addMhcIProcessingNewFormGroup()\">MHC-I Processing\n\n          </button>\n<!--            TODO take all of mhcnp prediction model out - it will be added to PredictionModel-->\n<!--          <button class=\"dropdown-item\" type=\"button\" (click)=\"addMhcNPFormGroup()\">MHC-NP-->\n<!--          </button>-->\n        </div>\n      </div>\n    </div>\n  </div>\n  <hr/>\n\n  <div class=\"form-group d-flex flex-row-reverse pt-2\">\n\n    <div class=\"p-2\">\n      <!--        [disabled]=\"filteredSequences.length===0\"-->\n      <button type=\"button\" class=\"reset-button btn btn-secondary btn-lg\" [disabled]=\"loading\"\n              (click)=\"onReset(); alleleSearch.value='';\">\n        <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-arrow-clockwise\" viewBox=\"0 0 16 16\">\n          <path fill-rule=\"evenodd\" d=\"M8 3a5 5 0 1 0 4.546 2.914.5.5 0 0 1 .908-.417A6 6 0 1 1 8 2v1z\"/>\n          <path\n            d=\"M8 4.466V.534a.25.25 0 0 1 .41-.192l2.36 1.966c.12.1.12.284 0 .384L8.41 4.658A.25.25 0 0 1 8 4.466z\"/>\n        </svg>\n      </button>\n      &nbsp;\n      <span *ngIf=\"loading; else elseBlock\">\n        <button type=\"button\" class=\"btn btn-danger btn-lg\" (click)=\"onCancel()\"> Cancel Run </button>\n      </span>\n      <ng-template #elseBlock>\n        <div *ngIf=\"index!==0; else runButtonBlock\" class=\"btn-group\">\n          <div class=\"btn-group\">\n            <button type=\"submit\" class=\"run-button btn btn-dark-blue-grey btn-lg text-white\"\n                    [disabled]=\"\n                    (!tCellForm.get('predictionModels')!.value.length) ||\n                    (index>0 && !tools[index-1].submitted) ||\n                    pipelineLoading\"\n            >\n              <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\" class=\"bi bi-play-fill\" viewBox=\"0 0 16 16\">\n                <path d=\"m11.596 8.697-6.363 3.692c-.54.313-1.233-.066-1.233-.697V4.308c0-.63.692-1.01 1.233-.696l6.363 3.692a.802.802 0 0 1 0 1.393z\"/>\n              </svg>\n            </button>\n            <button type=\"button\" class=\"btn btn-dark-blue-grey text-white dropdown-toggle dropdown-toggle-split\"\n                    data-toggle=\"dropdown\"\n                    data-bs-toggle=\"dropdown\" aria-haspopup=\"true\" aria-expanded=\"false\"\n                    [disabled]=\"\n                    (!tCellForm.get('predictionModels')!.value.length) ||\n                    pipelineLoading\">\n              <!--              <span class=\"sr-only\">Toggle Dropdown</span>-->\n            </button>\n            <div class=\"dropdown-menu\">\n              <a class=\"dropdown-item\" (click)=\"onRunAll()\">Run All Above</a>\n            </div>\n          </div>\n        </div>\n        <ng-template #runButtonBlock>\n          <button type=\"submit\" class=\"run-button btn btn-dark-blue-grey btn-lg text-white\"\n                  [disabled]=\"\n                    (!tCellForm.get('predictionModels')!.value.length) ||\n                    (index>0 && !tools[index-1].submitted) ||\n                    pipelineLoading\"\n          >\n            <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\" class=\"bi bi-play-fill\" viewBox=\"0 0 16 16\">\n              <path d=\"m11.596 8.697-6.363 3.692c-.54.313-1.233-.066-1.233-.697V4.308c0-.63.692-1.01 1.233-.696l6.363 3.692a.802.802 0 0 1 0 1.393z\"/>\n            </svg>\n          </button>\n        </ng-template>\n\n      </ng-template>\n    </div>\n  </div>\n</form>\n<!--Errors and Warnings accordion -->\n<div ngbAccordion>\n  <!--  Error -->\n  <div ngbAccordionItem=\"first\" *ngIf=\"errorMessages.length\" #first=\"ngbAccordionItem\" [collapsed]=\"true\">\n    <h2 ngbAccordionHeader>\n      <button ngbAccordionButton class=\"accordion-button justify-content-center\">\n        <span class=\"text-danger-new m-1\">Errors ({{errorMessages.length}})</span>\n        <!--        <div>-->\n        <svg *ngIf=\"first.collapsed\" xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-arrow-left-circle-fill\" style=\"color: #E89A91;\" viewBox=\"0 0 16 16\">\n          <path\n            d=\"M8 0a8 8 0 1 0 0 16A8 8 0 0 0 8 0zm3.5 7.5a.5.5 0 0 1 0 1H5.707l2.147 2.146a.5.5 0 0 1-.708.708l-3-3a.5.5 0 0 1 0-.708l3-3a.5.5 0 1 1 .708.708L5.707 7.5H11.5z\"/>\n        </svg>\n        <!--        </div>-->\n        <!--        <div>-->\n        <svg *ngIf=\"!first.collapsed\" xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-arrow-down-circle-fill\" style=\"color: #E89A91;\" viewBox=\"0 0 16 16\">\n          <path\n            d=\"M16 8A8 8 0 1 1 0 8a8 8 0 0 1 16 0zM8.5 4.5a.5.5 0 0 0-1 0v5.793L5.354 8.146a.5.5 0 1 0-.708.708l3 3a.5.5 0 0 0 .708 0l3-3a.5.5 0 0 0-.708-.708L8.5 10.293V4.5z\"/>\n        </svg>\n        <!--        </div>-->\n      </button>\n    </h2>\n    <div ngbAccordionCollapse>\n      <div ngbAccordionBody>\n        <ng-template>\n          <ol>\n            <li *ngFor=\"let message of errorMessages; let i=index;\">{{message}}</li>\n          </ol>\n        </ng-template>\n      </div>\n    </div>\n  </div>\n  <!--  Warning -->\n  <div ngbAccordionItem=\"second\" *ngIf=\"warningMessages.length\" #second=\"ngbAccordionItem\" [collapsed]=\"true\">\n    <h2 ngbAccordionHeader>\n      <button ngbAccordionButton class=\"accordion-button justify-content-center\">\n        <span class=\"text-warning-new m-1\">Warnings ({{warningMessages.length}})</span>\n        <svg *ngIf=\"second.collapsed\"  xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-arrow-left-circle-fill\" style=\"color: #E8D491;\" viewBox=\"0 0 16 16\">\n          <path\n            d=\"M8 0a8 8 0 1 0 0 16A8 8 0 0 0 8 0zm3.5 7.5a.5.5 0 0 1 0 1H5.707l2.147 2.146a.5.5 0 0 1-.708.708l-3-3a.5.5 0 0 1 0-.708l3-3a.5.5 0 1 1 .708.708L5.707 7.5H11.5z\"/>\n        </svg>\n        <svg *ngIf=\"!second.collapsed\" xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-arrow-down-circle-fill\" style=\"color: #E8D491;\" viewBox=\"0 0 16 16\">\n          <path\n            d=\"M16 8A8 8 0 1 1 0 8a8 8 0 0 1 16 0zM8.5 4.5a.5.5 0 0 0-1 0v5.793L5.354 8.146a.5.5 0 1 0-.708.708l3 3a.5.5 0 0 0 .708 0l3-3a.5.5 0 0 0-.708-.708L8.5 10.293V4.5z\"/>\n        </svg>\n      </button>\n    </h2>\n    <div ngbAccordionCollapse>\n      <div ngbAccordionBody>\n        <ng-template>\n          <ol>\n            <li *ngFor=\"let message of warningMessages; let i=index;\">{{message}}</li>\n          </ol>\n        </ng-template>\n      </div>\n    </div>\n  </div>\n</div>\n\n<div *ngIf=\"!loading && !submitted && !(errorMessages.length && warningMessages.length)\"\n     class=\"p-2 d-flex justify-content-center col\"\n     [style.borderStyle]=\"styleResultContainer\">\n  <label class=\"p-2 font-italic\">\n    Results will load once step is run.\n  </label>\n</div>\n\n<div *ngIf=\"loading\" class=\"p-2 d-flex justify-content-center col\" [style.borderStyle]=\"styleResultContainer\">\n  <div class=\"spinner-border text-primary align-self-center p-3 mb-3\" role=\"status\">\n    <span class=\"visually-hidden sr-only\">Loading...</span>\n  </div>\n  <label *ngIf=\"!getResultsClicked\" class=\"p-2 font-italic\">\n    Calculating results, please wait... Click <a href=\"javascript:void(0)\" (click)=\"openEmailModal.emit()\">here</a> to\n    receive email.\n  </label>\n  <label *ngIf=\"getResultsClicked\" class=\"p-2 font-italic\">\n    Checking job status, please wait...\n  </label>\n</div>\n\n<div class=\"container-fluid p-2\" id=\"table-result-container\"\n     *ngIf=\"!loading && submitted  && !(errorMessages.length && warningMessages.length)\">\n  <ul ngbNav #nav=\"ngbNav\" [(activeId)]=\"active\" [animation]='false' [destroyOnHide]=\"false\" class=\"nav-tabs text-warning\">\n    <li *ngIf=\"peptide_table[0].length\" [ngbNavItem]=\"'peptide_table'\">\n      <a ngbNavLink>Peptide Table</a>\n      <ng-template ngbNavContent>\n<!--        <app-result-table-angular [table_data]=\"peptide_table\"-->\n<!--                                  [columns]=\"peptide_table_columns\"-->\n<!--                                  [tool_group]=\"formGroupName\"-->\n<!--                                  table_name=\"peptide_table\"></app-result-table-angular>-->\n\n        <app-result-table [table_data]=\"peptide_table\"\n                          table_name=\"peptide_table\"\n                          [order]=\"peptide_table_order\"\n                          [columns]=\"peptide_table_columns\"\n                          [tool_group]=\"formGroupName\"\n                          [index]=\"index\"\n                          [inputChange]=\"inputChange.table_state\"\n                          [tableStateSaving]=\"tableStateSaving\"\n                          (emitFilterApplied)=\"onFilterApplied()\"\n                          (emitResetTableState)=\"onClearTableState()\"\n                          (emitSaveTableState)=\"onSaveTableStateMain()\"></app-result-table>\n      </ng-template>\n    </li>\n    <li *ngIf=\"residue_table[0].length\" [ngbNavItem]=\"'residue_table'\">\n      <a ngbNavLink>Residue Table</a>\n      <ng-template ngbNavContent>\n        <app-result-table [table_data]=\"residue_table\"\n                          table_name=\"residue_table\"\n                          [order]=\"residue_table_order\"\n                          [columns]=\"residue_table_columns\"\n                          [tool_group]=\"formGroupName\"></app-result-table>\n      </ng-template>\n    </li>\n    <li *ngIf=\"allele_distances_table[0].length\" [ngbNavItem]=\"'allele_distances_table'\">\n      <a ngbNavLink>NetMHCpan Allele Distance</a>\n      <ng-template ngbNavContent>\n        <app-result-table [table_data]=\"allele_distances_table\"\n                          table_name=\"allele_distances_table\"\n                          [order]=\"allele_distances_table_order\"\n                          [columns]=\"allele_distances_table_columns\"\n                          [tool_group]=\"formGroupName\"></app-result-table>\n      </ng-template>\n    </li>\n    <li *ngIf=\"selectedSeqNumPlots && selectedLengthPlots && selectedAllelePlots\"\n        [ngbNavItem]=\"'processing_plots'\">\n      <a ngbNavLink>Processing Plots</a>\n      <ng-template ngbNavContent>\n        <div class=\"container p-2 d-flex flex-column justify-content-center\">\n          <div class=\"d-flex justify-content-center mb-5\">\n            <div class=\"input-group input-group-lg\">\n              <span class=\"input-group-text\">Seq #</span>\n              <select class=\"form-select\" aria-label=\"Default select example\" [(ngModel)]=\"selectedSeqNumPlots\"\n                      (change)=\"changePlotsBySequence($event)\">\n                <option *ngFor=\"let st of sequenceNumbers\"\n                        [value]=\"st\"> {{st}}</option>\n              </select>\n\n            </div>\n\n            <div class=\"input-group input-group-lg\">\n              <span class=\"input-group-text\">Allele</span>\n              <select class=\"form-select\" aria-label=\"Default select example\" [(ngModel)]=\"selectedAllelePlots\"\n                      (change)=\"changePlotsByAllele($event)\">\n                <option *ngFor=\"let st of stageAlleles;\" [value]=\"st\"> {{st}}</option>\n              </select>\n\n            </div>\n\n            <div class=\"input-group input-group-lg\">\n              <span class=\"input-group-text\">Length</span>\n              <select class=\"form-select\" aria-label=\"Default select example\" [(ngModel)]=\"selectedLengthPlots\"\n                      (change)=\"changePlotsByLength($event)\">\n                <option *ngFor=\"let st of range(stagePeptideLengthRange[0], stagePeptideLengthRange[1]);\"\n                        [value]=\"st\"> {{st}}</option>\n              </select>\n\n            </div>\n          </div>\n\n          <div *ngIf=\"plotLoading; else plots\" class=\"d-flex justify-content-center col\">\n            <div class=\"spinner-border text-primary align-self-center\" role=\"status\">\n              <span class=\"visually-hidden sr-only\">Loading...</span>\n            </div>\n          </div>\n          <ng-template #plots>\n            <div class=\"d-flex flex-column justify-content-center\" *ngFor=\"let plot of processingPlots; let i=index\">\n              <div class=\"row d-flex flex-row justify-content-between\">\n                <h2 class=\"col-3\"> {{plot.method}}</h2>\n                <div class=\"col-3 float-end\">\n                  <div class=\"input-group input-group-sm mb-3\">\n                    <span *ngIf=\"plot.method==='processing.netctlpan' else scoreThreshold\" class=\"input-group-text\">Percentile Threshold</span>\n                    <ng-template #scoreThreshold>\n                      <span class=\"input-group-text\">Score Threshold</span>\n                    </ng-template>\n                    <input type=\"number\" class=\"form-control\" [(ngModel)]=\"plot.thresholdInput\">\n                    <button class=\"btn btn-sm btn-dark-blue-grey text-white\" (click)=\"changePlotThreshold(plot.url, i)\">submit</button>\n                  </div>\n                </div>\n              </div>\n\n              <img [src]=\"plot.url\" [alt]=\"plot.method\">\n            </div>\n          </ng-template>\n          <div *ngIf=\"!plotLoading && !processingPlots.length;\" class=\"d-flex justify-content-center col\">\n            <div>NO DATA AVAILABLE</div>\n          </div>\n        </div>\n      </ng-template>\n    </li>\n    <li *ngIf=\"sequence_table[0].length\" [ngbNavItem]=\"'sequence_table'\">\n      <a ngbNavLink> Sequence Table </a>\n      <ng-template ngbNavContent>\n        <app-result-table [table_data]=\"sequence_table\"\n                          table_name=\"sequence_table\"\n                          [order]=\"sequence_table_order\"\n                          [columns]=\"sequence_table_columns\"\n                          [tool_group]=\"formGroupName\"\n                          (emitResetTableState)=\"onClearTableState()\"></app-result-table>\n      </ng-template>\n    </li>\n  </ul>\n\n  <div [ngbNavOutlet]=\"nav\"></div>\n</div>\n\n<!--Allele Select Modal-->\n<ng-template #alleleModal let-modal2>\n  <div class=\"modal-header\">\n    <h4 class=\"modal-title\" id=\"modal-allele-title\">\n      Number of Selected Alleles: {{modalAlleles.length}}\n    </h4>\n    <button type=\"button\" class=\"btn-close\" aria-label=\"Close\"\n            (click)=\"dismissAlleleModal();\">\n    </button>\n  </div>\n\n  <div class=\"modal-body\">\n    <div class=\"form-group row p-2\">\n      <div class=\"col-sm-3 col-form-label\">\n        <label [className]=\"'font-weight-bold'\">\n          MHC Allele(s)\n        </label>\n      </div>\n      <div class=\"col-sm-7 d-flex flex-row\">\n        <!--        <input class=\"form-control\" formControlName=\"allele\" type=\"text\" placeholder=\"HLA-A*02:01,HLA-A*01:01\">-->\n        <input #alleleSearchModal type=\"text\" class=\"form-control\"\n               [ngbTypeahead]=\"search\"\n               [inputFormatter]=\"inputFormatter\"\n               [resultTemplate]=\"rt\"\n               [editable]=\"false\"\n               [disabled]=\"loading\"\n               (selectItem)=\"onAlleleSelectModal({e : $event, input : alleleSearchModal})\"\n               (blur)=\"onBlurAlleleSelectModal($event, alleleSearchModal)\"\n               (focus)=\"alleleSearchModal.value=''; alleleSearchModal.placeholder=''\"\n               [defaultValue]=\"modalAlleles.length ? selectedModalAlleleLabels : ''\"\n               [placeholder]=\"'Ex: HLA-A*02:01'\"\n               placement=\"bottom-left\"\n        />\n      </div>\n      <div class=\"col-sm-2\">\n        <div *ngIf=\"searching\" class=\"d-flex justify-content-center col\">\n          <div class=\"spinner-border text-primary align-self-center\" role=\"status\">\n            <span class=\"visually-hidden sr-only\">Loading...</span>\n          </div>\n        </div>\n      </div>\n    </div>\n\n    <div *ngIf=\"modalAlleles.length > 0\" class=\"p-2 d-flex flex-column justify-content-start\">\n\n      <ul class=\"list-group\">\n        <!--<li *ngFor=\"let i of selectedAssayProtocols;\" class=\"list-group-item list-group-item-success\">{{i['allele']['allele']}} {{i['assayCondition'] && '+'}} {{i['assayCondition']}}</li>-->\n        <li *ngFor=\"let i of modalAlleles; let j=index;\" class=\"list-group-item list-group-item-primary list-group-item-action\">{{i['label']}}\n          <button class=\"btn-close float-end\" type=\"button\" (click)=\"onAlleleDeselect2(j, alleleSearchModal)\"\n                  [disabled]=\"loading\">\n          </button>\n        </li>\n      </ul>\n    </div>\n    <div class=\"modal-footer\" style=\"overflow-x: auto; overflow-y: auto\">\n      <fieldset class=\"w-100\">\n        <button type=\"button\" class=\"btn btn-secondary\" (click)=\"generate27Alleles(alleleSearchModal)\"\n                ngbTooltip=\"Covers ~97% of the human population\"\n                placement=\"bottom\">27 Allele Panel\n        </button>\n        <button type=\"button\" class=\"btn btn-sm\" placement=\"bottom\"\n                [ngbPopover]=\"popOverContent\"\n                popoverTitle=\"27 Allele Panel Source\">\n          <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\" class=\"bi bi-info-circle\"\n               viewBox=\"0 0 16 16\">\n            <path d=\"M8 15A7 7 0 1 1 8 1a7 7 0 0 1 0 14zm0 1A8 8 0 1 0 8 0a8 8 0 0 0 0 16z\"/>\n            <path\n              d=\"m8.93 6.588-2.29.287-.082.38.45.083c.294.07.352.176.288.469l-.738 3.468c-.194.897.105 1.319.808 1.319.545 0 1.178-.252 1.465-.598l.088-.416c-.2.176-.492.246-.686.246-.275 0-.375-.193-.304-.533L8.93 6.588zM9 4.5a1 1 0 1 1-2 0 1 1 0 0 1 2 0z\"/>\n          </svg>\n        </button>\n        <ng-template #popOverContent>\n          <a target=\"_blank\"\n             href=\"https://help.iedb.org/hc/en-us/articles/114094151851-HLA-allele-frequencies-and-reference-sets-with-maximal-population-coverage\">\n            HLA allele frequencies and reference sets with maximal population coverage\n          </a>\n        </ng-template>\n        <div class=\"float-end\">\n        <button type=\"button\" class=\"btn btn-secondary mx-1\" (click)=\"onAlleleClearModal(alleleSearchModal);\">\n          Clear Selected Allele(s)\n        </button>\n          <button type=\"button\" class=\"btn btn-dark-blue-grey text-white mx-1\" (click)=\"onSubmitModalAlleles();\">\n            Submit\n          </button>\n        </div>\n      </fieldset>\n    </div>\n\n\n  </div>\n</ng-template>\n\n<!--Alert Modal -->\n<ng-template #alertModal let-modal4>\n  <div class=\"modal-header\">\n    <h4 class=\"modal-title\" id=\"alert-modal-title\">Validation Error(s)</h4>\n    <button type=\"button\" class=\"btn-close\" aria-label=\"Close\" (click)=\"modal4.dismiss('Cross click'); modalOpen=false;\">\n    </button>\n  </div>\n  <div class=\"modal-body\">\n    <app-alert-component></app-alert-component>\n  </div>\n  <div class=\"modal-footer\">\n    <!--    <button type=\"button\" class=\"btn btn-secondary\" (click)=\"null\">Reset</button>-->\n    <!--    <button type=\"button\" class=\"btn btn-primary\" (click)=\"null\">Display</button>-->\n  </div>\n</ng-template>\n\n<!--Confirm Modal -->\n<ng-template #confirmModal let-confirmModal>\n  <div class=\"modal-header\">\n    <h4 class=\"modal-title\" id=\"modal-title\">Are you sure?</h4>\n    <button type=\"button\" class=\"btn-close\" aria-label=\"Close\" (click)=\"confirmModal.dismiss('Cross click'); modalOpen=false;\">\n    </button>\n  </div>\n  <div class=\"modal-body\">\n    <div *ngIf=\"!saveState; else saveStateConfirmation\">\n      <p><strong>Re-running this step of the pipeline will delete all downstream results, including:</strong></p>\n      <ol>\n        <li *ngFor=\"let tool of tools.slice(this.index+1)\"> {{tool.name}} </li>\n      </ol>\n      <p><strong>To access the current results, you can use this link</strong></p>\n    </div>\n    <ng-template #saveStateConfirmation>\n      <p><strong>Applying these filters for input to the next stage will delete results from all downstream steps in\n        this session, including:</strong></p>\n      <ol>\n        <li *ngFor=\"let tool of tools.slice(this.index+1)\"> {{tool.name}} </li>\n      </ol>\n      <p><strong>To access the current results, you can use this link</strong></p>\n    </ng-template>\n    <!-- pipeline URL input group-->\n    <div class=\"input-group\">\n      <input type=\"text\" class=\"form-control\" id=\"pipeline-url-input\" [value]=\"pipelineUrl\">\n      <button class=\"btn btn-secondary\" [cdkCopyToClipboard]=\"pipelineUrl\" ngbTooltip=\"copy url\" placement=\"top\">\n        <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-clipboard\" viewBox=\"0 0 16 16\">\n          <path\n            d=\"M4 1.5H3a2 2 0 0 0-2 2V14a2 2 0 0 0 2 2h10a2 2 0 0 0 2-2V3.5a2 2 0 0 0-2-2h-1v1h1a1 1 0 0 1 1 1V14a1 1 0 0 1-1 1H3a1 1 0 0 1-1-1V3.5a1 1 0 0 1 1-1h1v-1z\"/>\n          <path\n            d=\"M9.5 1a.5.5 0 0 1 .5.5v1a.5.5 0 0 1-.5.5h-3a.5.5 0 0 1-.5-.5v-1a.5.5 0 0 1 .5-.5h3zm-3-1A1.5 1.5 0 0 0 5 1.5v1A1.5 1.5 0 0 0 6.5 4h3A1.5 1.5 0 0 0 11 2.5v-1A1.5 1.5 0 0 0 9.5 0h-3z\"/>\n        </svg>\n      </button>\n    </div>\n  </div>\n  <div class=\"modal-footer\">\n    <button type=\"button\" class=\"btn btn-outline-secondary\" (click)=\"confirmModal.dismiss('cancel click')\">No\n    </button>\n    <button type=\"button\" class=\"btn btn-danger\" (click)=\"confirmModal.close('Ok click'); onRunConfirm();\">Yes, continue\n      and destroy downstream steps\n    </button>\n  </div>\n</ng-template>\n\n<!--Email Modal-->\n<!--<ng-template #emailModal let-modal3>-->\n<!--  <div class=\"modal-header\">-->\n<!--    <h4 class=\"modal-title\" id=\"modal-email-title\">-->\n<!--      Email and Job Title-->\n<!--    </h4>-->\n<!--    <button type=\"button\" id=\"emailModalCloseButton\" class=\"btn-close\" aria-label=\"Close\"-->\n<!--            (click)=\"modal3.dismiss('Cross click');\">-->\n<!--    </button>-->\n<!--  </div>-->\n<!--  <form [formGroup]=\"emailForm\" (ngSubmit)=\"sendNotification()\">-->\n<!--    <div class=\"modal-body\">-->\n<!--      <p>-->\n<!--        Your job is queued. Please send your email and job title, and we will send you an email when your job has-->\n<!--        finished.-->\n<!--      </p>-->\n<!--      <div class=\"clearfix\"></div>-->\n<!--      <div class=\"form-group row\">-->\n<!--        <label for=\"email\" class=\"col-sm-2 col-form-label font-weight-bold\">Email</label>-->\n<!--        <div class=\"col-sm-10\">-->\n<!--          <input type=\"email\"-->\n<!--                 id=\"email\"-->\n<!--                 class=\"form-control\"-->\n<!--                 formControlName=\"email\"-->\n<!--                 placeholder=\"Ex: abc@lji.org\"/>-->\n<!--        </div>-->\n<!--      </div>-->\n<!--      <div class=\"form-group row\">-->\n<!--        <label for=\"jobTitle\" class=\"col-sm-2 col-form-label font-weight-bold\">Job Title</label>-->\n<!--        <div class=\"col-sm-10\">-->\n<!--          <input id=\"jobTitle\" type=\"text\" class=\"form-control\" formControlName=\"jobTitle\"/>-->\n<!--        </div>-->\n<!--      </div>-->\n<!--    </div>-->\n<!--    <div class=\"modal-footer\">-->\n<!--      <button type=\"submit\" class=\"btn btn-outline-primary\">Submit</button>-->\n<!--    </div>-->\n<!--  </form>-->\n<!--</ng-template>-->\n","import {\n  Component,\n  OnInit,\n  OnDestroy,\n  Input,\n  Output,\n  EventEmitter,\n  ViewChild,\n  ElementRef,\n  OnChanges,\n  SimpleChanges,\n  AfterViewInit,\n  isDevMode\n} from '@angular/core';\nimport {HttpClient} from \"@angular/common/http\";\nimport {UntypedFormBuilder, UntypedFormGroup, FormControl, UntypedFormArray, FormGroupDirective, Validators} from \"@angular/forms\";\nimport {CdkDragDrop} from '@angular/cdk/drag-drop';\nimport {Location} from '@angular/common';\nimport {Title} from \"@angular/platform-browser\";\n\nimport {Observable, timer, of, from, Subject, Subscription} from \"rxjs\";\nimport {NgbModal, NgbActiveModal} from '@ng-bootstrap/ng-bootstrap';\n\nimport {catchError, debounce, debounceTime, distinctUntilChanged, tap, switchMap, takeUntil} from 'rxjs/operators';\n\n// import {Options, ChangeContext} from '@angular-slider/ngx-slider';\nimport {Options, ChangeContext} from 'ngx-slider-v2';\nimport {isASCII, IsJsonString, ltrim}from \"../../util/string-helpers\";\nimport {isMaxLength} from \"../../util/is-max-length\";\nimport {SequenceParserService} from \"../../services/sequence-parser/sequence-parser.service\";\nimport {AlleleSearchService} from \"../../services/allele-search/allele-search.service\";\nimport {PipelineService} from \"../../services/pipeline-service/pipeline.service\";\nimport {AlertServiceService} from \"../../services/alert-service/alert-service.service\";\nimport Columns from \"../../_global/Columns\";\nimport Allele from \"../../_global/Allele\";\n\nimport onCsvDownloadAllClickedNew from '../../util/on-csv-download';\nimport * as sarsSampleData from \"../../services/data/t-cell-sample.json\";\nimport * as pipelineData from \"../../services/data/pipeline-example.json\";\nimport * as alleleData from \"../../services/data/27-alleles.json\";\nimport _ from \"lodash\";\n\nimport {environment} from '../../../environments/environment';\nimport {ActivatedRoute, Router} from \"@angular/router\";\nimport {PipelineStateService} from \"../../services/state-services/pipeline-state-service/pipeline-state.service\";\nimport Stage from \"../../_global/Stage\";\nimport PipelineParams from \"../../_global/PipelineParams\";\nimport Tool from \"../../_global/Tool\";\nimport {\n  initTCellPredictionTool\n} from \"../../services/state-services/default-stage-states\";\n\nimport {columnListToObject} from \"../../util/convert-columns\";\n\nconst API_URL = `${environment['api_url']}/api/v1/mhci`;\n\n@Component({\n  selector: 'app-t-cell-prediction',\n  templateUrl: './t-cell-prediction.component.html',\n  styleUrls: ['./t-cell-prediction.component.scss']\n})\nexport class TCellPredictionComponent implements OnInit, OnDestroy, AfterViewInit, OnChanges {\n  /** Pipeline form */\n  @Input() formGroupName!: string\n  @Input() index!: number;\n  @Input() resultUrl!: string | undefined;\n  @Input() emailForm!: UntypedFormGroup;\n\n  active = 'processing_plots'\n\n  @Output() emitIndex = new EventEmitter<number>(); // used for run all\n\n  @Output() openEmailModal = new EventEmitter<any>();\n\n  @Output() emitOnCancel = new EventEmitter<any>();\n\n  @ViewChild('alleleSearch') alleleSearch!: ElementRef;\n  @ViewChild('alertModal') alertModal!: ElementRef;\n  @ViewChild('confirmModal') confirmModal!: ElementRef;\n  @ViewChild('alleleModal') alleleModal!: ElementRef;\n\n  unsubscribe$ = new Subject();\n\n  stages$: Observable<Stage[]> = this._stateService.stages$;\n  tools$: Observable<Tool[]> = this._stateService.tools$;\n  pipelineId$: Observable<string> = this._stateService.pipelineId$;\n  params$: Observable<PipelineParams> = this._stateService.params$;\n\n  stages: Stage[] = [];\n  tools: Tool[] = [];\n  pipelineId = '';\n  params!: PipelineParams;\n\n  sequence_table_result_link = ''\n\n  /** Form variables */\n  tCellForm!: UntypedFormGroup;\n  // emailForm!: FormGroup;\n\n  inputChange = {\n    /** Keeps track of inputChanges to highlight selected parameter table row*/\n    input_sequence_text: false,\n    alleles: false,\n    lengths: false,\n    predictors: false,\n    table_state: false,\n  }\n  peptideLengthSliderOptions: Options = { // ngx-slider option\n    showTicksValues: true,\n    disabled: false,\n    stepsArray: [\n      {value: 8},\n      {value: 9},\n      {value: 10},\n      {value: 11},\n      {value: 12},\n      {value: 13},\n      {value: 14}\n    ]\n  };\n\n  predictionOptions: {display_name: string, short_name: string, group: string, source: string, has_ic50: boolean}[] = [];\n  basicProcessingPredictionOption: {display_name: string, short_name: string, group: string, source: string, has_ic50: boolean}[] = []\n  processingOptions: {display_name: string, short_name: string, group: string, source: string, has_ic50: boolean}[] = [];\n\n  mhciLoading: boolean = false;\n  mhciPredictors: any[] = [];\n  // bindingPredictors: object[] = [];\n\n  /** sequence variables */\n  synthesisDownloadLinks = {\n    sequence_list_json_uri: '',\n    sequence_list_fasta_uri: '',\n    download_sequences: ''\n  };\n\n  swaggerUrl = `${environment['api_url']}/apidocs`\n\n  filteredSequences: { name: string, sequences: string }[] = [];\n  numOfAA: number = 0;\n  numOfCharacters: number = 0;\n  seqFormat: string = 'Unknown';\n\n  /** API Call variables */\n  runSetInterval: any;\n  submitted = false;\n  loading = false;\n  getResultsClicked = true;\n  pipelineLoading = false;\n  tableStateSaving = false;\n  saveState = false;\n\n  resultId: number = 0;\n\n  plotLoading = false;\n  processingPlots: {method: string, url: string, thresholdInput: number}[] = []\n  selectedSeqNumPlots = '';\n  selectedAllelePlots = '';\n  selectedLengthPlots = ''\n  sequenceNumbers = []\n\n  sequence_table_order: any[] = [];\n  sequence_table_columns: Columns[] | any;\n  sequence_table: [(string | number)[]] = [[]]\n\n  residue_table_order: any[] = [];\n  residue_table_columns: Columns[] | any;\n  residue_table: [(string | number)[]] = [[]]\n\n  allele_distances_table_order: any[] = [];\n  allele_distances_table_columns: Columns[] | any;\n  allele_distances_table: [(string | number)[]] = [[]]\n\n  peptide_table_order: any[] = [];\n  peptide_table_columns: Columns[] | any;\n  peptide_table: [(string | number)[]] = [[]]\n\n  defaultOrder: any[] = [];\n\n  // apiStatus: string;\n  errorMessages: string[] = [];\n  warningMessages: string[] = [];\n  closeResult = '';\n\n  /** Alleles */\n  searching = false;\n  searchFailed = false;\n\n  modalAlleles: Allele[] = [];\n  modalOpen = false;\n\n  /** sequence files */\n  maxCharacters = 1000000;\n  files: any[] = [];\n  fileName = '';\n\n  pipelineUrl: string = ''\n\n  data: any\n\n  @Input() events: Observable<void> = of();\n  private eventsSubscription: Subscription  = new Subscription();\n\n  @Input() runAllEvent: Observable<void> = of();\n  private runAllSubscription: Subscription  = new Subscription();\n\n  constructor(\n    public alertService: AlertServiceService,\n    private http: HttpClient,\n    private fb: UntypedFormBuilder,\n    private _alleleSearchService: AlleleSearchService,\n    private _pipelineService: PipelineService,\n    private _stateService: PipelineStateService,\n    private rootFormGroup: FormGroupDirective, // pipeline component\n    private route: ActivatedRoute,\n    private router: Router,\n    private titleService: Title,\n    private location: Location,\n    private sequenceParserService: SequenceParserService,\n    private modalService: NgbModal,\n  ) {\n  }\n\n  ngOnInit(): void {\n    if (isDevMode()) {\n      console.log('Development!');\n    } else {\n      console.log('Production!');\n    }\n\n    this.getMHCIList();\n    // this.tCellForm = this.fb.group(this.initialControlConfig);\n    this.tCellForm = this.rootFormGroup.control.get(this.formGroupName) as UntypedFormGroup;\n    this.peptideLengthSliderOptions = Object.assign({}, this.peptideLengthSliderOptions, {disabled: this.breakPeptides});\n\n    this.pipelineId$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n      console.log(`pipelineId=${value}`);\n      this.pipelineId = value;\n      this.pipelineUrl = `${window.location.origin}/pipeline/${value}`;\n    })\n    this.stages$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n      console.log(value);\n      this.stages = value;\n      this.errorMessages = this.stages[this.index]?.stage_messages!.errors\n      this.warningMessages = this.stages[this.index]?.stage_messages!.warnings\n    })\n    this.tools$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n      console.log('tools$');\n      console.log(value);\n      this.tools = value;\n      this.submitted = this.tools[this.index]?.submitted\n\n      const inputSequenceTextId = this.tools[this.index]?.input_data_uri?.input_sequence_text_id\n\n      this.synthesisDownloadLinks.sequence_list_json_uri = `${environment['api_url']}/api/v1/sequence_list_json/${inputSequenceTextId}`\n      this.synthesisDownloadLinks.sequence_list_fasta_uri = `${environment['api_url']}/api/v1/sequence_list_fasta/${inputSequenceTextId}`\n      this.synthesisDownloadLinks.download_sequences = `${environment['api_url']}/api/v1/download_sequences/${inputSequenceTextId}`\n\n      // this.loading = this.tools[this.index]?.loading\n      if(!this.tools[this.index]?.loading) {\n        this.loading = false;\n        clearInterval(this.runSetInterval)\n      }\n\n      /** pipeline Loading */\n      this.pipelineLoading = _.some(this.tools, {loading: true})\n      // if(this.pipelineLoading) {\n      //   this.disableInputs();\n      // } else {\n      //   this.enableInputs();\n      // }\n      console.log('pipelineLoading')\n      console.log(this.pipelineLoading)\n\n    })\n\n    this.params$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n      console.log(`params`);\n      console.log(value);\n      this.params = value;\n    })\n\n    this.eventsSubscription = this.events.subscribe(() => this.onRunMain());\n    this.runAllSubscription = this.runAllEvent.subscribe(() => this.onRunAll())\n\n    this.onChanges();\n\n    if(this.tCellForm.get('inputSequenceText')?.value) {\n      this.sequenceParser(this.tCellForm.get('inputSequenceText')?.value)\n    }\n\n    // if(this.loading) {\n    //   this.disableInputs()\n    // }\n\n    // if(this.resultUrl) {\n    //   this.loading = true\n    //   this.getResultsSetInterval(this.resultUrl)\n    // }\n  }\n\n  ngOnDestroy() {\n    clearInterval(this.runSetInterval);\n    clearInterval(this._pipelineService.runSetInterval)\n    this.unsubscribe$.next();\n    this.unsubscribe$.complete();\n\n    this.eventsSubscription.unsubscribe();\n    this.runAllSubscription.unsubscribe();\n  }\n\n  ngAfterViewInit() {\n    setTimeout(() => {\n      const run = history.state?.run;\n      // console.log(run);\n      run && this.onRunMain();\n    }, 0)\n  }\n\n  ngOnChanges(changes: SimpleChanges) {\n    if(changes.resultUrl?.currentValue) {\n      console.log(changes.resultUrl.currentValue);\n      console.log('ngOnChanges t-cell')\n      this.loading = true;\n      this.getResultsSetInterval(changes.resultUrl.currentValue);\n    }\n  }\n\n  get selectedAlleleLabels() {\n    return this.alleles.value.map(((o: { label: string; }) => o.label)).join(', ');\n  }\n\n  get selectedModalAlleleLabels() {\n    return this.modalAlleles.map(((o: { label: string; }) => o.label)).join(', ');\n  }\n\n  get predictionModels() {\n    return this.tCellForm.get('predictionModels') as UntypedFormArray;\n  }\n\n  get alleles() {\n    return this.tCellForm.get('alleles') as UntypedFormArray;\n  }\n\n  get breakPeptides() : boolean {\n    return this.tCellForm.get('breakPeptides')?.value;\n  }\n\n  get inputSequenceText(){\n    return this.tCellForm.get('inputSequenceText')?.value\n  }\n\n  get peptideLength() {\n    return this.tCellForm.get('peptideLength')?.value;\n  }\n\n  /** processing plot filters **/\n\n  // get sequenceNumberRange() {\n  //   const seq_num_arr =_.map(this.peptide_table, (o) => o[0])\n  //   return [_.min(seq_num_arr), _.max(seq_num_arr)] as number[]\n  // }\n\n  get stageAlleles() {\n    return this.stages[this.index]?.input_parameters?.alleles?.split(',');\n  }\n\n  get stagePeptideLengthRange() {\n    return this.stages[this.index]?.input_parameters?.peptide_length_range;\n  }\n\n  range(start: number, end: number) {\n    return (new Array(end - start + 1)).fill(undefined).map((_, i) => i + start);\n  }\n\n  getMHCIList() {\n    this.mhciLoading = true;\n    this.http.get<any[]>(API_URL)\n      .pipe().subscribe(\n      resp => {\n        // @ts-ignore\n        this.mhciPredictors = resp['predictors'];\n        // console.log(this.mhciPredictors);\n        this.predictionOptions = _.filter(this.mhciPredictors, {'group': 'binding'});\n        this.basicProcessingPredictionOption = _.filter(this.mhciPredictors, {'group': 'binding', 'has_ic50': true})\n        this.processingOptions = _.filter(this.mhciPredictors, {'group': 'processing'});\n        console.log(this.processingOptions)\n        this.mhciLoading = false;\n      }\n    )\n  }\n\n  onRunAll() {\n    this.setDefaultFormValues()\n    this.emitIndex.emit(this.index);\n  }\n\n  onRunMain() {\n    if(this.tCellForm.invalid){\n\n      this.alertService.add(`Input sequence text is too long. The maximum number of characters allowed is ${this.maxCharacters.toLocaleString()}\\nYour sequence contains ${this.inputSequenceText.length.toLocaleString()}`, 'alert-danger');\n      this.open(this.alertModal)\n      return;\n    }\n\n    const hasResult = _.find(this.tools.slice(this.index+1), (o) => o.submitted || o.loading)\n    if(this.stages.length > 1 && hasResult) {\n      this.open(this.confirmModal);\n    } else {\n      this.getResultsClicked = true;\n      if(this.index===0) {\n        this.onRun();\n      } else {\n        this.onRun2()\n      }\n    }\n  }\n\n\n  setDefaultFormValues() {\n    /** defaults - use Sars placeholders*/\n    let seq: string = ''\n    let all: string = ''\n    if(environment.production || environment['name'] === 'DEV') { // prod or dev\n      const {input_sequence_text, alleles } = sarsSampleData; // correct examples\n      seq = input_sequence_text\n      all = alleles\n    } else {\n      const {input_sequence_text, alleles } = pipelineData;\n      seq = input_sequence_text\n      all = alleles\n    }\n\n    /** Sequences */\n    let sequences = this.tCellForm.value.inputSequenceText\n    if(!sequences && this.index===0) {\n      this._stateService.setInputSequenceText(seq);\n      this.tCellForm.controls.inputSequenceText.setValue(seq);\n    }\n\n    /** Alleles */\n    const patchValues = (allele: string, synonym = '', score = null) => {\n      /** patchValues - helper function */\n      return this.fb.group({\n        label: [allele],\n        synonym: [synonym],\n        score: [score]\n      })\n    }\n    if(this.alleles.length===0) {\n      _.forEach(all.split(','), (allele) => {\n        this.alleles.push(patchValues(allele));\n      })\n      // this.alleleSearch!.nativeElement.value = alleles;\n    }\n  }\n\n  onRunConfirm() {\n      let indicies = _.range(this.index + 1, this.stages.length)\n      let initTool: Tool;\n      console.log(indicies);\n      _.forEach(indicies, i => {\n        initTool = this.tools[i];\n        const unSubmittedTool = {\n          ...initTool,\n          loading: false,\n          submitted: false,\n        }\n        this._stateService.insertTool(unSubmittedTool, i);\n      })\n      this.saveState ? this.onSaveTableState() : this.onRunMain();\n  }\n\n  onRun() {\n    /**\n     Update pipeline State\n     *\n     * */\n    /** Reset global datatables search ext */\n    $.fn.dataTable.ext.search = [];\n\n    const stage_number = this.index + 1;\n    /** run_stage_range */\n    const run_stage_range: [number, number] = [stage_number, stage_number]\n    /** default formValue */\n    this.setDefaultFormValues()\n    /** Sequences */\n    let sequences = this.tCellForm.value.inputSequenceText\n\n    /** input parameters */\n    const inputParameters = this._pipelineService.convertTCellForm(this.tCellForm)\n\n    /** Table State */\n    const { table_state } = this.stages[this.index];\n\n    const newStage = {\n      \"stage_display_name\": \"T-Cell Prediction\",\n      \"stage_number\": stage_number,\n      \"stage_type\": \"prediction\",\n      \"tool_group\": \"mhci\",\n      \"input_sequence_text\": sequences,\n      \"input_parameters\": inputParameters,\n      \"table_state\": table_state\n    }\n\n    const params = {\n      \"pipeline_id\": '',\n      \"pipeline_title\": this.emailForm.controls['name'].value,\n      \"email\": this.emailForm.controls['email'].value,\n      \"run_stage_range\": run_stage_range,\n      \"stages\": [\n        newStage\n      ]\n    }\n\n    /** set params */\n    const loadingTCellPredictionTool = Object.assign(initTCellPredictionTool, {\n      loading: true,\n      submitted: false,\n      appliedFilters: !_.isEmpty(table_state?.columns)\n    })\n    this._stateService.setParams(params);\n    this._stateService.insertTool(loadingTCellPredictionTool, this.index);\n    this._stateService.insertInputParametersToStage(inputParameters, this.index);\n\n    // this._stateService.insertTableStateToStage({columns: {}}, this.index);\n\n    this.postPipelineAPI(params);\n  }\n\n\n  onRun2() {\n\n    const params = this.params;\n    const stage_number = this.index + 1;\n    const input_stage_number = this.index; // previous index\n\n    /** run_stage_range */\n    const run_stage_range: [number, number] = [stage_number, stage_number]\n    /** default formValue */\n    this.setDefaultFormValues()\n\n    /** input parameters */\n    const inputParameters = this._pipelineService.convertTCellForm(this.tCellForm)\n    const initialStage = this.stages[this.index];\n\n    /** Table State */\n    const { table_state } = this.stages[this.index];\n\n    const stage: Stage = {\n      ...initialStage,\n      result_url: undefined,\n      stage_number: stage_number,\n      input_stage_number: input_stage_number,\n      input_parameters: inputParameters,\n      table_state\n    }\n\n    // this.params.stages.push(stage);\n    params.stages[this.index] = stage;\n    params.run_stage_range = run_stage_range;\n    params.pipeline_title = this.emailForm.controls['name'].value;\n    params.email = this.emailForm.controls['email'].value;\n\n    // console.log(params)\n\n    /** set params */\n    const initToolLoading = Object.assign(initTCellPredictionTool, {\n      loading: true,\n      submitted: false,\n      appliedFilters: !_.isEmpty(table_state?.columns)\n    })\n\n    this._stateService.setParams(params);\n    this._stateService.insertTool(initToolLoading, this.index);\n    this._stateService.insertInputParametersToStage(inputParameters, this.index);\n\n    this.postPipelineAPI(params);\n  }\n\n  getResultsSetInterval(result_url: string) {\n    /** */\n    this.getResultsClicked = true\n\n    this.residue_table_order = [];\n    this.residue_table_columns = null;\n    this.residue_table = [[]]\n\n    this.sequence_table = [[]]\n    this.allele_distances_table = [[]]\n    this.residue_table = [[]]\n    this.peptide_table = [[]]\n    this.processingPlots = []\n\n    this.resultUrl = result_url;\n    console.log(result_url)\n    this.inputChange = _.mapValues(this.inputChange, () => false);\n    let increment = 0;\n    const milliseconds = 3000;\n    this.runSetInterval = setInterval(() => {\n      this._pipelineService.getResults(`${result_url}?statusOnly=true`).subscribe(\n        {\n          next: resp => {\n        console.log(resp);\n        if (resp['status'] === 'error' || resp['errors']) {\n          // this.errorMessages = resp['errors'];\n          // this.warningMessages = resp['warnings'];\n          this.submitted = false;\n          this.loading = false;\n          const prevTool = this.tools[this.index];\n          const submittedTool = Object.assign(prevTool, {\n            submitted: this.submitted,\n            loading: this.loading,\n          })\n          this._stateService.insertTool(submittedTool, this.index);\n          clearInterval(this.runSetInterval);\n          this.enableInputs();\n        }\n        if (resp['data']['warnings']?.length) {\n          // console.log(resp['warnings']);\n          this.warningMessages = resp['data']['warnings'];\n        }\n        if (resp['data']['errors']?.length) {\n          // console.log(resp['warnings']);\n          this.errorMessages = resp['data']['errors'];\n        }\n        if (resp['status'] === 'done') {\n          clearInterval(this.runSetInterval);\n\n          this._pipelineService.getResults(result_url).subscribe(resp => {\n            // clearInterval(this.runSetInterval);\n            console.log(resp)\n            this.defaultOrder = [[]]\n            /** 1) Create Column */\n            const data = resp['data']['results'];\n            // check for residue_table\n            this.active = data[0].type\n            _.forEach(data, table => {\n\n\n              if (table.type === 'residue_table') {\n                this.residue_table_columns = _.map(table.table_columns, (column, i) => {\n                  if (column.default_order && Number.isFinite(column.row_sort_priority)) { // set defaultOrder\n                    this.residue_table_order[column.row_sort_priority] = [i, column.default_order === \"ascending\" ? 'asc' : 'desc'];\n                  }\n                  column['title'] = `${column['display_name']}`; // required\n                  column['data'] = `${column['name']}`;\n                  let source = column['source'];\n\n                  column['filterKey'] = `${source}.${column.name}`\n\n                  // console.log(`source=${source}`);\n                  let tempSource = source.split('.')\n                  // console.log(tempSource);\n                  source = tempSource[tempSource.length - 1];\n                  // console.log(`source=${source}`);\n                  column['data'] = `${source}_${column['name']}`;\n                  /** remove `core` from name */\n                  // column['name'] = column['display_name'] ? column['display_name'] : column['name']\n                  column['value_limits'] = column['type'] === 'int' ? {\n                    minValue: NaN,\n                    maxValue: NaN,\n                    applied: false\n                  } : {\n                    possibleValues: [],\n                    textValue: null,\n                    selectedValues: [],\n                    applied: false\n                  }\n                  return column\n                });\n                // this.currentOrder = [...this.defaultOrder];\n                if (this.residue_table_columns) {\n                  this.residue_table = table.table_data;\n                }\n                // console.log(this.residue_table_order);\n                // console.log(this.residue_table_columns);\n                // console.log(this.residue_table);\n              }\n              if (table.type === 'netmhcpan_allele_distance') {\n                this.allele_distances_table_columns = _.map(table.table_columns, (column, i) => {\n                  if (column.default_order && Number.isFinite(column.row_sort_priority)) { // set defaultOrder\n                    this.allele_distances_table[column.row_sort_priority] = [i, column.default_order === \"ascending\" ? 'asc' : 'desc'];\n                  }\n                  column['title'] = `${column['display_name']}`; // required\n                  column['data'] = `${column['name']}`;\n                  let source = column['source'];\n\n                  column['filterKey'] = `${source}.${column.name}`\n\n                  // console.log(`source=${source}`);\n                  let tempSource = source.split('.')\n                  // console.log(tempSource);\n                  source = tempSource[tempSource.length - 1];\n                  // console.log(`source=${source}`);\n                  column['data'] = `${source}_${column['name']}`;\n                  /** remove `core` from name */\n                  // column['name'] = column['display_name'] ? column['display_name'] : column['name']\n                  // column['value_limits'] = column['type'] === 'int' ? {\n                  //   minValue: NaN,\n                  //   maxValue: NaN,\n                  //   applied: false\n                  // } : {\n                  //   possibleValues: [],\n                  //   textValue: null,\n                  //   selectedValues: [],\n                  //   applied: false\n                  // }\n                  column['value_limits'] = column['value_limits'] ? this.setValueLimits(column) : undefined\n                  return column\n                });\n                // this.currentOrder = [...this.defaultOrder];\n                if (this.allele_distances_table_columns) {\n                  this.allele_distances_table = table.table_data;\n                }\n              }\n              if (table.type === 'peptide_table') {\n                this.peptide_table_columns = _.map(table.table_columns, (column, i) => {\n                  if (column.default_order && Number.isFinite(column.row_sort_priority)) { // set defaultOrder\n                    this.defaultOrder[column.row_sort_priority] = [i, column.default_order === \"ascending\" ? 'asc' : 'desc'];\n                  }\n                  column['title'] = `${column['display_name']}`; // required\n                  column['data'] = `${column['name']}`;\n                  let source = column['source'];\n\n                  column['filterKey'] = `${source}.${column.name}`\n\n                  // console.log(`source=${source}`);\n                  let tempSource = source.split('.')\n                  // console.log(tempSource);\n                  source = tempSource[tempSource.length - 1];\n                  // console.log(`source=${source}`);\n                  column['data'] = `${source}_${column['name']}`;\n                  /** remove `core` from name */\n                  // column['name'] = column['display_name'] ? column['display_name'] : column['name']\n\n                  column['value_limits'] = column['value_limits'] &&  this.setValueLimits(column)\n\n                  // console.log(column['value_limits'])\n                  // column['value_limits'] = column['value_limits'] ? {...column['value_limits'], applied: false, possibleValues: []} : undefined\n\n                  return column\n                });\n                this.peptide_table_order = [...this.defaultOrder];\n                if (this.peptide_table_columns) {\n                  this.peptide_table = table.table_data;\n                }\n                // console.log(this.peptide_table_order);\n                // console.log(this.peptide_table_columns);\n                // console.log(this.peptide_table);\n              }\n              if (table.type === 'input_sequence_table') {\n                this.sequence_table_columns = _.map(table.table_columns, (column, i) => {\n                  // if (column.default_order && Number.isFinite(column.row_sort_priority)) { // set defaultOrder\n                  //   this.defaultOrder[column.row_sort_priority] = [i, column.default_order === \"ascending\" ? 'asc' : 'desc'];\n                  // }\n                  column['title'] = `${column['display_name']}`; // required\n                  column['data'] = `${column['name']}`;\n                  let source = column['source'];\n\n                  column['filterKey'] = `${source}.${column.name}`\n\n                  // console.log(`source=${source}`);\n                  let tempSource = source.split('.')\n                  // console.log(tempSource);\n                  source = tempSource[tempSource.length - 1];\n                  // console.log(`source=${source}`);\n                  column['data'] = `${source}_${column['name']}`;\n                  /** remove `core` from name */\n                  // column['name'] = column['display_name'] ? column['display_name'] : column['name']\n                  // column['value_limits'] = column['type'] === 'int' ? {\n                  //   minValue: NaN,\n                  //   maxValue: NaN,\n                  //   applied: false\n                  // } : {\n                  //   possibleValues: [],\n                  //   textValue: null,\n                  //   selectedValues: [],\n                  //   applied: false\n                  // }\n\n                  column['value_limits'] = column['value_limits'] ? this.setValueLimits(column) : undefined\n                  // column['value_limits'] = column['value_limits'] && this.setValueLimits(column)\n                  return column\n\n\n\n                });\n                this.sequence_table_order = []\n                if (this.sequence_table_columns) {\n\n                  this.sequence_table = table.table_data\n                }\n              }\n              if (table.type === 'processing_plots') {\n                const all_plots_uri = new URL(table.all_plots_uri)\n\n                this.selectedSeqNumPlots = all_plots_uri.searchParams.get('sequence_number') || ''\n                this.selectedLengthPlots = all_plots_uri.searchParams.get('length') || ''\n                this.selectedAllelePlots = all_plots_uri.searchParams.get('allele') || ''\n\n                this.sequenceNumbers = table.sequence_numbers\n\n                this.processingPlots = _.map(table.urls, (plot) => {\n\n                  const url = new URL(plot.url)\n                  const thresholdInput = url.searchParams.get('threshold')\n\n                  return {\n                    thresholdInput,\n                    ...plot\n                  }\n                })\n                // this.processingPlots = table.urls\n                console.log(this.processingPlots)\n              }\n\n            })\n\n            this.submitted = true; this.loading = false;\n            const prevTool = this.tools[this.index];\n            console.log(prevTool)\n            const submittedTCellPredictionTool = Object.assign(prevTool, {\n              submitted: this.submitted,\n              loading: this.loading,\n            })\n            this._stateService.insertTool(submittedTCellPredictionTool, this.index);\n            // clearInterval(this.runSetInterval); // remove later\n            console.log(data);\n            console.log(resp.pipeline_id)\n            this.enableInputs();\n          })\n        }\n        if (resp['status'] === 'canceled') {\n          /** if status is canceled, then just stop loader **/\n          this.submitted = false;\n          this.loading = false;\n          const prevTool = this.tools[this.index];\n          console.log(prevTool)\n          const submittedTCellPredictionTool = Object.assign(prevTool, {\n            submitted: this.submitted,\n            loading: this.loading,\n          })\n          this._stateService.insertTool(submittedTCellPredictionTool, this.index);\n          clearInterval(this.runSetInterval);\n          // console.log(data);\n          this.enableInputs();\n          // set error message\n          // this.errorMessages = [`PIPELINE_ID=${this.pipelineId} w/ STATUS=${resp['status']}`]\n        }\n        else {\n          this.getResultsClicked = false;\n          console.log(`current status: ${resp['status']} - ${increment}`);\n          increment += 1;\n        }\n      },\n          error: error => {\n            console.error(error);\n            this.enableInputs();\n            clearInterval(this.runSetInterval);\n            this.loading = false;\n          }\n        }\n      )\n    }, milliseconds);\n  }\n\n  setValueLimits(column: Columns) : any {\n    /* set value_limits (i.e. filters) for each column based on if type is a number/string */\n    return column['type'] === 'int' || column['type'] === 'float' ? {\n      ...column['value_limits'],\n      minValue: NaN,\n      maxValue: NaN,\n      applied: false\n    } : {\n      // ...column['value_limits'],\n      possibleValues: column['value_limits']['unique_values'],\n      textValue: null,\n      selectedValues: [],\n      applied: false\n    }\n  }\n\n  postPipelineAPI(params: PipelineParams, getResults: boolean = true) {\n    /**\n     * params\n     * getResults: boolean\n     *  false - used in 'Save Table State'\n     * */\n    /** initial set up */\n    this.disableInputs();\n    if (getResults) {\n      this.errorMessages = [];\n      this.warningMessages = [];\n    }\n    this.loading = getResults; // true - defaults\n    this.submitted = !getResults; // false - defaults\n    this.tableStateSaving = !getResults\n    // this.residue_table_order = [];\n    // this.residue_table_columns = null;\n    // this.residue_table = [[]]\n    //\n    // this.sequence_table = [[]]\n    // this.allele_distances_table = [[]]\n    // this.residue_table = [[]]\n    // this.peptide_table = [[]]\n    // this.processingPlots = []\n\n    this._pipelineService.postPipeline(params).subscribe(\n      (resp) => {\n      // Errors and Warnings\n      if (resp['errors'] && resp['errors'].length) {\n        console.log(resp);\n        console.error(resp['errors']);\n        this.errorMessages = resp['errors'];\n        if (resp['warnings'].length) {\n          console.log(resp['warnings']);\n          this.warningMessages = resp['warnings'];\n        }\n        this.loading = false;\n        this.submitted = true;\n        const submittedTCellPredictionTool = Object.assign(initTCellPredictionTool, {\n          submitted: false,\n          loading: false,\n        })\n        this._stateService.insertTool(submittedTCellPredictionTool, this.index);\n        this.enableInputs();\n        return;\n      }\n      // Warnings\n      if (resp['warnings'].length) {\n        console.log(resp['warnings']);\n        this.warningMessages = resp['warnings'];\n      }\n\n      const inputDataUri = {input_sequence_text_id: resp.input_sequence_text_id}\n      this._stateService.insertInputDataUriToTool(inputDataUri, this.index)\n\n      this._stateService.setPipelineId(resp.pipeline_id);\n      this._stateService.setPipelineIdToParams(resp.pipeline_id);\n      this._stateService.setPipelineSpecId(resp.pipeline_spec_id);\n      /** Display email Modal if emailModalShow=true */\n      this.location.go(`pipeline/${resp.pipeline_id}`)\n      // this.titleService.setTitle(`IEDB NG Tools Pipeline`);\n\n      // this.location.replaceState(`pipeline/${resp.pipeline_id}`)\n      // this.router.createUrlTree([`pipeline/${resp.pipeline_id}`])\n      if (getResults) {\n        const result_url = `${resp.results_uri}`;\n        console.log(result_url);\n        this.getResultsSetInterval(result_url);\n      } else {\n        this.inputChange.table_state = false;\n        this.submitted = true;\n        this.loading = false;\n        this.tableStateSaving = false;\n        this.enableInputs();\n      }\n    },\n      (error) => {\n        console.error(error);\n        this.errorMessages.push(error.error);\n        this.submitted = false;\n        this.loading = false;\n        const prevTool = this.tools[this.index];\n        const submittedTool = Object.assign(prevTool, {\n          submitted: this.submitted,\n          loading: this.loading,\n        })\n        this._stateService.insertTool(submittedTool, this.index);\n        clearInterval(this.runSetInterval);\n        this.enableInputs();\n      }\n      )\n  }\n\n\n  onSaveTableStateMain() {\n    const hasResult = _.find(this.tools.slice(this.index+1), {submitted: true})\n    if (hasResult) {\n      this.saveState = true;\n      this.open(this.confirmModal);\n    } else {\n      this.onSaveTableState();\n    }\n  }\n\n  onSaveTableState() {\n    const tool_group = 'mhci'\n\n    const params = this.params\n    // create colObj and params\n    let colObj = columnListToObject(this.peptide_table_columns, tool_group)\n    const stages = params.stages;\n    const stageTemp = stages[this.index];\n\n    stageTemp.table_state = [{table: 'peptide_table', columns: colObj}];\n    stages[this.index] = stageTemp\n    params.stages = stages;\n    // run_stage_range\n    const stage_number = this.index + 1;\n    params.run_stage_range = [stage_number, stage_number];\n    this._stateService.setParams(params);\n    // appliedFilters\n    let appliedFilters = !_.isEmpty(colObj);\n    this._stateService.setToolAppliedFilters(appliedFilters, this.index)\n    this.postPipelineAPI(params, false);\n    this.saveState = false;\n  }\n\n  onFilterApplied() {\n    this.inputChange.table_state = this.submitted;\n  }\n\n  onClearTableState() {\n    this.peptide_table_columns = _.map(this.peptide_table_columns, (c) => {\n      c.value_limits = c.type === 'int'? {\n        minValue: NaN,\n        maxValue: NaN,\n        applied: false\n      } :\n        {\n          possibleValues: [],\n          textValue: null,\n          selectedValues: [],\n          applied: false\n        }\n      return c\n    })\n    this.inputChange.table_state = this.submitted;\n  }\n\n  onCancel() {\n    console.log(this.runSetInterval)\n    clearInterval(this.runSetInterval);\n    this.emitOnCancel.emit()\n\n    this.inputChange.table_state = false;\n    // this.submitted = false;\n    const currentTool = this.tools[this.index];\n    const unSubmittedTool = {\n      ...currentTool,\n      loading: false,\n      submitted: false,\n      appliedFilters: undefined\n    }\n    this._stateService.insertTool(unSubmittedTool, this.index);\n    this.warningMessages = [];\n    this.loading = false;\n    this.tableStateSaving = false;\n    this.enableInputs();\n  }\n\n  onReset() {\n    this.alertService.clear();\n    this.errorMessages = [];\n    this.warningMessages = [];\n\n    const oldSequence = this.stages[this.index].input_sequence_text\n    const input_parameters = this.params.stages[this.index].input_parameters\n\n    console.log(input_parameters)\n\n    // sequences\n    this.filteredSequences = [];\n    this.numOfAA = 0;\n    // order\n    this.peptide_table_order = [];\n    this.defaultOrder = [];\n    // tCellForm values\n    const peptideLength = [9, 10];\n    this.tCellForm.patchValue({\n      inputSequenceText: '',\n      peptideLength,\n    }, {emitEvent: false});\n\n    // selected alleles\n    this.alleles.clear()\n\n    // predictors\n    const initPredictor = {\n      type: 'binding',\n      method: 'netmhcpan_el',\n    }\n    const pm = this.tCellForm.controls.predictionModels as UntypedFormArray\n    pm.clear({emitEvent: false})\n    pm.push(this.fb.group(initPredictor), {emitEvent: false});\n\n    this.enableInputs();\n\n    if(this.submitted){\n      this.inputChange =  {\n        ...this.inputChange,\n        /** Keeps track of inputChanges to highlight selected parameter table row*/\n        input_sequence_text: oldSequence !== '',\n        alleles: !_.isEqual([], input_parameters.alleles),\n        lengths: !_.isEqual(peptideLength, input_parameters.peptide_length_range),\n        predictors: !_.isEqual([initPredictor], input_parameters.predictors),\n      }\n    }\n  }\n\n  onFileDropped($event: any[]) {\n    console.log($event);\n    const file = $event[0];\n    const fileSize = file.size / 1024; // in kB\n    console.log(file.type);\n    if (fileSize > 20000) {\n      this.alertService.add('File Size is too big! (20mB max)', 'alert-danger');\n      this.open(this.alertModal);\n    }\n    else {\n      this.prepareSequenceFileList($event);\n    }\n  }\n\n  prepareSequenceFileList(files: Array<any>) {\n    console.log(files);\n    this.fileName = files[0].name;\n    const reader = new FileReader();\n    const myForm = this.tCellForm;\n    for (const item of files) {\n      // console.log(item);\n      reader.readAsText(item);\n      reader.onload = () => {\n        const val = reader.result?.toString() || '';\n        console.log(val);\n        const v = isASCII(val);\n        console.log(v);\n        if (v) {\n          // myForm.patchValue({inputSequenceText: val.substring(0, this.maxCharacters)});\n          const w = isMaxLength(val, this.maxCharacters)\n          if (w) {\n            myForm.patchValue({inputSequenceText: val});\n          } else {\n            this.alertService.add(`Sequence is too long - max Sequence length is ${this.maxCharacters.toLocaleString(\"en-US\")} characters`, 'alert-danger');\n            this.open(this.alertModal);\n          }\n          // this.sequenceParser(val);  // auto parser\n        } else {\n          this.alertService.add('Invalid file type.\\nValid file types are .txt, .fa, .fasta, .json, .faa,', 'alert-danger');\n          this.open(this.alertModal);\n        }\n      };\n\n      reader.onerror = () => {\n        console.log(reader.error);\n      };\n      item.progress = 0;\n      this.files.push(item);\n    }\n  }\n\n  /** Add Prediction Model FormGroups */\n\n  mhcBindingFormGroup(method = 'netmhcpan_el') {\n    /**\n     * Creates mhcBindingFormGroup using formBuilder\n     *\n     * Currently defaulted to 'netmhcpan_el'\n     * */\n    return this.fb.group({\n      type: 'binding',\n      method: this.fb.control(method),\n    })\n  }\n\n  pmhcImmunogencityFormGroup(mask_choice = 'default', position_to_mask = '2,5,9') {\n    /**\n     * */\n    return this.fb.group({\n      type: 'immunogenicity',\n      mask_choice: mask_choice,\n      position_to_mask: this.fb.control(position_to_mask),\n    })\n  }\n\n  mhcIProcessingFormGroup(proteasome = 'immuno', tap_precursor = 1, tap_alpha = 0.2) {\n    /**\n     *\n     * Defaults:\n     * {\n     *   type: 'processing'\n     *   proteasome: 'immuno'\n     *   tap_precursor: 1,\n     *   tap_alpha: 0.2\n     * }\n     * */\n    return this.fb.group({\n      type: 'processing',\n      proteasome: this.fb.control(proteasome),\n      tap_precursor: this.fb.control(tap_precursor),\n      tap_alpha: this.fb.control(tap_alpha)\n    })\n  }\n\n  mhcIProcessingNewFormGroup(method='basic_processing') {\n    /**\n     *\n     * Defaults:\n     * {\n     *   type: 'processing'\n     *   proteasome: 'immuno'\n     *   tap_precursor: 1,\n     *   tap_alpha: 0.2\n     * }\n     * */\n    return this.fb.group({\n      type: 'processing',\n      method: this.fb.control(method),\n      mhc_binding_method: \"netmhcpan_ba\",\n      proteasome: \"immuno\",\n      tap_precursor: 1,\n      tap_alpha: 0.2\n    })\n  }\n\n  mhcINPNewFormGroup() {\n    /**\n     *\n     * Defaults:\n     * {\n     *   type: 'processing'\n     *   proteasome: 'immuno'\n     *   tap_precursor: 1,\n     *   tap_alpha: 0.2\n     * }\n     * */\n    return this.fb.group({\n      type: 'mhcnp'\n    })\n  }\n\n  /** Download Sequence File API calls\n   * onDownloadJson()\n   * onDownloadFasta()\n   * onDownloadOriginal()\n   * */\n\n  onDownloadJson() {\n    onCsvDownloadAllClickedNew(this.synthesisDownloadLinks.sequence_list_json_uri, this.http, 'json');\n  }\n\n  onDownloadFasta() {\n    onCsvDownloadAllClickedNew(this.synthesisDownloadLinks.sequence_list_fasta_uri, this.http, 'fasta');\n  }\n\n  onDownloadOriginal() {\n    onCsvDownloadAllClickedNew(this.synthesisDownloadLinks.download_sequences, this.http, 'txt');\n  }\n\n  /** Allele Search Functions */\n  onAlleleSelect({e, input}: { e: any, input: any }) {\n    e.preventDefault();\n    const selectedAllele = e.item;\n    let labels = _.map(this.alleles.value, (allele) => allele.label)\n    if (!labels.includes(selectedAllele.label)) {\n      this.alleles.push(this.fb.group(selectedAllele));\n    }\n    // sessionStorage.setItem('selectedAlleles', JSON.stringify(this.selectedAlleles));\n    input.value = '';\n    this.inputChange.alleles = this.submitted;\n  }\n\n  onAlleleSelectModal({e, input}: { e: any, input: any }) {\n    e.preventDefault();\n    const selectedAllele = e.item;\n    let labels = _.map(this.modalAlleles, (allele) => allele.label)\n    if (!labels.includes(selectedAllele.label)) {\n      this.modalAlleles.push(selectedAllele);\n    }\n    input.value = '';\n  }\n\n  onBlurAlleleSelect(e: { preventDefault: () => void; }, input: { value: string; placeholder: string; }) {\n    /**\n     * Displays alleles in the text box when out of focus.\n     * */\n    e.preventDefault();\n    input.value = '';\n    input.placeholder = 'Ex. HLA-A*02:01'\n    if (this.alleles.length) {\n      const labels = _.map(this.alleles.value, (o) => {\n        return o.label;\n      });\n      input.value = labels.join(', ');\n    }\n  }\n\n  onBlurAlleleSelectModal(e: { preventDefault: () => void; }, input: { value: string; placeholder: string; }) {\n    /**\n     * Displays alleles in the text box when out of focus.\n     * */\n    e.preventDefault();\n    input.placeholder = 'Ex. HLA-A*02:01'\n    input.value = this.modalAlleles.length ? this.selectedModalAlleleLabels : ''\n  }\n\n  onAlleleClear(input: { value: string; }) {\n    this.inputChange.alleles = this.submitted;\n    this.alleles.clear()\n    input.value = '';\n  }\n\n  onAlleleClearModal(input: { value: string; }) {\n    this.modalAlleles = []\n    input.value = ''\n  }\n\n  onAlleleDeselect(index: number) {\n    this.alleles.removeAt(index)\n    this.inputChange.alleles = this.submitted;\n    // input.value = '';\n    // if (this.alleles.length) {\n    //   input.value = this.selectedAlleleLabels\n    // }\n  }\n\n\n  onAlleleDeselect2(index: number, input: { value: string }) {\n    console.log(index)\n    _.pullAt(this.modalAlleles, [index])\n    const labels = this.modalAlleles.map(((o: { label: string; }) => o.label)).join(', ')\n    input.value = this.modalAlleles.length ? labels : ''\n  }\n\n  search = (text$: Observable<string>) =>\n    text$.pipe(\n      debounceTime(1000),\n      distinctUntilChanged(),\n      tap(() => this.searching = true),\n      switchMap(term => {\n          // console.log(term);\n          return this._alleleSearchService.search(term).pipe(\n            tap(() => this.searchFailed = false),\n            catchError(() => {\n              this.searchFailed = true;\n              return of([]);\n            }))\n        }\n      ),\n      tap(() => this.searching = false)\n    )\n\n  resultFormatter = (result: any) => {\n    /**\n     *  The function that converts an item from the result list to a string to display in the popup.\n     * */\n    return result.synonyms.length > 0 ? `${result.label} - (${result.synonyms})` : result.label;\n  }\n\n  inputFormatter(value: any): any {\n    /**\n     * The function that converts an item from the result list to a string to display in the <input> field.\n     * */\n    if (value.label) {\n      return `${value.label}`;\n    }\n  }\n\n  /** Predictors Drag and Drop */\n\n  dropPredictionModel(event: CdkDragDrop<string[]>) {\n    const {previousIndex, currentIndex} = event;\n\n    const control = this.predictionModels.at(previousIndex);\n    this.predictionModels.removeAt(previousIndex);\n    this.predictionModels.insert(currentIndex, control);\n\n    if (previousIndex !== currentIndex) {\n      this.inputChange.predictors = this.submitted;\n    }\n  }\n\n  setInputChangePredictors(value: boolean) {\n    this.inputChange.predictors = this.submitted;\n  }\n\n  removePredictorByIndex(index: number) {\n    this.predictionModels.removeAt(index);\n    this.inputChange.predictors = this.submitted;\n  }\n\n  addpredictionModel() {\n    this.predictionModels.push(this.mhcBindingFormGroup());\n    this.inputChange.predictors = this.submitted;\n  }\n\n  addPmhcImmungencityFormGroup() {\n    this.predictionModels.push(this.pmhcImmunogencityFormGroup());\n    this.inputChange.predictors = this.submitted;\n  }\n\n  // addMhcIProcessingFormGroup() {\n  //   this.predictionModels.push(this.mhcIProcessingFormGroup());\n  //   this.inputChange.predictors = this.submitted;\n  // }\n\n  addMhcIProcessingNewFormGroup() {\n    this.predictionModels.push(this.mhcIProcessingNewFormGroup());\n    this.inputChange.predictors = this.submitted;\n  }\n\n  addMhcNPFormGroup() {\n    this.predictionModels.push(this.mhcINPNewFormGroup());\n    this.inputChange.predictors = this.submitted;\n  }\n\n  get styleResultContainer(){\n    return !this.loading && this.submitted ? 'none' : 'dotted';\n  }\n\n  /** Prediction Parameter Functions */\n\n  formUrl() {\n    /**\n     http://localhost:4200/t-cell-prediction?params=\n     * */\n  }\n\n  onDownloadParameter() {\n    const data = this._pipelineService.convertTCellForm(this.tCellForm)\n\n    const a = document.createElement('a');\n    a.setAttribute('style', 'display:none;');\n    document.body.appendChild(a);\n    // const contentType = 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet;charset=UTF-16';\n    // var blob = new Blob([csvData], { type: contentType });\n    const blob = new Blob([JSON.stringify(data, null, 2)], ); // thx: http://stackoverflow.com/a/18925211\n    a.href = window.URL.createObjectURL(blob);\n    a.download = 'parameter.json';\n\n    a.click();\n  }\n\n  /** File Download/Upload*/\n  uploadSequenceFile($event: any) {\n    $event.preventDefault();\n    /**\n     * Used for 'Upload' button\n     * */\n    const {files} = $event.target;\n    files && this.onFileDropped(files);\n  }\n\n  uploadParameterFile($event: any, input: any) {\n    console.log($event);\n    $event.preventDefault();\n    /**\n     * Used for 'Upload' button to upload parameters\n     * */\n    // const {files} = $event.target;\n    // files && this.onParameterFileDropped(files, input);\n  }\n\n  sequenceParser(val: string) {\n\n    const firstChar = ltrim(val)[0];\n    const firstLine = val.split('\\n')[0]\n    console.log(firstLine)\n\n    /** Named white space */\n    let firstLineNumOfElements = 0\n    let separator = ' '\n    if(firstLine.includes(' ')){\n      separator = ' '\n    } else if (firstLine.includes('\\t')){\n      separator = '\\t'\n    } else if (firstLine.includes('\\s')){\n      separator = '\\s'\n    }\n    firstLineNumOfElements = firstLine.split(separator).length\n    console.log(firstLineNumOfElements)\n    console.log(separator)\n\n    const slicedVal = val.slice(0, this.maxCharacters)\n\n    if(val.length > this.maxCharacters) {\n      //  Skip parsing\n    } else if (firstChar === '>' && this.sequenceParserService.fastaValidate(val)) { // fasta\n      this.seqFormat = this.sequenceParserService.seqFormat;\n      this.numOfCharacters = slicedVal.length\n    } else if ((firstChar === '{' || firstChar === '[') && IsJsonString(val)) { // json\n      this.seqFormat = 'JSON'\n      this.numOfCharacters = slicedVal.length\n    } else if (firstLineNumOfElements === 2 && this.sequenceParserService.namedWhiteSpaceValidate(val, separator)) {\n      // named white space\n      this.seqFormat = this.sequenceParserService.seqFormat;\n      this.numOfCharacters = slicedVal.length\n    } else if (val.length > 3 && !val.includes('>') && this.sequenceParserService.unnamedWhiteSpaceValidate(val)) {\n      // Unnamed\n      this.seqFormat = this.sequenceParserService.seqFormat;\n      this.numOfCharacters = slicedVal.length\n    } else if (val === '') {  // delete\n      /**\n       * Takes care of it up top - still need this if statement\n       * */\n      this.seqFormat = 'Unknown';\n      this.numOfCharacters = 0\n    } else { // error\n      this.seqFormat = 'Error';\n      this.numOfCharacters = 0\n    }\n  }\n\n  onLengthChange(changeContext: ChangeContext): void {\n    /**\n     * used in (userChangeEnd)\n     * Saves minPeptideLength and maxPeptideLength in session storage\n     * */\n    // sessionStorage.setItem('minPeptideLength', JSON.stringify(changeContext.value));\n    // sessionStorage.setItem('maxPeptideLength', JSON.stringify(changeContext.highValue));\n    this.inputChange.lengths = this.submitted;\n  }\n\n  onChanges(): void {\n    /** PredictionModel sessionStorage */\n    this.tCellForm.get('predictionModels')?.valueChanges.subscribe(val => {\n      // sessionStorage.setItem('predictionModels', JSON.stringify(val));\n      this.inputChange.predictors = this.submitted\n    });\n\n    const sequenceFieldChange = this.tCellForm.get('inputSequenceText')?.valueChanges.pipe(\n      debounce(v => timer(1000)),\n    );\n\n    this.tCellForm.get('breakPeptides')?.valueChanges.subscribe(val => {\n      this.peptideLengthSliderOptions = Object.assign({}, this.peptideLengthSliderOptions, {disabled: val});\n    })\n\n    sequenceFieldChange?.subscribe(val => {\n      console.log('sequenceFieldChange')\n      // sessionStorage.setItem('sequences', val);\n      this.sequenceParser(val);\n      this.inputChange.input_sequence_text = this.submitted;\n      if (val === '') {  // delete\n        this.filteredSequences = [];\n        this.numOfAA = 0;\n        // this.alertService.clear();\n        // this.myForm.patchValue({\n        //   inputFormat: 0\n        // });\n      }\n    });\n  }\n\n  /** Allele Modal Functions */\n  open(content: any) {\n    this.modalOpen = true;\n    this.modalService.open(content, {\n      ariaLabelledBy: 'modal-basic-title',\n      size: 'lg',\n      animation: true,\n      backdrop: 'static'\n    }).result.then((result) => {\n      // this.closeResult = `Closed with: ${result}`;\n      this.saveState = false;\n      this.modalOpen = false;\n    }, (reason) => {\n      this.saveState = false;\n      this.alleleSearch.nativeElement.focus();\n      // this.closeResult = `Dismissed ${TCellPredictionComponent.getDismissReason(reason)}`;\n    });\n  }\n\n  onOpenAlleleModal() {\n    this.open(this.alleleModal)\n    this.modalAlleles = [...this.alleles.value]\n    console.log(this.modalAlleles)\n  }\n\n  dismissAlleleModal() {\n    this.modalOpen = false;\n    this.modalService.dismissAll()\n  }\n\n  onSubmitModalAlleles() {\n    this.alleles.clear()\n    _.forEach(this.modalAlleles, (selectedAllele) => {\n      this.alleles.push(this.fb.group(selectedAllele));\n    })\n    this.inputChange.alleles = this.submitted;\n    this.modalService.dismissAll()\n    this.modalOpen = false;\n  }\n\n  generate27Alleles(input: any) {\n    this.modalAlleles = []\n    // this.alleles.clear()\n    const { alleles } = alleleData;\n    _.forEach(alleles.split(','), (allele) => {this.modalAlleles.push({label: allele, synonym: null, score: null})})\n    input.value = this.selectedModalAlleleLabels;\n  }\n\n  enableInputs() {\n    // this.tCellForm.enable({emitEvent: false});\n    this.peptideLengthSliderOptions = Object.assign({}, this.peptideLengthSliderOptions, {disabled: this.breakPeptides});\n  }\n\n  disableInputs() {\n    // this.tCellForm.disable({emitEvent: false});\n    this.peptideLengthSliderOptions = Object.assign({}, this.peptideLengthSliderOptions, {disabled: true});\n  }\n\n  onErrorMessageDeselect(message: string, index: number) {\n    if (index > -1) {\n      this.errorMessages.splice(index, 1);\n    }\n    this.errorMessages = _.filter(this.errorMessages, (em) => em !== message);\n  }\n\n  onWarningMessageDeselect(message: string, index: number) {\n    if (index > -1) {\n      this.warningMessages.splice(index, 1);\n    }\n    this.warningMessages = _.filter(this.warningMessages, (wm) => wm !== message);\n  }\n\n  changePlotThreshold(url: string, i: number) {\n    const value = this.processingPlots[i].thresholdInput\n    const tempUrl = url.split('?')[0]\n    const params = new URL(url).searchParams\n    params.set('threshold', `${value}`)\n    this.processingPlots[i].url = `${tempUrl}?${params}`\n  }\n\n\n\n  changePlotsBySequence(e: any) {\n    const newUrl = `${this.resultUrl}/plots?sequence_number=${e.target.value}&length=${this.selectedLengthPlots}&allele=${this.selectedAllelePlots}`\n    console.log(newUrl)\n    this.plotLoading = true;\n    this.http.get(newUrl).subscribe((value: any) => {\n      console.log(value)\n      this.processingPlots = _.map(value.urls, (plot) => {\n\n        const url = new URL(plot.url)\n        const thresholdInput = url.searchParams.get('threshold')\n\n        return {\n          thresholdInput,\n          ...plot\n        }\n      })\n      this.plotLoading = false;\n    })\n  }\n\n  changePlotsByAllele(e: any) {\n    const newUrl = `${this.resultUrl}/plots?sequence_number=${this.selectedSeqNumPlots}&length=${this.selectedLengthPlots}&allele=${e.target.value}`\n    console.log(newUrl)\n    this.plotLoading = true;\n    this.http.get(newUrl).subscribe((value: any) => {\n      console.log(value)\n      this.processingPlots = _.map(value.urls, (plot) => {\n\n        const url = new URL(plot.url)\n        const thresholdInput = url.searchParams.get('threshold')\n\n        return {\n          thresholdInput,\n          ...plot\n        }\n      })\n      this.plotLoading = false;\n    })\n  }\n\n  changePlotsByLength(e: any) {\n    const newUrl = `${this.resultUrl}/plots?sequence_number=${this.selectedSeqNumPlots}&length=${e.target.value}&allele=${this.selectedAllelePlots}`\n    console.log(newUrl)\n    this.plotLoading = true;\n    this.http.get(newUrl).subscribe((value: any) => {\n      console.log(value)\n      this.processingPlots = _.map(value.urls, (plot) => {\n\n        const url = new URL(plot.url)\n        const thresholdInput = url.searchParams.get('threshold')\n\n        return {\n          thresholdInput,\n          ...plot\n        }\n      })\n      this.plotLoading = false;\n    })\n  }\n\n  // sendNotification() {\n  //   const param = {\n  //     request_id: this.resultId,\n  //     email: this.emailForm.get('email')?.value,\n  //     job_title: this.emailForm.get('jobTitle')?.value\n  //   }\n  //   this.http.post<any[]>(EMAIL_URL, param)\n  //     .subscribe(resp => {\n  //       console.log(resp);\n  //       this.modalService.dismissAll('sendNotification()');\n  //     })\n  // }\n\n}\n","import { Pipe, PipeTransform } from '@angular/core';\n\n@Pipe({ name: 'dashToDecimal' })\nexport class DashToDecimalPipe implements PipeTransform {\n  transform(value: string): any {\n    if (!value) return null;\n    return value.replace('_', '.');\n  }\n}\n","<div class=\"container-fluid p-2 d-flex flex-column\" id=\"visualization-result-container\">\n<!--  <div class=\"d-flex flex-row p-2 align-self-center\" role=\"group\" aria-label=\"button-groups\">-->\n<!--    <button type=\"button\"-->\n<!--            class=\"btn btn-link text-dark d-flex flex-column justify-content-center align-items-center\">-->\n<!--      <svg width=\"1em\" height=\"1em\" viewBox=\"0 0 16 16\" class=\"bi bi-download\" fill=\"currentColor\"-->\n<!--           xmlns=\"http://www.w3.org/2000/svg\">-->\n<!--        <path fill-rule=\"evenodd\"-->\n<!--              d=\"M.5 8a.5.5 0 0 1 .5.5V12a1 1 0 0 0 1 1h12a1 1 0 0 0 1-1V8.5a.5.5 0 0 1 1 0V12a2 2 0 0 1-2 2H2a2 2 0 0 1-2-2V8.5A.5.5 0 0 1 .5 8z\"/>-->\n<!--        <path fill-rule=\"evenodd\"-->\n<!--              d=\"M5 7.5a.5.5 0 0 1 .707 0L8 9.793 10.293 7.5a.5.5 0 1 1 .707.707l-2.646 2.647a.5.5 0 0 1-.708 0L5 8.207A.5.5 0 0 1 5 7.5z\"/>-->\n<!--        <path fill-rule=\"evenodd\" d=\"M8 1a.5.5 0 0 1 .5.5v8a.5.5 0 0 1-1 0v-8A.5.5 0 0 1 8 1z\"/>-->\n<!--      </svg>-->\n<!--      Download-->\n<!--    </button>-->\n<!--    <button type=\"button\"-->\n<!--            class=\"btn btn-link text-dark d-flex flex-column justify-content-center align-items-center\">-->\n<!--      <svg width=\"1em\" height=\"1em\" viewBox=\"0 0 16 16\" class=\"bi bi-share\" fill=\"currentColor\"-->\n<!--           xmlns=\"http://www.w3.org/2000/svg\">-->\n<!--        <path fill-rule=\"evenodd\"-->\n<!--              d=\"M11.724 3.947l-7 3.5-.448-.894 7-3.5.448.894zm-.448 9l-7-3.5.448-.894 7 3.5-.448.894z\"/>-->\n<!--        <path fill-rule=\"evenodd\"-->\n<!--              d=\"M13.5 4a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3zm0 1a2.5 2.5 0 1 0 0-5 2.5 2.5 0 0 0 0 5zm0 10a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3zm0 1a2.5 2.5 0 1 0 0-5 2.5 2.5 0 0 0 0 5zm-11-6.5a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3zm0 1a2.5 2.5 0 1 0 0-5 2.5 2.5 0 0 0 0 5z\"/>-->\n<!--      </svg>-->\n<!--      Share-->\n<!--    </button>-->\n<!--    <button type=\"button\"-->\n<!--            class=\"btn btn-link text-dark d-flex flex-column justify-content-center align-items-center\">-->\n<!--      <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"-->\n<!--           class=\"bi bi-arrow-clockwise\" viewBox=\"0 0 16 16\">-->\n<!--        <path fill-rule=\"evenodd\" d=\"M8 3a5 5 0 1 0 4.546 2.914.5.5 0 0 1 .908-.417A6 6 0 1 1 8 2v1z\"/>-->\n<!--        <path-->\n<!--          d=\"M8 4.466V.534a.25.25 0 0 1 .41-.192l2.36 1.966c.12.1.12.284 0 .384L8.41 4.658A.25.25 0 0 1 8 4.466z\"/>-->\n<!--      </svg>-->\n<!--      Reset Graph-->\n<!--    </button>-->\n<!--  </div>-->\n<div #d3force class=\"p-2 m-4 align-self-center border\">\n  <h3>Interactive Cluster Visualization</h3>\n  <span>\n        Visualize a selected Sub-cluster\n          <select (change)=\"onFilterGraph($event)\">\n            <option value=\"all\"> All </option>\n            <option *ngFor=\"let cluster of uniqueClusters\" [value]=\"cluster\"> {{cluster | dashToDecimal }} </option>\n          </select>\n      </span>\n  <div #containerForceChart></div>\n</div>\n</div>\n","import {AfterViewInit, Component, ElementRef, Input, ViewChild} from '@angular/core';\nimport {HttpClient} from \"@angular/common/http\";\nimport * as d3 from \"d3\";\nimport _ from 'lodash';\nimport {BehaviorSubject} from \"rxjs\";\n\ninterface IAData {\n  label: string,\n  value: number\n}\n\n\n@Component({\n  selector: 'app-d3-force',\n  templateUrl: './d3-force.component.html',\n  styleUrls: ['./d3-force.component.scss']\n})\n\nexport class D3ForceComponent implements AfterViewInit {\n  @ViewChild(\"containerForceChart\") element: ElementRef | undefined\n\n  // initialize a private variable _data, it's a BehaviorSubject\n  private _data = new BehaviorSubject<IAData[]>([]);\n\n  // change data to use getter and setter\n  @Input()\n  set data(value) {\n    // set the latest value for _data BehaviorSubject\n    this._data.next(value);\n  };\n\n  get data() {\n    // get the latest value from _data BehaviorSubject\n    return this._data.getValue();\n  }\n\n  @Input() uniqueClusters: string[] = [];\n\n  private host: d3.Selection<d3.BaseType, {}, d3.BaseType, any> | undefined\n  private svg?: d3.Selection<SVGElement, {}, d3.BaseType, any>\n  private width: number = 960;\n  private height: number = 600;\n  private radius: number = 10;\n\n  private htmlElement?: HTMLElement;\n\n  private links: any[] = [];\n  nodes = {}\n\n  constructor(private http: HttpClient) { }\n\n  ngAfterViewInit() {\n    this.htmlElement = this.element?.nativeElement;\n    // @ts-ignore\n    this.host = d3.select(this.htmlElement);\n    this.buildSVG()\n\n    this._data\n      .subscribe(data => {\n        this.links = data;\n        this.buildForce()\n      })\n  }\n\n  private buildSVG(): void {\n    this.host?.html(\"\");\n\n    // zoom\n    const zoom: d3.ZoomBehavior<any, any> = d3.zoom()\n      .scaleExtent([-1, 3])\n      .on(\"zoom\", event => {\n        this.svg?.attr('transform', event.transform)\n      })\n\n\n    // @ts-ignore\n    this.svg = this.host?.append(\"svg\")\n      .attr(\"width\", this.width)\n      .attr(\"height\", this.height) // add zoom feature here\n      .call(zoom)\n      .append(\"g\")\n  }\n\n  private buildForce(): void {\n    _.forEach(this.links, (link) => {\n      // @ts-ignore\n      link.source = this.nodes[link.source] || (this.nodes[link.source] = {name: link.source, cluster: link.cluster});\n      // @ts-ignore\n      link.target = this.nodes[link.target] || (this.nodes[link.target] = {name: link.target, cluster: link.cluster});\n    })\n\n    this.nodes = {}\n\n    _.forEach(this.links, (link) => {\n      // @ts-ignore\n      if( this.nodes[link.source.name] ){\n        // @ts-ignore\n        this.nodes[link.source.name].cluster = this.nodes[link.source.name].cluster.concat(link.cluster)\n      }\n      else{ // @ts-ignore\n        this.nodes[link.source.name] = {\n          name: link.source.name,\n          cluster: link.cluster\n        }\n      }\n      // @ts-ignore\n      link.source = this.nodes[link.source.name]\n      // @ts-ignore\n      if( this.nodes[link.target.name] ){\n        // @ts-ignore\n        this.nodes[link.target.name].cluster = this.nodes[link.target.name].cluster.concat(link.cluster)\n      }\n      else{\n        // @ts-ignore\n        this.nodes[link.target.name] = {\n          name: link.target.name,\n          cluster: link.cluster\n        }\n      }\n      // @ts-ignore\n      link.target = this.nodes[link.target.name]\n    })\n\n    // @ts-ignore\n    let simulation = d3.forceSimulation(Object.values(this.nodes))\n      .force(\"charge\", d3.forceManyBody().strength(-10))\n      .force(\"link\", d3.forceLink(this.links))\n      .force('center', d3.forceCenter(this.width/2, this.height/2))\n    // @ts-ignore\n    const link = this.svg\n      .selectAll(\".link\")\n      .data(this.links)\n      .enter().append(\"line\")\n      .style(\"stroke\", \"#6b7071\")\n      .attr(\"class\", (d) => \"link \"+ d.cluster.join(' '));\n\n    // mouseover\n    const mouseover = (event: { currentTarget: any; }, d: any) => {\n      d3.select(event.currentTarget).select(\"circle\").transition()\n        .duration(750)\n        .attr(\"r\", 8)\n\n      d3.select(event.currentTarget).select(\"text\").transition()\n        .duration(750)\n        .attr(\"visibility\", \"visible\");\n    }\n\n    // mouseout\n    const mouseout = (event: { currentTarget: any; }, d: any) => {\n      d3.select(event.currentTarget).select(\"circle\").transition()\n        .duration(750)\n        .attr(\"r\", 4.5);\n\n      d3.select(event.currentTarget).select(\"text\").transition()\n        .duration(750)\n        .attr(\"visibility\", \"hidden\");\n    }\n    // @ts-ignore\n    const drag = simulation => {\n\n      function dragstarted(event: { active: any; subject: { fx: any; x: any; fy: any; y: any; }; }) {\n        if (!event.active) simulation.alphaTarget(0.3).restart();\n        event.subject.fx = event.subject.x;\n        event.subject.fy = event.subject.y;\n      }\n\n      function dragged(event: { subject: { fx: any; fy: any; }; x: any; y: any; }) {\n        event.subject.fx = event.x;\n        event.subject.fy = event.y;\n      }\n\n      function dragended(event: { active: any; subject: { fx: null; fy: null; }; }) {\n        if (!event.active) simulation.alphaTarget(0);\n        event.subject.fx = null;\n        event.subject.fy = null;\n      }\n\n      return d3.drag()\n        .on(\"start\", dragstarted)\n        .on(\"drag\", dragged)\n        .on(\"end\", dragended);\n    }\n    // @ts-ignore\n    let node = this.svg\n      .selectAll(\".node\")\n      .data(Object.values(this.nodes))\n      .enter().append(\"g\")\n      .attr(\"class\", (d: any) => \"node \"+ d['cluster'].join(' '))\n      .on('mouseover', mouseover)\n      .on('mouseout', mouseout)\n      // @ts-ignore\n      .call(drag(simulation))\n\n    const circle = node.append(\"circle\")\n      .attr(\"r\", 4.5);\n\n    const label = node.append(\"text\")\n      .attr(\"dy\", \".35em\")\n      .attr('visibility','hidden')\n      .text(function(d: any) { return d['name']; });\n\n    simulation.on(\"tick\", () => {\n      link\n        .attr(\"x1\", d => d.source.x)\n        .attr(\"y1\", d => d.source.y)\n        .attr(\"x2\", d => d.target.x)\n        .attr(\"y2\", d => d.target.y);\n      circle.attr(\"cx\", (d:any) => d['x']).attr(\"cy\", (d: any) => d['y']);\n      label.attr(\"x\", function(d: any) { return d['x'] + 8; }).attr(\"y\", function(d: any) { return d['y']; });\n    });\n  }\n\n  private populateForce(): void {\n    /** can break down buildForce to populate Force here.*/\n  }\n\n  onFilterGraph(e: any) {\n    e.preventDefault();\n    const value = e.target.value;\n    /* https://gitlab.lji.org/iedb/tools/djangotools/-/blob/master/cluster2/templates/cluster2/results.html#L340 */\n    if (value == 'all'){\n      $(\".node\").show();\n      $(\".link\").show();\n    }\n    else{\n\n      $(\".node\").hide();\n      $(\".link\").hide();\n\n      $(\".\"+value).show();\n    }\n  }\n\n}\n","<form [formGroup]=\"clusterForm\" (ngSubmit)=\"onRunMain()\" class=\"container\">\n  <div class=\"d-flex flex-row p-2\">\n    <h2 class=\"pe-2 display-5\">{{index + 1}}</h2>\n    <hr class=\"mt-4 flex-grow-1 divider\"/>\n  </div>\n  <div class=\"d-flex pb-3\">\n    <h4 class=\"p-2 tool-name\" id=\"cluster-label\">Cluster</h4>\n    <div class=\"d-flex flex-row tool-links\" role=\"group\" aria-label=\"tool-links\">\n      <button type=\"button\" class=\"btn btn-link text-dark d-flex flex-column justify-content-center align-items-center\">\n        <a target=\"_blank\" routerLink=\"/docs/tools/cluster/index.html\" class=\"text-dark d-flex flex-column justify-content-center align-items-center\">\n          <svg width=\"1em\" height=\"1em\" viewBox=\"0 0 16 16\" class=\"bi bi-file-earmark-text\" fill=\"currentColor\"\n               xmlns=\"http://www.w3.org/2000/svg\">\n            <path\n              d=\"M4 1h5v1H4a1 1 0 0 0-1 1v10a1 1 0 0 0 1 1h8a1 1 0 0 0 1-1V6h1v7a2 2 0 0 1-2 2H4a2 2 0 0 1-2-2V3a2 2 0 0 1 2-2z\"/>\n            <path d=\"M9 4.5V1l5 5h-3.5A1.5 1.5 0 0 1 9 4.5z\"/>\n            <path fill-rule=\"evenodd\"\n                  d=\"M5 11.5a.5.5 0 0 1 .5-.5h2a.5.5 0 0 1 0 1h-2a.5.5 0 0 1-.5-.5zm0-2a.5.5 0 0 1 .5-.5h5a.5.5 0 0 1 0 1h-5a.5.5 0 0 1-.5-.5zm0-2a.5.5 0 0 1 .5-.5h5a.5.5 0 0 1 0 1h-5a.5.5 0 0 1-.5-.5z\"/>\n          </svg>\n          Docs\n        </a>\n      </button>\n      <button type=\"button\" class=\"btn btn-link\">\n        <a target=\"_blank\" [href]=\"swaggerUrl\" class=\"text-dark d-flex flex-column justify-content-center align-items-center\">\n          <svg width=\"1em\" height=\"1em\" viewBox=\"0 0 16 16\" class=\"bi bi-gear\" fill=\"currentColor\"\n               xmlns=\"http://www.w3.org/2000/svg\">\n            <path fill-rule=\"evenodd\"\n                  d=\"M8.837 1.626c-.246-.835-1.428-.835-1.674 0l-.094.319A1.873 1.873 0 0 1 4.377 3.06l-.292-.16c-.764-.415-1.6.42-1.184 1.185l.159.292a1.873 1.873 0 0 1-1.115 2.692l-.319.094c-.835.246-.835 1.428 0 1.674l.319.094a1.873 1.873 0 0 1 1.115 2.693l-.16.291c-.415.764.42 1.6 1.185 1.184l.292-.159a1.873 1.873 0 0 1 2.692 1.116l.094.318c.246.835 1.428.835 1.674 0l.094-.319a1.873 1.873 0 0 1 2.693-1.115l.291.16c.764.415 1.6-.42 1.184-1.185l-.159-.291a1.873 1.873 0 0 1 1.116-2.693l.318-.094c.835-.246.835-1.428 0-1.674l-.319-.094a1.873 1.873 0 0 1-1.115-2.692l.16-.292c.415-.764-.42-1.6-1.185-1.184l-.291.159A1.873 1.873 0 0 1 8.93 1.945l-.094-.319zm-2.633-.283c.527-1.79 3.065-1.79 3.592 0l.094.319a.873.873 0 0 0 1.255.52l.292-.16c1.64-.892 3.434.901 2.54 2.541l-.159.292a.873.873 0 0 0 .52 1.255l.319.094c1.79.527 1.79 3.065 0 3.592l-.319.094a.873.873 0 0 0-.52 1.255l.16.292c.893 1.64-.902 3.434-2.541 2.54l-.292-.159a.873.873 0 0 0-1.255.52l-.094.319c-.527 1.79-3.065 1.79-3.592 0l-.094-.319a.873.873 0 0 0-1.255-.52l-.292.16c-1.64.893-3.433-.902-2.54-2.541l.159-.292a.873.873 0 0 0-.52-1.255l-.319-.094c-1.79-.527-1.79-3.065 0-3.592l.319-.094a.873.873 0 0 0 .52-1.255l-.16-.292c-.892-1.64.902-3.433 2.541-2.54l.292.159a.873.873 0 0 0 1.255-.52l.094-.319z\"/>\n            <path fill-rule=\"evenodd\"\n                  d=\"M8 5.754a2.246 2.246 0 1 0 0 4.492 2.246 2.246 0 0 0 0-4.492zM4.754 8a3.246 3.246 0 1 1 6.492 0 3.246 3.246 0 0 1-6.492 0z\"/>\n          </svg>\n          API\n        </a>\n      </button>\n      <button type=\"button\" class=\"btn btn-link text-dark d-flex flex-column justify-content-center align-items-center\"\n              routerLink=\"/download-all\"\n              [state]=\"{tool: 'cluster'}\">\n        <svg width=\"1em\" height=\"1em\" viewBox=\"0 0 16 16\" class=\"bi bi-cloud-arrow-down\" fill=\"currentColor\"\n             xmlns=\"http://www.w3.org/2000/svg\">\n          <path fill-rule=\"evenodd\"\n                d=\"M4.406 3.342A5.53 5.53 0 0 1 8 2c2.69 0 4.923 2 5.166 4.579C14.758 6.804 16 8.137 16 9.773 16 11.569 14.502 13 12.687 13H3.781C1.708 13 0 11.366 0 9.318c0-1.763 1.266-3.223 2.942-3.593.143-.863.698-1.723 1.464-2.383zm.653.757c-.757.653-1.153 1.44-1.153 2.056v.448l-.445.049C2.064 6.805 1 7.952 1 9.318 1 10.785 2.23 12 3.781 12h8.906C13.98 12 15 10.988 15 9.773c0-1.216-1.02-2.228-2.313-2.228h-.5v-.5C12.188 4.825 10.328 3 8 3a4.53 4.53 0 0 0-2.941 1.1z\"/>\n          <path fill-rule=\"evenodd\"\n                d=\"M7.646 10.854a.5.5 0 0 0 .708 0l2-2a.5.5 0 0 0-.708-.708L8.5 9.293V5.5a.5.5 0 0 0-1 0v3.793L6.354 8.146a.5.5 0 1 0-.708.708l2 2z\"/>\n        </svg>\n        Download\n      </button>\n      <button type=\"button\" class=\"btn btn-link text-dark d-flex flex-column justify-content-center align-items-center\"\n              routerLink=\"/citation\">\n        <svg width=\"1em\" height=\"1em\" viewBox=\"0 0 16 16\" class=\"bi bi-chat-square-quote\" fill=\"currentColor\"\n             xmlns=\"http://www.w3.org/2000/svg\">\n          <path fill-rule=\"evenodd\"\n                d=\"M14 1H2a1 1 0 0 0-1 1v8a1 1 0 0 0 1 1h2.5a2 2 0 0 1 1.6.8L8 14.333 9.9 11.8a2 2 0 0 1 1.6-.8H14a1 1 0 0 0 1-1V2a1 1 0 0 0-1-1zM2 0a2 2 0 0 0-2 2v8a2 2 0 0 0 2 2h2.5a1 1 0 0 1 .8.4l1.9 2.533a1 1 0 0 0 1.6 0l1.9-2.533a1 1 0 0 1 .8-.4H14a2 2 0 0 0 2-2V2a2 2 0 0 0-2-2H2z\"/>\n          <path fill-rule=\"evenodd\"\n                d=\"M7.066 4.76A1.665 1.665 0 0 0 4 5.668a1.667 1.667 0 0 0 2.561 1.406c-.131.389-.375.804-.777 1.22a.417.417 0 1 0 .6.58c1.486-1.54 1.293-3.214.682-4.112zm4 0A1.665 1.665 0 0 0 8 5.668a1.667 1.667 0 0 0 2.561 1.406c-.131.389-.375.804-.777 1.22a.417.417 0 1 0 .6.58c1.486-1.54 1.293-3.214.682-4.112z\"/>\n        </svg>\n        Cite\n      </button>\n    </div>\n  </div>\n\n  <ng-container *ngIf=\"index===0\"> <!-- display sequence input -->\n    <div class=\"d-flex flex-row p-2\">\n      <h5 class=\"col-3 text-left\">Input Sequence(s)</h5>\n\n      <div class=\"col-9\">\n        <!--          <div class=\"btn-group btn-group-sm ml-auto\">-->\n        <button type=\"button\" class=\"btn btn-sm btn-dark-blue-grey text-white\" (click)=\"null\"\n                [disabled]=\"!submitted\"\n                data-toggle=\"dropdown\"\n                data-bs-toggle=\"dropdown\" aria-haspopup=\"true\" aria-expanded=\"false\">\n          <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n               class=\"bi bi-download\" viewBox=\"0 0 16 16\">\n            <path\n              d=\"M.5 9.9a.5.5 0 0 1 .5.5v2.5a1 1 0 0 0 1 1h12a1 1 0 0 0 1-1v-2.5a.5.5 0 0 1 1 0v2.5a2 2 0 0 1-2 2H2a2 2 0 0 1-2-2v-2.5a.5.5 0 0 1 .5-.5z\"/>\n            <path\n              d=\"M7.646 11.854a.5.5 0 0 0 .708 0l3-3a.5.5 0 0 0-.708-.708L8.5 10.293V1.5a.5.5 0 0 0-1 0v8.793L5.354 8.146a.5.5 0 1 0-.708.708l3 3z\"/>\n          </svg>\n        </button>\n        <div class=\"dropdown-menu\" aria-labelledby=\"dropdownMenuButton\">\n          <div class=\"dropdown-item\">\n            <label>Download as: </label>\n            &nbsp;\n            <div class=\"btn-group\">\n              <button\n                [className]=\"submitted ? 'btn btn-sky-blue text-white' : 'btn btn-outline-secondary'\"\n                type=\"button\" (click)=\"onDownloadJson()\">\n                JSON\n              </button>\n              <button\n                [className]=\"submitted ? 'btn btn-sky-blue text-white' : 'btn btn-outline-secondary'\"\n                type=\"button\" (click)=\"onDownloadFasta()\">\n                FASTA\n              </button>\n              <button\n                [className]=\"submitted ? 'btn btn-sky-blue text-white' : 'btn btn-outline-secondary'\"\n                type=\"button\" (click)=\"onDownloadOriginal()\">Original\n              </button>\n            </div>\n          </div>\n        </div>\n        &nbsp;\n        <input type=\"file\"\n               #uploader\n               style=\"display: none\"\n               id=\"file\"\n               (change)=\"uploadSequenceFile($event)\">\n\n        <ng-template #uploadSequencesTipContent>\n          <div>\n            Upload sequence file <br> (.txt, .json, .fasta)\n          </div>\n\n        </ng-template>\n        <button type=\"button\" class=\"btn btn-sm btn-dark-blue-grey text-white\" (click)=\"uploader.click()\" [disabled]=\"loading\"\n                ngbTooltip='Clear allele(s)'\n                [ngbTooltip]=\"uploadSequencesTipContent\" placement=\"right\">\n          <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\" class=\"bi bi-upload\"\n               viewBox=\"0 0 16 16\">\n            <path\n              d=\"M.5 9.9a.5.5 0 0 1 .5.5v2.5a1 1 0 0 0 1 1h12a1 1 0 0 0 1-1v-2.5a.5.5 0 0 1 1 0v2.5a2 2 0 0 1-2 2H2a2 2 0 0 1-2-2v-2.5a.5.5 0 0 1 .5-.5z\"/>\n            <path\n              d=\"M7.646 1.146a.5.5 0 0 1 .708 0l3 3a.5.5 0 0 1-.708.708L8.5 2.707V11.5a.5.5 0 0 1-1 0V2.707L5.354 4.854a.5.5 0 1 1-.708-.708l3-3z\"/>\n          </svg>\n        </button>\n        &nbsp;\n      </div>\n    </div>\n    <div class=\"d-flex flex-column p-2\" appDnd (fileDropped)=\"onFileDropped($event)\">\n        <textarea class='form-control'\n                  [style.border-color]=\"inputChange.input_sequence_text ? '#f0ad4d' : null\"\n                  id=\"sequenceFormControlTextArea\"\n                  rows=\"10\"\n                  formControlName=\"inputSequenceText\"\n                  [readOnly]=\"loading\"\n                  [placeholder]=\"'Type/paste/drag a set of peptides (max: 1,000) into this box or click \\'Run\\' to use the example sequence:\\n >Mus Pep1\\nLEQIHVLENSLVL\\n>Mus Pep2\\nFVEHIHVLENSLAFK\\n>Mus Pep3\\nGLYGREPDLSSDIKERFA\\n>Mus Pep4\\nEWFSILLASDKREKI\\n>Mus Pep5\\nDGFNTFTILKTDYDN\\n>Mus Pep6\\nNEKDGETFQLMGLY\\n>Mus Pep7\\nYGREPDLSLDIKEK\\n>Mus Pep8\\nLENSLVLKFHTVRDE\\n>Mus Pep9\\nAHLINEKDGETFQLM\\n>Mus Pep10\\nEEASSTGRNFNVQKINGEWHTIIL\\n>Mus Pep11\\nEKALVSSVRQRMKCS\\n>Mus Pep12\\nSRPFIFQEVIDLGGE\\n>Mus Pep13\\nNVEKINGEWHTIIL\\n>Mus Pep14\\nGIYYLNYDGFNTFTI\\n>Mus Pep15\\nDDVVASEALNSVWSGF\\n>Mus Pep16\\nGSMRVFVEHIHVLEN\\n>Mus Pep17\\nENIIDLTKTNRCLKA\\n>Mus Pep18\\nILGKLVKDYHLQFHR\\n>Mus Pep19\\nIGGPDDGVITPWQSSF\\n>Mus Pep20\\nDKETLSLEELKALLL\\n>Mus Pep21\\nLQSGFYSLSSLVTVP\\n>Mus Pep22\\nEELRRLAPITSDPTE\\n>Mus Pep23\\nTIFISLFLLSVCYSA\\n>Rat Pep1\\nASNKREKIEENGSMRVFMQH\\n>Rat Pep2\\nDIKEKFAKLCEAHGITRDNI\\n>Rat Pep3\\nEEASSTRGNLDVAKLNGDWF\\n>Rat Pep4\\nEENGSMRVFMQHIDVLENSL\\n>Rat Pep5\\nENSLGFKFRIKENGECRELY\\n>Rat Pep6\\nFMQHIDVLENSLGFKFRIKE\\n>Rat Pep7\\nFVEYDGGNTFTILKTDYDRY\\n>Rat Pep8\\nGDWFSIVVASNKREKIEENG\\n>Rat Pep9\\nGRTKDLSSDIKEKFAKLCEA\\n>Rat Pep10\\nKTPEDGEYFVEYDGGNTFTI\\n>Rat Pep11\\nLCEAHGITRDNIIDLTKTDR\\n>Rat Pep12\\nLINFKNGETFQLMVLYGRTK\\n>Rat Pep13\\nNLDVAKLNGDWFSIVVASNK\\n>Rat Pep14\\nRDNIIDLTKTDRCLQARG\\n>Rat Pep15\\nRELYLVAYKTPEDGEYFVEY\\n>Rat Pep16\\nRIKENGECRELYLVAYKTPE\\n>Rat Pep17\\nTFQLMVLYGRTKDLSSDIKE\\n>Rat Pep18\\nTFTILKTDYDRYVMFHLINF\\n>Rat Pep19\\nYDRYVMFHLINFKNGETFQL'\"></textarea>\n\n      <div class=\"d-flex flex-row-reverse justify-content-between p-2\">\n        <small *ngIf=\"inputSequenceText.length >= maxCharacters; else sequenceCounter\" class=\"text-danger\">\n          Sequence text is too long -  {{maxCharacters | number}} characters allowed\n        </small>\n        <ng-template #sequenceCounter>\n          <small class=\"text-muted\">\n            Format: {{seqFormat}} | {{numOfCharacters | number}} characters\n          </small>\n        </ng-template>\n        <small *ngIf=\"inputChange.input_sequence_text\"  class=\"help-block form-text text-warning\">\n          Parameter changed since prediction.\n        </small>\n      </div>\n    </div>\n  </ng-container>\n  <!--  Prediction Parameters -->\n  <div class=\"row p-2\">\n    <h5 class=\"col-3 text-left p-2\">Prediction Parameters</h5>\n    <div class=\"col-9\">\n      <button type=\"button\" class=\"btn btn-sm btn-dark-blue-grey text-white\" (click)=\"onDownloadParameter()\"\n              data-toggle=\"dropdown\" aria-haspopup=\"true\" aria-expanded=\"false\">\n        <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-download\" viewBox=\"0 0 16 16\">\n          <path\n            d=\"M.5 9.9a.5.5 0 0 1 .5.5v2.5a1 1 0 0 0 1 1h12a1 1 0 0 0 1-1v-2.5a.5.5 0 0 1 1 0v2.5a2 2 0 0 1-2 2H2a2 2 0 0 1-2-2v-2.5a.5.5 0 0 1 .5-.5z\"/>\n          <path\n            d=\"M7.646 11.854a.5.5 0 0 0 .708 0l3-3a.5.5 0 0 0-.708-.708L8.5 10.293V1.5a.5.5 0 0 0-1 0v8.793L5.354 8.146a.5.5 0 1 0-.708.708l3 3z\"/>\n        </svg>\n      </button>\n      <div class=\"dropdown-menu\" aria-labelledby=\"dropdownMenuButton\">\n        <div class=\"dropdown-item\">\n          <button disabled class='btn btn-dark-blue-grey' type=\"button\" (click)=\"null\"\n                  ngbTooltip=\"Download a JSON file that includes the parameters set on this page.\"\n                  placement=\"left\">\n            Download Prediction Parameters\n          </button>\n        </div>\n      </div>\n      &nbsp;\n<!--      <ng-template #uploadJsonTipContent>-->\n<!--        Upload inputs as JSON-->\n<!--      </ng-template>-->\n<!--      <button type=\"button\" class=\"btn btn-info btn-sm text-white\" (click)=\"paramUploader.click()\" [disabled]=\"loading\"-->\n<!--              datatype=\"html\" [ngbTooltip]=\"uploadJsonTipContent\">-->\n<!--        Upload Parameters-->\n<!--      </button>-->\n<!--      <input type=\"file\"-->\n<!--             #paramUploader-->\n<!--             style=\"display: none\"-->\n<!--             id=\"paramUploader\"-->\n<!--             (change)=\"uploadParameterFile($event, null)\">-->\n    </div>\n  </div>\n<!--  Sequence Identity Threshold -->\n  <div class=\"form-group row p-2\" id=\"minThresholdRow\">\n    <div class=\"col-sm-3 col-form-label\">\n      <label class=\"text-left\">Sequence Identity Threshold</label>\n    </div>\n    <div class=\"col-sm-9\">\n      <div [className]=\"inputChange.threshold ? 'input-change-slider' : 'custom-ngx-slider'\">\n      <ngx-slider formControlName=\"threshold\"\n                  (userChangeEnd)=\"onThresholdChange($event)\"\n                  [options]=\"thresholdSliderOptions\"></ngx-slider>\n        <small *ngIf=\"inputChange.threshold\" class=\"help-block form-text text-warning\">\n          Parameter changed since prediction.\n        </small>\n      </div>\n    </div>\n    <!--    <div class=\"col-sm-1\">-->\n    <!--      <div class=\"form-check pt-4\">-->\n    <!--        <input #asIsCheckbox-->\n    <!--               class=\"form-check-input\"-->\n    <!--               type=\"checkbox\"-->\n    <!--               id=\"asIsCheckbox\"-->\n    <!--               [checked]=\"asIs\"-->\n    <!--               (change)=\"onAsIsChecked(asIsCheckbox.checked)\">-->\n    <!--        <label class=\"form-check-label\" for=\"asIsCheckbox\">-->\n    <!--          as-is-->\n    <!--        </label>-->\n    <!--      </div>-->\n    <!--    </div>-->\n  </div>\n\n  <div class=\"form-group row p-2\" id=\"peptideLengthRow\">\n    <div class=\"col-sm-3 col-form-label\">\n      <label class=\"text-left\">Peptide Length(s)</label>\n    </div>\n    <div class=\"col-sm-9\">\n      <div [className]=\"inputChange.lengths ? 'input-change-slider' : 'custom-ngx-slider'\">\n      <ngx-slider\n        formControlName=\"peptideLength\"\n        (userChangeEnd)=\"onLengthChange($event)\"\n        [options]=\"peptideLengthOptions\"></ngx-slider>\n        <small *ngIf=\"inputChange.lengths\" class=\"help-block form-text text-warning\">\n          Parameter changed since prediction.\n        </small>\n      </div>\n      </div>\n  </div>\n\n  <div class=\"form-group row p-2\" id=\"methodRow\">\n    <div class=\"col-sm-3 col-form-label\">\n      <label class=\"text-left\">Cluster Method</label>\n    </div>\n    <div class=\"col-sm-9\">\n      <select class=\"form-select form-control w-100\" formControlName=\"method\"\n              [style.border-color]=\"inputChange.predictors ? '#f0ad4d' : null\">\n        <option value=\"cluster\"> All the connected Peptides in a cluster</option>\n        <option value=\"cluster-break\"> Cluster-break for clear representative sequence</option>\n        <option value=\"cliques\">Fully interconnected clusters (cliques)</option>\n      </select>\n      <small *ngIf=\"inputChange.predictors\" class=\"help-block form-text text-warning\">\n        Parameter changed since prediction.\n      </small>\n    </div>\n  </div>\n  <hr/>\n\n<!--  <div class=\"form-check row pt-2\">-->\n<!--    <div class=\"col text-right\">-->\n<!--      <input class=\"form-check-input\" type=\"checkbox\" value=\"\" id=\"emailModalShow\" [checked]=\"showEmailModal\"-->\n<!--             (change)=onShowEmailModalChange()>-->\n<!--      <label class=\"form-check-label\" for=\"emailModalShow\">-->\n<!--        Notify me when prediction is complete-->\n<!--      </label>-->\n<!--    </div>-->\n<!--  </div>-->\n\n  <!--    Run/Reset Buttons -->\n  <div class=\"form-group d-flex flex-row-reverse pt-2\">\n\n    <div class=\"p-2\">\n      <button type=\"button\" class=\"reset-button btn btn-secondary btn-lg\" [disabled]=\"loading\"\n              (click)=\"onReset();\">\n        <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-arrow-clockwise\" viewBox=\"0 0 16 16\">\n          <path fill-rule=\"evenodd\" d=\"M8 3a5 5 0 1 0 4.546 2.914.5.5 0 0 1 .908-.417A6 6 0 1 1 8 2v1z\"/>\n          <path\n            d=\"M8 4.466V.534a.25.25 0 0 1 .41-.192l2.36 1.966c.12.1.12.284 0 .384L8.41 4.658A.25.25 0 0 1 8 4.466z\"/>\n        </svg>\n      </button>\n      &nbsp;\n      <span *ngIf=\"loading; else elseBlock\">\n          <button type=\"button\" class=\"btn btn-danger btn-lg\" (click)=\"onCancel()\"> Cancel Run </button>\n        </span>\n      <ng-template #elseBlock>\n        <div *ngIf=\"index!==0; else runButtonBlock\" class=\"btn-group\">\n          <div class=\"btn-group\">\n            <button type=\"submit\" class=\"run-button btn btn-dark-blue-grey btn-lg text-white\"\n                    [disabled]=\"(index>0 && !tools[index-1].submitted) || pipelineLoading\"\n            >\n              <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\" class=\"bi bi-play-fill\" viewBox=\"0 0 16 16\">\n                <path d=\"m11.596 8.697-6.363 3.692c-.54.313-1.233-.066-1.233-.697V4.308c0-.63.692-1.01 1.233-.696l6.363 3.692a.802.802 0 0 1 0 1.393z\"/>\n              </svg>\n            </button>\n            <button  type=\"button\" class=\"btn btn-dark-blue-grey text-white dropdown-toggle dropdown-toggle-split\"\n                     data-toggle=\"dropdown\"\n                     data-bs-toggle=\"dropdown\"\n                     aria-haspopup=\"true\" aria-expanded=\"false\"\n                     [disabled]=\"pipelineLoading\">\n            </button>\n            <div class=\"dropdown-menu\">\n              <a class=\"dropdown-item\" (click)=\"onRunAll()\">Run All Above</a>\n            </div>\n          </div>\n        </div>\n        <ng-template #runButtonBlock>\n          <button type=\"submit\" class=\"run-button btn btn-dark-blue-grey btn-lg text-white\"\n                  [disabled]=\"(index>0 && !tools[index-1].submitted) || pipelineLoading\"\n          >\n            <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\" class=\"bi bi-play-fill\" viewBox=\"0 0 16 16\">\n              <path d=\"m11.596 8.697-6.363 3.692c-.54.313-1.233-.066-1.233-.697V4.308c0-.63.692-1.01 1.233-.696l6.363 3.692a.802.802 0 0 1 0 1.393z\"/>\n            </svg>\n          </button>\n        </ng-template>\n\n      </ng-template>\n    </div>\n  </div>\n\n</form>\n\n<div ngbAccordion>\n  <!--  Error -->\n  <div ngbAccordionItem=\"first\" *ngIf=\"errorMessages.length\" #first=\"ngbAccordionItem\" [collapsed]=\"true\">\n    <h2 ngbAccordionHeader>\n      <button ngbAccordionButton class=\"accordion-button justify-content-center\">\n        <span class=\"text-danger m-1\">Errors ({{errorMessages.length}})</span>\n<!--        <div>-->\n          <svg *ngIf=\"first.collapsed\" xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n               class=\"bi bi-arrow-left-circle-fill\" style=\"color: #dc3545;\" viewBox=\"0 0 16 16\">\n            <path\n              d=\"M8 0a8 8 0 1 0 0 16A8 8 0 0 0 8 0zm3.5 7.5a.5.5 0 0 1 0 1H5.707l2.147 2.146a.5.5 0 0 1-.708.708l-3-3a.5.5 0 0 1 0-.708l3-3a.5.5 0 1 1 .708.708L5.707 7.5H11.5z\"/>\n          </svg>\n<!--        </div>-->\n<!--        <div>-->\n          <svg *ngIf=\"!first.collapsed\" xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n               class=\"bi bi-arrow-down-circle-fill\" style=\"color: #dc3545;\" viewBox=\"0 0 16 16\">\n            <path\n              d=\"M16 8A8 8 0 1 1 0 8a8 8 0 0 1 16 0zM8.5 4.5a.5.5 0 0 0-1 0v5.793L5.354 8.146a.5.5 0 1 0-.708.708l3 3a.5.5 0 0 0 .708 0l3-3a.5.5 0 0 0-.708-.708L8.5 10.293V4.5z\"/>\n          </svg>\n<!--        </div>-->\n      </button>\n    </h2>\n    <div ngbAccordionCollapse>\n      <div ngbAccordionBody>\n        <ng-template>\n          <ol>\n            <li *ngFor=\"let message of errorMessages; let i=index;\">{{message}}</li>\n          </ol>\n        </ng-template>\n      </div>\n    </div>\n  </div>\n  <!--  Warning -->\n  <div ngbAccordionItem=\"second\" *ngIf=\"warningMessages.length\" #second=\"ngbAccordionItem\" [collapsed]=\"true\">\n    <h2 ngbAccordionHeader>\n      <button ngbAccordionButton class=\"accordion-button justify-content-center\">\n        <span class=\"text-warning m-1\">Warnings ({{warningMessages.length}})</span>\n          <svg *ngIf=\"second.collapsed\"  xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n               class=\"bi bi-arrow-left-circle-fill\" style=\"color: #f0ad4d;\" viewBox=\"0 0 16 16\">\n            <path\n              d=\"M8 0a8 8 0 1 0 0 16A8 8 0 0 0 8 0zm3.5 7.5a.5.5 0 0 1 0 1H5.707l2.147 2.146a.5.5 0 0 1-.708.708l-3-3a.5.5 0 0 1 0-.708l3-3a.5.5 0 1 1 .708.708L5.707 7.5H11.5z\"/>\n          </svg>\n          <svg *ngIf=\"!second.collapsed\" xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n               class=\"bi bi-arrow-down-circle-fill\" style=\"color: #f0ad4d;\" viewBox=\"0 0 16 16\">\n            <path\n              d=\"M16 8A8 8 0 1 1 0 8a8 8 0 0 1 16 0zM8.5 4.5a.5.5 0 0 0-1 0v5.793L5.354 8.146a.5.5 0 1 0-.708.708l3 3a.5.5 0 0 0 .708 0l3-3a.5.5 0 0 0-.708-.708L8.5 10.293V4.5z\"/>\n          </svg>\n      </button>\n    </h2>\n    <div ngbAccordionCollapse>\n      <div ngbAccordionBody>\n        <ng-template>\n          <ol>\n            <li *ngFor=\"let message of warningMessages; let i=index;\">{{message}}</li>\n          </ol>\n        </ng-template>\n      </div>\n    </div>\n  </div>\n</div>\n\n<div *ngIf=\"!loading && !submitted && !errorMessages.length && !warningMessages.length\" class=\"p-2 d-flex justify-content-center col\" [style.borderStyle]=\"styleResultContainer\">\n  <label class=\"p-2 font-italic\">\n    Results will load once step is run\n  </label>\n</div>\n\n<div *ngIf=\"loading\" class=\"p-2 d-flex justify-content-center col\" [style.borderStyle]=\"styleResultContainer\">\n  <div class=\"spinner-border text-primary align-self-center p-3 mb-3\" role=\"status\">\n    <span class=\"visually-hidden sr-only\" >Loading...</span>\n  </div>\n  <label *ngIf=\"!getResultsClicked\" class=\"p-2 font-italic\">\n    Calculating results, please wait... Click <a href=\"javascript:void(0)\" (click)=\"openEmailModal.emit()\">here</a> to\n    receive email.\n  </label>\n  <label *ngIf=\"getResultsClicked\" class=\"p-2 font-italic\">\n    Checking job status, please wait...\n  </label>\n</div>\n\n\n<div class=\"container-fluid p-2\" id=\"table-result-container\" *ngIf=\"!loading && submitted  && !(errorMessages.length && warningMessages.length)\">\n  <ul ngbNav #nav=\"ngbNav\" [(activeId)]=\"active\" [animation]='false' [destroyOnHide]=\"false\" class=\"nav-tabs\">\n    <li *ngIf=\"peptide_table[0].length\" [ngbNavItem]=\"'peptide_table'\">\n      <a ngbNavLink>Peptide Table</a>\n      <ng-template ngbNavContent>\n      <app-result-table [table_data]=\"peptide_table\"\n                        table_name=\"peptide_table\"\n                        [inputChange]=\"inputChange.table_state\"\n                        [order]=\"peptide_table_order\"\n                        [columns]=\"peptide_table_columns\"\n                        [tool_group]=\"formGroupName\"\n                        [index]=\"index\"\n                        [tableStateSaving]=\"tableStateSaving\"\n                        (emitFilterApplied)=\"onFilterApplied()\"\n                        (emitResetTableState)=\"onClearTableState()\"\n                        (emitSaveTableState)=\"onSaveTableStateMain()\"></app-result-table>\n      </ng-template>\n    </li>\n    <li [ngbNavItem]=\"'network_graph'\">\n      <a ngbNavLink>Visualization</a>\n      <ng-template ngbNavContent>\n          <app-d3-force [data]=\"links\" [uniqueClusters]=\"uniqueClusters\"></app-d3-force>\n      </ng-template>\n    </li>\n    <li *ngIf=\"sequence_table[0].length\" [ngbNavItem]=\"'sequence_table'\">\n      <a ngbNavLink> Sequence Table </a>\n      <ng-template ngbNavContent>\n        <app-result-table [table_data]=\"sequence_table\"\n                          table_name=\"sequence_table\"\n                          [order]=\"sequence_table_order\"\n                          [columns]=\"sequence_table_columns\"\n                          [tool_group]=\"formGroupName\"></app-result-table>\n      </ng-template>\n    </li>\n  </ul>\n  <div [ngbNavOutlet]=\"nav\"></div>\n</div>\n\n<!--Alert Modal -->\n<ng-template #alertModal let-modal4>\n  <div class=\"modal-header\">\n    <h4 class=\"modal-title\" id=\"alert-modal-title\">Validation Error(s)</h4>\n    <button type=\"button\" class=\"btn-close\" aria-label=\"Close\" (click)=\"modal4.dismiss('Cross click');\">\n    </button>\n  </div>\n  <div class=\"modal-body\">\n    <app-alert-component></app-alert-component>\n  </div>\n  <div class=\"modal-footer\">\n  </div>\n</ng-template>\n\n<!--Confirm Modal -->\n<ng-template #confirmModal let-confirmModal>\n  <div class=\"modal-header\">\n    <h4 class=\"modal-title\" id=\"modal-title\">Are you sure?</h4>\n    <button type=\"button\" class=\"btn-close\" aria-label=\"Close\" (click)=\"confirmModal.dismiss('Cross click')\"></button>\n  </div>\n  <div class=\"modal-body\">\n    <div *ngIf=\"!saveState; else saveStateConfirmation\">\n      <p><strong>Re-running this step of the pipeline will delete all downstream results, including:</strong></p>\n      <ol>\n        <li *ngFor=\"let tool of tools.slice(this.index+1)\"> {{tool.name}} </li>\n      </ol>\n      <p><strong>To access the current results, you can use this link</strong></p>\n    </div>\n    <ng-template #saveStateConfirmation>\n      <p><strong>Applying these filters for input to the next stage will delete results from all downstream steps in\n        this session, including:</strong></p>\n      <ol>\n        <li *ngFor=\"let tool of tools.slice(this.index+1)\"> {{tool.name}} </li>\n      </ol>\n      <p><strong>To access the current results, you can use this link</strong></p>\n    </ng-template>\n    <!-- pipeline URL input group-->\n    <div class=\"input-group\">\n      <input type=\"text\" class=\"form-control\" id=\"pipeline-url-input\" [value]=\"pipelineUrl\">\n      <button class=\"btn btn-secondary\" [cdkCopyToClipboard]=\"pipelineUrl\" ngbTooltip=\"copy url\" placement=\"top\">\n        <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-clipboard\" viewBox=\"0 0 16 16\">\n          <path\n            d=\"M4 1.5H3a2 2 0 0 0-2 2V14a2 2 0 0 0 2 2h10a2 2 0 0 0 2-2V3.5a2 2 0 0 0-2-2h-1v1h1a1 1 0 0 1 1 1V14a1 1 0 0 1-1 1H3a1 1 0 0 1-1-1V3.5a1 1 0 0 1 1-1h1v-1z\"/>\n          <path\n            d=\"M9.5 1a.5.5 0 0 1 .5.5v1a.5.5 0 0 1-.5.5h-3a.5.5 0 0 1-.5-.5v-1a.5.5 0 0 1 .5-.5h3zm-3-1A1.5 1.5 0 0 0 5 1.5v1A1.5 1.5 0 0 0 6.5 4h3A1.5 1.5 0 0 0 11 2.5v-1A1.5 1.5 0 0 0 9.5 0h-3z\"/>\n        </svg>\n      </button>\n    </div>\n  </div>\n  <div class=\"modal-footer\">\n    <button type=\"button\" class=\"btn btn-outline-secondary\" (click)=\"confirmModal.dismiss('cancel click')\">No\n    </button>\n    <button type=\"button\" class=\"btn btn-danger\" (click)=\"confirmModal.close('Ok click'); onRunConfirm();\">Yes, continue\n      and destroy downstream steps\n    </button>\n  </div>\n</ng-template>\n","import {Component, OnInit, OnDestroy, OnChanges, Input, Output, EventEmitter, ViewChild, ElementRef, SimpleChanges} from '@angular/core';\nimport {UntypedFormGroup, UntypedFormBuilder, FormGroupDirective} from \"@angular/forms\";\nimport {Title} from \"@angular/platform-browser\";\nimport {takeUntil, debounce} from \"rxjs/operators\";\nimport {Observable, timer, of, from, Subject, concat, Subscription} from \"rxjs\";\nimport _ from 'lodash';\n\n// import {ChangeContext, Options} from '@angular-slider/ngx-slider';\nimport {ChangeContext, Options, CustomStepDefinition} from 'ngx-slider-v2'\n\nimport Columns from \"../_global/Columns\";\nimport {PipelineService} from \"../services/pipeline-service/pipeline.service\";\nimport {PipelineStateService} from \"../services/state-services/pipeline-state-service/pipeline-state.service\";\nimport {SequenceParserService} from \"../services/sequence-parser/sequence-parser.service\";\n\nimport Stage from \"../_global/Stage\";\nimport PipelineParams from \"../_global/PipelineParams\";\nimport * as pipelineData from \"../services/data/cluster-sample.json\";\nimport {\n  initClusterTool,\n} from \"../services/state-services/default-stage-states\";\nimport {isASCII, IsJsonString, ltrim} from \"../util/string-helpers\";\nimport {NgbModal} from \"@ng-bootstrap/ng-bootstrap\";\nimport {Location} from \"@angular/common\";\nimport Tool from \"../_global/Tool\";\nimport {AlertServiceService} from \"../services/alert-service/alert-service.service\";\nimport {columnListToObject} from \"../util/convert-columns\";\nimport {environment} from \"../../environments/environment\";\nimport onCsvDownloadAllClickedNew from \"../util/on-csv-download\";\nimport {HttpClient} from \"@angular/common/http\";\nimport {isMaxLength} from \"../util/is-max-length\";\n\n@Component({\n  selector: 'app-cluster',\n  templateUrl: './cluster.component.html',\n  styleUrls: ['./cluster.component.scss']\n})\nexport class ClusterComponent implements OnInit, OnDestroy, OnChanges {\n\n  swaggerUrl = `${environment['api_url']}/apidocs`\n\n  unsubscribe$ = new Subject();\n  tools$: Observable<Tool[]> = this._stateService.tools$;\n  stages$: Observable<Stage[]> = this._stateService.stages$;\n  pipelineId$: Observable<string> = this._stateService.pipelineId$;\n  params$: Observable<PipelineParams> = this._stateService.params$;\n\n  active = 1\n\n  pipelineUrl: string = ''\n\n  pipelineId = '';\n  tools: Tool[] = [];\n  stages: Stage[] = [];\n  params!: PipelineParams;\n\n  /** Form variables */\n  clusterForm!: UntypedFormGroup;\n  @Input() emailForm!: UntypedFormGroup;\n\n  inputChange = {\n    /** Keeps track of inputChanges to highlight selected parameter table row*/\n    input_sequence_text: false,\n    threshold: false,\n    lengths: false,\n    predictors: false,\n    table_state: false,\n  }\n\n  @Output() emitIndex = new EventEmitter<number>(); // used for run all\n  @Output() emitOnCancel = new EventEmitter<any>();\n\n  @Input() formGroupName!: string\n  @Input() index!: number\n  // @Input() index!: number\n  @Input() resultUrl!: string | undefined;\n\n\n  @Input() showEmailModal: boolean = false;\n  @Output() shoeEmailModalChange = new EventEmitter<boolean>(); // used for run all\n  @Output() openEmailModal = new EventEmitter<any>();\n\n  @ViewChild('confirmModal') confirmModal!: ElementRef;\n  @ViewChild('alertModal') alertModal!: ElementRef;\n  @ViewChild('emailModal') emailModal! : ElementRef;\n  // showEmailModal: boolean = false;\n\n  @Input() events: Observable<void> = of();\n  private eventsSubscription: Subscription  = new Subscription();\n\n  @Input() runAllEvent: Observable<void> = of();\n  private runAllSubscription: Subscription  = new Subscription();\n\n  /** sequence files */\n  maxCharacters = 1000000;\n  files: any[] = [];\n  fileName = '';\n\n\n  thresholdSliderOptions: Options = {\n    floor: 0,\n    ceil: 100,\n    showTicksValues: true,\n    translate: (value) => `${value * 100}%`,\n    stepsArray: [\n      {value: 0.1},\n      {value: 0.2},\n      {value: 0.3},\n      {value: 0.4},\n      {value: 0.5},\n      {value: 0.6},\n      {value: 0.7},\n      {value: 0.8},\n      {value: 0.9},\n      {value: 1},\n    ]\n  }\n\n  // minValue: number = 5;\n  // maxValue: number = 26;\n  peptideLengthOptions: Options = {\n    showTicks: true,\n    stepsArray: _.map(_.range(4, 27), (num): CustomStepDefinition => {return {value: num, legend: num % 5 === 0 ? `${num}` : undefined}}),\n    minRange: 1,\n    noSwitching: true,\n    translate: (value) => {\n      if (value === 4) return 'No Min';\n      if (value === 26) return 'No Max';\n      else return `${value}`;\n    }\n  }\n  /** sequence variables */\n  synthesisDownloadLinks = {\n    sequence_list_json_uri: '',\n    sequence_list_fasta_uri: '',\n    download_sequences: ''\n  };\n\n  filteredSequences: { name: string, sequences: string }[] = [];\n  numOfAA: number = 0;\n  numOfCharacters: number = 0;\n  seqFormat: string = 'Unknown';\n\n  pipelineLoading = false;\n  /** API Call variables */\n  runSetInterval: any;\n  submitted = false;\n  loading = false;\n  getResultsClicked = true;\n\n  tableStateSaving = false;\n  saveState = false;\n\n  resultId: number = 0;\n\n  peptide_table_columns: Columns[] | any;\n  peptide_table: [(string | number)[]] = [[]]\n  peptide_table_order: any[] = [];\n\n  sequence_table_order: any[] = [];\n  sequence_table_columns: Columns[] | any;\n  sequence_table: [(string | number)[]] = [[]]\n\n  defaultOrder: any[] = [];\n\n  // apiStatus: string;\n  errorMessages: string[] = [];\n  warningMessages: string[] = [];\n  closeResult = '';\n\n  // d3-force variable\n  links: any[] = [];\n  uniqueClusters: string[] = [];\n  constructor(\n    public alertService: AlertServiceService,\n    private http: HttpClient,\n    private fb: UntypedFormBuilder,\n    private location: Location,\n    private titleService: Title,\n    private modalService: NgbModal,\n    private _pipelineService: PipelineService,\n    private _stateService: PipelineStateService,\n    private rootFormGroup: FormGroupDirective, // pipeline component\n    private sequenceParserService: SequenceParserService\n  ) { }\n\n  ngOnInit(): void {\n    this.clusterForm = this.rootFormGroup.control.get(this.formGroupName) as UntypedFormGroup;\n\n    this.pipelineId$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n      console.log(`pipelineId=${value}`);\n      this.pipelineId = value;\n      this.pipelineUrl = `${window.location.origin}/pipeline/${value}`;\n    })\n\n    this.tools$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n      console.log('tools$');\n      console.log(value);\n      this.tools = value;\n      this.submitted = this.tools[this.index]?.submitted\n\n      const inputSequenceTextId = this.tools[this.index]?.input_data_uri?.input_sequence_text_id\n\n      this.synthesisDownloadLinks.sequence_list_json_uri = `${environment['api_url']}/api/v1/sequence_list_json/${inputSequenceTextId}`\n      this.synthesisDownloadLinks.sequence_list_fasta_uri = `${environment['api_url']}/api/v1/sequence_list_fasta/${inputSequenceTextId}`\n      this.synthesisDownloadLinks.download_sequences = `${environment['api_url']}/api/v1/download_sequences/${inputSequenceTextId}`\n\n      /** pipeline Loading */\n      this.pipelineLoading = _.some(this.tools, {loading: true})\n\n      if(!this.tools[this.index]?.loading) {\n        this.loading = false;\n        clearInterval(this.runSetInterval)\n      }\n    })\n\n    this.stages$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n      console.log(value);\n      this.stages = value;\n      this.errorMessages = this.stages[this.index]?.stage_messages!.errors\n      this.warningMessages = this.stages[this.index]?.stage_messages!.warnings\n    })\n\n    this.params$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n      console.log(`params`);\n      console.log(value);\n      this.params = value;\n      // if (this.tools[this.index]?.submitted){this.submitted = true}\n    })\n\n    this.eventsSubscription = this.events.subscribe(() => this.onRunMain());\n    this.runAllSubscription = this.runAllEvent.subscribe(() => this.onRunAll())\n\n    this.onChanges();\n    if(this.clusterForm.get('inputSequenceText')?.value) {\n      this.sequenceParser(this.clusterForm.get('inputSequenceText')?.value)\n    }\n\n    // if(this.loading) {\n    //   this.disableInputs()\n    // }\n\n    // if (this.resultUrl) {\n    //   this.loading = true;\n    //   this.getResultsSetInterval(this.resultUrl);\n    // }\n  }\n\n  ngOnChanges(changes: SimpleChanges) {\n    if(changes.resultUrl?.currentValue) {\n      console.log(changes.resultUrl.currentValue);\n      console.log('ngOnChanges cluster')\n      this.loading = true;\n      this.getResultsSetInterval(changes.resultUrl.currentValue);\n    }\n  }\n\n  getResultsSetInterval(result_url: string) {\n    /** */\n    this.getResultsClicked = true\n\n    this.sequence_table = [[]]\n    this.peptide_table = [[]]\n    this.uniqueClusters = []\n\n\n    this.inputChange = _.mapValues(this.inputChange, () => false);\n    let increment = 0;\n    const milliseconds = 3000;\n    this.runSetInterval = setInterval(() => {\n      this._pipelineService.getResults(result_url).subscribe(resp => {\n        if (resp['status'] === 'error' || resp['errors']) {\n          this.errorMessages = resp['data']['errors'];\n          this.warningMessages = resp['data']['warnings'];\n          this.submitted = false;\n          this.loading = false;\n          const prevTool = this.tools[this.index];\n          console.log(prevTool)\n          const submittedTCellPredictionTool = Object.assign(prevTool, {\n            submitted: this.submitted,\n            loading: this.loading,\n          })\n          this._stateService.insertTool(submittedTCellPredictionTool, this.index);\n          clearInterval(this.runSetInterval);\n          this.enableInputs();\n        }\n        if (resp['data']['warnings']?.length) {\n          // console.log(resp['warnings']);\n          this.warningMessages = resp['data']['warnings'];\n        }\n        if (resp['data']['errors']?.length) {\n          // console.log(resp['warnings']);\n          this.errorMessages = resp['data']['errors'];\n        }\n        if (resp['status'] === 'done') {\n          /** 1) Create Column */\n          const data = resp['data']['results'];\n          console.log(data);\n\n          this.active = data[0].type\n\n          _.forEach(data, table => {\n            if (table.type === 'peptide_table') {\n              this.peptide_table_columns = _.map(table.table_columns, (column, i) => {\n                if (column.default_order && Number.isFinite(column.row_sort_priority)) { // set defaultOrder\n                  // console.log(column);\n                  this.defaultOrder[column.row_sort_priority] = [i, column.default_order === \"ascending\" ? 'asc' : 'desc'];\n                }\n                column['title'] = `${column['display_name']}`; // required\n                column['data'] = `${column['name']}`;\n                let source = column['source'];\n\n                column['filterKey'] = `${source}.${column.name}`\n                // console.log(`source=${source}`);\n                let tempSource = source.split('.')\n                // console.log(tempSource);\n                source = tempSource[tempSource.length - 1];\n                // console.log(`source=${source}`);\n                column['data'] = `${source}_${column['name']}`;\n                /** remove `core` from name */\n                // column['name'] = column['display_name'] ? column['display_name'] : column['name']\n                // column['name'] = source === 'core' ? display_name: `${source} ${display_name}`;\n                // column['filters'] = column['type'] === 'int' ? {\n                //   minValue: NaN,\n                //   maxValue: NaN,\n                //   applied: false\n                // } : {\n                //   possibleValues: [],\n                //   textValue: null,\n                //   selectedValues: [],\n                //   applied: false\n                // }\n                column['value_limits'] = column['value_limits'] &&  this.setValueLimits(column)\n                return column\n              });\n              this.peptide_table_order = [...this.defaultOrder];\n              if (this.peptide_table_columns) {\n                this.peptide_table = table.table_data;\n              }\n            }\n            if (table.type === 'network_graph') {\n              // set d3-force inputs\n              this.links = data[1].graph_data;\n              this.uniqueClusters = [];\n              _.forEach(this.links, (link) => {\n                if(!this.uniqueClusters.includes(link.cluster[0])) {\n                  this.uniqueClusters.push(link.cluster[0]);\n                }\n              });\n            }\n            if (table.type === 'input_sequence_table') {\n              this.sequence_table_columns = _.map(table.table_columns, (column, i) => {\n                // if (column.default_order && Number.isFinite(column.row_sort_priority)) { // set defaultOrder\n                //   this.defaultOrder[column.row_sort_priority] = [i, column.default_order === \"ascending\" ? 'asc' : 'desc'];\n                // }\n                column['title'] = `${column['display_name']}`; // required\n                column['data'] = `${column['name']}`;\n                let source = column['source'];\n\n                column['filterKey'] = `${source}.${column.name}`\n\n                // console.log(`source=${source}`);\n                let tempSource = source.split('.')\n                // console.log(tempSource);\n                source = tempSource[tempSource.length - 1];\n                // console.log(`source=${source}`);\n                column['data'] = `${source}_${column['name']}`;\n                /** remove `core` from name */\n                // column['name'] = column['display_name'] ? column['display_name'] : column['name']\n                // column['filters'] = column['type'] === 'int' ? {\n                //   minValue: NaN,\n                //   maxValue: NaN,\n                //   applied: false\n                // } : {\n                //   possibleValues: [],\n                //   textValue: null,\n                //   selectedValues: [],\n                //   applied: false\n                // }\n                column['value_limits'] = column['value_limits'] ? this.setValueLimits(column) : undefined\n                return column\n              });\n              this.sequence_table_order = []\n              if (this.sequence_table_columns) {\n\n                this.sequence_table = table.table_data\n              }\n            }\n          })\n\n          this.submitted = true; this.loading = false;\n          const prevTool = this.tools[this.index];\n          console.log(prevTool)\n          const submittedTCellPredictionTool = Object.assign(prevTool, {\n            submitted: this.submitted,\n            loading: this.loading,\n          })\n          this._stateService.insertTool(submittedTCellPredictionTool, this.index);\n          clearInterval(this.runSetInterval);\n          console.log(data);\n          this.enableInputs();\n\n        }\n        if (resp['status'] === 'canceled') {\n          /** if status is canceled, then just stop loader **/\n          this.submitted = false;\n          this.loading = false;\n          const prevTool = this.tools[this.index];\n          console.log(prevTool)\n          const submittedTCellPredictionTool = Object.assign(prevTool, {\n            submitted: this.submitted,\n            loading: this.loading,\n          })\n          this._stateService.insertTool(submittedTCellPredictionTool, this.index);\n          clearInterval(this.runSetInterval);\n          // console.log(data);\n          this.enableInputs();\n          // set error message\n          // this.errorMessages = [`PIPELINE_ID=${this.pipelineId} w/ STATUS=${resp['status']}`]\n        }\n        else {\n          this.getResultsClicked = false;\n          // this.apiStatus = resp['status'];\n          console.log(`current status: ${resp['status']} - ${increment}`);\n          increment += 1;\n        }\n      }, error => {\n        console.error(error);\n        this.enableInputs();\n        clearInterval(this.runSetInterval);\n        this.submitted = true;\n        this.loading = false;\n      })\n    }, milliseconds);\n  }\n\n  ngOnDestroy() {\n    clearInterval(this.runSetInterval);\n    clearInterval(this._pipelineService.runSetInterval)\n    this.unsubscribe$.next();\n    this.unsubscribe$.complete();\n\n    this.eventsSubscription.unsubscribe();\n    this.runAllSubscription.unsubscribe();\n  }\n\n  get inputSequenceText(){\n    return this.clusterForm.get('inputSequenceText')?.value\n  }\n\n  onLengthChange(changeContext: ChangeContext): void {\n    this.inputChange.lengths = this.submitted;\n  }\n\n  onThresholdChange(changeContext: ChangeContext): void {\n    this.inputChange.threshold = this.submitted;\n  }\n\n  onChanges(): void {\n    /** Immediate - Deletion, */\n    // this.clusterForm.get('inputSequenceText').valueChanges.subscribe(val => {\n    //   if (val === '') {  // delete\n    //     this.filteredSequences = [];\n    //     this.numOfAA = 0;\n    //     // this.alertService.clear();\n    //     // this.myForm.patchValue({\n    //     //   inputFormat: 0\n    //     // });\n    //   }\n    // })\n\n    /** PredictionModel sessionStorage */\n    this.clusterForm.get('method')?.valueChanges.subscribe(() => {\n      this.inputChange.predictors = this.submitted\n    });\n\n    const sequenceFieldChange = this.clusterForm.get('inputSequenceText')?.valueChanges.pipe(\n      debounce(v => timer(1000)),\n    );\n\n    sequenceFieldChange?.subscribe((val: string) => {\n      sessionStorage.setItem('clusterSequences', val);\n      this.sequenceParser(val);\n      this.inputChange.input_sequence_text = this.submitted;\n      if (val === '') {  // delete\n        this.filteredSequences = [];\n        this.numOfAA = 0;\n        // this.alertService.clear();\n        // this.myForm.patchValue({\n        //   inputFormat: 0\n        // });\n      }\n    });\n  }\n\n  /** Download Sequence File API calls*/\n\n  onDownloadJson() {\n    console.log(this.synthesisDownloadLinks.sequence_list_json_uri);\n    onCsvDownloadAllClickedNew(this.synthesisDownloadLinks.sequence_list_json_uri, this.http, 'json');\n  }\n\n  onDownloadFasta() {\n    console.log(this.synthesisDownloadLinks.sequence_list_fasta_uri);\n    onCsvDownloadAllClickedNew(this.synthesisDownloadLinks.sequence_list_fasta_uri, this.http, 'fasta');\n  }\n  onDownloadOriginal() {\n    console.log(this.synthesisDownloadLinks.download_sequences);\n    onCsvDownloadAllClickedNew(this.synthesisDownloadLinks.download_sequences, this.http, 'txt');\n  }\n\n  open(content: any) {\n    this.modalService.open(content, {\n      ariaLabelledBy: 'modal-basic-title',\n      size: 'lg',\n      animation: true\n    }).result.then((result) => {\n      this.saveState = false;\n      // this.closeResult = `Closed with: ${result}`;\n    }, (reason) => {\n      this.saveState = false;\n      // this.alleleSearch.nativeElement.focus();\n      // this.closeResult = `Dismissed ${TCellPredictionComponent.getDismissReason(reason)}`;\n    });\n  }\n\n  sequenceParser(val: string) {\n\n    const firstChar = ltrim(val)[0];\n    const firstLine = val.split('\\n')[0]\n    console.log(firstLine)\n\n    /** Named white space */\n    let firstLineNumOfElements = 0\n    let separator = ' '\n    if(firstLine.includes(' ')){\n      separator = ' '\n    } else if (firstLine.includes('\\t')){\n      separator = '\\t'\n    } else if (firstLine.includes('\\s')){\n      separator = '\\s'\n    }\n    firstLineNumOfElements = firstLine.split(separator).length\n    console.log(firstLineNumOfElements)\n    console.log(separator)\n\n    const slicedVal = val.slice(0, this.maxCharacters)\n\n    if(val.length > this.maxCharacters) {\n      //  Skip parsing\n    } else if (firstChar === '>' && this.sequenceParserService.fastaValidate(val)) { // fasta\n      this.seqFormat = this.sequenceParserService.seqFormat;\n      this.numOfCharacters = slicedVal.length\n    } else if ((firstChar === '{' || firstChar === '[') && IsJsonString(val)) { // json\n      this.seqFormat = 'JSON'\n      this.numOfCharacters = slicedVal.length\n    } else if (firstLineNumOfElements === 2 && this.sequenceParserService.namedWhiteSpaceValidate(val, separator)) {\n      // named white space\n      this.seqFormat = this.sequenceParserService.seqFormat;\n      this.numOfCharacters = slicedVal.length\n    } else if (val.length > 3 && !val.includes('>') && this.sequenceParserService.unnamedWhiteSpaceValidate(val)) {\n      // Unnamed\n      this.seqFormat = this.sequenceParserService.seqFormat;\n      this.numOfCharacters = slicedVal.length\n    } else if (val === '') {  // delete\n      /**\n       * Takes care of it up top - still need this if statement\n       * */\n      this.seqFormat = 'Unknown';\n      this.numOfCharacters = 0\n    } else { // error\n      this.seqFormat = 'Error';\n      this.numOfCharacters = 0\n    }\n  }\n\n  onDownloadParameter() {\n    const data = this._pipelineService.convertClusterForm(this.clusterForm)\n\n    const a = document.createElement('a');\n    a.setAttribute('style', 'display:none;');\n    document.body.appendChild(a);\n    // const contentType = 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet;charset=UTF-16';\n    // var blob = new Blob([csvData], { type: contentType });\n    const blob = new Blob([JSON.stringify(data, null, 2)], ); // thx: http://stackoverflow.com/a/18925211\n    a.href = window.URL.createObjectURL(blob);\n    a.download = 'parameter.json';\n\n    a.click();\n  }\n\n  setValueLimits(column: Columns) : any {\n    /* set value_limits (i.e. filters) for each column based on if type is a number/string */\n    return column['type'] === 'int' || column['type'] === 'float' ? {\n      ...column['value_limits'],\n      minValue: NaN,\n      maxValue: NaN,\n      applied: false\n    } : {\n      // ...column['value_limits'],\n      possibleValues: column['value_limits']['unique_values'],\n      textValue: null,\n      selectedValues: [],\n      applied: false\n    }\n  }\n\n  postPipelineAPI(params: PipelineParams, getResults: boolean = true) {\n    this.disableInputs();\n    if (getResults) {\n      this.errorMessages = [];\n      this.warningMessages = [];\n    }\n\n    this.loading = getResults; // true - defaults\n    this.submitted = !getResults; // false - defaults\n    this.tableStateSaving = !getResults\n\n    this._pipelineService.postPipeline(params).subscribe(\n      (resp) => {\n        if (resp['errors'] && resp['errors'].length) {\n          console.error(resp['errors']);\n          this.errorMessages = resp['errors'];\n          if (resp['warnings'].length) {\n            console.log(resp['warnings']);\n            this.warningMessages = resp['warnings'];\n          }\n          this.loading = false;\n          const submittedClusterTool = Object.assign(initClusterTool, {\n            submitted: false,\n            loading: false,\n          })\n          this._stateService.insertTool(submittedClusterTool, this.index);\n          this.enableInputs();\n          return;\n        }\n        if (resp['warnings'].length) {\n          console.log(resp['warnings']);\n          this.warningMessages = resp['warnings'];\n        }\n\n        if (this.showEmailModal) {\n          this.open(this.emailModal);\n        }\n\n        const inputDataUri = {input_sequence_text_id: resp.input_sequence_text_id}\n        this._stateService.insertInputDataUriToTool(inputDataUri, this.index)\n\n        this._stateService.setPipelineId(resp.pipeline_id);\n        this._stateService.setPipelineIdToParams(resp.pipeline_id);\n        this._stateService.setPipelineSpecId(resp.pipeline_spec_id);\n        this.location.go(`pipeline/${resp.pipeline_id}`);\n        // this.titleService.setTitle(`IEDB NG Tools Pipeline`);\n\n        if (getResults) {\n          const result_url = `${resp.results_uri}`;\n          console.log(result_url);\n          this.getResultsSetInterval(result_url);\n        } else {\n          this.inputChange.table_state = false;\n          this.enableInputs();\n          this.submitted = true;\n          this.loading = false;\n          this.tableStateSaving = false;\n        }\n      },\n      error => {\n        console.error(error);\n        this.errorMessages.push(error.error);\n        this.submitted = false;\n        this.loading = false;\n        const prevTool = this.tools[this.index];\n        const submittedTool = Object.assign(prevTool, {\n          submitted: this.submitted,\n          loading: this.loading,\n        })\n        this._stateService.insertTool(submittedTool, this.index);\n        clearInterval(this.runSetInterval);\n        this.enableInputs();\n      });\n  }\n\n  onRunAll() {\n    // this.setDefaultFormValues() // not needed because all defaults are already set in formValues\n    this.emitIndex.emit(this.index);\n  }\n\n  onRunMain() {\n    if(this.clusterForm.invalid){\n      this.alertService.add(`Input sequence text is too long. The maximum number of characters allowed is ${this.maxCharacters.toLocaleString()}\\nYour sequence contains ${this.inputSequenceText.length.toLocaleString()}`, 'alert-danger');\n      this.open(this.alertModal)\n      return;\n    }\n\n    const hasResult = _.find(this.tools.slice(this.index+1), (o) => o.submitted || o.loading)\n    if(this.stages.length > 1 && hasResult) {\n      this.open(this.confirmModal);\n    } else {\n      this.getResultsClicked = true;\n      if(this.index===0) {\n        this.onRun();\n      } else {\n        this.onRun2()\n      }\n    }\n  }\n\n  onRunConfirm() {\n    let indicies = _.range(this.index + 1, this.stages.length)\n    let initTool: Tool;\n    console.log(indicies);\n    _.forEach(indicies, i => {\n      initTool = this.tools[i];\n      const unSubmittedTool = {\n        ...initTool,\n        loading: false,\n        submitted: false,\n      }\n      this._stateService.insertTool(unSubmittedTool, i);\n    })\n    this.saveState ? this.onSaveTableState() : this.onRun();\n  }\n\n  setDefaultFormValues() {\n    /** defaults - use Sars placeholders*/\n    const {input_sequence_text } = pipelineData;\n    /** Sequences */\n    let sequences = this.clusterForm.value.inputSequenceText\n    if(!sequences && this.index===0) {\n      this._stateService.setInputSequenceText(input_sequence_text);\n      this.clusterForm.controls.inputSequenceText.setValue(input_sequence_text);\n    }\n  }\n\n  onRun() {\n    /** Reset global datatables search ext */\n    $.fn.dataTable.ext.search = [];\n    const stage_number = this.index + 1;\n    /** run_stage_range */\n    const run_stage_range: [number, number] = [stage_number, stage_number]\n    /** default formValue */\n    this.setDefaultFormValues()\n    /** Sequences */\n    let sequences = this.clusterForm.value.inputSequenceText\n\n    /** input_parameters */\n    const input = this._pipelineService.convertClusterForm(this.clusterForm)\n\n    /** Table State */\n    const { table_state } = this.stages[this.index];\n\n    const params = {\n      \"pipeline_id\": '',\n      \"pipeline_title\": this.emailForm.controls['name'].value,\n      \"email\": this.emailForm.controls['email'].value,\n      \"run_stage_range\": run_stage_range,\n      \"stages\": [\n        {\n          \"stage_display_name\": \"Cluster\",\n          \"stage_number\": stage_number,\n          \"stage_type\": \"prediction\",\n          \"tool_group\": \"cluster\",\n          \"input_sequence_text\": sequences,\n          // \"input_stage_number\": 1,\n          \"input_parameters\": input,\n          \"table_state\": table_state\n        }\n      ]\n    }\n    /** set params */\n    this._stateService.setParams(params);\n    const loadingClusterTool = Object.assign(initClusterTool, {\n      loading: true,\n      submitted: false,\n      appliedFilters: !_.isEmpty(table_state?.columns)\n    })\n    console.log(loadingClusterTool)\n    console.log(`this.index=${this.index}`);\n    this._stateService.insertTool(loadingClusterTool, this.index);\n    // this._stateService.insertTableStateToStage({columns: {}}, this.index);\n    this.loading = true;\n    this.postPipelineAPI(params);\n  }\n\n  onRun2() {\n\n    const params = this.params;\n    const stage_number = this.index + 1;\n    const input_stage_number = this.index;\n    /** run_stage_range */\n    const run_stage_range: [number, number] = [stage_number, stage_number]\n    /** default formValue */\n    // this.setDefaultFormValues() // no need because no sequences\n    /** input_parameters */\n    const input = this._pipelineService.convertClusterForm(this.clusterForm)\n\n    const initialStage = this.stages[this.index];\n\n    /** Table State */\n    const { table_state } = this.stages[this.index];\n\n    const stage = {\n      ...initialStage,\n      result_url: undefined,\n      \"input_stage_number\": input_stage_number,\n      \"input_parameters\": input,\n      table_state\n    }\n\n    params.stages[this.index] = stage;\n    params.run_stage_range = run_stage_range;\n    params.pipeline_title = this.emailForm.controls['name'].value;\n    params.email = this.emailForm.controls['email'].value;\n\n    console.log(params)\n\n    /** set params */\n    this._stateService.setParams(params);\n    const loadingClusterTool = Object.assign(initClusterTool, {\n      loading: true,\n      submitted: false,\n      appliedFilters: !_.isEmpty(table_state?.columns)\n    })\n    console.log(loadingClusterTool)\n    console.log(`onRun2() - this.index=${this.index}`);\n    this._stateService.insertTool(loadingClusterTool, this.index);\n    this.loading = true;\n    this.postPipelineAPI(params);\n  }\n\n  onCancel() {\n    console.log(this.runSetInterval)\n    clearInterval(this.runSetInterval);\n    this.emitOnCancel.emit()\n\n    this.inputChange.table_state = false;\n    // this.submitted = false;\n    const currentTool = this.tools[this.index];\n    const unSubmittedTool = {\n      ...currentTool,\n      loading: false,\n      submitted: false,\n      appliedFilters: undefined\n    }\n    this._stateService.insertTool(unSubmittedTool, this.index);\n    this.warningMessages = [];\n    this.loading = false;\n    this.tableStateSaving = false;\n    this.enableInputs();\n  }\n\n  onFilterApplied() {\n    this.inputChange.table_state = this.submitted;\n  }\n\n  onClearTableState() {\n    this.peptide_table_columns = _.map(this.peptide_table_columns, (c) => {\n      c.filters = ['int', 'float'].includes(c.type) ? {\n          minValue: NaN,\n          maxValue: NaN,\n          applied: false\n        } :\n        {\n          possibleValues: [],\n          textValue: null,\n          selectedValues: [],\n          applied: false\n        }\n      return c\n    })\n    this.inputChange.table_state = this.submitted;\n  }\n\n  onShowEmailModalChange() {\n    this.showEmailModal = !this.showEmailModal\n    this.shoeEmailModalChange.emit(this.showEmailModal)\n  }\n\n  onSaveTableStateMain() {\n    const hasResult = _.find(this.tools.slice(this.index+1), {submitted: true})\n    if (hasResult) {\n      this.saveState = true;\n      this.open(this.confirmModal);\n    } else {\n      this.onSaveTableState();\n    }\n  }\n\n  onSaveTableState() {\n    const tool_group = 'cluster'\n\n    const params = this.params\n    // create colObj and params\n    let colObj = columnListToObject(this.peptide_table_columns, tool_group)\n    const stages = params.stages;\n    const stageTemp = stages[this.index];\n\n    // stageTemp.table_state.columns = colObj;\n    stageTemp.table_state = [{table: 'peptide_table', columns: colObj}];\n\n    stages[this.index] = stageTemp\n    params.stages = stages;\n    // run_stage_range\n    const stage_number = this.index + 1;\n    params.run_stage_range = [stage_number, stage_number];\n    this._stateService.setParams(params);\n    // appliedFilters\n    let appliedFilters = !_.isEmpty(colObj);\n    this._stateService.setToolAppliedFilters(appliedFilters, this.index)\n    this.postPipelineAPI(params, false);\n    this.saveState = false;\n  }\n\n  onFileDropped($event: any[]) {\n    console.log($event);\n    const file = $event[0];\n    const fileSize = file.size / 1024; // in kB\n    console.log(file.type);\n    if (fileSize > 20000) {\n      this.alertService.add('File Size is too big! (20mB max)', 'alert-danger');\n      this.open(this.alertModal);\n    }\n    else {\n      this.prepareSequenceFileList($event);\n    }\n  }\n\n  prepareSequenceFileList(files: Array<any>) {\n    console.log(files);\n    this.fileName = files[0].name;\n    const reader = new FileReader();\n    const myForm = this.clusterForm;\n    for (const item of files) {\n      // console.log(item);\n      reader.readAsText(item);\n      reader.onload = () => {\n        const val = reader.result?.toString() || '';\n        console.log(val);\n        const v = isASCII(val);\n        console.log(v);\n        if (v) {\n          // myForm.patchValue({inputSequenceText: val.substring(0, this.maxCharacters)});\n          const w = isMaxLength(val, this.maxCharacters)\n          if (w) {\n            myForm.patchValue({inputSequenceText: val});\n          } else {\n            this.alertService.add(`Sequence is too long - max Sequence length is ${this.maxCharacters.toLocaleString(\"en-US\")} characters`, 'alert-danger');\n            this.open(this.alertModal);\n          }\n        } else {\n          this.alertService.add('Invalid file type.\\nValid file types are .txt, .fa, .fasta, .json, .faa,', 'alert-danger');\n          this.open(this.alertModal);\n        }\n      };\n\n      reader.onerror = () => {\n        console.log(reader.error);\n      };\n      item.progress = 0;\n      this.files.push(item);\n    }\n  }\n\n  sendNotification() {\n  //    TODO - used in email modal\n  }\n\n  onReset() {\n    this.alertService.clear();\n    this.errorMessages = [];\n    this.warningMessages = [];\n\n    const oldSequence = this.stages[this.index].input_sequence_text\n    const input_parameters = this.params.stages[this.index].input_parameters\n\n    // sequences\n    this.filteredSequences = [];\n    this.numOfAA = 0;\n    // order\n    this.peptide_table_order = [];\n    this.defaultOrder = [];\n    // clusterForm values\n\n    this.clusterForm.patchValue({\n      inputSequenceText: '',\n      peptideLength: [4, 26],\n      threshold: 0.7,\n      method: 'cluster-break'\n    }, {emitEvent: false});\n\n    this.enableInputs()\n\n    const method = input_parameters.predictors[0].method\n\n    if(this.submitted){\n      this.inputChange =  {\n        ...this.inputChange,\n        /** Keeps track of inputChanges to highlight selected parameter table row*/\n        input_sequence_text: oldSequence !== '',\n        threshold: input_parameters.cluster_pct_identity !== 0.7,\n        lengths: !_.isEqual([0, 0], input_parameters.peptide_length_range),\n        predictors: method !== 'cluster-break',\n      }\n    }\n\n    // this.errorMessages = [];\n    // this.warningMessages = [];\n    // this.loading = false;\n    // this.submitted = false;\n    // this.saveState = false;\n    // this.tableStateSaving = false;\n  }\n\n  get styleResultContainer(){\n    return !this.loading && this.submitted ? 'none' : 'dotted';\n  }\n\n  /** File Download/Upload*/\n  uploadSequenceFile($event: any) {\n    $event.preventDefault();\n    /**\n     * Used for 'Upload' button\n     * */\n    const {files} = $event.target;\n    files && this.onFileDropped(files);\n  }\n\n  uploadParameterFile($event: any, input: any) {\n    console.log($event);\n    $event.preventDefault();\n    // /**\n    //  * Used for 'Upload' button to upload parameters\n    //  * */\n    // const {files} = $event.target;\n    // files && this.onParameterFileDropped(files, input);\n  }\n\n  /** changes peptideLengthSliderOptions */\n\n  enableInputs() {\n    // this.clusterForm.enable({emitEvent: false});\n    this.clusterForm.controls['method'].enable({emitEvent: false})\n    this.thresholdSliderOptions = Object.assign({}, this.thresholdSliderOptions, {disabled: false});\n    this.peptideLengthOptions = Object.assign({}, this.peptideLengthOptions, {disabled: false})\n  }\n\n  disableInputs() {\n    // this.clusterForm.disable({emitEvent: false});\n    this.clusterForm.controls['method'].disable({emitEvent: false})\n    this.thresholdSliderOptions = Object.assign({}, this.thresholdSliderOptions, {disabled: true});\n    this.peptideLengthOptions = Object.assign({}, this.peptideLengthOptions, {disabled: true})\n  }\n\n  onErrorMessageDeselect(message: string, index: number) {\n    if (index > -1) {\n      this.errorMessages.splice(index, 1);\n    }\n    this.errorMessages = _.filter(this.errorMessages, (em) => em !== message);\n  }\n\n  onWarningMessageDeselect(message: string, index: number) {\n    if (index > -1) {\n      this.warningMessages.splice(index, 1);\n    }\n    this.warningMessages = _.filter(this.warningMessages, (wm) => wm !== message);\n  }\n\n}\n","<form [formGroup]=\"pepmatchForm\" (ngSubmit)=\"onRunMain()\" class=\"container\">\n  <div class=\"d-flex flex-row p-2\">\n    <h2 class=\"pe-2 display-5\">{{index + 1}}</h2>\n    <hr class=\"mt-4 flex-grow-1 divider\"/>\n  </div>\n  <div class=\"d-flex pb-3\">\n    <h4 class=\"p-2 tool-name\" id=\"pepmatch-label\">PEPMatch</h4>\n    <div class=\"d-flex flex-row tool-links\" role=\"group\" aria-label=\"tool-links\">\n      <button type=\"button\" class=\"btn btn-link text-dark d-flex flex-column justify-content-center align-items-center\">\n        <a target=\"_blank\" routerLink=\"/docs/tools/pepmatch/index.html\"\n           class=\"text-dark d-flex flex-column justify-content-center align-items-center\">\n          <svg width=\"1em\" height=\"1em\" viewBox=\"0 0 16 16\" class=\"bi bi-file-earmark-text\" fill=\"currentColor\"\n               xmlns=\"http://www.w3.org/2000/svg\">\n            <path\n              d=\"M4 1h5v1H4a1 1 0 0 0-1 1v10a1 1 0 0 0 1 1h8a1 1 0 0 0 1-1V6h1v7a2 2 0 0 1-2 2H4a2 2 0 0 1-2-2V3a2 2 0 0 1 2-2z\"/>\n            <path d=\"M9 4.5V1l5 5h-3.5A1.5 1.5 0 0 1 9 4.5z\"/>\n            <path fill-rule=\"evenodd\"\n                  d=\"M5 11.5a.5.5 0 0 1 .5-.5h2a.5.5 0 0 1 0 1h-2a.5.5 0 0 1-.5-.5zm0-2a.5.5 0 0 1 .5-.5h5a.5.5 0 0 1 0 1h-5a.5.5 0 0 1-.5-.5zm0-2a.5.5 0 0 1 .5-.5h5a.5.5 0 0 1 0 1h-5a.5.5 0 0 1-.5-.5z\"/>\n          </svg>\n          Docs\n        </a>\n      </button>\n      <button type=\"button\" class=\"btn btn-link\">\n        <a target=\"_blank\" [href]=\"swaggerUrl\"\n           class=\"text-dark d-flex flex-column justify-content-center align-items-center\">\n          <svg width=\"1em\" height=\"1em\" viewBox=\"0 0 16 16\" class=\"bi bi-gear\" fill=\"currentColor\"\n               xmlns=\"http://www.w3.org/2000/svg\">\n            <path fill-rule=\"evenodd\"\n                  d=\"M8.837 1.626c-.246-.835-1.428-.835-1.674 0l-.094.319A1.873 1.873 0 0 1 4.377 3.06l-.292-.16c-.764-.415-1.6.42-1.184 1.185l.159.292a1.873 1.873 0 0 1-1.115 2.692l-.319.094c-.835.246-.835 1.428 0 1.674l.319.094a1.873 1.873 0 0 1 1.115 2.693l-.16.291c-.415.764.42 1.6 1.185 1.184l.292-.159a1.873 1.873 0 0 1 2.692 1.116l.094.318c.246.835 1.428.835 1.674 0l.094-.319a1.873 1.873 0 0 1 2.693-1.115l.291.16c.764.415 1.6-.42 1.184-1.185l-.159-.291a1.873 1.873 0 0 1 1.116-2.693l.318-.094c.835-.246.835-1.428 0-1.674l-.319-.094a1.873 1.873 0 0 1-1.115-2.692l.16-.292c.415-.764-.42-1.6-1.185-1.184l-.291.159A1.873 1.873 0 0 1 8.93 1.945l-.094-.319zm-2.633-.283c.527-1.79 3.065-1.79 3.592 0l.094.319a.873.873 0 0 0 1.255.52l.292-.16c1.64-.892 3.434.901 2.54 2.541l-.159.292a.873.873 0 0 0 .52 1.255l.319.094c1.79.527 1.79 3.065 0 3.592l-.319.094a.873.873 0 0 0-.52 1.255l.16.292c.893 1.64-.902 3.434-2.541 2.54l-.292-.159a.873.873 0 0 0-1.255.52l-.094.319c-.527 1.79-3.065 1.79-3.592 0l-.094-.319a.873.873 0 0 0-1.255-.52l-.292.16c-1.64.893-3.433-.902-2.54-2.541l.159-.292a.873.873 0 0 0-.52-1.255l-.319-.094c-1.79-.527-1.79-3.065 0-3.592l.319-.094a.873.873 0 0 0 .52-1.255l-.16-.292c-.892-1.64.902-3.433 2.541-2.54l.292.159a.873.873 0 0 0 1.255-.52l.094-.319z\"/>\n            <path fill-rule=\"evenodd\"\n                  d=\"M8 5.754a2.246 2.246 0 1 0 0 4.492 2.246 2.246 0 0 0 0-4.492zM4.754 8a3.246 3.246 0 1 1 6.492 0 3.246 3.246 0 0 1-6.492 0z\"/>\n          </svg>\n          API\n        </a>\n      </button>\n      <button type=\"button\" class=\"btn btn-link text-dark d-flex flex-column justify-content-center align-items-center\"\n              routerLink=\"/download-all\"\n              [state]=\"{tool: 'pepmatch'}\">\n        <svg width=\"1em\" height=\"1em\" viewBox=\"0 0 16 16\" class=\"bi bi-cloud-arrow-down\" fill=\"currentColor\"\n             xmlns=\"http://www.w3.org/2000/svg\">\n          <path fill-rule=\"evenodd\"\n                d=\"M4.406 3.342A5.53 5.53 0 0 1 8 2c2.69 0 4.923 2 5.166 4.579C14.758 6.804 16 8.137 16 9.773 16 11.569 14.502 13 12.687 13H3.781C1.708 13 0 11.366 0 9.318c0-1.763 1.266-3.223 2.942-3.593.143-.863.698-1.723 1.464-2.383zm.653.757c-.757.653-1.153 1.44-1.153 2.056v.448l-.445.049C2.064 6.805 1 7.952 1 9.318 1 10.785 2.23 12 3.781 12h8.906C13.98 12 15 10.988 15 9.773c0-1.216-1.02-2.228-2.313-2.228h-.5v-.5C12.188 4.825 10.328 3 8 3a4.53 4.53 0 0 0-2.941 1.1z\"/>\n          <path fill-rule=\"evenodd\"\n                d=\"M7.646 10.854a.5.5 0 0 0 .708 0l2-2a.5.5 0 0 0-.708-.708L8.5 9.293V5.5a.5.5 0 0 0-1 0v3.793L6.354 8.146a.5.5 0 1 0-.708.708l2 2z\"/>\n        </svg>\n        Download\n      </button>\n      <button type=\"button\" class=\"btn btn-link text-dark d-flex flex-column justify-content-center align-items-center\"\n              routerLink=\"/citation\">\n        <svg width=\"1em\" height=\"1em\" viewBox=\"0 0 16 16\" class=\"bi bi-chat-square-quote\" fill=\"currentColor\"\n             xmlns=\"http://www.w3.org/2000/svg\">\n          <path fill-rule=\"evenodd\"\n                d=\"M14 1H2a1 1 0 0 0-1 1v8a1 1 0 0 0 1 1h2.5a2 2 0 0 1 1.6.8L8 14.333 9.9 11.8a2 2 0 0 1 1.6-.8H14a1 1 0 0 0 1-1V2a1 1 0 0 0-1-1zM2 0a2 2 0 0 0-2 2v8a2 2 0 0 0 2 2h2.5a1 1 0 0 1 .8.4l1.9 2.533a1 1 0 0 0 1.6 0l1.9-2.533a1 1 0 0 1 .8-.4H14a2 2 0 0 0 2-2V2a2 2 0 0 0-2-2H2z\"/>\n          <path fill-rule=\"evenodd\"\n                d=\"M7.066 4.76A1.665 1.665 0 0 0 4 5.668a1.667 1.667 0 0 0 2.561 1.406c-.131.389-.375.804-.777 1.22a.417.417 0 1 0 .6.58c1.486-1.54 1.293-3.214.682-4.112zm4 0A1.665 1.665 0 0 0 8 5.668a1.667 1.667 0 0 0 2.561 1.406c-.131.389-.375.804-.777 1.22a.417.417 0 1 0 .6.58c1.486-1.54 1.293-3.214.682-4.112z\"/>\n        </svg>\n        Cite\n      </button>\n    </div>\n  </div>\n  <!--  Sequence Input-->\n  <ng-container *ngIf=\"index===0\">\n    <div class=\"d-flex flex-row p-2\">\n      <h5 class=\"col-3 text-left\">Input Sequence(s)</h5>\n\n      <div class=\"col-9\">\n        <!--          <div class=\"btn-group btn-group-sm ml-auto\">-->\n        <button type=\"button\" class=\"btn btn-sm btn-dark-blue-grey text-white\" (click)=\"null\"\n                [disabled]=\"!submitted\"\n                data-bs-toggle=\"dropdown\"\n                data-toggle=\"dropdown\" aria-haspopup=\"true\" aria-expanded=\"false\">\n          <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n               class=\"bi bi-download\" viewBox=\"0 0 16 16\">\n            <path\n              d=\"M.5 9.9a.5.5 0 0 1 .5.5v2.5a1 1 0 0 0 1 1h12a1 1 0 0 0 1-1v-2.5a.5.5 0 0 1 1 0v2.5a2 2 0 0 1-2 2H2a2 2 0 0 1-2-2v-2.5a.5.5 0 0 1 .5-.5z\"/>\n            <path\n              d=\"M7.646 11.854a.5.5 0 0 0 .708 0l3-3a.5.5 0 0 0-.708-.708L8.5 10.293V1.5a.5.5 0 0 0-1 0v8.793L5.354 8.146a.5.5 0 1 0-.708.708l3 3z\"/>\n          </svg>\n        </button>\n        <div class=\"dropdown-menu\" aria-labelledby=\"dropdownMenuButton\">\n          <div class=\"dropdown-item\">\n            <label>Download as: </label>\n            &nbsp;\n            <div class=\"btn-group\">\n              <button\n                [className]=\"submitted ? 'btn btn-sky-blue text-white' : 'btn btn-outline-secondary'\"\n                type=\"button\" (click)=\"onDownloadJson()\">\n                JSON\n              </button>\n              <button\n                [className]=\"submitted ? 'btn btn-sky-blue text-white' : 'btn btn-outline-secondary'\"\n                type=\"button\" (click)=\"onDownloadFasta()\">\n                FASTA\n              </button>\n              <button\n                [className]=\"submitted ? 'btn btn-sky-blue text-white' : 'btn btn-outline-secondary'\"\n                type=\"button\" (click)=\"onDownloadOriginal()\">\n                Original\n              </button>\n            </div>\n          </div>\n        </div>\n        &nbsp;\n\n        <input type=\"file\"\n               #uploader\n               style=\"display: none\"\n               id=\"file\"\n               (change)=\"uploadSequenceFile($event)\">\n\n        <ng-template #uploadSequencesTipContent>\n          <div>\n            Upload sequence file <br> (.txt, .json, .fasta)\n          </div>\n\n        </ng-template>\n        <button type=\"button\" class=\"btn btn-dark-blue-grey text-white btn-sm\" (click)=\"uploader.click()\" [disabled]=\"loading\"\n                ngbTooltip='Clear allele(s)'\n                [ngbTooltip]=\"uploadSequencesTipContent\" placement=\"right\">\n          <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\" class=\"bi bi-upload\"\n               viewBox=\"0 0 16 16\">\n            <path\n              d=\"M.5 9.9a.5.5 0 0 1 .5.5v2.5a1 1 0 0 0 1 1h12a1 1 0 0 0 1-1v-2.5a.5.5 0 0 1 1 0v2.5a2 2 0 0 1-2 2H2a2 2 0 0 1-2-2v-2.5a.5.5 0 0 1 .5-.5z\"/>\n            <path\n              d=\"M7.646 1.146a.5.5 0 0 1 .708 0l3 3a.5.5 0 0 1-.708.708L8.5 2.707V11.5a.5.5 0 0 1-1 0V2.707L5.354 4.854a.5.5 0 1 1-.708-.708l3-3z\"/>\n          </svg>\n        </button>\n        &nbsp;\n      </div>\n    </div>\n    <div class=\"d-flex flex-column p-2\" appDnd (fileDropped)=\"onFileDropped($event)\">\n      <!--      [style.border-color]=\"inputChange.input_sequence_text ? '#f0ad4d' : null\"    -->\n      <textarea class='form-control'\n                [style.border-color]=\"inputChange.input_sequence_text ? '#f0ad4d' : null\"\n                id=\"sequenceFormControlTextArea\"\n                rows=\"10\"\n                formControlName=\"inputSequenceText\"\n                [readOnly]=\"loading\"\n                [placeholder]=\"sequencePlaceHolder\"></textarea>\n\n      <div class=\"d-flex flex-row-reverse justify-content-between p-2\">\n        <small *ngIf=\"inputSequenceText.length >= maxCharacters; else sequenceCounter\" class=\"text-danger\">\n          Sequence text is too long -  {{maxCharacters | number}} characters allowed\n        </small>\n        <ng-template #sequenceCounter>\n          <small class=\"text-muted\">\n            Format: {{seqFormat}} | {{numOfCharacters | number}} characters\n          </small>\n        </ng-template>\n\n        <small *ngIf=\"inputChange.input_sequence_text\" class=\"help-block form-text text-warning\">\n          Parameter changed since prediction.\n        </small>\n      </div>\n    </div>\n  </ng-container>\n\n  <!--  Prediction parameter -->\n  <div class=\"row p-2\">\n    <h5 class=\"col-3 text-left p-2\">Prediction Parameters</h5>\n    <div class=\"col-9\">\n      <!--  (click)=\"formUrl()\"    -->\n      <button type=\"button\" class=\"btn btn-sm btn-dark-blue-grey text-white\" (click)=\"onDownloadParameter()\"\n              aria-haspopup=\"true\" aria-expanded=\"false\">\n        <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-download\" viewBox=\"0 0 16 16\">\n          <path\n            d=\"M.5 9.9a.5.5 0 0 1 .5.5v2.5a1 1 0 0 0 1 1h12a1 1 0 0 0 1-1v-2.5a.5.5 0 0 1 1 0v2.5a2 2 0 0 1-2 2H2a2 2 0 0 1-2-2v-2.5a.5.5 0 0 1 .5-.5z\"/>\n          <path\n            d=\"M7.646 11.854a.5.5 0 0 0 .708 0l3-3a.5.5 0 0 0-.708-.708L8.5 10.293V1.5a.5.5 0 0 0-1 0v8.793L5.354 8.146a.5.5 0 1 0-.708.708l3 3z\"/>\n        </svg>\n      </button>\n      &nbsp;\n      <!--      <ng-template #uploadJsonTipContent>-->\n      <!--        Upload inputs as JSON-->\n      <!--      </ng-template>-->\n      <!--      <button type=\"button\" class=\"btn btn-info btn-sm text-white\" (click)=\"paramUploader.click()\" [disabled]=\"loading\"-->\n      <!--              datatype=\"html\" [ngbTooltip]=\"uploadJsonTipContent\">-->\n      <!--        Upload Parameters-->\n      <!--      </button>-->\n      <!--      <input type=\"file\"-->\n      <!--             #paramUploader-->\n      <!--             style=\"display: none\"-->\n      <!--             id=\"paramUploader\">-->\n      <!--      (change)=\"uploadParameterFile($event, alleleSearch)\"-->\n    </div>\n  </div>\n  <!--  Number of Mismatches -->\n  <div class=\"form-group row p-2\">\n    <div class=\"col-sm-3 col-form-label\">\n      <label class=\"'font-weight-bold'\">Maximum number of mismatches</label>\n    </div>\n    <div class=\"col-sm-9\">\n      <div [className]=\"inputChange.mismatch ? 'input-change-slider' : 'custom-ngx-slider'\">\n        <ngx-slider\n          formControlName=\"mismatch\"\n          (userChangeEnd)=\"onNumOfMismatchesChange($event)\"\n          [options]=\"options\"></ngx-slider>\n        <small *ngIf=\"inputChange.mismatch\" class=\"help-block form-text text-warning\">\n          Parameter changed since prediction.\n        </small>\n      </div>\n    </div>\n  </div>\n  <!--  Proteome -->\n  <div class=\"form-group row p-2\">\n    <div class=\"col-sm-3 col-form-label\">\n      <label class=\"'font-weight-bold'\">Proteome</label>\n    </div>\n    <div class=\"col-sm-9\">\n      <select class=\"form-control\" id=\"proteomeSelect\" formControlName=\"proteome\"\n              [style.border-color]=\"inputChange.proteome ? '#f0ad4d' : null\">\n        <option *ngFor=\"let o of proteomeOptions\" [value]=\"o\">{{o}}</option>\n      </select>\n      <small *ngIf=\"inputChange.proteome\" class=\"help-block form-text text-warning\">\n        Parameter changed since prediction.\n      </small>\n    </div>\n  </div>\n\n  <div class=\"form-group row p-2\">\n    <div class=\"col-sm-3 col-form-label\">\n      <label class=\"'font-weight-bold'\">Include all matches or best match per peptide</label>\n    </div>\n    <div class=\"col-sm-3\">\n      <div class=\"form-check\">\n        <input class=\"form-check-input\" type=\"radio\" id=\"bestMatchRadioButton\" formControlName=\"bestMatch\"\n               [value]=\"true\">\n        <label class=\"form-check-label\" for=\"bestMatchRadioButton\">\n          Best match per peptide\n        </label>\n      </div>\n      <div class=\"form-check\">\n        <input class=\"form-check-input\" type=\"radio\" id=\"allMatchRadioButton\" formControlName=\"bestMatch\"\n               [value]=\"false\">\n        <label class=\"form-check-label\" for=\"allMatchRadioButton\">\n          All matches\n        </label>\n      </div>\n      <small *ngIf=\"inputChange.bestMatch\" class=\"help-block form-text text-warning\">\n        Parameter changed since prediction.\n      </small>\n    </div>\n      <div class=\"col-sm-6\">\n        <div class=\"form-check pt-4\">\n        <input class=\"form-check-input\"\n               type=\"checkbox\"\n               id=\"includeUnmatchedPeptidesCheckbox\"\n               formControlName=\"include_unmatched_peptides\"\n               [attr.disabled]=\"loading ? true : null\"\n        >\n        <label class=\"form-check-label\" for=\"includeUnmatchedPeptidesCheckbox\">\n          Include unmatched peptides\n        </label>\n        </div>\n      </div>\n  </div>\n\n  <!--  <div class=\"form-check row pt-2\">-->\n  <!--    <div class=\"col text-right\">-->\n  <!--      <input class=\"form-check-input\" type=\"checkbox\" value=\"\" id=\"emailModalShow\" [checked]=\"showEmailModal\"-->\n  <!--             (change)=\"onShowEmailModalChange()\">-->\n  <!--      <label class=\"form-check-label\" for=\"emailModalShow\">-->\n  <!--        Notify me when prediction is complete-->\n  <!--      </label>-->\n  <!--    </div>-->\n  <!--  </div>-->\n  <hr/>\n  <div class=\"form-group d-flex flex-row-reverse pt-2\">\n\n    <div class=\"p-2\">\n      <button type=\"button\" class=\"reset-button btn btn-secondary btn-lg\" [disabled]=\"loading\"\n              (click)=\"onReset()\">\n        <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-arrow-clockwise\" viewBox=\"0 0 16 16\">\n          <path fill-rule=\"evenodd\" d=\"M8 3a5 5 0 1 0 4.546 2.914.5.5 0 0 1 .908-.417A6 6 0 1 1 8 2v1z\"/>\n          <path\n            d=\"M8 4.466V.534a.25.25 0 0 1 .41-.192l2.36 1.966c.12.1.12.284 0 .384L8.41 4.658A.25.25 0 0 1 8 4.466z\"/>\n        </svg>\n      </button>\n      &nbsp;\n      <span *ngIf=\"loading; else elseBlock\">\n            <button type=\"button\" class=\"btn btn-danger btn-lg\" (click)=\"onCancel()\"> Cancel Run </button>\n          </span>\n      <ng-template #elseBlock>\n        <div *ngIf=\"index!==0; else runButtonBlock\" class=\"btn-group\">\n          <div class=\"btn-group\">\n            <button type=\"submit\" class=\"run-button btn btn-dark-blue-grey text-white btn-lg\"\n                    [disabled]=\"(index>0 && !tools[index-1].submitted) || pipelineLoading\"\n            >\n              <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\" class=\"bi bi-play-fill\"\n                   viewBox=\"0 0 16 16\">\n                <path\n                  d=\"m11.596 8.697-6.363 3.692c-.54.313-1.233-.066-1.233-.697V4.308c0-.63.692-1.01 1.233-.696l6.363 3.692a.802.802 0 0 1 0 1.393z\"/>\n              </svg>\n            </button>\n            <button type=\"button\" class=\"btn btn-dark-blue-grey text-white dropdown-toggle dropdown-toggle-split\"\n                    data-toggle=\"dropdown\"\n                    data-bs-toggle=\"dropdown\"\n                    aria-haspopup=\"true\" aria-expanded=\"false\"\n                    [disabled]=\"pipelineLoading\">\n            </button>\n            <div class=\"dropdown-menu\">\n              <a class=\"dropdown-item\" (click)=\"onRunAll()\">Run All Above</a>\n            </div>\n          </div>\n        </div>\n        <ng-template #runButtonBlock>\n          <button type=\"submit\" class=\"run-button btn btn-dark-blue-grey btn-lg text-white\"\n                  [disabled]=\"(index>0 && !tools[index-1].submitted) || pipelineLoading\"\n          >\n            <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\" class=\"bi bi-play-fill\"\n                 viewBox=\"0 0 16 16\">\n              <path\n                d=\"m11.596 8.697-6.363 3.692c-.54.313-1.233-.066-1.233-.697V4.308c0-.63.692-1.01 1.233-.696l6.363 3.692a.802.802 0 0 1 0 1.393z\"/>\n            </svg>\n          </button>\n        </ng-template>\n\n      </ng-template>\n    </div>\n  </div>\n</form>\n\n<!--Errors and Warnings accordion -->\n<div ngbAccordion>\n  <!--  Error -->\n  <div ngbAccordionItem=\"first\" *ngIf=\"errorMessages.length\" #first=\"ngbAccordionItem\" [collapsed]=\"true\">\n    <h2 ngbAccordionHeader>\n      <button ngbAccordionButton class=\"accordion-button justify-content-center\">\n        <span class=\"text-danger m-1\">Errors ({{errorMessages.length}})</span>\n        <!--        <div>-->\n        <svg *ngIf=\"first.collapsed\" xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-arrow-left-circle-fill\" style=\"color: #dc3545;\" viewBox=\"0 0 16 16\">\n          <path\n            d=\"M8 0a8 8 0 1 0 0 16A8 8 0 0 0 8 0zm3.5 7.5a.5.5 0 0 1 0 1H5.707l2.147 2.146a.5.5 0 0 1-.708.708l-3-3a.5.5 0 0 1 0-.708l3-3a.5.5 0 1 1 .708.708L5.707 7.5H11.5z\"/>\n        </svg>\n        <!--        </div>-->\n        <!--        <div>-->\n        <svg *ngIf=\"!first.collapsed\" xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-arrow-down-circle-fill\" style=\"color: #dc3545;\" viewBox=\"0 0 16 16\">\n          <path\n            d=\"M16 8A8 8 0 1 1 0 8a8 8 0 0 1 16 0zM8.5 4.5a.5.5 0 0 0-1 0v5.793L5.354 8.146a.5.5 0 1 0-.708.708l3 3a.5.5 0 0 0 .708 0l3-3a.5.5 0 0 0-.708-.708L8.5 10.293V4.5z\"/>\n        </svg>\n        <!--        </div>-->\n      </button>\n    </h2>\n    <div ngbAccordionCollapse>\n      <div ngbAccordionBody>\n        <ng-template>\n          <ol>\n            <li *ngFor=\"let message of errorMessages; let i=index;\">{{message}}</li>\n          </ol>\n        </ng-template>\n      </div>\n    </div>\n  </div>\n  <!--  Warning -->\n  <div ngbAccordionItem=\"second\" *ngIf=\"warningMessages.length\" #second=\"ngbAccordionItem\" [collapsed]=\"true\">\n    <h2 ngbAccordionHeader>\n      <button ngbAccordionButton class=\"accordion-button justify-content-center\">\n        <span class=\"text-warning m-1\">Warnings ({{warningMessages.length}})</span>\n        <svg *ngIf=\"second.collapsed\"  xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-arrow-left-circle-fill\" style=\"color: #f0ad4d;\" viewBox=\"0 0 16 16\">\n          <path\n            d=\"M8 0a8 8 0 1 0 0 16A8 8 0 0 0 8 0zm3.5 7.5a.5.5 0 0 1 0 1H5.707l2.147 2.146a.5.5 0 0 1-.708.708l-3-3a.5.5 0 0 1 0-.708l3-3a.5.5 0 1 1 .708.708L5.707 7.5H11.5z\"/>\n        </svg>\n        <svg *ngIf=\"!second.collapsed\" xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-arrow-down-circle-fill\" style=\"color: #f0ad4d;\" viewBox=\"0 0 16 16\">\n          <path\n            d=\"M16 8A8 8 0 1 1 0 8a8 8 0 0 1 16 0zM8.5 4.5a.5.5 0 0 0-1 0v5.793L5.354 8.146a.5.5 0 1 0-.708.708l3 3a.5.5 0 0 0 .708 0l3-3a.5.5 0 0 0-.708-.708L8.5 10.293V4.5z\"/>\n        </svg>\n      </button>\n    </h2>\n    <div ngbAccordionCollapse>\n      <div ngbAccordionBody>\n        <ng-template>\n          <ol>\n            <li *ngFor=\"let message of warningMessages; let i=index;\">{{message}}</li>\n          </ol>\n        </ng-template>\n      </div>\n    </div>\n  </div>\n</div>\n\n<div *ngIf=\"!loading && !submitted && !(errorMessages.length && warningMessages.length)\"\n     class=\"p-2 d-flex justify-content-center col\"\n     [style.borderStyle]=\"styleResultContainer\">\n  <label class=\"p-2 font-italic\">\n    Results will load once step is run\n  </label>\n</div>\n\n<div *ngIf=\"loading\" class=\"p-2 d-flex justify-content-center col\" [style.borderStyle]=\"styleResultContainer\">\n  <div class=\"spinner-border text-primary align-self-center p-3 mb-3\" role=\"status\">\n    <span class=\"visually-hidden sr-only\">Loading...</span>\n  </div>\n  <label class=\"p-2 font-italic\">\n    <!--     TODO change when POST request returns a pipeline ID immediately-->\n    Calculating results, please wait...\n  </label>\n</div>\n\n<div class=\"container-fluid p-2\" id=\"table-result-container\"\n     *ngIf=\"!loading && submitted && peptide_table && !(errorMessages.length && warningMessages.length)\">\n  <ul ngbNav #nav=\"ngbNav\" [(activeId)]=\"active\" [animation]='false' [destroyOnHide]=\"false\" class=\"nav-tabs\">\n    <!--    peptide_table-->\n    <li [ngbNavItem]=\"'peptide_table'\">\n      <a ngbNavLink>Peptide Table</a>\n      <ng-template ngbNavContent>\n        <app-result-table *ngIf=\"peptide_table[0]?.length\" [table_data]=\"peptide_table\"\n                          table_name=\"peptide_table\"\n                          [order]=\"currentOrder\"\n                          [columns]=\"columns\"\n                          [tool_group]=\"formGroupName\"\n                          [index]=\"index\"\n                          [inputChange]=\"inputChange.table_state\"\n                          [tableStateSaving]=\"tableStateSaving\"\n                          (emitFilterApplied)=\"onFilterApplied()\"\n                          (emitResetTableState)=\"onClearTableState()\"\n                          (emitSaveTableState)=\"onSaveTableStateMain()\"></app-result-table>\n        <div *ngIf=\"!peptide_table[0]?.length\" class=\"pt-2\">\n            <ngb-alert [dismissible]=\"false\">\n              No matches found with the given input peptides and selected parameters.\n            </ngb-alert>\n        </div>\n\n      </ng-template>\n    </li>\n    <!--    sequence_table-->\n    <li *ngIf=\"sequence_table[0]?.length\" [ngbNavItem]=\"'input_sequence_table'\">\n      <a ngbNavLink> Sequence Table </a>\n      <ng-template ngbNavContent>\n        <app-result-table [table_data]=\"sequence_table\"\n                          table_name=\"input_sequence_table\"\n                          [order]=\"sequence_table_order\"\n                          [columns]=\"sequence_table_columns\"\n                          [tool_group]=\"formGroupName\"></app-result-table>\n      </ng-template>\n    </li>\n  </ul>\n  <div [ngbNavOutlet]=\"nav\"></div>\n</div>\n\n<!--Confirm Modal -->\n<ng-template #confirmModal let-confirmModal>\n  <div class=\"modal-header\">\n    <h4 class=\"modal-title\" id=\"modal-title\">Are you sure?</h4>\n    <button type=\"button\" class=\"btn-close\" aria-label=\"Close\" (click)=\"confirmModal.dismiss('Cross click')\"></button>\n  </div>\n  <div class=\"modal-body\">\n    <div *ngIf=\"!saveState; else saveStateConfirmation\">\n      <p><strong>Re-running this step of the pipeline will delete all downstream results, including:</strong></p>\n      <ol>\n        <li *ngFor=\"let stage of stages.slice(this.index+1)\"> {{stage.stage_display_name}} </li>\n      </ol>\n      <p><strong>To access the current results, you can use this link</strong></p>\n    </div>\n    <ng-template #saveStateConfirmation>\n      <p><strong>Applying these filters for input to the next stage will delete results from all downstream steps in\n        this session, including:</strong></p>\n      <ol>\n        <li *ngFor=\"let stage of stages.slice(this.index+1)\"> {{stage.stage_display_name}} </li>\n      </ol>\n      <p><strong>To access the current results, you can use this link</strong></p>\n    </ng-template>\n    <!-- pipeline URL input group-->\n    <div class=\"input-group\">\n      <input type=\"text\" class=\"form-control\" id=\"pipeline-url-input\" [value]=\"pipelineUrl\">\n      <button class=\"btn btn-secondary\" [cdkCopyToClipboard]=\"pipelineUrl\" ngbTooltip=\"copy url\" placement=\"top\">\n        <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-clipboard\" viewBox=\"0 0 16 16\">\n          <path\n            d=\"M4 1.5H3a2 2 0 0 0-2 2V14a2 2 0 0 0 2 2h10a2 2 0 0 0 2-2V3.5a2 2 0 0 0-2-2h-1v1h1a1 1 0 0 1 1 1V14a1 1 0 0 1-1 1H3a1 1 0 0 1-1-1V3.5a1 1 0 0 1 1-1h1v-1z\"/>\n          <path\n            d=\"M9.5 1a.5.5 0 0 1 .5.5v1a.5.5 0 0 1-.5.5h-3a.5.5 0 0 1-.5-.5v-1a.5.5 0 0 1 .5-.5h3zm-3-1A1.5 1.5 0 0 0 5 1.5v1A1.5 1.5 0 0 0 6.5 4h3A1.5 1.5 0 0 0 11 2.5v-1A1.5 1.5 0 0 0 9.5 0h-3z\"/>\n        </svg>\n      </button>\n    </div>\n  </div>\n  <div class=\"modal-footer\">\n    <button type=\"button\" class=\"btn btn-outline-secondary\" (click)=\"confirmModal.dismiss('cancel click')\">No\n    </button>\n    <button type=\"button\" class=\"btn btn-danger\" (click)=\"confirmModal.close('Ok click'); onRunConfirm();\">Yes, continue\n      and destroy downstream steps\n    </button>\n  </div>\n</ng-template>\n\n<!--Alert Modal -->\n<ng-template #alertModal let-modal4>\n  <div class=\"modal-header\">\n    <h4 class=\"modal-title\" id=\"alert-modal-title\">Validation Error(s)</h4>\n    <button type=\"button\" class=\"btn-close\" aria-label=\"Close\" (click)=\"modal4.dismiss('Cross click');\">\n    </button>\n  </div>\n  <div class=\"modal-body\">\n    <app-alert-component></app-alert-component>\n  </div>\n  <div class=\"modal-footer\">\n  </div>\n</ng-template>\n","import {\n  Component,\n  OnInit,\n  OnDestroy,\n  Input,\n  Output,\n  EventEmitter,\n  ViewChild,\n  ElementRef,\n  OnChanges, SimpleChanges\n} from '@angular/core';\nimport {HttpClient} from \"@angular/common/http\";\nimport {Title} from \"@angular/platform-browser\";\nimport {ActivatedRoute, Router} from \"@angular/router\";\nimport {FormBuilder, UntypedFormGroup, FormControl, FormArray, FormGroupDirective} from \"@angular/forms\";\nimport {CdkDragDrop} from '@angular/cdk/drag-drop';\nimport { Location } from '@angular/common';\n\nimport {Observable, timer, of, from, Subject, Subscription} from \"rxjs\";\nimport {NgbModal, NgbActiveModal} from '@ng-bootstrap/ng-bootstrap';\nimport {Options, ChangeContext} from '@angular-slider/ngx-slider';\n\nimport Columns from \"../_global/Columns\";\nimport {PipelineService} from \"../services/pipeline-service/pipeline.service\";\nimport {PipelineStateService} from \"../services/state-services/pipeline-state-service/pipeline-state.service\";\nimport {SequenceParserService} from \"../services/sequence-parser/sequence-parser.service\";\n\nimport Stage from \"../_global/Stage\";\nimport PipelineParams from \"../_global/PipelineParams\";\nimport * as pipelineData from \"../services/data/cluster-sample.json\";\nimport * as pepmatchData from \"../services/data/pepmatch-mismatch-sample.json\";\nimport {\n  initClusterTool, initParams, initClusterState, initTCellPredictionTool, initPepmatchTool\n} from \"../services/state-services/default-stage-states\";\nimport {isASCII, IsJsonString, ltrim} from \"../util/string-helpers\";\nimport Tool from \"../_global/Tool\";\nimport {AlertServiceService} from \"../services/alert-service/alert-service.service\";\nimport {columnListToObject} from \"../util/convert-columns\";\nimport {AlleleSearchService} from \"../services/allele-search/allele-search.service\";\nimport * as _ from \"lodash\";\nimport {environment} from \"../../environments/environment\";\nimport {debounce, takeUntil} from \"rxjs/operators\";\nimport onCsvDownloadAllClickedNew from '../util/on-csv-download';\nimport {isMaxLength} from \"../util/is-max-length\";\n\nconst API_URL = `${environment['api_url']}/api/v1/pepmatch`;\nconst EMAIL_URL = `${environment['api_url']}/api/v1/request`;\n\n@Component({\n  selector: 'app-pepmatch',\n  templateUrl: './pepmatch.component.html',\n  styleUrls: ['./pepmatch.component.scss'],\n  styles: [\n    `\n\t\t\t.accordion-button::after {\n\t\t\t\tcontent: none;\n\t\t\t}\n\t\t`,\n  ]\n})\nexport class PepmatchComponent implements OnInit, OnDestroy, OnChanges  {\n\n  sequencePlaceHolder = `Type/paste/drag a set of peptides (max: 1,000) into this box or click 'Run' to use the example sequence:\nDDEDSKQNIFHFLYR\nADPGPHLMGGGGRAK\nKAVELGVKLLHAFHT\nQLQNLGINPANIGLS\nHEVWFFGLQYVDSKG\n`\n\n  /** Pipeline form */\n  @Input() formGroupName!: string\n  @Input() index!: number;\n  @Input() resultUrl!: string | undefined;\n  @Input() showEmailModal: boolean = false;\n\n  @Input() emailForm!: UntypedFormGroup;\n  @Output() openEmailModal = new EventEmitter<any>();\n\n\n  @Output() emitIndex = new EventEmitter<number>(); // used for run all\n  @Output() emitOnCancel = new EventEmitter<any>();\n\n  @ViewChild('alertModal') alertModal!: ElementRef;\n  @ViewChild('confirmModal') confirmModal!: ElementRef;\n\n  @Input() events: Observable<void> = of();\n  private eventsSubscription: Subscription  = new Subscription();\n\n  @Input() runAllEvent: Observable<void> = of();\n  private runAllSubscription: Subscription  = new Subscription();\n\n  unsubscribe$ = new Subject();\n\n  stages$: Observable<Stage[]> = this._stateService.stages$;\n  tools$: Observable<Tool[]> = this._stateService.tools$;\n  pipelineId$: Observable<string> = this._stateService.pipelineId$;\n  params$: Observable<PipelineParams> = this._stateService.params$;\n\n  stages: Stage[] = [];\n  tools: Tool[] = [];\n  pipelineId = '';\n  params!: PipelineParams;\n  pipelineUrl: string = ''\n\n  swaggerUrl = `${environment['api_url']}/apidocs`\n\n  /** sequence variables */\n  synthesisDownloadLinks = {\n    sequence_list_json_uri: '',\n    sequence_list_fasta_uri: '',\n    download_sequences: ''\n  };\n\n  /** Form variables */\n  pepmatchForm!: UntypedFormGroup;\n\n  filteredSequences: { name: string, sequences: string }[] = [];\n  numOfAA: number = 0;\n  numOfCharacters = 0\n  seqFormat: string = 'Unknown';\n\n  inputChange = {\n    /** Keeps track of inputChanges to highlight selected parameter table row*/\n    input_sequence_text: false,\n    proteome: false,\n    mismatch: false,\n    bestMatch: false,\n    table_state: false,\n  }\n\n  options: Options = {\n    floor: 0,\n    ceil: 5,\n    step: 1,\n    showTicks: true,\n    showTicksValues: true\n  };\n\n  predictionOptions: {display_name: string, short_name: string, group: string, source: string, has_ic50: boolean}[] = [];\n  proteomeOptions: string[] = [];\n\n  pepmatchLoading: boolean = false;\n\n  /** API Call variables */\n  runSetInterval: any;\n  submitted = false;\n  loading = false;\n  getResultsClicked = true;\n\n  pipelineLoading = false;\n  tableStateSaving = false;\n  saveState = false;\n\n  errorMessages: string[] = [];\n  warningMessages: string[] = [];\n\n  columns: Columns[] | any;\n  peptide_table: [(string | number)[]] = [[]]\n  currentOrder: any[] = [];\n  defaultOrder: any[] = [];\n\n  sequence_table_order: any[] = [];\n  sequence_table_columns: Columns[] | any;\n  sequence_table: [(string | number)[]] = [[]]\n\n  /** sequence files */\n  maxCharacters = 1000000;\n  files: any[] = [];\n  fileName = '';\n\n  active = 'peptide_table'\n\n  constructor(\n    public alertService: AlertServiceService,\n    private http: HttpClient,\n    // private fb: FormBuilder,\n    private location: Location,\n    private titleService: Title,\n    private _alleleSearchService: AlleleSearchService,\n    private _pipelineService: PipelineService,\n    private _stateService: PipelineStateService,\n    private rootFormGroup: FormGroupDirective, // pipeline component\n    private sequenceParserService: SequenceParserService,\n    private modalService: NgbModal,\n  ) { }\n\n  ngOnInit(): void {\n    this.getPepmatch()\n    this.pepmatchForm = this.rootFormGroup.control.get(this.formGroupName) as UntypedFormGroup;\n\n    this.pipelineId$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n      this.pipelineId = value;\n      this.pipelineUrl = `${window.location.origin}/pipeline/${value}`;\n    })\n    this.stages$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n      this.stages = value;\n      this.errorMessages = this.stages[this.index]?.stage_messages!.errors\n      this.warningMessages = this.stages[this.index]?.stage_messages!.warnings\n    })\n    this.tools$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n      console.log('tools$');\n      console.log(value);\n      this.tools = value;\n      this.submitted = this.tools[this.index]?.submitted\n\n      // inputSequenceTextURIs\n      const inputSequenceTextId = this.tools[this.index]?.input_data_uri?.input_sequence_text_id\n\n      this.synthesisDownloadLinks.sequence_list_json_uri = `${environment['api_url']}/api/v1/sequence_list_json/${inputSequenceTextId}`\n      this.synthesisDownloadLinks.sequence_list_fasta_uri = `${environment['api_url']}/api/v1/sequence_list_fasta/${inputSequenceTextId}`\n      this.synthesisDownloadLinks.download_sequences = `${environment['api_url']}/api/v1/download_sequences/${inputSequenceTextId}`\n      /** pipeline Loading */\n      this.pipelineLoading = _.some(this.tools, {loading: true})\n\n      /** cancel run all  */\n      if(!this.tools[this.index]?.loading) {\n        this.loading = false;\n        clearInterval(this.runSetInterval)\n      }\n      // this.loading = this.tools[this.index]?.loading\n      // if (this.tools[this.index]?.submitted){this.submitted = true}\n      // if (this.tools[this.index].appliedFilters){this.submitted = true}\n      // this.componentDisabled = value[this.index].disabled;\n    })\n\n    this.params$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n      console.log(`params`);\n      console.log(value);\n      this.params = value;\n    })\n\n    this.eventsSubscription = this.events.subscribe(() => this.onRunMain());\n    this.runAllSubscription = this.runAllEvent.subscribe(() => this.onRunAll())\n\n    this.onChanges()\n\n    if(this.pepmatchForm.get('inputSequenceText')?.value) {\n      this.sequenceParser(this.pepmatchForm.get('inputSequenceText')?.value)\n    }\n    // if(this.loading) {\n    //   this.disableInputs()\n    // }\n\n    // if(this.resultUrl) {\n    //   this.loading = true;\n    //   this.getResultsSetInterval(this.resultUrl);\n    // }\n\n    // filteredSequences\n    // numOfAA\n  }\n\n  ngOnDestroy() {\n    clearInterval(this.runSetInterval);\n    clearInterval(this._pipelineService.runSetInterval)\n    this.unsubscribe$.next();\n    this.unsubscribe$.complete();\n    this.eventsSubscription.unsubscribe();\n  }\n\n  ngOnChanges(changes: SimpleChanges) {\n    if (changes.resultUrl?.currentValue) {\n      console.log(changes.resultUrl.currentValue);\n      console.log('ngOnChanges pepmatch')\n      this.loading = true;\n      this.getResultsSetInterval(changes.resultUrl.currentValue);\n    }\n  }\n\n  get styleResultContainer(){\n    return !this.loading && this.submitted ? 'none' : 'dotted';\n  }\n\n  get inputSequenceText(){\n    return this.pepmatchForm.get('inputSequenceText')?.value\n  }\n\n  /** Download Sequence File API calls*/\n\n  onDownloadJson() {\n    onCsvDownloadAllClickedNew(this.synthesisDownloadLinks.sequence_list_json_uri, this.http, 'json');\n  }\n\n  onDownloadFasta() {\n    onCsvDownloadAllClickedNew(this.synthesisDownloadLinks.sequence_list_fasta_uri, this.http, 'fasta');\n  }\n  onDownloadOriginal() {\n    onCsvDownloadAllClickedNew(this.synthesisDownloadLinks.download_sequences, this.http, 'txt');\n  }\n\n\n  /** File Download/Upload*/\n  uploadSequenceFile($event: any) {\n    $event.preventDefault();\n    /**\n     * Used for 'Upload' button\n     * */\n    const {files} = $event.target;\n    files && this.onFileDropped(files);\n  }\n\n  uploadParameterFile($event: any, input: any) {\n    console.log($event);\n    $event.preventDefault();\n    /**\n     * Used for 'Upload' button to upload parameters\n     * */\n    // const {files} = $event.target;\n    // files && this.onParameterFileDropped(files, input);\n  }\n\n  onDownloadParameter() {\n    const data = this._pipelineService.convertPepmatchForm(this.pepmatchForm)\n\n    const a = document.createElement('a');\n    a.setAttribute('style', 'display:none;');\n    document.body.appendChild(a);\n    // const contentType = 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet;charset=UTF-16';\n    // var blob = new Blob([csvData], { type: contentType });\n    const blob = new Blob([JSON.stringify(data, null, 2)], ); // thx: http://stackoverflow.com/a/18925211\n    a.href = window.URL.createObjectURL(blob);\n    a.download = 'parameter.json';\n\n    a.click();\n  }\n\n  getPepmatch() {\n    this.pepmatchLoading = true;\n    this.http.get<any[]>(API_URL)\n      .pipe().subscribe(\n      resp => {\n        // @ts-ignore\n        // this.mhciPredictors = resp['predictors'];\n        this.proteomeOptions = resp.optional_parameters[0].choice\n        // console.log(resp.optional_parameters[0]);\n\n        console.log(this.proteomeOptions)\n        this.pepmatchLoading = false;\n      }\n    )\n  }\n\n  onChanges(): void {\n    /** PredictionModel sessionStorage */\n    this.pepmatchForm.get('proteome')?.valueChanges.subscribe(() => {\n      this.inputChange.proteome = this.submitted\n    });\n\n    this.pepmatchForm.get('bestMatch')?.valueChanges.subscribe(() => {\n      this.inputChange.bestMatch = this.submitted\n    });\n\n    const sequenceFieldChange = this.pepmatchForm.get('inputSequenceText')?.valueChanges.pipe(\n      debounce(v => timer(1000)),\n    );\n\n    sequenceFieldChange?.subscribe(val => {\n      // sessionStorage.setItem('sequences', val);\n      this.sequenceParser(val);\n      this.inputChange.input_sequence_text = this.submitted;\n      if (val === '') {  // delete\n        this.filteredSequences = [];\n        this.numOfAA = 0;\n      }\n    });\n  }\n\n  onRunAll() {\n    this.setDefaultFormValues()\n    this.errorMessages = [];\n    this.warningMessages = [];\n    this.emitIndex.emit(this.index);\n  }\n\n  onRunMain() {\n    if(this.pepmatchForm.invalid){\n      this.alertService.add(`Input sequence text is too long. The maximum number of characters allowed is ${this.maxCharacters.toLocaleString()}\\nYour sequence contains ${this.inputSequenceText.length.toLocaleString()}`, 'alert-danger');\n      this.open(this.alertModal)\n      return;\n    }\n\n    const hasResult = _.find(this.tools.slice(this.index+1), (o) => o.submitted || o.loading)\n    if(this.stages.length > 1 && hasResult) {\n      this.open(this.confirmModal);\n    } else {\n      this.getResultsClicked = true;\n      if(this.index===0) {\n        this.onRun();\n      } else {\n        this.onRun2()\n      }\n    }\n  }\n\n  setDefaultFormValues() {\n    /** defaults - use Sars placeholders*/\n    const {input_sequence_text} = pepmatchData;\n    /** Sequences */\n    let sequences = this.pepmatchForm.value.inputSequenceText\n    if(!sequences && this.index===0) {\n      this._stateService.setInputSequenceText(input_sequence_text);\n      this.pepmatchForm.controls.inputSequenceText.setValue(input_sequence_text);\n    }\n  }\n\n  onRunConfirm() {\n    let indicies = _.range(this.index + 1, this.stages.length)\n    let initTool: Tool;\n    console.log(indicies);\n    _.forEach(indicies, i => {\n      initTool = this.tools[i];\n      const unSubmittedTool = {\n        ...initTool,\n        loading: false,\n        submitted: false,\n      }\n      this._stateService.insertTool(unSubmittedTool, i);\n    })\n    this.saveState ? this.onSaveTableState() : this.onRun();\n  }\n\n  onRun() {\n    /**\n     Update pipeline State\n     *\n     * */\n    /** Reset global datatables search ext */\n    $.fn.dataTable.ext.search = [];\n\n    const stage_number = this.index + 1;\n    /** run_stage_range */\n    const run_stage_range: [number, number] = [stage_number, stage_number]\n    /** default formValue */\n    this.setDefaultFormValues()\n    /** Sequences */\n    let sequences = this.pepmatchForm.value.inputSequenceText\n\n    /** input parameters */\n    const inputParameters = this._pipelineService.convertPepmatchForm(this.pepmatchForm)\n\n    /** Table State */\n\n    const { table_state } = this.stages[this.index];\n\n    const newStage = {\n      \"stage_display_name\": \"Pepmatch\",\n      \"stage_number\": stage_number,\n      \"stage_type\": \"prediction\",\n      \"tool_group\": \"pepmatch\",\n      \"input_sequence_text\": sequences,\n      \"input_parameters\": inputParameters,\n      \"table_state\": table_state\n    }\n\n    const params = {\n      \"pipeline_id\": '',\n      \"pipeline_title\": this.emailForm.controls['name'].value,\n      \"email\": this.emailForm.controls['email'].value,\n      \"run_stage_range\": run_stage_range,\n      \"stages\": [\n        newStage\n      ]\n    }\n\n    /** set params */\n    const initTool = Object.assign(initPepmatchTool, {\n      loading: true,\n      submitted: false,\n      appliedFilters: !_.isEmpty(table_state?.columns)\n    })\n    this._stateService.setParams(params);\n    this._stateService.insertTool(initTool, this.index);\n    // this._stateService.insertTableStateToStage({columns: {}}, this.index);\n\n    this.postPipelineAPI(params);\n  }\n\n  onRun2() {\n\n    const params = this.params;\n    const stage_number = this.index + 1;\n    const input_stage_number = this.index; // previous index\n\n    /** run_stage_range */\n    const run_stage_range: [number, number] = [stage_number, stage_number]\n    /** default formValue */\n    this.setDefaultFormValues()\n\n    /** input parameters */\n    const inputParameters = this._pipelineService.convertPepmatchForm(this.pepmatchForm)\n\n    const initialStage = this.stages[this.index];\n    console.log('initialStage');\n    console.log(initialStage);\n\n    /** Table State */\n    const { table_state } = this.stages[this.index];\n\n    const stage: Stage = {\n      ...initialStage,\n      result_url: undefined,\n      stage_number: stage_number,\n      input_stage_number: input_stage_number,\n      input_parameters: inputParameters,\n      table_state\n    }\n\n    // this.params.stages.push(stage);\n    params.stages[this.index] = stage;\n    params.run_stage_range = run_stage_range;\n    params.pipeline_title = this.emailForm.controls['name'].value;\n    params.email = this.emailForm.controls['email'].value;\n\n    console.log(params)\n\n    /** set params */\n    this._stateService.setParams(params);\n    const loadingTCellPredictionTool = Object.assign(initPepmatchTool, {\n      loading: true,\n      submitted: false,\n      appliedFilters: !_.isEmpty(table_state?.columns)\n    })\n    console.log('loadingTCellPredictionTool')\n    console.log(loadingTCellPredictionTool)\n    this._stateService.insertTool(loadingTCellPredictionTool, this.index);\n\n    this.postPipelineAPI(params);\n  }\n\n  setValueLimits(column: Columns) : any {\n    /* set value_limits (i.e. filters) for each column based on if type is a number/string */\n    return column['type'] === 'int' || column['type'] === 'float' ? {\n      ...column['value_limits'],\n      minValue: NaN,\n      maxValue: NaN,\n      applied: false\n    } : {\n      // ...column['value_limits'],\n      possibleValues: column['value_limits']['unique_values'],\n      textValue: null,\n      selectedValues: [],\n      applied: false\n    }\n  }\n\n  postPipelineAPI(params: PipelineParams, getResults: boolean = true) {\n    /**\n     * params\n     * getResults: boolean\n     *  false - used in 'Save Table State'\n     * */\n    /** initial set up */\n    this.disableInputs();\n    this.loading = getResults; // true - defaults\n    this.submitted = !getResults; // false - defaults\n    this.tableStateSaving = !getResults\n    if (getResults) {\n      this.errorMessages = [];\n      this.warningMessages = [];\n    }\n    this._pipelineService.postPipeline(params).subscribe(\n      (resp) => {\n      // Errors and Warnings\n      if (resp['errors'] && resp['errors'].length) {\n        console.log(resp);\n        console.error(resp['errors']);\n        this.errorMessages = resp['errors'];\n        if (resp['warnings'].length) {\n          console.log(resp['warnings']);\n          this.warningMessages = resp['warnings'];\n        }\n        this.loading = false;\n        this.submitted = true;\n        const submittedTool = Object.assign(initPepmatchTool, {\n          submitted: false,\n          loading: false,\n        })\n        this._stateService.insertTool(submittedTool, this.index);\n        this.enableInputs();\n        return;\n      }\n      // Warnings\n      if (resp['warnings'].length) {\n        console.log(resp['warnings']);\n        this.warningMessages = resp['warnings'];\n      }\n\n      console.log(resp.pipeline_id);\n\n      const inputDataUri = {input_sequence_text_id: resp.input_sequence_text_id}\n      this._stateService.insertInputDataUriToTool(inputDataUri, this.index)\n\n      this._stateService.setPipelineId(resp.pipeline_id);\n      this._stateService.setPipelineIdToParams(resp.pipeline_id);\n      this._stateService.setPipelineSpecId(resp.pipeline_spec_id);\n      /** Display email Modal if emailModalShow=true */\n      if (this.showEmailModal) {\n        // this.open(this.emailModal);\n      }\n      this.location.replaceState(`pipeline/${resp.pipeline_id}`)\n      // this.titleService.setTitle(`IEDB NG Tools Pipeline`);\n\n      if (getResults) {\n        const result_url = `${resp.results_uri}`;\n        console.log(result_url);\n        this.getResultsSetInterval(result_url);\n      } else {\n        this.inputChange.table_state = false;\n        this.submitted = true;\n        this.loading = false;\n        this.tableStateSaving = false;\n        this.enableInputs();\n      }\n    },\n      error => {\n        console.error(error);\n        this.errorMessages.push(error.error);\n        this.submitted = false;\n        this.loading = false;\n        const prevTool = this.tools[this.index];\n        const submittedTool = Object.assign(prevTool, {\n          submitted: this.submitted,\n          loading: this.loading,\n        })\n        this._stateService.insertTool(submittedTool, this.index);\n        clearInterval(this.runSetInterval);\n        this.enableInputs();\n      })\n  }\n\n  getResultsSetInterval(result_url: string) {\n    this.getResultsClicked = true\n\n    this.sequence_table = [[]]\n    this.peptide_table = [[]]\n\n    this.inputChange = _.mapValues(this.inputChange, () => false);\n    let increment = 0;\n    const milliseconds = 3000;\n    this.runSetInterval = setInterval(() => {\n      this._pipelineService.getResults(result_url).subscribe(resp => {\n        if (resp['status'] === 'error' || resp['errors']) {\n          this.errorMessages = resp['data']['errors'];\n          this.warningMessages = resp['data']['warnings'];\n          this.submitted = false;\n          this.loading = false;\n          const prevTool = this.tools[this.index];\n          console.log(prevTool)\n          const submittedTool = Object.assign(prevTool, {\n            submitted: this.submitted,\n            loading: this.loading,\n          })\n          this._stateService.insertTool(submittedTool, this.index);\n          clearInterval(this.runSetInterval);\n          this.enableInputs();\n        }\n        if (resp['data']['warnings']?.length) {\n          // console.log(resp['warnings']);\n          this.warningMessages = resp['data']['warnings'];\n        }\n        if (resp['data']['errors']?.length) {\n          // console.log(resp['warnings']);\n          this.errorMessages = resp['data']['errors'];\n        }\n        if (resp['status'] === 'done') {\n          /** 1) Create Column */\n          const data = resp['data']['results'];\n          console.log(data);\n\n          this.active = data[0].type\n\n          // this.active = data[0].table_data.length ? data[0].type : data[1].type\n\n          _.forEach(data, table => {\n            if (table.type === 'peptide_table') {\n              this.columns = _.map(table.table_columns, (column, i) => {\n                if (column.default_order && Number.isFinite(column.row_sort_priority)) { // set defaultOrder\n                  // console.log(column);\n                  this.defaultOrder[column.row_sort_priority] = [i, column.default_order === \"ascending\" ? 'asc' : 'desc'];\n                }\n                column['title'] = `${column['display_name']}`; // required\n                column['data'] = `${column['name']}`;\n                let source = column['source'];\n\n                column['filterKey'] = `${source}.${column.name}`\n                // console.log(`source=${source}`);\n                let tempSource = source.split('.')\n                // console.log(tempSource);\n                source = tempSource[tempSource.length - 1];\n                // console.log(`source=${source}`);\n                column['data'] = `${source}_${column['name']}`;\n                /** remove `core` from name */\n                // column['name'] = column['display_name'] ? column['display_name'] : column['name']\n                // column['name'] = source === 'core' ? display_name: `${source} ${display_name}`;\n                // column['filters'] = column['type'] === 'int' ? {\n                //   minValue: NaN,\n                //   maxValue: NaN,\n                //   applied: false\n                // } : {\n                //   possibleValues: [],\n                //   textValue: null,\n                //   selectedValues: [],\n                //   applied: false\n                // }\n                column['value_limits'] = column['value_limits'] &&  this.setValueLimits(column)\n                return column\n              });\n              this.currentOrder = [...this.defaultOrder];\n              if (this.columns) {\n                this.peptide_table = table.table_data;\n                const prevTool = this.tools[this.index];\n                console.log(prevTool)\n                const submittedClusterTool = Object.assign(prevTool, {\n                  submitted: true,\n                  loading: false,\n                })\n\n                this._stateService.insertTool(submittedClusterTool, this.index);\n\n                clearInterval(this.runSetInterval);\n                this.enableInputs();\n\n                this.submitted = true;\n                this.loading = false;\n              }\n            }\n            if (table.type === 'input_sequence_table') {\n              this.sequence_table_columns = _.map(table.table_columns, (column, i) => {\n                // if (column.default_order && Number.isFinite(column.row_sort_priority)) { // set defaultOrder\n                //   this.defaultOrder[column.row_sort_priority] = [i, column.default_order === \"ascending\" ? 'asc' : 'desc'];\n                // }\n                column['title'] = `${column['display_name']}`; // required\n                column['data'] = `${column['name']}`;\n                let source = column['source'];\n\n                column['filterKey'] = `${source}.${column.name}`\n\n                // console.log(`source=${source}`);\n                let tempSource = source.split('.')\n                // console.log(tempSource);\n                source = tempSource[tempSource.length - 1];\n                // console.log(`source=${source}`);\n                column['data'] = `${source}_${column['name']}`;\n                /** remove `core` from name */\n                // column['name'] = column['display_name'] ? column['display_name'] : column['name']\n                // column['filters'] = column['type'] === 'int' ? {\n                //   minValue: NaN,\n                //   maxValue: NaN,\n                //   applied: false\n                // } : {\n                //   possibleValues: [],\n                //   textValue: null,\n                //   selectedValues: [],\n                //   applied: false\n                // }\n                column['value_limits'] = column['value_limits'] ? this.setValueLimits(column) : undefined\n                return column\n              });\n              this.sequence_table_order = []\n              if (this.sequence_table_columns) {\n\n                this.sequence_table = table.table_data\n              }\n            }\n          })\n        }\n        if (resp['status'] === 'canceled') {\n          /** if status is canceled, then just stop loader **/\n          this.submitted = false;\n          this.loading = false;\n          const prevTool = this.tools[this.index];\n          console.log(prevTool)\n          const submittedTCellPredictionTool = Object.assign(prevTool, {\n            submitted: this.submitted,\n            loading: this.loading,\n          })\n          this._stateService.insertTool(submittedTCellPredictionTool, this.index);\n          clearInterval(this.runSetInterval);\n          // console.log(data);\n          this.enableInputs();\n          // set error message\n          // this.errorMessages = [`PIPELINE_ID=${this.pipelineId} w/ STATUS=${resp['status']}`]\n        }\n        else {\n          this.getResultsClicked = false;\n          // this.apiStatus = resp['status'];\n          console.log(`current status: ${resp['status']} - ${increment}`);\n          increment += 1;\n        }\n      }, error => {\n        console.error(error);\n        this.enableInputs();\n        clearInterval(this.runSetInterval);\n        this.submitted = true;\n        this.loading = false;\n      })\n    }, milliseconds);\n  }\n\n  onFileDropped($event: any[]) {\n    console.log($event);\n    const file = $event[0];\n    const fileSize = file.size / 1024; // in kB\n    console.log(file.type);\n    if (fileSize > 20000) {\n      this.alertService.add('File Size is too big! (20mB max)', 'alert-danger');\n      this.open(this.alertModal);\n    }\n    else {\n      this.prepareSequenceFileList($event);\n    }\n  }\n\n  prepareSequenceFileList(files: Array<any>) {\n    console.log(files);\n    this.fileName = files[0].name;\n    const reader = new FileReader();\n    const myForm = this.pepmatchForm;\n    for (const item of files) {\n      // console.log(item);\n      reader.readAsText(item);\n      reader.onload = () => {\n        const val = reader.result?.toString() || '';\n        console.log(val);\n        const v = isASCII(val);\n        console.log(v);\n        if (v) {\n          // myForm.patchValue({inputSequenceText: val.substring(0, this.maxCharacters)});\n          const w = isMaxLength(val, this.maxCharacters)\n          if (w) {\n            myForm.patchValue({inputSequenceText: val});\n          } else {\n            this.alertService.add(`Sequence is too long - max Sequence length is ${this.maxCharacters.toLocaleString(\"en-US\")} characters`, 'alert-danger');\n            this.open(this.alertModal);\n          }\n          // this.sequenceParser(val);  // auto parser\n        } else {\n          this.alertService.add('Invalid file type.\\nValid file types are .txt, .fa, .fasta, .json, .faa,', 'alert-danger');\n          this.open(this.alertModal);\n        }\n      };\n\n      reader.onerror = () => {\n        console.log(reader.error);\n      };\n      item.progress = 0;\n      this.files.push(item);\n    }\n  }\n\n  // Allele Modal Functions\n\n  open(content: any) {\n    this.modalService.open(content, {\n      ariaLabelledBy: 'modal-basic-title',\n      size: 'lg',\n      animation: true,\n    }).result.then((result) => {\n      // this.closeResult = `Closed with: ${result}`;\n      this.saveState = false;\n    }, (reason) => {\n      this.saveState = false;\n      // this.alleleSearch.nativeElement.focus();\n      // this.closeResult = `Dismissed ${TCellPredictionComponent.getDismissReason(reason)}`;\n    });\n  }\n\n\n  onCancel() {\n    console.log(this.runSetInterval)\n    clearInterval(this.runSetInterval);\n    this.emitOnCancel.emit()\n\n    // this.inputChange.table_state = false;\n    // // this.submitted = false;\n    const currentTool = this.tools[this.index]\n    const unSubmittedTool = {\n      ...currentTool,\n      loading: false,\n      submitted: false,\n      appliedFilters: undefined\n    }\n    this._stateService.insertTool(unSubmittedTool, this.index);\n    this.warningMessages = [];\n    this.loading = false;\n    this.tableStateSaving = false;\n    this.enableInputs();\n  }\n\n  onReset() {\n    this.alertService.clear();\n    this.errorMessages = [];\n    this.warningMessages = [];\n  }\n\n  enableInputs() {\n    // this.pepmatchForm.enable({emitEvent: false});\n    this.pepmatchForm.controls['bestMatch'].enable({emitEvent: false})\n    this.pepmatchForm.controls['proteome'].enable({emitEvent: false})\n    this.options = Object.assign({}, this.options, {disabled: false});\n  }\n\n  disableInputs() {\n    // this.pepmatchForm.disable({emitEvent: false});\n    this.pepmatchForm.controls['bestMatch'].disable({emitEvent: false})\n    this.pepmatchForm.controls['proteome'].disable({emitEvent: false})\n    this.options = Object.assign({}, this.options, {disabled: true});\n  }\n\n  onFilterApplied() {\n    this.inputChange.table_state = this.submitted;\n  }\n\n  onClearTableState() {\n    this.columns = _.map(this.columns, (c) => {\n      c.filters = c.type === 'int'? {\n          minValue: NaN,\n          maxValue: NaN,\n          applied: false\n        } :\n        {\n          possibleValues: [],\n          textValue: null,\n          selectedValues: [],\n          applied: false\n        }\n      return c\n    })\n    this.inputChange.table_state = this.submitted;\n  }\n\n  onSaveTableStateMain() {\n    const hasResult = _.find(this.tools.slice(this.index+1), {submitted: true})\n    if (hasResult) {\n      this.saveState = true;\n      this.open(this.confirmModal);\n    } else {\n      this.onSaveTableState();\n    }\n  }\n\n  onSaveTableState() {\n    const tool_group = 'pepmatch'\n\n    const params = this.params\n    // create colObj and params\n    let colObj = columnListToObject(this.columns, tool_group)\n    const stages = params.stages;\n    const stageTemp = stages[this.index];\n\n    // stageTemp.table_state.columns = colObj;\n    stageTemp.table_state = [{table: 'peptide_table', columns: colObj}];\n\n    stages[this.index] = stageTemp\n    params.stages = stages;\n    // run_stage_range\n    const stage_number = this.index + 1;\n    params.run_stage_range = [stage_number, stage_number];\n    this._stateService.setParams(params);\n    // appliedFilters\n    let appliedFilters = !_.isEmpty(colObj);\n    this._stateService.setToolAppliedFilters(appliedFilters, this.index)\n    this.postPipelineAPI(params, false);\n    this.saveState = false;\n  }\n\n  onNumOfMismatchesChange(changeContext: ChangeContext) : void {\n    this.inputChange.mismatch = this.submitted;\n  }\n\n  sequenceParser(val: string) {\n\n    const firstChar = ltrim(val)[0];\n    const firstLine = val.split('\\n')[0]\n    console.log(firstLine)\n\n    /** Named white space */\n    let firstLineNumOfElements = 0\n    let separator = ' '\n    if(firstLine.includes(' ')){\n      separator = ' '\n    } else if (firstLine.includes('\\t')){\n      separator = '\\t'\n    } else if (firstLine.includes('\\s')){\n      separator = '\\s'\n    }\n    firstLineNumOfElements = firstLine.split(separator).length\n    console.log(firstLineNumOfElements)\n    console.log(separator)\n\n    const slicedVal = val.slice(0, this.maxCharacters)\n\n    if(val.length > this.maxCharacters) {\n      //  Skip parsing\n    } else if (firstChar === '>' && this.sequenceParserService.fastaValidate(val)) { // fasta\n      this.seqFormat = this.sequenceParserService.seqFormat;\n      this.numOfCharacters = slicedVal.length\n    } else if ((firstChar === '{' || firstChar === '[') && IsJsonString(val)) { // json\n      this.seqFormat = 'JSON'\n      this.numOfCharacters = slicedVal.length\n    } else if (firstLineNumOfElements === 2 && this.sequenceParserService.namedWhiteSpaceValidate(val, separator)) {\n      // named white space\n      this.seqFormat = this.sequenceParserService.seqFormat;\n      this.numOfCharacters = slicedVal.length\n    } else if (val.length > 3 && !val.includes('>') && this.sequenceParserService.unnamedWhiteSpaceValidate(val)) {\n      // Unnamed\n      this.seqFormat = this.sequenceParserService.seqFormat;\n      this.numOfCharacters = slicedVal.length\n    } else if (val === '') {  // delete\n      /**\n       * Takes care of it up top - still need this if statement\n       * */\n      this.seqFormat = 'Unknown';\n      this.numOfCharacters = 0\n    } else { // error\n      this.seqFormat = 'Error';\n      this.numOfCharacters = 0\n    }\n  }\n\n}\n","<form [formGroup]=\"pepxForm\" (ngSubmit)=\"onRunMain()\" class=\"container\">\n  <div class=\"d-flex flex-row p-2\">\n    <h2 class=\"pe-2 display-5\">{{index + 1}}</h2>\n    <hr class=\"mt-4 flex-grow-1 divider\"/>\n  </div>\n  <div class=\"d-flex pb-3\">\n    <h4 class=\"p-2 tool-name\" id=\"pepx-label\">\n      PepX - Peptide Expression Annotation\n      <img class='pb-1' src=\"/assets/symbols/cedar/symbol.svg\" alt=\"cedar\" height=\"24\" width=\"24\">\n    </h4>\n    <div class=\"d-flex flex-row tool-links\" role=\"group\" aria-label=\"tool-links\">\n      <button type=\"button\" class=\"btn btn-link text-dark d-flex flex-column justify-content-center align-items-center\">\n        <a target=\"_blank\" routerLink=\"/docs/tools/pepx/index.html\"\n           class=\"text-dark d-flex flex-column justify-content-center align-items-center\">\n          <svg width=\"1em\" height=\"1em\" viewBox=\"0 0 16 16\" class=\"bi bi-file-earmark-text\" fill=\"currentColor\"\n               xmlns=\"http://www.w3.org/2000/svg\">\n            <path\n              d=\"M4 1h5v1H4a1 1 0 0 0-1 1v10a1 1 0 0 0 1 1h8a1 1 0 0 0 1-1V6h1v7a2 2 0 0 1-2 2H4a2 2 0 0 1-2-2V3a2 2 0 0 1 2-2z\"/>\n            <path d=\"M9 4.5V1l5 5h-3.5A1.5 1.5 0 0 1 9 4.5z\"/>\n            <path fill-rule=\"evenodd\"\n                  d=\"M5 11.5a.5.5 0 0 1 .5-.5h2a.5.5 0 0 1 0 1h-2a.5.5 0 0 1-.5-.5zm0-2a.5.5 0 0 1 .5-.5h5a.5.5 0 0 1 0 1h-5a.5.5 0 0 1-.5-.5zm0-2a.5.5 0 0 1 .5-.5h5a.5.5 0 0 1 0 1h-5a.5.5 0 0 1-.5-.5z\"/>\n          </svg>\n          Docs\n        </a>\n      </button>\n      <button type=\"button\" class=\"btn btn-link\">\n        <a target=\"_blank\" [href]=\"swaggerUrl\"\n           class=\"text-dark d-flex flex-column justify-content-center align-items-center\">\n          <svg width=\"1em\" height=\"1em\" viewBox=\"0 0 16 16\" class=\"bi bi-gear\" fill=\"currentColor\"\n               xmlns=\"http://www.w3.org/2000/svg\">\n            <path fill-rule=\"evenodd\"\n                  d=\"M8.837 1.626c-.246-.835-1.428-.835-1.674 0l-.094.319A1.873 1.873 0 0 1 4.377 3.06l-.292-.16c-.764-.415-1.6.42-1.184 1.185l.159.292a1.873 1.873 0 0 1-1.115 2.692l-.319.094c-.835.246-.835 1.428 0 1.674l.319.094a1.873 1.873 0 0 1 1.115 2.693l-.16.291c-.415.764.42 1.6 1.185 1.184l.292-.159a1.873 1.873 0 0 1 2.692 1.116l.094.318c.246.835 1.428.835 1.674 0l.094-.319a1.873 1.873 0 0 1 2.693-1.115l.291.16c.764.415 1.6-.42 1.184-1.185l-.159-.291a1.873 1.873 0 0 1 1.116-2.693l.318-.094c.835-.246.835-1.428 0-1.674l-.319-.094a1.873 1.873 0 0 1-1.115-2.692l.16-.292c.415-.764-.42-1.6-1.185-1.184l-.291.159A1.873 1.873 0 0 1 8.93 1.945l-.094-.319zm-2.633-.283c.527-1.79 3.065-1.79 3.592 0l.094.319a.873.873 0 0 0 1.255.52l.292-.16c1.64-.892 3.434.901 2.54 2.541l-.159.292a.873.873 0 0 0 .52 1.255l.319.094c1.79.527 1.79 3.065 0 3.592l-.319.094a.873.873 0 0 0-.52 1.255l.16.292c.893 1.64-.902 3.434-2.541 2.54l-.292-.159a.873.873 0 0 0-1.255.52l-.094.319c-.527 1.79-3.065 1.79-3.592 0l-.094-.319a.873.873 0 0 0-1.255-.52l-.292.16c-1.64.893-3.433-.902-2.54-2.541l.159-.292a.873.873 0 0 0-.52-1.255l-.319-.094c-1.79-.527-1.79-3.065 0-3.592l.319-.094a.873.873 0 0 0 .52-1.255l-.16-.292c-.892-1.64.902-3.433 2.541-2.54l.292.159a.873.873 0 0 0 1.255-.52l.094-.319z\"/>\n            <path fill-rule=\"evenodd\"\n                  d=\"M8 5.754a2.246 2.246 0 1 0 0 4.492 2.246 2.246 0 0 0 0-4.492zM4.754 8a3.246 3.246 0 1 1 6.492 0 3.246 3.246 0 0 1-6.492 0z\"/>\n          </svg>\n          API\n        </a>\n      </button>\n      <button type=\"button\" class=\"btn btn-link text-dark d-flex flex-column justify-content-center align-items-center\"\n              routerLink=\"/download-all\"\n              [state]=\"{tool: 'pepx'}\">\n        <svg width=\"1em\" height=\"1em\" viewBox=\"0 0 16 16\" class=\"bi bi-cloud-arrow-down\" fill=\"currentColor\"\n             xmlns=\"http://www.w3.org/2000/svg\">\n          <path fill-rule=\"evenodd\"\n                d=\"M4.406 3.342A5.53 5.53 0 0 1 8 2c2.69 0 4.923 2 5.166 4.579C14.758 6.804 16 8.137 16 9.773 16 11.569 14.502 13 12.687 13H3.781C1.708 13 0 11.366 0 9.318c0-1.763 1.266-3.223 2.942-3.593.143-.863.698-1.723 1.464-2.383zm.653.757c-.757.653-1.153 1.44-1.153 2.056v.448l-.445.049C2.064 6.805 1 7.952 1 9.318 1 10.785 2.23 12 3.781 12h8.906C13.98 12 15 10.988 15 9.773c0-1.216-1.02-2.228-2.313-2.228h-.5v-.5C12.188 4.825 10.328 3 8 3a4.53 4.53 0 0 0-2.941 1.1z\"/>\n          <path fill-rule=\"evenodd\"\n                d=\"M7.646 10.854a.5.5 0 0 0 .708 0l2-2a.5.5 0 0 0-.708-.708L8.5 9.293V5.5a.5.5 0 0 0-1 0v3.793L6.354 8.146a.5.5 0 1 0-.708.708l2 2z\"/>\n        </svg>\n        Download\n      </button>\n      <button type=\"button\" class=\"btn btn-link text-dark d-flex flex-column justify-content-center align-items-center\"\n              routerLink=\"/citation\">\n        <svg width=\"1em\" height=\"1em\" viewBox=\"0 0 16 16\" class=\"bi bi-chat-square-quote\" fill=\"currentColor\"\n             xmlns=\"http://www.w3.org/2000/svg\">\n          <path fill-rule=\"evenodd\"\n                d=\"M14 1H2a1 1 0 0 0-1 1v8a1 1 0 0 0 1 1h2.5a2 2 0 0 1 1.6.8L8 14.333 9.9 11.8a2 2 0 0 1 1.6-.8H14a1 1 0 0 0 1-1V2a1 1 0 0 0-1-1zM2 0a2 2 0 0 0-2 2v8a2 2 0 0 0 2 2h2.5a1 1 0 0 1 .8.4l1.9 2.533a1 1 0 0 0 1.6 0l1.9-2.533a1 1 0 0 1 .8-.4H14a2 2 0 0 0 2-2V2a2 2 0 0 0-2-2H2z\"/>\n          <path fill-rule=\"evenodd\"\n                d=\"M7.066 4.76A1.665 1.665 0 0 0 4 5.668a1.667 1.667 0 0 0 2.561 1.406c-.131.389-.375.804-.777 1.22a.417.417 0 1 0 .6.58c1.486-1.54 1.293-3.214.682-4.112zm4 0A1.665 1.665 0 0 0 8 5.668a1.667 1.667 0 0 0 2.561 1.406c-.131.389-.375.804-.777 1.22a.417.417 0 1 0 .6.58c1.486-1.54 1.293-3.214.682-4.112z\"/>\n        </svg>\n        Cite\n      </button>\n    </div>\n  </div>\n  <!--  Sequence Input-->\n  <ng-container *ngIf=\"index===0\">\n    <div class=\"d-flex flex-row p-2\">\n      <h5 class=\"col-3 text-left\">Input Sequence(s)</h5>\n\n      <div class=\"col-9\">\n        <button type=\"button\" class=\"btn btn-sm btn-dark-blue-grey text-white\" (click)=\"null\"\n                [disabled]=\"!submitted\"\n                data-bs-toggle=\"dropdown\"\n                data-toggle=\"dropdown\" aria-haspopup=\"true\" aria-expanded=\"false\">\n          <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n               class=\"bi bi-download\" viewBox=\"0 0 16 16\">\n            <path\n              d=\"M.5 9.9a.5.5 0 0 1 .5.5v2.5a1 1 0 0 0 1 1h12a1 1 0 0 0 1-1v-2.5a.5.5 0 0 1 1 0v2.5a2 2 0 0 1-2 2H2a2 2 0 0 1-2-2v-2.5a.5.5 0 0 1 .5-.5z\"/>\n            <path\n              d=\"M7.646 11.854a.5.5 0 0 0 .708 0l3-3a.5.5 0 0 0-.708-.708L8.5 10.293V1.5a.5.5 0 0 0-1 0v8.793L5.354 8.146a.5.5 0 1 0-.708.708l3 3z\"/>\n          </svg>\n        </button>\n        <div class=\"dropdown-menu\" aria-labelledby=\"dropdownMenuButton\">\n          <div class=\"dropdown-item\">\n            <label>Download as: </label>\n            &nbsp;\n            <div class=\"btn-group\">\n              <button\n                [className]=\"submitted ? 'btn btn-sky-blue text-white' : 'btn btn-outline-secondary'\"\n                type=\"button\" (click)=\"onDownloadJson()\">\n                JSON\n              </button>\n              <button\n                [className]=\"submitted ? 'btn btn-sky-blue text-white' : 'btn btn-outline-secondary'\"\n                type=\"button\" (click)=\"onDownloadFasta()\">\n                FASTA\n              </button>\n              <button\n                [className]=\"submitted ? 'btn btn-sky-blue text-white' : 'btn btn-outline-secondary'\"\n                type=\"button\" (click)=\"onDownloadOriginal()\">\n                Original\n              </button>\n            </div>\n          </div>\n        </div>\n        &nbsp;\n\n        <input type=\"file\"\n               #uploader\n               style=\"display: none\"\n               id=\"file\"\n               (change)=\"uploadSequenceFile($event)\">\n\n        <ng-template #uploadSequencesTipContent>\n          <div>\n            Upload sequence file <br> (.txt, .json, .fasta)\n          </div>\n\n        </ng-template>\n        <button type=\"button\" class=\"btn btn-dark-blue-grey btn-sm text-white\" (click)=\"uploader.click()\" [disabled]=\"loading\"\n                ngbTooltip='Clear allele(s)'\n                [ngbTooltip]=\"uploadSequencesTipContent\" placement=\"right\">\n          <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\" class=\"bi bi-upload\"\n               viewBox=\"0 0 16 16\">\n            <path\n              d=\"M.5 9.9a.5.5 0 0 1 .5.5v2.5a1 1 0 0 0 1 1h12a1 1 0 0 0 1-1v-2.5a.5.5 0 0 1 1 0v2.5a2 2 0 0 1-2 2H2a2 2 0 0 1-2-2v-2.5a.5.5 0 0 1 .5-.5z\"/>\n            <path\n              d=\"M7.646 1.146a.5.5 0 0 1 .708 0l3 3a.5.5 0 0 1-.708.708L8.5 2.707V11.5a.5.5 0 0 1-1 0V2.707L5.354 4.854a.5.5 0 1 1-.708-.708l3-3z\"/>\n          </svg>\n        </button>\n        &nbsp;\n      </div>\n    </div>\n    <div class=\"d-flex flex-column p-2\" appDnd (fileDropped)=\"onFileDropped($event)\">\n      <!--      [style.border-color]=\"inputChange.input_sequence_text ? '#f0ad4d' : null\"    -->\n      <textarea class='form-control'\n                [style.border-color]=\"inputChange.input_sequence_text ? '#f0ad4d' : null\"\n                id=\"sequenceFormControlTextArea\"\n                rows=\"10\"\n                formControlName=\"inputSequenceText\"\n                [readOnly]=\"loading\"\n                [placeholder]=\"sequencePlaceHolder\"></textarea>\n\n      <div class=\"d-flex flex-row-reverse justify-content-between p-2\">\n        <small *ngIf=\"inputSequenceText.length >= maxCharacters; else sequenceCounter\" class=\"text-danger\">\n          Sequence text is too long -  {{maxCharacters | number}} characters allowed\n        </small>\n        <ng-template #sequenceCounter>\n          <small class=\"text-muted\">\n            Format: {{seqFormat}} | {{numOfCharacters | number}} characters\n          </small>\n        </ng-template>\n\n        <small *ngIf=\"inputChange.input_sequence_text\" class=\"help-block form-text text-warning\">\n          Parameter changed since prediction.\n        </small>\n      </div>\n    </div>\n  </ng-container>\n  <!--  Prediction parameter -->\n  <div class=\"row p-2\">\n    <h5 class=\"col-3 text-left p-2\">Prediction Parameters</h5>\n    <div class=\"col-9\">\n      <button type=\"button\" class=\"btn btn-sm btn-dark-blue-grey text-white\" (click)=\"onDownloadParameter()\"\n              aria-haspopup=\"true\" aria-expanded=\"false\">\n        <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-download\" viewBox=\"0 0 16 16\">\n          <path\n            d=\"M.5 9.9a.5.5 0 0 1 .5.5v2.5a1 1 0 0 0 1 1h12a1 1 0 0 0 1-1v-2.5a.5.5 0 0 1 1 0v2.5a2 2 0 0 1-2 2H2a2 2 0 0 1-2-2v-2.5a.5.5 0 0 1 .5-.5z\"/>\n          <path\n            d=\"M7.646 11.854a.5.5 0 0 0 .708 0l3-3a.5.5 0 0 0-.708-.708L8.5 10.293V1.5a.5.5 0 0 0-1 0v8.793L5.354 8.146a.5.5 0 1 0-.708.708l3 3z\"/>\n        </svg>\n      </button>\n    </div>\n  </div>\n  <!--  Number of Mismatches -->\n  <div class=\"form-group row p-2\">\n    <div class=\"col-sm-3 col-form-label\">\n      <label class=\"'font-weight-bold'\">Quantitation Level</label>\n    </div>\n    <div class=\"col-sm-9\">\n      <div class=\"radio-button-group\">\n        <div class=\"form-check form-check-inline\">\n          <input class=\"form-check-input\" type=\"radio\" name=\"qlevel\" id=\"geneRadioButton\"\n                 formControlName=\"qlevel\" value=\"gene\" (change)=\"onQuantitationLevelChange('gene')\">\n          <label class=\"form-check-label\" for=\"geneRadioButton\">\n            Gene\n          </label>\n        </div>\n        <div class=\"form-check form-check-inline\">\n          <input class=\"form-check-input\" type=\"radio\" name=\"qlevel\" id=\"transcriptRadioButton\"\n                 formControlName=\"qlevel\" value=\"transcript\" (change)=\"onQuantitationLevelChange('transcript')\">\n          <label class=\"form-check-label\" for=\"transcriptRadioButton\">\n            Transcript\n          </label>\n        </div>\n      </div>\n      <small *ngIf=\"inputChange.quantitation_level\" class=\"help-block form-text text-warning\">\n        Parameter changed since prediction.\n      </small>\n    </div>\n  </div>\n  <!--  Data Source -->\n  <div class=\"form-group row p-2\" id=\"dataSourceRow\">\n    <div class=\"col-sm-3 col-form-label\">\n      <label class=\"text-left\">Data Source</label>\n    </div>\n    <div class=\"col-sm-9\">\n      <div *ngIf=\"datasourceLoading; else datasourceSelect\" class=\"d-flex justify-content-center col\">\n        <div class=\"spinner-border text-primary align-self-center\" role=\"status\">\n          <span class=\"visually-hidden sr-only\">Loading...</span>\n        </div>\n      </div>\n      <ng-template #datasourceSelect>\n        <select class=\"form-select form-control w-100\" formControlName=\"datasource\"\n                [style.border-color]=\"inputChange.data_source ? '#f0ad4d' : null\"\n                (change)=\"onDataSourceChange($event)\">\n          <option *ngFor=\"let v of datasources\" [value]=\"v\">{{ v }}</option>\n        </select>\n        <small *ngIf=\"inputChange.data_source\" class=\"help-block form-text text-warning\">\n          Parameter changed since prediction.\n        </small>\n      </ng-template>\n    </div>\n  </div>\n  <!--  Dataset -->\n  <div class=\"form-group row p-2\" id=\"datasetRow\">\n    <div class=\"col-sm-3 col-form-label\">\n      <label class=\"text-left\">Dataset</label>\n    </div>\n    <div class=\"col-sm-9\">\n      <div *ngIf=\"datasetLoading; else datasetSelect\" class=\"d-flex justify-content-center col\">\n        <div class=\"spinner-border text-primary align-self-center\" role=\"status\">\n          <span class=\"visually-hidden sr-only\">Loading...</span>\n        </div>\n      </div>\n      <ng-template #datasetSelect>\n      <select class=\"form-select form-control w-100\" formControlName=\"dataset_id\"\n              [style.border-color]=\"inputChange.data_source ? '#f0ad4d' : null\">\n        <option *ngFor=\"let v of dataSets\" [value]=\"v.dataset_id\">{{v.title}}</option>\n      </select>\n      <small *ngIf=\"inputChange.data_source\" class=\"help-block form-text text-warning\">\n        Parameter changed since prediction.\n      </small>\n      </ng-template>\n    </div>\n  </div>\n\n  <hr/>\n  <div class=\"form-group d-flex flex-row-reverse pt-2\">\n\n    <div class=\"p-2\">\n      <button type=\"button\" class=\"reset-button btn btn-secondary btn-lg\" [disabled]=\"loading\"\n              (click)=\"null\">\n        <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-arrow-clockwise\" viewBox=\"0 0 16 16\">\n          <path fill-rule=\"evenodd\" d=\"M8 3a5 5 0 1 0 4.546 2.914.5.5 0 0 1 .908-.417A6 6 0 1 1 8 2v1z\"/>\n          <path\n            d=\"M8 4.466V.534a.25.25 0 0 1 .41-.192l2.36 1.966c.12.1.12.284 0 .384L8.41 4.658A.25.25 0 0 1 8 4.466z\"/>\n        </svg>\n      </button>\n      &nbsp;\n      <span *ngIf=\"loading; else elseBlock\">\n            <button type=\"button\" class=\"btn btn-danger btn-lg\" (click)=\"null\"> Cancel Run </button>\n          </span>\n      <ng-template #elseBlock>\n        <div *ngIf=\"index!==0; else runButtonBlock\" class=\"btn-group\">\n          <div class=\"btn-group\">\n            <button type=\"submit\" class=\"run-button btn btn-dark-blue-grey btn-lg text-white\"\n                    [disabled]=\"(index>0 && !tools[index-1].submitted) || pipelineLoading\"\n            >\n              <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\" class=\"bi bi-play-fill\"\n                   viewBox=\"0 0 16 16\">\n                <path\n                  d=\"m11.596 8.697-6.363 3.692c-.54.313-1.233-.066-1.233-.697V4.308c0-.63.692-1.01 1.233-.696l6.363 3.692a.802.802 0 0 1 0 1.393z\"/>\n              </svg>\n            </button>\n            <button type=\"button\" class=\"btn btn-dark-blue-grey text-white dropdown-toggle dropdown-toggle-split\"\n                    data-toggle=\"dropdown\"\n                    data-bs-toggle=\"dropdown\"\n                    aria-haspopup=\"true\" aria-expanded=\"false\"\n                    [disabled]=\"pipelineLoading\">\n            </button>\n            <div class=\"dropdown-menu\">\n              <a class=\"dropdown-item\" (click)=\"null\">Run All Above</a>\n            </div>\n          </div>\n        </div>\n        <ng-template #runButtonBlock>\n          <button type=\"submit\" class=\"run-button btn btn-dark-blue-grey btn-lg text-white\"\n                  [disabled]=\"(index>0 && !tools[index-1].submitted) || pipelineLoading\"\n          >\n            <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\" class=\"bi bi-play-fill\"\n                 viewBox=\"0 0 16 16\">\n              <path\n                d=\"m11.596 8.697-6.363 3.692c-.54.313-1.233-.066-1.233-.697V4.308c0-.63.692-1.01 1.233-.696l6.363 3.692a.802.802 0 0 1 0 1.393z\"/>\n            </svg>\n          </button>\n        </ng-template>\n\n      </ng-template>\n    </div>\n  </div>\n\n</form>\n\n<!--Errors and Warnings accordion -->\n<div ngbAccordion>\n  <!--  Error -->\n  <div ngbAccordionItem=\"first\" *ngIf=\"errorMessages.length\" #first=\"ngbAccordionItem\" [collapsed]=\"true\">\n    <h2 ngbAccordionHeader>\n      <button ngbAccordionButton class=\"accordion-button justify-content-center\">\n        <span class=\"text-danger m-1\">Errors ({{errorMessages.length}})</span>\n        <!--        <div>-->\n        <svg *ngIf=\"first.collapsed\" xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-arrow-left-circle-fill\" style=\"color: #dc3545;\" viewBox=\"0 0 16 16\">\n          <path\n            d=\"M8 0a8 8 0 1 0 0 16A8 8 0 0 0 8 0zm3.5 7.5a.5.5 0 0 1 0 1H5.707l2.147 2.146a.5.5 0 0 1-.708.708l-3-3a.5.5 0 0 1 0-.708l3-3a.5.5 0 1 1 .708.708L5.707 7.5H11.5z\"/>\n        </svg>\n        <!--        </div>-->\n        <!--        <div>-->\n        <svg *ngIf=\"!first.collapsed\" xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-arrow-down-circle-fill\" style=\"color: #dc3545;\" viewBox=\"0 0 16 16\">\n          <path\n            d=\"M16 8A8 8 0 1 1 0 8a8 8 0 0 1 16 0zM8.5 4.5a.5.5 0 0 0-1 0v5.793L5.354 8.146a.5.5 0 1 0-.708.708l3 3a.5.5 0 0 0 .708 0l3-3a.5.5 0 0 0-.708-.708L8.5 10.293V4.5z\"/>\n        </svg>\n        <!--        </div>-->\n      </button>\n    </h2>\n    <div ngbAccordionCollapse>\n      <div ngbAccordionBody>\n        <ng-template>\n          <ol>\n            <li *ngFor=\"let message of errorMessages; let i=index;\">{{message}}</li>\n          </ol>\n        </ng-template>\n      </div>\n    </div>\n  </div>\n  <!--  Warning -->\n  <div ngbAccordionItem=\"second\" *ngIf=\"warningMessages.length\" #second=\"ngbAccordionItem\" [collapsed]=\"true\">\n    <h2 ngbAccordionHeader>\n      <button ngbAccordionButton class=\"accordion-button justify-content-center\">\n        <span class=\"text-warning m-1\">Warnings ({{warningMessages.length}})</span>\n        <svg *ngIf=\"second.collapsed\"  xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-arrow-left-circle-fill\" style=\"color: #f0ad4d;\" viewBox=\"0 0 16 16\">\n          <path\n            d=\"M8 0a8 8 0 1 0 0 16A8 8 0 0 0 8 0zm3.5 7.5a.5.5 0 0 1 0 1H5.707l2.147 2.146a.5.5 0 0 1-.708.708l-3-3a.5.5 0 0 1 0-.708l3-3a.5.5 0 1 1 .708.708L5.707 7.5H11.5z\"/>\n        </svg>\n        <svg *ngIf=\"!second.collapsed\" xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-arrow-down-circle-fill\" style=\"color: #f0ad4d;\" viewBox=\"0 0 16 16\">\n          <path\n            d=\"M16 8A8 8 0 1 1 0 8a8 8 0 0 1 16 0zM8.5 4.5a.5.5 0 0 0-1 0v5.793L5.354 8.146a.5.5 0 1 0-.708.708l3 3a.5.5 0 0 0 .708 0l3-3a.5.5 0 0 0-.708-.708L8.5 10.293V4.5z\"/>\n        </svg>\n      </button>\n    </h2>\n    <div ngbAccordionCollapse>\n      <div ngbAccordionBody>\n        <ng-template>\n          <ol>\n            <li *ngFor=\"let message of warningMessages; let i=index;\">{{message}}</li>\n          </ol>\n        </ng-template>\n      </div>\n    </div>\n  </div>\n</div>\n\n<div *ngIf=\"!loading && !submitted && !(errorMessages.length && warningMessages.length)\"\n     class=\"p-2 d-flex justify-content-center col\"\n     [style.borderStyle]=\"styleResultContainer\">\n  <label class=\"p-2 font-italic\">\n    Results will load once step is run\n  </label>\n</div>\n\n<div *ngIf=\"loading\" class=\"p-2 d-flex justify-content-center col\" [style.borderStyle]=\"styleResultContainer\">\n  <div class=\"spinner-border text-primary align-self-center p-3 mb-3\" role=\"status\">\n    <span class=\"visually-hidden sr-only\">Loading...</span>\n  </div>\n  <label class=\"p-2 font-italic\">\n    <!--     TODO change when POST request returns a pipeline ID immediately-->\n    Calculating results, please wait...\n  </label>\n</div>\n\n<div class=\"container-fluid p-2\" id=\"table-result-container\"\n     *ngIf=\"!loading && submitted && peptide_table && !(errorMessages.length && warningMessages.length)\">\n  <ul ngbNav #nav=\"ngbNav\" [(activeId)]=\"active\" [animation]='false' [destroyOnHide]=\"false\" class=\"nav-tabs\">\n    <!--    peptide_table-->\n    <li [ngbNavItem]=\"'peptide_table'\">\n      <a ngbNavLink>Peptide Table</a>\n      <ng-template ngbNavContent>\n        <app-result-table *ngIf=\"peptide_table[0]?.length\" [table_data]=\"peptide_table\"\n                          table_name=\"peptide_table\"\n                          [order]=\"peptide_table_currentOrder\"\n                          [columns]=\"peptide_table_columns\"\n                          [tool_group]=\"formGroupName\"\n                          [index]=\"index\"\n                          [inputChange]=\"inputChange.table_state_1\"\n                          [tableStateSaving]=\"tableStateSaving\"\n                          (emitFilterApplied)=\"onFilterApplied()\"\n                          (emitResetTableState)=\"onClearTableState()\"\n                          (emitSaveTableState)=\"onSaveTableStateMain('peptide_table')\"></app-result-table>\n        <div *ngIf=\"!peptide_table[0]?.length\" class=\"pt-2\">\n          <ngb-alert [dismissible]=\"false\">\n            No matches found with the given input peptides and selected parameters.\n          </ngb-alert>\n        </div>\n\n      </ng-template>\n    </li>\n    <!--    peptide_gene_summary_table-->\n    <li [ngbNavItem]=\"'peptide_gene_summary_table'\">\n      <a ngbNavLink>Peptide Gene Summary Table</a>\n      <ng-template ngbNavContent>\n        <app-result-table *ngIf=\"peptide_gene_summary_table[0]?.length\" [table_data]=\"peptide_gene_summary_table\"\n                          table_name=\"peptide_gene_summary_table\"\n                          [order]=\"peptide_gene_currentOrder\"\n                          [columns]=\"peptide_gene_columns\"\n                          [tool_group]=\"formGroupName\"\n                          [index]=\"index\"\n                          [inputChange]=\"inputChange.table_state_2\"\n                          (emitFilterApplied)=\"onFilterApplied2()\"\n                          (emitResetTableState)=\"onClearTable2State()\"\n                          (emitSaveTableState)=\"onSaveTableStateMain('peptide_gene_summary_table')\"\n        ></app-result-table>\n        <div *ngIf=\"!peptide_gene_summary_table[0]?.length\" class=\"pt-2\">\n          <ngb-alert [dismissible]=\"false\">\n            No matches found with the given input peptides and selected parameters.\n          </ngb-alert>\n        </div>\n\n      </ng-template>\n    </li>\n    <!--    sequence_table-->\n    <li *ngIf=\"sequence_table[0]?.length\" [ngbNavItem]=\"'input_sequence_table'\">\n      <a ngbNavLink> Sequence Table </a>\n      <ng-template ngbNavContent>\n        <app-result-table [table_data]=\"sequence_table\"\n                          table_name=\"input_sequence_table\"\n                          [order]=\"sequence_table_order\"\n                          [columns]=\"sequence_table_columns\"\n                          [tool_group]=\"formGroupName\"></app-result-table>\n      </ng-template>\n    </li>\n  </ul>\n  <div [ngbNavOutlet]=\"nav\"></div>\n</div>\n\n<!--Confirm Modal -->\n<ng-template #confirmModal let-confirmModal>\n  <div class=\"modal-header\">\n    <h4 class=\"modal-title\" id=\"modal-title\">Are you sure?</h4>\n    <button type=\"button\" class=\"btn-close\" aria-label=\"Close\" (click)=\"confirmModal.dismiss('Cross click')\"></button>\n  </div>\n  <div class=\"modal-body\">\n    <div *ngIf=\"!saveState; else saveStateConfirmation\">\n      <p><strong>Re-running this step of the pipeline will delete all downstream results, including:</strong></p>\n      <ol>\n        <li *ngFor=\"let stage of stages.slice(this.index+1)\"> {{stage.stage_display_name}} </li>\n      </ol>\n      <p><strong>To access the current results, you can use this link</strong></p>\n    </div>\n    <ng-template #saveStateConfirmation>\n      <p><strong>Applying these filters for input to the next stage will delete results from all downstream steps in\n        this session, including:</strong></p>\n      <ol>\n        <li *ngFor=\"let stage of stages.slice(this.index+1)\"> {{stage.stage_display_name}} </li>\n      </ol>\n      <p><strong>To access the current results, you can use this link</strong></p>\n    </ng-template>\n    <!-- pipeline URL input group-->\n    <div class=\"input-group\">\n      <input type=\"text\" class=\"form-control\" id=\"pipeline-url-input\" [value]=\"pipelineUrl\">\n      <button class=\"btn btn-secondary\" [cdkCopyToClipboard]=\"pipelineUrl\" ngbTooltip=\"copy url\" placement=\"top\">\n        <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-clipboard\" viewBox=\"0 0 16 16\">\n          <path\n            d=\"M4 1.5H3a2 2 0 0 0-2 2V14a2 2 0 0 0 2 2h10a2 2 0 0 0 2-2V3.5a2 2 0 0 0-2-2h-1v1h1a1 1 0 0 1 1 1V14a1 1 0 0 1-1 1H3a1 1 0 0 1-1-1V3.5a1 1 0 0 1 1-1h1v-1z\"/>\n          <path\n            d=\"M9.5 1a.5.5 0 0 1 .5.5v1a.5.5 0 0 1-.5.5h-3a.5.5 0 0 1-.5-.5v-1a.5.5 0 0 1 .5-.5h3zm-3-1A1.5 1.5 0 0 0 5 1.5v1A1.5 1.5 0 0 0 6.5 4h3A1.5 1.5 0 0 0 11 2.5v-1A1.5 1.5 0 0 0 9.5 0h-3z\"/>\n        </svg>\n      </button>\n    </div>\n  </div>\n  <div class=\"modal-footer\">\n    <button type=\"button\" class=\"btn btn-outline-secondary\" (click)=\"confirmModal.dismiss('cancel click')\">No\n    </button>\n    <button type=\"button\" class=\"btn btn-danger\" (click)=\"confirmModal.close('Ok click'); onRunConfirm();\">Yes, continue\n      and destroy downstream steps\n    </button>\n  </div>\n</ng-template>\n\n<!--Alert Modal -->\n<ng-template #alertModal let-modal4>\n  <div class=\"modal-header\">\n    <h4 class=\"modal-title\" id=\"alert-modal-title\">Validation Error(s)</h4>\n    <button type=\"button\" class=\"btn-close\" aria-label=\"Close\" (click)=\"modal4.dismiss('Cross click');\">\n    </button>\n  </div>\n  <div class=\"modal-body\">\n    <app-alert-component></app-alert-component>\n  </div>\n  <div class=\"modal-footer\">\n  </div>\n</ng-template>\n","import {\n  AfterViewInit,\n  Component,\n  ElementRef,\n  EventEmitter,\n  Input, OnChanges,\n  OnDestroy,\n  OnInit,\n  Output,\n  SimpleChanges,\n  ViewChild\n} from '@angular/core';\nimport {FormGroupDirective, UntypedFormGroup} from \"@angular/forms\";\nimport {Title} from \"@angular/platform-browser\";\n\nimport {Observable, of, Subject, Subscription, timer} from \"rxjs\";\nimport _ from \"lodash\";\nimport {AlertServiceService} from \"../services/alert-service/alert-service.service\";\nimport Stage from \"../_global/Stage\";\nimport Tool from \"../_global/Tool\";\nimport PipelineParams from \"../_global/PipelineParams\";\nimport {environment} from \"../../environments/environment\";\nimport {PipelineStateService} from \"../services/state-services/pipeline-state-service/pipeline-state.service\";\nimport {HttpClient} from \"@angular/common/http\";\nimport {Location} from \"@angular/common\";\nimport Columns from \"../_global/Columns\";\nimport {NgbModal} from \"@ng-bootstrap/ng-bootstrap\";\nimport {PipelineService} from \"../services/pipeline-service/pipeline.service\";\nimport {isASCII, IsJsonString, ltrim} from \"../util/string-helpers\";\nimport {isMaxLength} from \"../util/is-max-length\";\nimport onCsvDownloadAllClickedNew from \"../util/on-csv-download\";\nimport {debounce, takeUntil} from \"rxjs/operators\";\nimport {SequenceParserService} from \"../services/sequence-parser/sequence-parser.service\";\n// import {initPepmatchTool} from \"../services/state-services/default-stage-states\";\nimport {initPepxTool} from \"../services/state-services/default-stage-states\";\nimport * as pepxData from \"../services/data/pepx-sample.json\";\nimport {columnListToObject} from \"../util/convert-columns\";\nconst API_URL = `${environment['api_url']}/api/v1/pepx`;\n\n@Component({\n  selector: 'app-pepx',\n  templateUrl: './pepx.component.html',\n  styleUrls: ['./pepx.component.scss']\n})\nexport class PepxComponent implements OnInit, OnDestroy, AfterViewInit, OnChanges {\n  sequencePlaceHolder = `Ex:\nFVQMMTAK\nMRYVASYL\nEDIISFIK\nYEVSQLKD\nYISEHEHF\nAEMYVAKF\nSEFEARVI\nIESIVHAF\nKYGPVFSF\nWERLAVLV\nHETTFNSI\nYVHMVTHF\nKYPENFFL\nPNLAFLRF\nTEFIFTTI\nHESLSHEL\nYERSIVDY\nIEKLFQSV\nTDGKVFQF\nTEFKFPQI\nHQKQISSL\nNQKRLTVY\nHQVVVAKY\nLQNSVKQY\nHSVLIHEY\nVSAVVHEY\nMQKEITAL\nSQAIIHQY\nTQQLMRVY\n`\n\n  datasourceLoading = false;\n  datasetLoading = false;\n\n  datasources: string[] = []\n  dataSets: {dataset_id: number, nSamples: null | string, source: string, title: string}[] = []\n\n  /** Pipeline form */\n  @Input() formGroupName!: string\n  @Input() index!: number;\n  @Input() resultUrl!: string | undefined;\n  @Input() showEmailModal: boolean = false;\n\n  @Input() emailForm!: UntypedFormGroup;\n  @Output() openEmailModal = new EventEmitter<any>();\n\n\n  @Output() emitIndex = new EventEmitter<number>(); // used for run all\n  @Output() emitOnCancel = new EventEmitter<any>();\n\n  @ViewChild('alertModal') alertModal!: ElementRef;\n  @ViewChild('confirmModal') confirmModal!: ElementRef;\n\n  @Input() events: Observable<void> = of();\n  private eventsSubscription: Subscription  = new Subscription();\n\n  @Input() runAllEvent: Observable<void> = of();\n  private runAllSubscription: Subscription  = new Subscription();\n\n  unsubscribe$ = new Subject();\n\n  stages$: Observable<Stage[]> = this._stateService.stages$;\n  tools$: Observable<Tool[]> = this._stateService.tools$;\n  pipelineId$: Observable<string> = this._stateService.pipelineId$;\n  params$: Observable<PipelineParams> = this._stateService.params$;\n\n  stages: Stage[] = [];\n  tools: Tool[] = [];\n  pipelineId = '';\n  params!: PipelineParams;\n  pipelineUrl: string = ''\n\n  swaggerUrl = `${environment['api_url']}/apidocs`\n\n  /** sequence variables */\n  synthesisDownloadLinks = {\n    sequence_list_json_uri: '',\n    sequence_list_fasta_uri: '',\n    download_sequences: ''\n  };\n\n  /** Form variables */\n  pepxForm!: UntypedFormGroup;\n\n  filteredSequences: { name: string, sequences: string }[] = [];\n  numOfAA: number = 0;\n  numOfCharacters = 0\n  seqFormat: string = 'Unknown';\n\n  inputChange = {\n    /** Keeps track of inputChanges to highlight selected parameter table row*/\n    input_sequence_text: false,\n    quantitation_level: false,\n    data_source: false,\n    // lengths: false,\n    // predictors: false,\n    table_state_1: false,\n    table_state_2: false,\n  }\n\n  // pepxLoading: boolean = false;\n\n  /** API Call variables */\n  runSetInterval: any;\n  submitted = false;\n  loading = false;\n  getResultsClicked = true;\n\n  pipelineLoading = false;\n  tableStateSaving = false;\n  saveState = false;\n\n  errorMessages: string[] = [];\n  warningMessages: string[] = [];\n\n  peptide_table_columns: Columns[] | any;\n  peptide_table: [(string | number)[]] = [[]]\n  peptide_table_currentOrder: any[] = [];\n  peptide_table_defaultOrder: any[] = [];\n\n  peptide_gene_columns: Columns[] | any;\n  peptide_gene_summary_table: [(string | number)[]] = [[]]\n  peptide_gene_currentOrder: any[] = [];\n  peptide_gene_defaultOrder: any[] = [];\n\n  sequence_table_order: any[] = [];\n  sequence_table_columns: Columns[] | any;\n  sequence_table: [(string | number)[]] = [[]]\n\n  /** sequence files */\n  maxCharacters = 1000000;\n  files: any[] = [];\n  fileName = '';\n\n  active = 'peptide_table'\n\n  constructor(\n    public alertService: AlertServiceService,\n    private http: HttpClient,\n    private location: Location,\n    private _pipelineService: PipelineService,\n    private _stateService: PipelineStateService,\n    private rootFormGroup: FormGroupDirective, // pipeline component\n    private sequenceParserService: SequenceParserService,\n    private modalService: NgbModal,\n    private titleService: Title,\n  ) {\n  }\n\n  ngOnInit(): void {\n    this.pepxForm = this.rootFormGroup.control.get(this.formGroupName) as UntypedFormGroup;\n\n    const qlevel = this.pepxForm.controls['qlevel']?.value\n    const datasource = this.pepxForm.controls['datasource']?.value\n    this.getPepx(qlevel, datasource)\n\n    this.pipelineId$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n      this.pipelineId = value;\n      this.pipelineUrl = `${window.location.origin}/pipeline/${value}`;\n    })\n    this.stages$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n      this.stages = value;\n      this.errorMessages = this.stages[this.index]?.stage_messages!.errors\n      this.warningMessages = this.stages[this.index]?.stage_messages!.warnings\n    })\n    this.tools$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n      console.log('tools$');\n      console.log(value);\n      this.tools = value;\n      this.submitted = this.tools[this.index]?.submitted\n\n      // inputSequenceTextURIs\n      const inputSequenceTextId = this.tools[this.index]?.input_data_uri?.input_sequence_text_id\n\n      this.synthesisDownloadLinks.sequence_list_json_uri = `${environment['api_url']}/api/v1/sequence_list_json/${inputSequenceTextId}`\n      this.synthesisDownloadLinks.sequence_list_fasta_uri = `${environment['api_url']}/api/v1/sequence_list_fasta/${inputSequenceTextId}`\n      this.synthesisDownloadLinks.download_sequences = `${environment['api_url']}/api/v1/download_sequences/${inputSequenceTextId}`\n      /** pipeline Loading */\n      this.pipelineLoading = _.some(this.tools, {loading: true})\n\n      /** cancel run all  */\n      if(!this.tools[this.index]?.loading) {\n        this.loading = false;\n        clearInterval(this.runSetInterval)\n      }\n      // this.loading = this.tools[this.index]?.loading\n      // if (this.tools[this.index]?.submitted){this.submitted = true}\n      // if (this.tools[this.index].appliedFilters){this.submitted = true}\n      // this.componentDisabled = value[this.index].disabled;\n    })\n\n    this.params$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n      console.log(`params`);\n      console.log(value);\n      this.params = value;\n    })\n\n    this.eventsSubscription = this.events.subscribe(() => this.onRunMain());\n    this.runAllSubscription = this.runAllEvent.subscribe(() => this.onRunAll())\n\n    this.onChanges()\n\n    if(this.pepxForm.get('inputSequenceText')?.value) {\n      this.sequenceParser(this.pepxForm.get('inputSequenceText')?.value)\n    }\n    // if(this.loading) {\n    //   this.disableInputs()\n    // }\n\n    // if(this.resultUrl) {\n    //   this.loading = true;\n    //   this.getResultsSetInterval(this.resultUrl);\n    // }\n\n    // filteredSequences\n    // numOfAA\n  }\n\n  ngOnDestroy() {\n    clearInterval(this.runSetInterval);\n    clearInterval(this._pipelineService.runSetInterval)\n    this.unsubscribe$.next();\n    this.unsubscribe$.complete();\n    this.eventsSubscription.unsubscribe();\n  }\n\n  ngAfterViewInit() {\n    setTimeout(() => {\n      const run = history.state?.run;\n      // console.log(run);\n      run && this.onRunMain();\n    }, 0)\n  }\n\n  ngOnChanges(changes: SimpleChanges) {\n    if (changes.resultUrl?.currentValue) {\n      console.log(changes.resultUrl.currentValue);\n      console.log('ngOnChanges pepx')\n      this.loading = true;\n      this.getResultsSetInterval(changes.resultUrl.currentValue);\n    }\n  }\n\n  get styleResultContainer(){\n    return !this.loading && this.submitted ? 'none' : 'dotted';\n  }\n\n  get inputSequenceText(){\n    return this.pepxForm.get('inputSequenceText')?.value\n  }\n\n  get quantitationLevel(){\n    return this.pepxForm.get('qlevel')?.value\n  }\n\n  /** Download Sequence File API calls*/\n\n  onDownloadJson() {\n    onCsvDownloadAllClickedNew(this.synthesisDownloadLinks.sequence_list_json_uri, this.http, 'json');\n  }\n\n  onDownloadFasta() {\n    onCsvDownloadAllClickedNew(this.synthesisDownloadLinks.sequence_list_fasta_uri, this.http, 'fasta');\n  }\n  onDownloadOriginal() {\n    onCsvDownloadAllClickedNew(this.synthesisDownloadLinks.download_sequences, this.http, 'txt');\n  }\n\n  onDownloadParameter() {\n    const data = this._pipelineService.convertPepxForm(this.pepxForm)\n\n    const a = document.createElement('a');\n    a.setAttribute('style', 'display:none;');\n    document.body.appendChild(a);\n    // const contentType = 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet;charset=UTF-16';\n    // var blob = new Blob([csvData], { type: contentType });\n    const blob = new Blob([JSON.stringify(data, null, 2)], ); // thx: http://stackoverflow.com/a/18925211\n    a.href = window.URL.createObjectURL(blob);\n    a.download = 'parameter.json';\n\n    a.click();\n  }\n\n  getPepx(qlevel: string = 'gene', datasource='Abelin') {\n    // this.pepxLoading = true;\n    this.datasetLoading = true\n    this.datasourceLoading = true\n\n    // https://api-nextgen-tools-dev.iedb.org/api/v1/pepx?datasource=Abelin\n    this.http.get<any[]>(`${API_URL}?qlevel=${qlevel}&datasource=${datasource}`)\n      .pipe().subscribe(\n      resp => {\n        // @ts-ignore\n        // this.mhciPredictors = resp['predictors'];\n        console.log(resp)\n        // @ts-ignore\n        this.dataSets = resp.datasets\n        console.log(this.dataSets)\n        // @ts-ignore\n        this.datasources = resp.datasources\n        // this.pepxForm.patchValue({dataset_id: this.dataSets[0].dataset_id})\n        // this.proteomeOptions = resp.optional_parameters[0].choice\n        // console.log(resp.optional_parameters[0]);\n\n        // console.log(this.proteomeOptions)\n        // this.pepxLoading = false;\n        this.datasetLoading = false\n        this.datasourceLoading = false\n      }\n    )\n  }\n\n\n  /** File Download/Upload*/\n  uploadSequenceFile($event: any) {\n    $event.preventDefault();\n    /**\n     * Used for 'Upload' button\n     * */\n    const {files} = $event.target;\n    files && this.onFileDropped(files);\n  }\n\n  onRunAll() {\n    this.setDefaultFormValues()\n    this.emitIndex.emit(this.index);\n  }\n\n\n  onRunMain() {\n    if(this.pepxForm.invalid){\n      this.alertService.add(`Input sequence text is too long. The maximum number of characters allowed is ${this.maxCharacters.toLocaleString()}\\nYour sequence contains ${this.inputSequenceText.length.toLocaleString()}`, 'alert-danger');\n      this.open(this.alertModal)\n      return;\n    }\n\n    const hasResult = _.find(this.tools.slice(this.index+1), (o) => o.submitted || o.loading)\n    if(this.stages.length > 1 && hasResult) {\n      this.open(this.confirmModal);\n    } else {\n      this.getResultsClicked = true;\n      if(this.index===0) {\n        this.onRun();\n      } else {\n        this.onRun2()\n      }\n    }\n  }\n\n  setDefaultFormValues() {\n    /** defaults - use Sars placeholders*/\n    const {input_sequence_text} = pepxData;\n    /** Sequences */\n    let sequences = this.pepxForm.value.inputSequenceText\n    if(!sequences && this.index===0) {\n      this._stateService.setInputSequenceText(input_sequence_text);\n      this.pepxForm.controls.inputSequenceText.setValue(input_sequence_text);\n    }\n  }\n\n  onChanges(): void {\n    /** PredictionModel sessionStorage */\n    // this.pepxForm.get('predictionModels')?.valueChanges.subscribe(val => {\n    //   // sessionStorage.setItem('predictionModels', JSON.stringify(val));\n    //   this.inputChange.predictors = this.submitted\n    // });\n    //\n    const sequenceFieldChange = this.pepxForm.get('inputSequenceText')?.valueChanges.pipe(\n      debounce(v => timer(1000)),\n    );\n    //\n    // this.pepxForm.get('breakPeptides')?.valueChanges.subscribe(val => {\n    //   this.peptideLengthSliderOptions = Object.assign({}, this.peptideLengthSliderOptions, {disabled: val});\n    // })\n    //\n    sequenceFieldChange?.subscribe(val => {\n      console.log('sequenceFieldChange')\n      // sessionStorage.setItem('sequences', val);\n      this.sequenceParser(val);\n      this.inputChange.input_sequence_text = this.submitted;\n      if (val === '') {  // delete\n        this.filteredSequences = [];\n        this.numOfAA = 0;\n      }\n    });\n  }\n\n  // Allele Modal Functions\n\n  open(content: any) {\n    this.modalService.open(content, {\n      ariaLabelledBy: 'modal-basic-title',\n      size: 'lg',\n      animation: true,\n    }).result.then((result) => {\n      // this.closeResult = `Closed with: ${result}`;\n      this.saveState = false;\n    }, (reason) => {\n      this.saveState = false;\n      // this.alleleSearch.nativeElement.focus();\n      // this.closeResult = `Dismissed ${TCellPredictionComponent.getDismissReason(reason)}`;\n    });\n  }\n\n  onCancel() {\n    console.log(this.runSetInterval)\n    clearInterval(this.runSetInterval);\n    this.emitOnCancel.emit()\n\n    // this.inputChange.table_state = false;\n    // // this.submitted = false;\n    const currentTool = this.tools[this.index]\n    const unSubmittedTool = {\n      ...currentTool,\n      loading: false,\n      submitted: false,\n      appliedFilters: undefined\n    }\n    this._stateService.insertTool(unSubmittedTool, this.index);\n    this.warningMessages = [];\n    this.loading = false;\n    this.tableStateSaving = false;\n    this.enableInputs();\n  }\n\n  onReset() {\n    this.alertService.clear();\n    this.errorMessages = [];\n    this.warningMessages = [];\n  }\n\n  enableInputs() {\n    this.pepxForm.controls['qlevel'].enable({emitEvent: false})\n    this.pepxForm.controls['datasource'].enable({emitEvent: false})\n    this.pepxForm.controls['dataset_id'].enable({emitEvent: false})\n    // this.options = Object.assign({}, this.options, {disabled: false});\n  }\n\n  disableInputs() {\n    this.pepxForm.controls['qlevel'].disable({emitEvent: false})\n    this.pepxForm.controls['datasource'].disable({emitEvent: false})\n    this.pepxForm.controls['dataset_id'].disable({emitEvent: false})\n    // this.options = Object.assign({}, this.options, {disabled: true});\n  }\n\n  onFilterApplied() {\n    this.inputChange.table_state_1 = this.submitted;\n  }\n  onFilterApplied2() {\n    this.inputChange.table_state_2 = this.submitted;\n  }\n\n  onClearTableState() {\n    this.peptide_table_columns = _.map(this.peptide_table_columns, (c) => {\n      c.value_limits = c.type === 'int'? {\n          minValue: NaN,\n          maxValue: NaN,\n          applied: false\n        } :\n        {\n          possibleValues: [],\n          textValue: null,\n          selectedValues: [],\n          applied: false\n        }\n      return c\n    })\n    this.inputChange.table_state_1 = this.submitted;\n  }\n\n  onClearTable2State() {\n    this.peptide_gene_columns = _.map(this.peptide_gene_columns, (c) => {\n      c.value_limits = c.type === 'int'? {\n          minValue: NaN,\n          maxValue: NaN,\n          applied: false\n        } :\n        {\n          possibleValues: [],\n          textValue: null,\n          selectedValues: [],\n          applied: false\n        }\n      return c\n    })\n    this.inputChange.table_state_2 = this.submitted;\n  }\n\n  onSaveTableStateMain(table_name: string) {\n    /**\n     * @table_name: string - shows which table is used for save table state\n     * */\n    const hasResult = _.find(this.tools.slice(this.index+1), {submitted: true})\n    if (hasResult) {\n      this.saveState = true;\n      this.open(this.confirmModal);\n    } else {\n      switch (table_name) {\n        case 'peptide_gene_summary_table':\n          this.onSaveTable2State();\n          break;\n        default:\n          this.onSaveTable1State();\n      }\n    }\n  }\n\n  onSaveTable1State() {\n    const tool_group = 'pepx'\n\n    const params = this.params\n    // create colObj and params\n    let colObj = columnListToObject(this.peptide_table_columns, tool_group)\n    let colObj2 = columnListToObject(this.peptide_gene_columns, tool_group)\n\n    const table_state = [\n      {table: 'peptide_table', columns: colObj},\n      {table: 'peptide_gene_summary_table', columns: colObj2}\n    ]\n    this._stateService.insertTableStateToStage(table_state, this.index)\n    // this._stateService.insertTableStateToStage({columns: colObj}, this.index)\n\n    const stages = params.stages;\n    const stageTemp = stages[this.index];\n\n\n    stageTemp.table_state[0].columns = colObj\n\n    stages[this.index] = stageTemp\n    params.stages = stages;\n    // run_stage_range\n    const stage_number = this.index + 1;\n    params.run_stage_range = [stage_number, stage_number];\n    this._stateService.setParams(params);\n    // appliedFilters\n    let appliedFilters = !_.isEmpty(colObj);\n    this._stateService.setToolAppliedFilters(appliedFilters, this.index)\n    this.postPipelineAPI(params, false);\n    this.inputChange.table_state_1 = false;\n\n    this.saveState = false;\n  }\n\n  onSaveTable2State() {\n    const tool_group = 'pepx'\n\n    const params = this.params\n    /** create colObj and params */\n    let colObj = columnListToObject(this.peptide_table, tool_group)\n    let colObj2 = columnListToObject(this.peptide_gene_columns, tool_group)\n\n    const table_state = [\n      {table: 'peptide_table', columns: colObj},\n      {table: 'peptide_gene_summary_table', columns: colObj2}\n    ]\n    this._stateService.insertTableStateToStage(table_state, this.index)\n\n    const stages = params.stages;\n    const stageTemp = stages[this.index];\n    console.log(this.peptide_gene_summary_table)\n    console.log(stageTemp)\n\n    stageTemp.table_state[1].columns = colObj2\n\n    stages[this.index] = stageTemp\n    params.stages = stages;\n    /** run_stage_range */\n    const stage_number = this.index + 1;\n    params.run_stage_range = [stage_number, stage_number];\n    this._stateService.setParams(params);\n    /** appliedFilters */\n    let appliedFilters = !_.isEmpty(colObj);\n    this._stateService.setToolAppliedFilters(appliedFilters, this.index)\n    this.postPipelineAPI(params, false);\n    this.inputChange.table_state_2 = false;\n\n    this.saveState = false;\n  }\n\n  onFileDropped($event: any[]) {\n    console.log($event);\n    const file = $event[0];\n    const fileSize = file.size / 1024; // in kB\n    console.log(file.type);\n    if (fileSize > 20000) {\n      this.alertService.add('File Size is too big! (20mB max)', 'alert-danger');\n      this.open(this.alertModal);\n    }\n    else {\n      this.prepareSequenceFileList($event);\n    }\n  }\n\n  prepareSequenceFileList(files: Array<any>) {\n    console.log(files);\n    this.fileName = files[0].name;\n    const reader = new FileReader();\n    const myForm = this.pepxForm;\n    for (const item of files) {\n      // console.log(item);\n      reader.readAsText(item);\n      reader.onload = () => {\n        const val = reader.result?.toString() || '';\n        console.log(val);\n        const v = isASCII(val);\n        console.log(v);\n        if (v) {\n          // myForm.patchValue({inputSequenceText: val.substring(0, this.maxCharacters)});\n          const w = isMaxLength(val, this.maxCharacters)\n          if (w) {\n            myForm.patchValue({inputSequenceText: val});\n          } else {\n            this.alertService.add(`Sequence is too long - max Sequence length is ${this.maxCharacters.toLocaleString(\"en-US\")} characters`, 'alert-danger');\n            this.open(this.alertModal);\n          }\n          // this.sequenceParser(val);  // auto parser\n        } else {\n          this.alertService.add('Invalid file type.\\nValid file types are .txt, .fa, .fasta, .json, .faa,', 'alert-danger');\n          this.open(this.alertModal);\n        }\n      };\n\n      reader.onerror = () => {\n        console.log(reader.error);\n      };\n      item.progress = 0;\n      this.files.push(item);\n    }\n  }\n\n  sequenceParser(val: string) {\n\n    const firstChar = ltrim(val)[0];\n    const firstLine = val.split('\\n')[0]\n    console.log(firstLine)\n\n    /** Named white space */\n    let firstLineNumOfElements = 0\n    let separator = ' '\n    if(firstLine.includes(' ')){\n      separator = ' '\n    } else if (firstLine.includes('\\t')){\n      separator = '\\t'\n    } else if (firstLine.includes('\\s')){\n      separator = '\\s'\n    }\n    firstLineNumOfElements = firstLine.split(separator).length\n    console.log(firstLineNumOfElements)\n    console.log(separator)\n\n    const slicedVal = val.slice(0, this.maxCharacters)\n\n    if(val.length > this.maxCharacters) {\n      //  Skip parsing\n    } else if (firstChar === '>' && this.sequenceParserService.fastaValidate(val)) { // fasta\n      this.seqFormat = this.sequenceParserService.seqFormat;\n      this.numOfCharacters = slicedVal.length\n    } else if ((firstChar === '{' || firstChar === '[') && IsJsonString(val)) { // json\n      this.seqFormat = 'JSON'\n      this.numOfCharacters = slicedVal.length\n    } else if (firstLineNumOfElements === 2 && this.sequenceParserService.namedWhiteSpaceValidate(val, separator)) {\n      // named white space\n      this.seqFormat = this.sequenceParserService.seqFormat;\n      this.numOfCharacters = slicedVal.length\n    } else if (val.length > 3 && !val.includes('>') && this.sequenceParserService.unnamedWhiteSpaceValidate(val)) {\n      // Unnamed\n      this.seqFormat = this.sequenceParserService.seqFormat;\n      this.numOfCharacters = slicedVal.length\n    } else if (val === '') {  // delete\n      /**\n       * Takes care of it up top - still need this if statement\n       * */\n      this.seqFormat = 'Unknown';\n      this.numOfCharacters = 0\n    } else { // error\n      this.seqFormat = 'Error';\n      this.numOfCharacters = 0\n    }\n  }\n\n  // Function for dataSource and quanitation level on change\n  onDataSourceChange(value: any) {\n    console.log(value.target.value)\n    // this.getPepx(this.quantitationLevel, value.target.value)\n\n    const datasource = value.target.value\n\n    // this.datasourceLoading = true\n    this.datasetLoading = true\n    this.http.get<any[]>(`${API_URL}?qlevel=${this.quantitationLevel}&datasource=${datasource}`)\n      .pipe().subscribe(\n      resp => {\n        // @ts-ignore\n        // this.mhciPredictors = resp['predictors'];\n        console.log(resp)\n        // @ts-ignore\n        this.dataSets = resp.datasets\n        this.pepxForm.patchValue({dataset_id: this.dataSets[0].dataset_id})\n        // @ts-ignore\n        this.datasources = resp.datasources\n        // this.proteomeOptions = resp.optional_parameters[0].choice\n        // console.log(resp.optional_parameters[0]);\n\n        // console.log(this.proteomeOptions)\n        // this.pepxLoading = false;\n        // this.datasourceLoading = false\n        this.datasetLoading = false\n      }\n    )\n\n  }\n\n  onQuantitationLevelChange(value: any) {\n    console.log(value)\n    const qlevel = value\n    let datasource = ''\n    if(value==='gene'){\n      // qlevel = value;\n      // const datasource = this.pepxForm.get('datasource')\n      this.pepxForm.controls['datasource'].patchValue('Abelin')\n      // datasource = 'Abelin'\n      // this.getPepx('gene','Abelin')\n    }\n    if(value==='transcript'){\n      // qlevel = value;\n      // this.getPepx('transcript','CCLE')\n      this.pepxForm.controls['datasource'].patchValue('CCLE')\n      // datasource = 'CCLE'\n    }\n\n    this.datasourceLoading = true\n    this.datasetLoading = true\n    this.http.get<any[]>(`${API_URL}?qlevel=${qlevel}&datasource=${datasource}`)\n      .pipe().subscribe(\n      resp => {\n        // @ts-ignore\n        // this.mhciPredictors = resp['predictors'];\n        console.log(resp)\n        // @ts-ignore\n        this.dataSets = resp.datasets\n        // @ts-ignore\n        this.datasources = resp.datasources\n        this.pepxForm.patchValue({dataset_id: this.dataSets[0].dataset_id})\n        // this.proteomeOptions = resp.optional_parameters[0].choice\n        // console.log(resp.optional_parameters[0]);\n\n        // console.log(this.proteomeOptions)\n        // this.pepxLoading = false;\n        this.datasourceLoading = false\n        this.datasetLoading = false\n      }\n    )\n\n  }\n\n  onRun() {\n    /**\n     Update pipeline State\n     *\n     * */\n    /** Reset global datatables search ext */\n    $.fn.dataTable.ext.search = [];\n\n    const stage_number = this.index + 1;\n    /** run_stage_range */\n    const run_stage_range: [number, number] = [stage_number, stage_number]\n    /** default formValue */\n    this.setDefaultFormValues()\n    /** Sequences */\n    let sequences = this.pepxForm.value.inputSequenceText\n\n    /** input parameters */\n    const inputParameters = this._pipelineService.convertPepxForm(this.pepxForm)\n\n    /** Table State */\n    const { table_state } = this.stages[this.index];\n\n    const newStage = {\n      \"stage_display_name\": \"PepX\",\n      \"stage_number\": stage_number,\n      \"stage_type\": \"prediction\",\n      \"tool_group\": \"pepx\",\n      \"input_sequence_text\": sequences,\n      \"input_parameters\": inputParameters,\n      \"table_state\": table_state\n    }\n\n    const params = {\n      \"pipeline_id\": '',\n      \"pipeline_title\": this.emailForm.controls['name'].value,\n      \"email\": this.emailForm.controls['email'].value,\n      \"run_stage_range\": run_stage_range,\n      \"stages\": [\n        newStage\n      ]\n    }\n\n    /** set params */\n    const initTool = Object.assign(initPepxTool, {\n      loading: true,\n      submitted: false,\n      appliedFilters: !_.isEmpty(table_state?.columns)\n    })\n    this._stateService.setParams(params);\n    this._stateService.insertTool(initTool, this.index);\n    // this._stateService.insertTableStateToStage({columns: {}}, this.index);\n\n    console.log(params)\n    this.postPipelineAPI(params);\n  }\n\n  onRun2() {\n\n    const params = this.params;\n    const stage_number = this.index + 1;\n    const input_stage_number = this.index; // previous index\n\n    /** run_stage_range */\n    const run_stage_range: [number, number] = [stage_number, stage_number]\n    /** default formValue */\n    this.setDefaultFormValues()\n\n    /** input parameters */\n    const inputParameters = this._pipelineService.convertPepxForm(this.pepxForm)\n    const initialStage = this.stages[this.index];\n\n    /** Table State */\n    const { table_state } = this.stages[this.index];\n\n    const stage: Stage = {\n      ...initialStage,\n      result_url: undefined,\n      stage_number: stage_number,\n      input_stage_number: input_stage_number,\n      input_parameters: inputParameters,\n      table_state\n    }\n\n    // this.params.stages.push(stage);\n    params.stages[this.index] = stage;\n    params.run_stage_range = run_stage_range;\n    params.pipeline_title = this.emailForm.controls['name'].value;\n    params.email = this.emailForm.controls['email'].value;\n\n    console.log(params)\n\n    /** set params */\n    const loadingTool = Object.assign(initPepxTool, {\n      loading: true,\n      submitted: false,\n      appliedFilters: !_.isEmpty(table_state?.columns)\n    })\n    console.log('loadingPepxTool')\n    console.log(loadingTool)\n    this._stateService.setParams(params);\n    this._stateService.insertTool(loadingTool, this.index);\n    this._stateService.insertInputParametersToStage(inputParameters, this.index);\n\n    this.postPipelineAPI(params);\n  }\n\n  setValueLimits(column: Columns) : any {\n    /* set value_limits (i.e. filters) for each column based on if type is a number/string */\n    return column['type'] === 'int' || column['type'] === 'float' ? {\n      ...column['value_limits'],\n      minValue: NaN,\n      maxValue: NaN,\n      applied: false\n    } : {\n      // ...column['value_limits'],\n      possibleValues: column['value_limits']['unique_values'],\n      textValue: null,\n      selectedValues: [],\n      applied: false\n    }\n  }\n\n  postPipelineAPI(params: PipelineParams, getResults: boolean = true) {\n    /**\n     * params\n     * getResults: boolean\n     *  false - used in 'Save Table State'\n     * */\n    /** initial set up */\n    this.disableInputs();\n    this.loading = getResults; // true - defaults\n    this.submitted = !getResults; // false - defaults\n    this.tableStateSaving = !getResults\n    if (getResults) {\n      this.errorMessages = [];\n      this.warningMessages = [];\n    }\n    this._pipelineService.postPipeline(params).subscribe(\n      (resp) => {\n        // Errors and Warnings\n        if (resp['errors'] && resp['errors'].length) {\n          console.log(resp);\n          console.error(resp['errors']);\n          this.errorMessages = resp['errors'];\n          if (resp['warnings']?.length) {\n            console.log(resp['warnings']);\n            this.warningMessages = resp['warnings'];\n          }\n          this.loading = false;\n          this.submitted = true;\n          const submittedTool = Object.assign(initPepxTool, {\n            submitted: true,\n            loading: false,\n          })\n          this._stateService.insertTool(submittedTool, this.index);\n          this.enableInputs();\n          return;\n        }\n        // Warnings\n        if (resp['warnings'].length) {\n          console.log(resp['warnings']);\n          this.warningMessages = resp['warnings'];\n        }\n\n        console.log(resp.pipeline_id);\n\n        const inputDataUri = {input_sequence_text_id: resp.input_sequence_text_id}\n        this._stateService.insertInputDataUriToTool(inputDataUri, this.index)\n\n        this._stateService.setPipelineId(resp.pipeline_id);\n        this._stateService.setPipelineIdToParams(resp.pipeline_id);\n        this._stateService.setPipelineSpecId(resp.pipeline_spec_id);\n        /** Display email Modal if emailModalShow=true */\n        if (this.showEmailModal) {\n          // this.open(this.emailModal);\n        }\n        this.location.replaceState(`pipeline/${resp.pipeline_id}`)\n        // this.titleService.setTitle(`IEDB NG Tools Pipeline`);\n\n        if (getResults) {\n          const result_url = `${resp.results_uri}`;\n          console.log(result_url);\n          this.getResultsSetInterval(result_url);\n        } else {\n          // this.inputChange.table_state_1 = false;\n          // this.inputChange.table_state_2 = false;\n          this.submitted = true;\n          this.loading = false;\n          this.tableStateSaving = false;\n          this.enableInputs();\n        }\n      },\n      error => {\n        console.error(error);\n        this.errorMessages.push(error.error);\n        this.submitted = false;\n        this.loading = false;\n        const prevTool = this.tools[this.index];\n        const submittedTool = Object.assign(prevTool, {\n          submitted: this.submitted,\n          loading: this.loading,\n        })\n        this._stateService.insertTool(submittedTool, this.index);\n        clearInterval(this.runSetInterval);\n        this.enableInputs();\n      })\n  }\n\n  getResultsSetInterval(result_url: string) {\n    this.getResultsClicked = true\n\n    // this.sequence_table = [[]]\n    this.peptide_table = [[]]\n\n    this.inputChange = _.mapValues(this.inputChange, () => false);\n    let increment = 0;\n    const milliseconds = 3000;\n    this.runSetInterval = setInterval(() => {\n      this._pipelineService.getResults(result_url).subscribe(resp => {\n        if (resp['status'] === 'error' || resp['errors']) {\n          this.errorMessages = resp['data']['errors'];\n          this.warningMessages = resp['data']['warnings'];\n          this.submitted = false;\n          this.loading = false;\n          const prevTool = this.tools[this.index];\n          console.log(prevTool)\n          const submittedTool = Object.assign(prevTool, {\n            submitted: this.submitted,\n            loading: this.loading,\n          })\n          this._stateService.insertTool(submittedTool, this.index);\n          clearInterval(this.runSetInterval);\n          this.enableInputs();\n        }\n        if (resp['data']['warnings']?.length) {\n          // console.log(resp['warnings']);\n          this.warningMessages = resp['data']['warnings'];\n        }\n        if (resp['data']['errors']?.length) {\n          // console.log(resp['warnings']);\n          this.errorMessages = resp['data']['errors'];\n        }\n        if (resp['status'] === 'done') {\n          /** 1) Create Column */\n          const data = resp['data']['results'];\n          console.log(data);\n\n          this.active = data[0].type\n\n          // this.active = data[0].table_data.length ? data[0].type : data[1].type\n\n          _.forEach(data, table => {\n            if (table.type === 'peptide_table') {\n              this.peptide_table_columns = _.map(table.table_columns, (column, i) => {\n                if (column.default_order && Number.isFinite(column.row_sort_priority)) { // set defaultOrder\n                  // console.log(column);\n                  this.peptide_table_defaultOrder[column.row_sort_priority] = [i, column.default_order === \"ascending\" ? 'asc' : 'desc'];\n                }\n                column['title'] = `${column['display_name']}`; // required\n                column['data'] = `${column['name']}`;\n                let source = column['source'];\n\n                column['filterKey'] = `${source}.${column.name}`\n                // console.log(`source=${source}`);\n                let tempSource = source.split('.')\n                // console.log(tempSource);\n                source = tempSource[tempSource.length - 1];\n                // console.log(`source=${source}`);\n                column['data'] = `${source}_${column['name']}`;\n                /** remove `core` from name */\n                // column['name'] = column['display_name'] ? column['display_name'] : column['name']\n                // column['name'] = source === 'core' ? display_name: `${source} ${display_name}`;\n                // column['filters'] = column['type'] === 'int' ? {\n                //   minValue: NaN,\n                //   maxValue: NaN,\n                //   applied: false\n                // } : {\n                //   possibleValues: [],\n                //   textValue: null,\n                //   selectedValues: [],\n                //   applied: false\n                // }\n                column['value_limits'] = column['value_limits'] &&  this.setValueLimits(column)\n                return column\n              });\n              this.peptide_table_currentOrder = [...this.peptide_table_defaultOrder];\n              if (this.peptide_table_columns) {\n                this.peptide_table = table.table_data;\n                const prevTool = this.tools[this.index];\n                console.log(prevTool)\n                const submittedClusterTool = Object.assign(prevTool, {\n                  submitted: true,\n                  loading: false,\n                })\n\n                this._stateService.insertTool(submittedClusterTool, this.index);\n\n                clearInterval(this.runSetInterval);\n                this.enableInputs();\n\n                this.submitted = true;\n                this.loading = false;\n              }\n            }\n            if (table.type === 'peptide_gene_summary_table') {\n              this.peptide_gene_columns = _.map(table.table_columns, (column, i) => {\n                if (column.default_order && Number.isFinite(column.row_sort_priority)) { // set defaultOrder\n                  // console.log(column);\n                  this.peptide_gene_defaultOrder[column.row_sort_priority] = [i, column.default_order === \"ascending\" ? 'asc' : 'desc'];\n                }\n                column['title'] = `${column['display_name']}`; // required\n                column['data'] = `${column['name']}`;\n                let source = column['source'];\n\n                column['filterKey'] = `${source}.${column.name}`\n                // console.log(`source=${source}`);\n                let tempSource = source.split('.')\n                // console.log(tempSource);\n                source = tempSource[tempSource.length - 1];\n                // console.log(`source=${source}`);\n                column['data'] = `${source}_${column['name']}`;\n                /** remove `core` from name */\n                // column['name'] = column['display_name'] ? column['display_name'] : column['name']\n                // column['name'] = source === 'core' ? display_name: `${source} ${display_name}`;\n                // column['filters'] = column['type'] === 'int' ? {\n                //   minValue: NaN,\n                //   maxValue: NaN,\n                //   applied: false\n                // } : {\n                //   possibleValues: [],\n                //   textValue: null,\n                //   selectedValues: [],\n                //   applied: false\n                // }\n                column['value_limits'] = column['value_limits'] &&  this.setValueLimits(column)\n                return column\n              });\n              this.peptide_gene_currentOrder = [...this.peptide_gene_defaultOrder];\n              if (this.peptide_gene_columns) {\n                this.peptide_gene_summary_table = table.table_data;\n                // const prevTool = this.tools[this.index];\n                // console.log(prevTool)\n                // const submittedTool = Object.assign(prevTool, {\n                //   submitted: true,\n                //   loading: false,\n                // })\n                //\n                // this._stateService.insertTool(submittedTool, this.index);\n\n                // clearInterval(this.runSetInterval);\n                // this.enableInputs();\n                //\n                // this.submitted = true;\n                // this.loading = false;\n              }\n            }\n            if (table.type === 'input_sequence_table') {\n              this.sequence_table_columns = _.map(table.table_columns, (column, i) => {\n                // if (column.default_order && Number.isFinite(column.row_sort_priority)) { // set defaultOrder\n                //   this.defaultOrder[column.row_sort_priority] = [i, column.default_order === \"ascending\" ? 'asc' : 'desc'];\n                // }\n                column['title'] = `${column['display_name']}`; // required\n                column['data'] = `${column['name']}`;\n                let source = column['source'];\n\n                column['filterKey'] = `${source}.${column.name}`\n\n                // console.log(`source=${source}`);\n                let tempSource = source.split('.')\n                // console.log(tempSource);\n                source = tempSource[tempSource.length - 1];\n                // console.log(`source=${source}`);\n                column['data'] = `${source}_${column['name']}`;\n                /** remove `core` from name */\n                // column['name'] = column['display_name'] ? column['display_name'] : column['name']\n                // column['filters'] = column['type'] === 'int' ? {\n                //   minValue: NaN,\n                //   maxValue: NaN,\n                //   applied: false\n                // } : {\n                //   possibleValues: [],\n                //   textValue: null,\n                //   selectedValues: [],\n                //   applied: false\n                // }\n                column['value_limits'] = column['value_limits'] ? this.setValueLimits(column) : undefined\n                return column\n              });\n              this.sequence_table_order = []\n              if (this.sequence_table_columns) {\n\n                this.sequence_table = table.table_data\n              }\n            }\n          })\n        }\n        if (resp['status'] === 'canceled') {\n          /** if status is canceled, then just stop loader **/\n          this.submitted = false;\n          this.loading = false;\n          const prevTool = this.tools[this.index];\n          console.log(prevTool)\n          const submittedTCellPredictionTool = Object.assign(prevTool, {\n            submitted: this.submitted,\n            loading: this.loading,\n          })\n          this._stateService.insertTool(submittedTCellPredictionTool, this.index);\n          clearInterval(this.runSetInterval);\n          // console.log(data);\n          this.enableInputs();\n          // set error message\n          // this.errorMessages = [`PIPELINE_ID=${this.pipelineId} w/ STATUS=${resp['status']}`]\n        }\n        else {\n          this.getResultsClicked = false;\n          // this.apiStatus = resp['status'];\n          console.log(`current status: ${resp['status']} - ${increment}`);\n          increment += 1;\n        }\n      }, error => {\n        console.error(error);\n        this.enableInputs();\n        clearInterval(this.runSetInterval);\n        this.submitted = true;\n        this.loading = false;\n      })\n    }, milliseconds);\n  }\n\n  onRunConfirm() {\n    let indicies = _.range(this.index + 1, this.stages.length)\n    let initTool: Tool;\n    console.log(indicies);\n    _.forEach(indicies, i => {\n      initTool = this.tools[i];\n      const unSubmittedTool = {\n        ...initTool,\n        loading: false,\n        submitted: false,\n      }\n      this._stateService.insertTool(unSubmittedTool, i);\n    })\n\n    // TODO - work oout logic on how to save respecive table when confirm modal pops up...\n    this.saveState ? this.onSaveTableStateMain('peptide_table') : this.onRun();\n  }\n\n}\n","<div class=\"container-fluid p-2 d-flex flex-column\" id=\"visualization-result-container\">\n  <div class=\"p-2 m-4 align-self-center border\">\n      <span>\n        Metric\n          <select (change)=\"onSeriesPlotChange($event)\" [(ngModel)]=\"selectedSeries\">\n            <option *ngFor=\"let s of series\" [value]=\"s\"> {{ s }} </option>\n          </select>\n      </span>\n    <span>\n        Allele\n          <select (change)=\"onAllelePlotChange($event)\" [(ngModel)]=\"selectedAllele\">\n            <option *ngFor=\"let allele of uniqueAlleles\" [value]=\"allele\"> {{ allele }} </option>\n          </select>\n      </span>\n  </div>\n  <div class=\"p-2 m-4 align-self-center border\">\n    <div #containerScatterPlot></div>\n  </div>\n</div>\n","import {AfterViewInit, Component, ElementRef, Input, ViewChild} from '@angular/core';\nimport * as d3 from \"d3\";\nimport {BehaviorSubject} from \"rxjs\";\nimport _ from \"lodash\";\n\n@Component({\n  selector: 'app-d3-plot',\n  templateUrl: './d3-plot.component.html',\n  styleUrls: ['./d3-plot.component.scss']\n})\nexport class D3PlotComponent implements AfterViewInit {\n  @ViewChild(\"containerScatterPlot\") element: ElementRef | undefined\n\n  /** initialize a private variable _data, it's a BehaviorSubject */\n    // private _data = new BehaviorSubject<IAData[]>([]);\n  private _data = new BehaviorSubject<any>([]);\n\n  @Input() plotData!: any\n  /**\n   {\n   <allele_name>: {\n   <peptidea>: float, <peptideb>: float,\n   <sequenceA>: string, <sequenceB>: string\n   }\n   }\n   * */\n  plottedPoints: any = []\n  selectedAllele = ''\n  selectedSeries = ''\n  uniqueAlleles: string[] = []\n  series: string[] = []\n\n  // change data to use getter and setter\n  @Input()\n  set data(value) {\n    // set the latest value for _data BehaviorSubject\n    this._data.next(value);\n  };\n\n  get data() {\n    // get the latest value from _data BehaviorSubject\n    return this._data.getValue();\n  }\n\n  private svg: any; // private svg?: d3.Selection<SVGElement, {}, d3.BaseType, any>\n  private focus: any;\n\n  private margin = {top: 40, right: 70, bottom: 50, left: 70}\n  private width = 520 - this.margin.left - this.margin.right\n  private height = 470 - this.margin.top - this.margin.bottom\n\n  private htmlElement?: HTMLElement;\n\n  constructor() {}\n\n  ngOnInit(): void {\n    // this.createSvg();\n    // this.drawPlot();\n    console.log(this.plotData)\n\n\n    this.series = _.chain(this.plotData)\n      .map((series) => series.series_name)\n      .uniq()\n      .value()\n\n    // console.log(this.series)\n    this.selectedSeries = this.series[0]\n\n    this.uniqueAlleles = this.uniqueAlleles = _.chain(this.plotData)\n      .map((series) =>series.allele)\n      .uniq()\n      .value()\n\n    // console.log(this.uniqueAlleles)\n    this.selectedAllele = this.uniqueAlleles[0]\n  }\n\n  ngAfterViewInit() {\n\n    this.createSvg()\n    this.drawPlot()\n  }\n\n  private createSvg(): void {\n    this.htmlElement = this.element?.nativeElement;\n\n    // const zoom: d3.ZoomBehavior<any, any> = d3.zoom()\n    //   .scaleExtent([-1, 3])\n    //   .on(\"zoom\", event => {\n    //\n    //     this.svg?.attr('transform', event.transform)\n    //   })\n\n    // @ts-ignore\n    this.svg = d3.select(this.htmlElement)\n      .append(\"svg\")\n      .attr(\"width\", this.width + (this.margin.left + this.margin.right))\n      .attr(\"height\", this.height + (this.margin.top + this.margin.bottom))\n      .attr(\"class\", \"allele-plot\")\n\n    this.focus = this.svg.append(\"g\")\n      .attr(\"class\", \"focus\")\n      .attr(\"transform\", \"translate(\" + this.margin.left + \",\" + this.margin.top + \")\")\n    // .call(zoom)\n\n  }\n\n  private drawPlot(\n    selectedAllele: string = this.selectedAllele,\n    selectedSeries: string = this.selectedSeries,\n  ): void {\n    /**\n     * Set up plottedPoints\n     [\n     {\n     <peptidea>: float, <peptideb>: float,\n     <sequenceA>: string, <sequenceB>: string\n     }\n     ]\n     * */\n      // _.forEach(_.zip(['a', 'b', 'c'], [1, 2, 3]), _.spread(function(name, score){ /* */ }));\n\n    let selected = _.find(this.plotData, {series_name: selectedSeries, allele: selectedAllele})\n    // console.log(selected)\n    if (selected) {\n      // zip\n      this.plottedPoints = []\n      _.forEach(\n        _.zip(selected!['x_values'], selected!.y_values, selected!.x_labels, selected!.y_labels),\n        _.spread((x_val, y_val, x_lab, y_lab) => {\n          this.plottedPoints.push({\n            peptidea: x_val, peptideb: y_val,\n            sequenceA: x_lab, sequenceB: y_lab\n          })\n        }))\n\n      /**\n       * Set up D3 elements\n       * */\n\n      // this.htmlElement = this.element?.nativeElement;\n      /** TOOLTIPS\n       * tooltip - coordinates\n       * seqTooltip - sequences\n       * */\n        // @ts-ignore\n      let tooltip = d3.select(this.htmlElement)\n          .append(\"div\")\n          .style(\"opacity\", 0)\n          .attr(\"class\", \"tooltip\")\n          .style(\"background-color\", \"white\")\n          .style(\"border\", \"solid\")\n          .style(\"border-width\", \"2px\")\n          .style(\"border-radius\", \"5px\")\n          .style(\"padding\", \"5px\")\n\n      // @ts-ignore\n      let seqTooltip = d3.select(this.htmlElement)\n        .append(\"div\")\n        .style(\"position\", \"absolute\")\n        .style(\"opacity\", 0)\n        .attr(\"class\", \"tooltip\")\n        .style(\"background-color\", \"white\")\n        .style(\"border\", \"solid\")\n        .style(\"border-width\", \"2px\")\n        .style(\"border-radius\", \"5px\")\n        .style(\"padding\", \"5px\")\n\n      // Title\n      this.focus.append(\"text\")\n        .attr(\"x\", (this.width / 2))\n        .attr(\"y\", 0 - (this.margin.top / 2))\n        .attr(\"text-anchor\", \"middle\")\n        .style(\"font-size\", \"16px\")\n        .style(\"text-decoration\", \"underline\")\n        .text(selected.title);\n      // Add X axis\n\n      const x = d3.scaleLinear()\n        .domain(selected.x_range)\n        .range([0, this.width]);\n\n      const xAxis = this.focus.append(\"g\")\n        .attr(\"transform\", \"translate(0,\" + this.height + \")\")\n        .call(d3.axisBottom(x));\n\n      // Add X axis label:\n      this.focus.append(\"text\")\n        .attr(\"text-anchor\", \"middle\")\n        .attr(\"x\", (this.width / 2))\n        .attr(\"y\", 420)\n        .text(selected.x_title); // add here\n\n      // Add Y axis\n      const y = d3.scaleLinear()\n        .domain(selected.y_range)\n        .range([this.height, 0]);\n\n      const yAxis = this.focus.append(\"g\")\n        .call(d3.axisLeft(y));\n\n      // Y axis label:\n      this.focus.append(\"text\")\n        .attr(\"text-anchor\", \"end\")\n        .attr(\"transform\", \"rotate(-90)\")\n        .attr(\"y\", -this.margin.left + 20)\n        // .attr(\"y\", (this.height / 2))\n        .attr(\"x\", -150)\n        .text(selected.y_title) // add here\n\n      /** draw line old */\n      // const line = this.focus.append('line')\n      //   .style('stroke', 'black')\n      //   .style(\"stroke-dasharray\",\"5,5\")//dashed array for line\n      //   .style(\"stroke-width\", 1)\n      //   .attr(\"x1\", x(0))\n      //   .attr(\"y1\", y(0))\n      //   .attr(\"x2\", x(1))\n      //   .attr(\"y2\", y(1))\n\n      /** draw line */\n        // let lineData = {x1: -1, y1: -1, x2: 1, y2: 1, strokeWidth: 1}\n      let lineData = {\n          x1: selected.x_range[0],\n          y1: selected.y_range[0],\n          x2: selected.x_range[1],\n          y2: selected.y_range[1],\n          strokeWidth: 1\n        }\n      const line = this.focus.append('g')\n        .attr(\"clip-path\", \"url(#clip)\")\n        .attr('class', 'line-group')\n        .selectAll('line').data([lineData])\n        .enter().append(\"line\")\n        .attr(\"x1\", (d: any) => (x(d.x1)))\n        .attr(\"y1\", (d: any) => (y(d.y1)))\n        .attr(\"x2\", (d: any) => (x(d.x2)))\n        .attr(\"y2\", (d: any) => (y(d.y2)))\n        .style('stroke', 'grey')\n        .style(\"stroke-dasharray\", \"5,5\")//dashed array for line\n        .style(\"stroke-width\", (d: any) => d.strokeWidth)\n\n      let lineDataY = {x1: -1e100, y1: 0, x2: 1e100, y2: 0, strokeWidth: 1}\n      const lineY = this.focus.append('g')\n        .attr(\"clip-path\", \"url(#clip)\")\n        .attr('class', 'line-group')\n        .selectAll('line').data([lineDataY])\n        .enter().append(\"line\")\n        .attr(\"x1\", (d: any) => (x(d.x1)))\n        .attr(\"y1\", (d: any) => (y(d.y1)))\n        .attr(\"x2\", (d: any) => (x(d.x2)))\n        .attr(\"y2\", (d: any) => (y(d.y2)))\n        .style('stroke', 'grey')\n        // .style(\"stroke-dasharray\",\"5,5\")//dashed array for line\n        .style(\"stroke-width\", (d: any) => d.strokeWidth)\n\n      let lineDataX = {x1: 0, y1: -1e100, x2: 0, y2: 1e100, strokeWidth: 1}\n      const lineX = this.focus.append('g')\n        .attr(\"clip-path\", \"url(#clip)\")\n        .attr('class', 'line-group')\n        .selectAll('line').data([lineDataX])\n        .enter().append(\"line\")\n        .attr(\"x1\", (d: any) => (x(d.x1)))\n        .attr(\"y1\", (d: any) => (y(d.y1)))\n        .attr(\"x2\", (d: any) => (x(d.x2)))\n        .attr(\"y2\", (d: any) => (y(d.y2)))\n        .style('stroke', 'grey')\n        // .style(\"stroke-dasharray\",\"5,5\")//dashed array for line\n        .style(\"stroke-width\", (d: any) => d.strokeWidth)\n\n\n      // 1) mouseover - insert the data point’s value and place it near the mouse.\n      const mouseover = (event: any, d: any, n: any) => {\n        tooltip\n          .transition()\n          .style(\"opacity\", 1)\n\n        seqTooltip\n          .transition()\n          .style(\"opacity\", 1)\n        // d3.select(this)\n        //   .style(\"stroke\", \"black\")\n        //   .style(\"opacity\", 1)\n      }\n\n      /** 2) mousemove\n       * .toLocaleString() - format w/ commas for thousands separator\n       *\n       * */\n      const mousemove = function (event: any, d: any, n: any) {\n        tooltip\n          .html(`Coordinates: (${d.peptidea}, ${d.peptideb})`)\n          .style(\"left\", (event.x) / 2 + \"px\") // It is important to put the +90: other wise the tooltip is exactly where the point is an it creates a weird effect\n          .style(\"top\", (event.y) / 2 + \"px\")\n          .style('margin-top', '10px')\n\n        // const [left, top] = d3.pointer(event);\n\n        seqTooltip.html(`peptide A: <span style=\"font-family: monospace\">${d.sequenceA}</span> <br>\n                               peptide B: <span style=\"font-family: monospace\">${d.sequenceB}</span>`)\n                  .style(\"left\", (event.pageX - 400) + \"px\")\n                  .style(\"top\", (event.pageY - 100) + \"px\")\n        // .style(\"left\", (event.x+70) + \"px\")\n        // .style(\"top\", (event.y) + \"px\")\n      }\n\n      // 3) mouseleave - A function that change this tooltip when the leaves a point: just need to set opacity to 0 again\n      const mouseleave = function (event: any, d: any, n: any) {\n        tooltip\n          .transition()\n          .style(\"opacity\", 0)\n\n        seqTooltip\n          .transition()\n          .style(\"opacity\", 0)\n      }\n\n      // Add a clipPath: everything out of this area won't be drawn.\n      const clip = this.svg.append(\"defs\").append(\"SVG:clipPath\")\n        .attr(\"id\", \"clip\")\n        .append(\"SVG:rect\")\n        .attr(\"width\", this.width)\n        .attr(\"height\", this.height)\n        .attr(\"x\", 0)\n        .attr(\"y\", 0)\n\n\n      // Create the dot/scatter variable: where both the circles and the brush take place\n      // const scatter = this.svg.append('g')\n      const dots = this.focus.append('g')\n        .attr(\"clip-path\", \"url(#clip)\");\n      // add dots\n\n      // .data(this.plotData[selectedAllele])\n      dots.selectAll(\"dot\")\n        .data(this.plottedPoints)\n        .enter()\n        .append(\"circle\")\n        .attr(\"r\", 4.5)\n        .attr(\"cx\", (d: any) => x(d.peptidea))\n        .attr(\"cy\", (d: any) => y(d.peptideb))\n        .style(\"opacity\", .5)\n        .style(\"fill\", \"#8FC2E8\")\n        .attr(\"stroke\", \"#759dc3\")\n        .attr(\"stroke-width\", 1.5)\n        .on('mouseover', mouseover)\n        .on(\"mousemove\", mousemove)\n        .on(\"mouseleave\", mouseleave)\n\n\n      // A function that updates the chart when the user zoom and thus new boundaries are available\n      function updateChart(event: any, d: any) {\n\n        // recover the new scale\n        let newX = event.transform.rescaleX(x);\n        let newY = event.transform.rescaleY(y);\n\n        let scaleMultiplier = event.scale\n\n        // update axes with these new boundaries\n        xAxis.call(d3.axisBottom(newX))\n        yAxis.call(d3.axisLeft(newY))\n\n        // update circle position\n        dots\n          .selectAll(\"circle\")\n          .attr(\"cx\", (d: any) => newX(d.peptidea))\n          .attr(\"cy\", (d: any) => newY(d.peptideb))\n\n        // redraw lines\n        line\n          .attr(\"x1\", (d: any) => (newX(d.x1)))\n          .attr(\"y1\", (d: any) => (newY(d.y1)))\n          .attr(\"x2\", (d: any) => (newX(d.x2)))\n          .attr(\"y2\", (d: any) => (newY(d.y2)))\n          .attr('stroke-width', (d: any) => d.strokeWidth * scaleMultiplier)\n\n        lineX\n          .attr(\"x1\", (d: any) => (newX(d.x1)))\n          .attr(\"y1\", (d: any) => (newY(d.y1)))\n          .attr(\"x2\", (d: any) => (newX(d.x2)))\n          .attr(\"y2\", (d: any) => (newY(d.y2)))\n          .attr('stroke-width', (d: any) => d.strokeWidth * scaleMultiplier)\n\n        lineY\n          .attr(\"x1\", (d: any) => (newX(d.x1)))\n          .attr(\"y1\", (d: any) => (newY(d.y1)))\n          .attr(\"x2\", (d: any) => (newX(d.x2)))\n          .attr(\"y2\", (d: any) => (newY(d.y2)))\n          .attr('stroke-width', (d: any) => d.strokeWidth * scaleMultiplier)\n      }\n\n      // Set the zoom and Pan features: how much you can zoom, on which part, and what to do when there is a zoom\n      const zoom = d3.zoom()\n        .scaleExtent([1, 100])  // This control how much you can unzoom (x0.5) and zoom (x20)\n        .extent([[0, 0], [this.width, this.height]])\n        .on(\"zoom\", updateChart);\n\n      // This add an invisible rect on top of the chart area. This rect can recover pointer events: necessary to understand when the user zoom\n      this.focus.append(\"rect\")\n        .attr(\"width\", this.width)\n        .attr(\"height\", this.height)\n        .lower()\n        .style(\"fill\", \"none\")\n        .style(\"pointer-events\", \"all\")\n        .attr('transform', 'translate(' + 0 + ',' + 0 + ')');\n\n      this.focus.call(zoom)\n    }\n    else { // if there is no 'selected', then show 'No Data Available' in the plot\n      this.svg.append(\"text\")\n        .attr(\"x\", (this.width / 2))\n        .attr(\"y\", (this.height / 2))\n        .text('No Data Available'); // add here\n    }\n  }\n\n  // filterUniqueAlleles(selectedSeriesName: string): string[] {\n  //   return _.chain(this.plotData)\n  //     .filter(series => series.series_name == selectedSeriesName)\n  //     .map(series => series.allele)\n  //     // .uniqBy({series_name: selectedSeriesName})\n  //     .value()\n  // }\n\n  onAllelePlotChange(e: any) {\n    e.preventDefault();\n    this.selectedAllele = e.target.value;\n\n    d3.selectAll(\"svg.allele-plot\").remove();\n    d3.selectAll(\".tooltip\").remove();\n\n    this.createSvg()\n\n    this.drawPlot(this.selectedAllele, this.selectedSeries)\n  }\n\n  onSeriesPlotChange(e: any) {\n    e.preventDefault();\n    this.selectedSeries = e.target.value;\n    // this.uniqueAlleles = this.filterUniqueAlleles(this.selectedSeries)\n    // this.selectedAllele = this.uniqueAlleles[0]\n\n    d3.selectAll(\"svg.allele-plot\").remove();\n    d3.selectAll(\".tooltip\").remove();\n\n    this.createSvg()\n\n    this.drawPlot(this.selectedAllele, this.selectedSeries)\n  }\n}\n","<!--[ngClass]=\"{disabled: componentDisabled}\"-->\n<form [formGroup]=\"pepcompForm\" (ngSubmit)=\"onRunMain()\" class=\"container\">\n  <div class=\"d-flex flex-row p-2\">\n    <h2 class=\"pe-2 display-5\">{{index + 1}}</h2>\n    <hr class=\"mt-4 flex-grow-1 divider\"/>\n  </div>\n  <div class=\"d-flex pb-3\">\n    <h4 class=\"p-2 tool-name\" id=\"peptide_variant_comparison-label\">Peptide Variant Comparison\n      <img class='pb-1' src=\"/assets/symbols/cedar/symbol.svg\" alt=\"cedar\" height=\"24\" width=\"24\">\n    </h4>\n    <div class=\"d-flex flex-row tool-links\" role=\"group\" aria-label=\"tool-links\">\n      <button type=\"button\" class=\"btn btn-link text-dark d-flex flex-column justify-content-center align-items-center\">\n        <a target=\"_blank\" routerLink=\"/docs/tools/pvc/index.html\" class=\"text-dark d-flex flex-column justify-content-center align-items-center\">\n          <svg width=\"1em\" height=\"1em\" viewBox=\"0 0 16 16\" class=\"bi bi-file-earmark-text\" fill=\"currentColor\"\n               xmlns=\"http://www.w3.org/2000/svg\">\n            <path\n              d=\"M4 1h5v1H4a1 1 0 0 0-1 1v10a1 1 0 0 0 1 1h8a1 1 0 0 0 1-1V6h1v7a2 2 0 0 1-2 2H4a2 2 0 0 1-2-2V3a2 2 0 0 1 2-2z\"/>\n            <path d=\"M9 4.5V1l5 5h-3.5A1.5 1.5 0 0 1 9 4.5z\"/>\n            <path fill-rule=\"evenodd\"\n                  d=\"M5 11.5a.5.5 0 0 1 .5-.5h2a.5.5 0 0 1 0 1h-2a.5.5 0 0 1-.5-.5zm0-2a.5.5 0 0 1 .5-.5h5a.5.5 0 0 1 0 1h-5a.5.5 0 0 1-.5-.5zm0-2a.5.5 0 0 1 .5-.5h5a.5.5 0 0 1 0 1h-5a.5.5 0 0 1-.5-.5z\"/>\n          </svg>\n          Docs\n        </a>\n      </button>\n      <button type=\"button\" class=\"btn btn-link\">\n        <a target=\"_blank\" [href]=\"swaggerUrl\" class=\"text-dark d-flex flex-column justify-content-center align-items-center\">\n          <svg width=\"1em\" height=\"1em\" viewBox=\"0 0 16 16\" class=\"bi bi-gear\" fill=\"currentColor\"\n               xmlns=\"http://www.w3.org/2000/svg\">\n            <path fill-rule=\"evenodd\"\n                  d=\"M8.837 1.626c-.246-.835-1.428-.835-1.674 0l-.094.319A1.873 1.873 0 0 1 4.377 3.06l-.292-.16c-.764-.415-1.6.42-1.184 1.185l.159.292a1.873 1.873 0 0 1-1.115 2.692l-.319.094c-.835.246-.835 1.428 0 1.674l.319.094a1.873 1.873 0 0 1 1.115 2.693l-.16.291c-.415.764.42 1.6 1.185 1.184l.292-.159a1.873 1.873 0 0 1 2.692 1.116l.094.318c.246.835 1.428.835 1.674 0l.094-.319a1.873 1.873 0 0 1 2.693-1.115l.291.16c.764.415 1.6-.42 1.184-1.185l-.159-.291a1.873 1.873 0 0 1 1.116-2.693l.318-.094c.835-.246.835-1.428 0-1.674l-.319-.094a1.873 1.873 0 0 1-1.115-2.692l.16-.292c.415-.764-.42-1.6-1.185-1.184l-.291.159A1.873 1.873 0 0 1 8.93 1.945l-.094-.319zm-2.633-.283c.527-1.79 3.065-1.79 3.592 0l.094.319a.873.873 0 0 0 1.255.52l.292-.16c1.64-.892 3.434.901 2.54 2.541l-.159.292a.873.873 0 0 0 .52 1.255l.319.094c1.79.527 1.79 3.065 0 3.592l-.319.094a.873.873 0 0 0-.52 1.255l.16.292c.893 1.64-.902 3.434-2.541 2.54l-.292-.159a.873.873 0 0 0-1.255.52l-.094.319c-.527 1.79-3.065 1.79-3.592 0l-.094-.319a.873.873 0 0 0-1.255-.52l-.292.16c-1.64.893-3.433-.902-2.54-2.541l.159-.292a.873.873 0 0 0-.52-1.255l-.319-.094c-1.79-.527-1.79-3.065 0-3.592l.319-.094a.873.873 0 0 0 .52-1.255l-.16-.292c-.892-1.64.902-3.433 2.541-2.54l.292.159a.873.873 0 0 0 1.255-.52l.094-.319z\"/>\n            <path fill-rule=\"evenodd\"\n                  d=\"M8 5.754a2.246 2.246 0 1 0 0 4.492 2.246 2.246 0 0 0 0-4.492zM4.754 8a3.246 3.246 0 1 1 6.492 0 3.246 3.246 0 0 1-6.492 0z\"/>\n          </svg>\n          API\n        </a>\n      </button>\n      <button type=\"button\" class=\"btn btn-link text-dark d-flex flex-column justify-content-center align-items-center\"\n              routerLink=\"/download-all\"\n              [state]=\"{tool: 'mhc-class-i-binding'}\">\n        <svg width=\"1em\" height=\"1em\" viewBox=\"0 0 16 16\" class=\"bi bi-cloud-arrow-down\" fill=\"currentColor\"\n             xmlns=\"http://www.w3.org/2000/svg\">\n          <path fill-rule=\"evenodd\"\n                d=\"M4.406 3.342A5.53 5.53 0 0 1 8 2c2.69 0 4.923 2 5.166 4.579C14.758 6.804 16 8.137 16 9.773 16 11.569 14.502 13 12.687 13H3.781C1.708 13 0 11.366 0 9.318c0-1.763 1.266-3.223 2.942-3.593.143-.863.698-1.723 1.464-2.383zm.653.757c-.757.653-1.153 1.44-1.153 2.056v.448l-.445.049C2.064 6.805 1 7.952 1 9.318 1 10.785 2.23 12 3.781 12h8.906C13.98 12 15 10.988 15 9.773c0-1.216-1.02-2.228-2.313-2.228h-.5v-.5C12.188 4.825 10.328 3 8 3a4.53 4.53 0 0 0-2.941 1.1z\"/>\n          <path fill-rule=\"evenodd\"\n                d=\"M7.646 10.854a.5.5 0 0 0 .708 0l2-2a.5.5 0 0 0-.708-.708L8.5 9.293V5.5a.5.5 0 0 0-1 0v3.793L6.354 8.146a.5.5 0 1 0-.708.708l2 2z\"/>\n        </svg>\n        Download\n      </button>\n      <button type=\"button\" class=\"btn btn-link text-dark d-flex flex-column justify-content-center align-items-center\"\n              routerLink=\"/citation\">\n        <svg width=\"1em\" height=\"1em\" viewBox=\"0 0 16 16\" class=\"bi bi-chat-square-quote\" fill=\"currentColor\"\n             xmlns=\"http://www.w3.org/2000/svg\">\n          <path fill-rule=\"evenodd\"\n                d=\"M14 1H2a1 1 0 0 0-1 1v8a1 1 0 0 0 1 1h2.5a2 2 0 0 1 1.6.8L8 14.333 9.9 11.8a2 2 0 0 1 1.6-.8H14a1 1 0 0 0 1-1V2a1 1 0 0 0-1-1zM2 0a2 2 0 0 0-2 2v8a2 2 0 0 0 2 2h2.5a1 1 0 0 1 .8.4l1.9 2.533a1 1 0 0 0 1.6 0l1.9-2.533a1 1 0 0 1 .8-.4H14a2 2 0 0 0 2-2V2a2 2 0 0 0-2-2H2z\"/>\n          <path fill-rule=\"evenodd\"\n                d=\"M7.066 4.76A1.665 1.665 0 0 0 4 5.668a1.667 1.667 0 0 0 2.561 1.406c-.131.389-.375.804-.777 1.22a.417.417 0 1 0 .6.58c1.486-1.54 1.293-3.214.682-4.112zm4 0A1.665 1.665 0 0 0 8 5.668a1.667 1.667 0 0 0 2.561 1.406c-.131.389-.375.804-.777 1.22a.417.417 0 1 0 .6.58c1.486-1.54 1.293-3.214.682-4.112z\"/>\n        </svg>\n        Cite\n      </button>\n    </div>\n  </div>\n  <!--  Sequence Input-->\n  <ng-container *ngIf=\"index===0\">\n    <div class=\"row p-2\">\n      <h5 class=\"col-3 text-left\">Peptide Pairs</h5>\n\n      <div class=\"col-9\">\n        <!--          <div class=\"btn-group btn-group-sm ml-auto\">-->\n        <button type=\"button\" class=\"btn btn-sm btn-dark-blue-grey text-white\" (click)=\"null\"\n                [disabled]=\"!submitted\"\n                data-toggle=\"dropdown\"\n                data-bs-toggle=\"dropdown\" aria-haspopup=\"true\" aria-expanded=\"false\">\n          <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n               class=\"bi bi-download\" viewBox=\"0 0 16 16\">\n            <path\n              d=\"M.5 9.9a.5.5 0 0 1 .5.5v2.5a1 1 0 0 0 1 1h12a1 1 0 0 0 1-1v-2.5a.5.5 0 0 1 1 0v2.5a2 2 0 0 1-2 2H2a2 2 0 0 1-2-2v-2.5a.5.5 0 0 1 .5-.5z\"/>\n            <path\n              d=\"M7.646 11.854a.5.5 0 0 0 .708 0l3-3a.5.5 0 0 0-.708-.708L8.5 10.293V1.5a.5.5 0 0 0-1 0v8.793L5.354 8.146a.5.5 0 1 0-.708.708l3 3z\"/>\n          </svg>\n        </button>\n        <div class=\"dropdown-menu\" aria-labelledby=\"dropdownMenuButton\">\n          <div class=\"dropdown-item\">\n            <label>Download as: </label>\n            &nbsp;\n            <div class=\"btn-group\">\n              <button\n                [className]=\"submitted ? 'btn btn-sky-blue text-white' : 'btn btn-outline-secondary'\"\n                type=\"button\" (click)=\"onDownloadJson()\">\n                JSON\n              </button>\n              <button\n                [className]=\"submitted ? 'btn btn-sky-blue text-white' : 'btn btn-outline-secondary'\"\n                type=\"button\" (click)=\"onDownloadOriginal()\"\n              >Original\n              </button>\n            </div>\n          </div>\n        </div>\n        &nbsp;\n        <input type=\"file\"\n               #uploader\n               style=\"display: none\"\n               id=\"file\"\n               (change)=\"uploadSequenceFile($event)\">\n\n        <ng-template #uploadSequencesTipContent>\n          <div>\n            Upload sequence file <br> (.txt, .json, .fasta)\n          </div>\n\n        </ng-template>\n        <button type=\"button\" class=\"btn btn-dark-blue-grey btn-sm text-white\" (click)=\"uploader.click()\" [disabled]=\"loading\"\n                ngbTooltip='Clear allele(s)'\n                [ngbTooltip]=\"uploadSequencesTipContent\" placement=\"right\">\n          <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\" class=\"bi bi-upload\"\n               viewBox=\"0 0 16 16\">\n            <path\n              d=\"M.5 9.9a.5.5 0 0 1 .5.5v2.5a1 1 0 0 0 1 1h12a1 1 0 0 0 1-1v-2.5a.5.5 0 0 1 1 0v2.5a2 2 0 0 1-2 2H2a2 2 0 0 1-2-2v-2.5a.5.5 0 0 1 .5-.5z\"/>\n            <path\n              d=\"M7.646 1.146a.5.5 0 0 1 .708 0l3 3a.5.5 0 0 1-.708.708L8.5 2.707V11.5a.5.5 0 0 1-1 0V2.707L5.354 4.854a.5.5 0 1 1-.708-.708l3-3z\"/>\n          </svg>\n        </button>\n        &nbsp;\n      </div>\n    </div>\n    <div class=\"d-flex flex-column p-2\" appDnd (fileDropped)=\"onFileDropped($event)\">\n      <!--      [style.border-color]=\"inputChange.input_sequence_text ? '#f0ad4d' : null\"    -->\n      <textarea class='form-control'\n                [style.border-color]=\"inputChange.input_sequence_text ? '#f0ad4d' : null\"\n                id=\"sequenceFormControlTextArea\"\n                rows=\"10\"\n                formControlName=\"inputSequenceText\"\n                [maxlength]=\"maxCharacters\"\n                [readOnly]=\"loading\"\n                [placeholder]=\"'Type/paste/drag a sequence into this box or click \\'Run\\' to use the example sequence:\\n FLYNPLTRV\\tFLYNLLTRV\\nMLGERLFPL\\tMLGEQLFPL\\nFLDEFMEAV\\tFLDEFMEGV\\nVVLSWAPPV\\tVVMSWAPPV\\nLLLDDSLVSI\\tLLLDDLLVSI\\nGSFGDIYLA\\tGLFGDIYLA\\nALYGSVPVL\\tALYGFVPVL\\nILTGLNYEA\\tILTGLNYEV\\nSLADEAEVHL\\tSLADEAEVYL\\nCQWGRLWQL\\tCMWGRLWQL'\"></textarea>\n\n      <div class=\"d-flex flex-row-reverse justify-content-between p-2\">\n        <small *ngIf=\"inputSequenceText.length >= maxCharacters; else sequenceCounter\" class=\"text-danger\">\n          Sequence text is too long -  {{maxCharacters | number}} characters allowed\n        </small>\n        <ng-template #sequenceCounter>\n          <small class=\"text-muted\">\n            {{numOfCharacters | number}} characters\n          </small>\n        </ng-template>\n        <small *ngIf=\"inputChange.input_sequence_text\" class=\"help-block form-text text-warning\">\n          Parameter changed since prediction.\n        </small>\n      </div>\n    </div>\n  </ng-container>\n\n  <!--  Prediction parameter -->\n  <div class=\"row p-2\">\n    <h5 class=\"col-3 text-left\">Prediction Parameters</h5>\n    <div class=\"col-9\">\n      <!--      <button type=\"button\" class=\"btn btn-sm btn-primary\" (click)=\"formUrl()\"-->\n      <!--              data-toggle=\"dropdown\" aria-haspopup=\"true\" aria-expanded=\"false\">-->\n      <!--        <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"-->\n      <!--             class=\"bi bi-download\" viewBox=\"0 0 16 16\">-->\n      <!--          <path-->\n      <!--            d=\"M.5 9.9a.5.5 0 0 1 .5.5v2.5a1 1 0 0 0 1 1h12a1 1 0 0 0 1-1v-2.5a.5.5 0 0 1 1 0v2.5a2 2 0 0 1-2 2H2a2 2 0 0 1-2-2v-2.5a.5.5 0 0 1 .5-.5z\"/>-->\n      <!--          <path-->\n      <!--            d=\"M7.646 11.854a.5.5 0 0 0 .708 0l3-3a.5.5 0 0 0-.708-.708L8.5 10.293V1.5a.5.5 0 0 0-1 0v8.793L5.354 8.146a.5.5 0 1 0-.708.708l3 3z\"/>-->\n      <!--        </svg>-->\n      <!--      </button>-->\n      <!--      <div class=\"dropdown-menu\" aria-labelledby=\"dropdownMenuButton\">-->\n      <!--        <div class=\"dropdown-item\">-->\n      <!--          <button class='btn btn-primary' type=\"button\" (click)=\"onDownloadInput()\"-->\n      <!--                  ngbTooltip=\"Download a JSON file that includes the parameters set on this page.\"-->\n      <!--                  placement=\"left\">-->\n      <!--            Download Prediction Parameters-->\n      <!--          </button>-->\n      <!--        </div>-->\n      <!--      </div>-->\n\n      <ng-template #downloadParametersTipContent>\n        Download parameters\n      </ng-template>\n\n      <button class='btn btn-dark-blue-grey btn-sm text-white' type=\"button\" (click)=\"onDownloadParameter()\"\n              [ngbTooltip]=\"downloadParametersTipContent\" placement=\"right\">\n        <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-download\" viewBox=\"0 0 16 16\">\n          <path\n            d=\"M.5 9.9a.5.5 0 0 1 .5.5v2.5a1 1 0 0 0 1 1h12a1 1 0 0 0 1-1v-2.5a.5.5 0 0 1 1 0v2.5a2 2 0 0 1-2 2H2a2 2 0 0 1-2-2v-2.5a.5.5 0 0 1 .5-.5z\"/>\n          <path\n            d=\"M7.646 11.854a.5.5 0 0 0 .708 0l3-3a.5.5 0 0 0-.708-.708L8.5 10.293V1.5a.5.5 0 0 0-1 0v8.793L5.354 8.146a.5.5 0 1 0-.708.708l3 3z\"/>\n        </svg>\n      </button>\n    </div>\n  </div>\n  <!--  Peptide Length -->\n<!--  <div class=\"form-group row p-2\" id=\"peptideLengthRow\">-->\n<!--    <div class=\"col-sm-3 col-form-label\">-->\n<!--      <label class=\"text-left\">Peptide Length(s)</label>-->\n<!--    </div>-->\n\n<!--    <div class=\"col-sm-8\">-->\n<!--      <div [className]=\"inputChange.lengths ? 'input-change-slider' : null\">-->\n<!--        <ngx-slider-->\n<!--          formControlName=\"peptideLength\"-->\n<!--          (userChangeEnd)=\"onLengthChange($event)\"-->\n<!--          [options]=\"peptideLengthSliderOptions\"></ngx-slider>-->\n<!--        <small *ngIf=\"inputChange.lengths\" class=\"help-block form-text text-warning\">-->\n<!--          Parameter changed since prediction.-->\n<!--        </small>-->\n<!--      </div>-->\n\n<!--    </div>-->\n<!--    <div class=\"col-sm-1\">-->\n<!--      <div class=\"form-check pt-4\">-->\n<!--        <input class=\"form-check-input\"-->\n<!--               type=\"checkbox\"-->\n<!--               id=\"asIsCheckbox\"-->\n<!--               formControlName=\"breakPeptides\"-->\n<!--               [attr.disabled]=\"loading ? true : null\"-->\n<!--        >-->\n<!--        <label class=\"form-check-label\" for=\"asIsCheckbox\" ngbTooltip='as-is defintion' placement=\"right\">-->\n<!--          as-is-->\n<!--        </label>-->\n<!--      </div>-->\n<!--    </div>-->\n<!--  </div>-->\n\n  <div class=\"form-group row p-2\" id=\"alleleRow\">\n    <div class=\"col-sm-3 col-form-label\">\n      <label class=\"text-left\">\n        MHC Allele(s)\n      </label>\n    </div>\n    <div class=\"col-sm-4\">\n      <div class=\"d-flex flex-row\">\n        <ng-template #rt let-r=\"result\" let-t=\"term\">\n          <ngb-highlight [result]=\"resultFormatter(r)\" [term]=\"t\"></ngb-highlight>\n        </ng-template>\n        <input #alleleSearch id=\"allAlleles\" type=\"text\" class=\"form-control\"\n               [style.border-color]=\"inputChange.alleles ? '#f0ad4d' : null\"\n               [ngbTypeahead]=\"search\"\n               [inputFormatter]=\"inputFormatter\"\n               [resultTemplate]=\"rt\"\n               [editable]=\"false\"\n               [disabled]=\"loading\"\n               (selectItem)=\"onAlleleSelect({e : $event, input : alleleSearch})\"\n               [placeholder]=\"'Ex: HLA-A*02:01'\"\n        />\n      </div>\n    </div>\n    <div class=\"col-sm-1\">\n      <div *ngIf=\"searching && !modalOpen\" class=\"d-flex justify-content-center col\">\n        <div class=\"spinner-border text-primary align-self-center\" role=\"status\">\n          <span class=\"visually-hidden sr-only\">Loading...</span>\n        </div>\n      </div>\n    </div>\n    <div class=\"col-sm-4 text-start\">\n      <button type=\"button\" class=\"btn btn-dark-blue-grey text-white\"\n              (click)=\"onOpenAlleleModal()\"\n              [style]=\"{'whiteSpace': 'nowrap', 'textAlign': 'center'}\"\n              [disabled]=\"loading\">\n        Allele Finder\n      </button>\n    </div>\n  </div>\n  <div class=\"row p-2\">\n    <div class=\"offset-sm-3 col-sm-9\" style=\"min-height: 40px\">\n      <div [className]=\"inputChange.alleles ? 'p-2 input-change' : 'p-2 border'\">\n        <mat-chip-list>\n          <mat-chip *ngFor=\"let allele of alleles.value; let j=index;\">\n            {{allele.label}}\n            <button matChipRemove (click)=\"onAlleleDeselect(j)\" [disabled]=\"loading\">\n              <mat-icon>cancel</mat-icon>\n            </button>\n          </mat-chip>\n        </mat-chip-list>\n      </div>\n      <small *ngIf=\"inputChange.alleles\" class=\"help-block form-text text-warning\">\n        Parameter changed since prediction.\n      </small>\n    </div>\n  </div>\n\n  <div class=\"d-flex flex-row-reverse justify-content-between p-2\">\n    <small class=\"text-muted\">\n      {{alleles.length}} allele(s)\n    </small>\n  </div>\n\n\n  <div class=\"row p-2\">\n    <label class=\"col-sm-12 pb-2 text-left\">\n      Prediction Model(s)\n    </label>\n  </div>\n\n  <div cdkDropList id=\"prediction-model-list\" (cdkDropListDropped)=\"dropPredictionModel($event)\"\n       class=\"d-flex flex-column p-2\">\n    <!--    [className]=\"inputChange.predictors ? 'input-change' : null\"-->\n    <div [className]=\"inputChange.predictors ? 'input-change' : null\">\n      <div class=\"d-flex flex-row bg-secondary-new border\" *ngFor=\"let pm of predictionModels.controls; let i=index;\" cdkDrag [cdkDragDisabled]=\"loading\">\n        <!--Prediction Models-->\n        <div cdkDragHandle class=\"p-3 justify-content-start align-self-center align-content-center drag-handle\">\n          <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"24\" height=\"24\" fill=\"currentColor\" class=\"bi bi-justify\"\n               viewBox=\"0 0 16 16\">\n            <path fill-rule=\"evenodd\"\n                  d=\"M2 12.5a.5.5 0 0 1 .5-.5h11a.5.5 0 0 1 0 1h-11a.5.5 0 0 1-.5-.5zm0-3a.5.5 0 0 1 .5-.5h11a.5.5 0 0 1 0 1h-11a.5.5 0 0 1-.5-.5zm0-3a.5.5 0 0 1 .5-.5h11a.5.5 0 0 1 0 1h-11a.5.5 0 0 1-.5-.5zm0-3a.5.5 0 0 1 .5-.5h11a.5.5 0 0 1 0 1h-11a.5.5 0 0 1-.5-.5z\"/>\n          </svg>\n        </div>\n        <app-mhc-binding-formgroup *ngIf=\"pm.get('type')?.value === 'binding'\" [formGroup]=\"$any(pm)\"\n                                   style=\"width:100%\"\n                                   [modelIndex]=\"i\" [disabled]=\"loading\"\n                                   [predictionOption]=\"predictionOptions\"\n                                   (emitPredictionModelIndex)=\"removePredictorByIndex(i)\"></app-mhc-binding-formgroup>\n        <app-pmhc-immunogenicity-formgroup *ngIf=\"pm.get('type')?.value === 'immunogenicity'\" [formGroup]=\"$any(pm)\"\n                                           style=\"width:100%\"\n                                           [modelIndex]=\"i\" [disabled]=\"loading\"\n                                           (emitPredictionModelIndex)=\"removePredictorByIndex(i)\"></app-pmhc-immunogenicity-formgroup>\n<!--        <app-mhc-i-processing-formgroup-new *ngIf=\"pm.get('type')?.value === 'processing'\" [formGroup]=\"$any(pm)\"-->\n<!--                                            style=\"width:100%\"-->\n<!--                                            [modelIndex]=\"i\" [disabled]=\"loading\"-->\n<!--                                            [processingOptions]=\"processingOptions\"-->\n<!--                                            [basicProcessingPredictionOption]=\"basicProcessingPredictionOption\"-->\n<!--                                            (emitPredictionModelIndex)=\"removePredictorByIndex(i)\"></app-mhc-i-processing-formgroup-new>-->\n        <!--        <app-mhc-np-formgroup *ngIf=\"pm.get('type')?.value === 'mhcnp'\" [formGroup]=\"$any(pm)\"-->\n        <!--                              style=\"width:100%\"-->\n        <!--                              [modelIndex]=\"i\" [disabled]=\"loading\"-->\n        <!--                              [predictionOption]=\"predictionOptions\"-->\n        <!--                              (emitPredictionModelIndex)=\"removePredictorByIndex(i)\"></app-mhc-np-formgroup>-->\n      </div>\n    </div>\n  </div>\n  <small *ngIf=\"inputChange.predictors\" class=\"help-block form-text text-warning\">\n    Parameter changed since prediction.\n  </small>\n\n\n  <div class=\"d-flex flex-row-reverse p-2\">\n    <div class=\"p-2\">\n      <div class=\"dropdown\">\n        <button class=\"btn btn-dark-blue-grey text-white dropdown-toggle\" type=\"button\" id=\"predictionModelDropdownMenu\"\n                data-bs-toggle=\"dropdown\"\n                data-toggle=\"dropdown\"\n                aria-haspopup=\"true\" aria-expanded=\"false\" [disabled]=\"loading\">\n          Add Another Prediction\n        </button>\n        <div class=\"dropdown-menu\" aria-labelledby=\"dropdownMenu2\">\n<!--          addpredictionModel()-->\n<!--          addPmhcImmungencityFormGroup()-->\n          <button class=\"dropdown-item\" type=\"button\" (click)=\"addpredictionModel()\">MHC Binding/Elution</button>\n          <button class=\"dropdown-item\" type=\"button\" (click)=\"addPmhcImmungencityFormGroup()\">Class I pMHC\n            Immunogenicity\n          </button>\n<!--          <button class=\"dropdown-item\" type=\"button\" (click)=\"addMhcIProcessingNewFormGroup()\">MHC-I Processing-->\n\n<!--          </button>-->\n          <!--            TODO take all of mhcnp prediction model out - it will be added to PredictionModel-->\n          <!--          <button class=\"dropdown-item\" type=\"button\" (click)=\"addMhcNPFormGroup()\">MHC-NP-->\n          <!--          </button>-->\n        </div>\n      </div>\n    </div>\n  </div>\n  <hr/>\n\n  <div class=\"form-group d-flex flex-row-reverse pt-2\">\n\n    <div class=\"p-2\">\n      <!--        [disabled]=\"filteredSequences.length===0\"-->\n      <button type=\"button\" class=\"reset-button btn btn-secondary btn-lg\" [disabled]=\"loading\"\n              (click)=\"onReset(); alleleSearch.value='';\">\n        <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-arrow-clockwise\" viewBox=\"0 0 16 16\">\n          <path fill-rule=\"evenodd\" d=\"M8 3a5 5 0 1 0 4.546 2.914.5.5 0 0 1 .908-.417A6 6 0 1 1 8 2v1z\"/>\n          <path\n            d=\"M8 4.466V.534a.25.25 0 0 1 .41-.192l2.36 1.966c.12.1.12.284 0 .384L8.41 4.658A.25.25 0 0 1 8 4.466z\"/>\n        </svg>\n      </button>\n      &nbsp;\n      <span *ngIf=\"loading; else elseBlock\">\n        <button type=\"button\" class=\"btn btn-danger btn-lg\" (click)=\"onCancel()\"> Cancel Run </button>\n      </span>\n      <ng-template #elseBlock>\n        <div *ngIf=\"index!==0; else runButtonBlock\" class=\"btn-group\">\n          <div class=\"btn-group\">\n            <button type=\"submit\" class=\"run-button btn btn-dark-blue-grey btn-lg text-white\"\n                    [disabled]=\"\n                    (!pepcompForm.get('predictionModels')!.value.length) ||\n                    (index>0 && !tools[index-1].submitted) ||\n                    pipelineLoading\"\n            >\n              <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\" class=\"bi bi-play-fill\" viewBox=\"0 0 16 16\">\n                <path d=\"m11.596 8.697-6.363 3.692c-.54.313-1.233-.066-1.233-.697V4.308c0-.63.692-1.01 1.233-.696l6.363 3.692a.802.802 0 0 1 0 1.393z\"/>\n              </svg>\n            </button>\n            <button type=\"button\" class=\"btn btn-dark-blue-grey text-white dropdown-toggle dropdown-toggle-split\"\n                    data-toggle=\"dropdown\"\n                    data-bs-toggle=\"dropdown\" aria-haspopup=\"true\" aria-expanded=\"false\"\n                    [disabled]=\"\n                    (!pepcompForm.get('predictionModels')!.value.length) ||\n                    pipelineLoading\">\n              <!--              <span class=\"sr-only\">Toggle Dropdown</span>-->\n            </button>\n            <div class=\"dropdown-menu\">\n              <a class=\"dropdown-item\" (click)=\"onRunAll()\">Run All Above</a>\n            </div>\n          </div>\n        </div>\n        <ng-template #runButtonBlock>\n          <button type=\"submit\" class=\"run-button btn btn-dark-blue-grey btn-lg text-white\"\n                  [disabled]=\"\n                    (!pepcompForm.get('predictionModels')!.value.length) ||\n                    (index>0 && !tools[index-1].submitted) ||\n                    pipelineLoading\"\n          >\n            <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\" class=\"bi bi-play-fill\" viewBox=\"0 0 16 16\">\n              <path d=\"m11.596 8.697-6.363 3.692c-.54.313-1.233-.066-1.233-.697V4.308c0-.63.692-1.01 1.233-.696l6.363 3.692a.802.802 0 0 1 0 1.393z\"/>\n            </svg>\n          </button>\n        </ng-template>\n\n      </ng-template>\n    </div>\n  </div>\n</form>\n<!--Errors and Warnings accordion -->\n<div ngbAccordion>\n  <!--  Error -->\n  <div ngbAccordionItem=\"first\" *ngIf=\"errorMessages.length\" #first=\"ngbAccordionItem\" [collapsed]=\"true\">\n    <h2 ngbAccordionHeader>\n      <button ngbAccordionButton class=\"accordion-button justify-content-center\">\n        <span class=\"text-danger m-1\">Errors ({{errorMessages.length}})</span>\n        <!--        <div>-->\n        <svg *ngIf=\"first.collapsed\" xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-arrow-left-circle-fill\" style=\"color: #dc3545;\" viewBox=\"0 0 16 16\">\n          <path\n            d=\"M8 0a8 8 0 1 0 0 16A8 8 0 0 0 8 0zm3.5 7.5a.5.5 0 0 1 0 1H5.707l2.147 2.146a.5.5 0 0 1-.708.708l-3-3a.5.5 0 0 1 0-.708l3-3a.5.5 0 1 1 .708.708L5.707 7.5H11.5z\"/>\n        </svg>\n        <!--        </div>-->\n        <!--        <div>-->\n        <svg *ngIf=\"!first.collapsed\" xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-arrow-down-circle-fill\" style=\"color: #dc3545;\" viewBox=\"0 0 16 16\">\n          <path\n            d=\"M16 8A8 8 0 1 1 0 8a8 8 0 0 1 16 0zM8.5 4.5a.5.5 0 0 0-1 0v5.793L5.354 8.146a.5.5 0 1 0-.708.708l3 3a.5.5 0 0 0 .708 0l3-3a.5.5 0 0 0-.708-.708L8.5 10.293V4.5z\"/>\n        </svg>\n        <!--        </div>-->\n      </button>\n    </h2>\n    <div ngbAccordionCollapse>\n      <div ngbAccordionBody>\n        <ng-template>\n          <ol>\n            <li *ngFor=\"let message of errorMessages; let i=index;\">{{message}}</li>\n          </ol>\n        </ng-template>\n      </div>\n    </div>\n  </div>\n  <!--  Warning -->\n  <div ngbAccordionItem=\"second\" *ngIf=\"warningMessages.length\" #second=\"ngbAccordionItem\" [collapsed]=\"true\">\n    <h2 ngbAccordionHeader>\n      <button ngbAccordionButton class=\"accordion-button justify-content-center\">\n        <span class=\"text-warning m-1\">Warnings ({{warningMessages.length}})</span>\n        <svg *ngIf=\"second.collapsed\"  xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-arrow-left-circle-fill\" style=\"color: #f0ad4d;\" viewBox=\"0 0 16 16\">\n          <path\n            d=\"M8 0a8 8 0 1 0 0 16A8 8 0 0 0 8 0zm3.5 7.5a.5.5 0 0 1 0 1H5.707l2.147 2.146a.5.5 0 0 1-.708.708l-3-3a.5.5 0 0 1 0-.708l3-3a.5.5 0 1 1 .708.708L5.707 7.5H11.5z\"/>\n        </svg>\n        <svg *ngIf=\"!second.collapsed\" xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-arrow-down-circle-fill\" style=\"color: #f0ad4d;\" viewBox=\"0 0 16 16\">\n          <path\n            d=\"M16 8A8 8 0 1 1 0 8a8 8 0 0 1 16 0zM8.5 4.5a.5.5 0 0 0-1 0v5.793L5.354 8.146a.5.5 0 1 0-.708.708l3 3a.5.5 0 0 0 .708 0l3-3a.5.5 0 0 0-.708-.708L8.5 10.293V4.5z\"/>\n        </svg>\n      </button>\n    </h2>\n    <div ngbAccordionCollapse>\n      <div ngbAccordionBody>\n        <ng-template>\n          <ol>\n            <li *ngFor=\"let message of warningMessages; let i=index;\">{{message}}</li>\n          </ol>\n        </ng-template>\n      </div>\n    </div>\n  </div>\n</div>\n\n<div *ngIf=\"!loading && !submitted && !(errorMessages.length && warningMessages.length)\"\n     class=\"p-2 d-flex justify-content-center col\"\n     [style.borderStyle]=\"styleResultContainer\">\n  <label class=\"p-2 font-italic\">\n    Results will load once step is run.\n  </label>\n</div>\n\n<div *ngIf=\"loading\" class=\"p-2 d-flex justify-content-center col\" [style.borderStyle]=\"styleResultContainer\">\n  <div class=\"spinner-border text-primary align-self-center p-3 mb-3\" role=\"status\">\n    <span class=\"visually-hidden sr-only\">Loading...</span>\n  </div>\n  <label *ngIf=\"!getResultsClicked\" class=\"p-2 font-italic\">\n    Calculating results, please wait... Click <a href=\"javascript:void(0)\" (click)=\"openEmailModal.emit()\">here</a> to\n    receive email.\n  </label>\n  <label *ngIf=\"getResultsClicked\" class=\"p-2 font-italic\">\n    Checking job status, please wait...\n  </label>\n</div>\n\n<div class=\"container-fluid p-2\" id=\"table-result-container\"\n     *ngIf=\"!loading && submitted  && !(errorMessages.length && warningMessages.length)\">\n  <ul ngbNav #nav=\"ngbNav\" [(activeId)]=\"active\" [animation]='false' [destroyOnHide]=\"false\" class=\"nav-tabs\">\n    <!--    Peptide Table -->\n    <li *ngIf=\"peptide_table[0].length\" [ngbNavItem]=\"'peptide_table'\">\n      <a ngbNavLink>Peptide Table</a>\n      <ng-template ngbNavContent>\n<!--        Result Table -->\n        <app-result-table [table_data]=\"peptide_table\"\n                          table_name=\"peptide_table\"\n                          [order]=\"peptide_table_order\"\n                          [columns]=\"peptide_table_columns\"\n                          [tool_group]=\"formGroupName\"\n                          [index]=\"index\"\n                          [inputChange]=\"inputChange.table_state\"\n                          [tableStateSaving]=\"tableStateSaving\"\n                          (emitFilterApplied)=\"onFilterApplied()\"\n                          (emitResetTableState)=\"onClearTableState()\"\n                          (emitSaveTableState)=\"onSaveTableStateMain()\"></app-result-table>\n      </ng-template>\n    </li>\n    <!--    Sequence Table -->\n    <li *ngIf=\"sequence_table[0].length\" [ngbNavItem]=\"'sequence_table'\">\n      <a ngbNavLink> Sequence Table </a>\n      <ng-template ngbNavContent>\n        <app-result-table [table_data]=\"sequence_table\"\n                          table_name=\"sequence_table\"\n                          [order]=\"sequence_table_order\"\n                          [columns]=\"sequence_table_columns\"\n                          [tool_group]=\"formGroupName\"\n                          (emitResetTableState)=\"onClearTableState()\"></app-result-table>\n      </ng-template>\n    </li>\n\n    <li [ngbNavItem]=\"'scatter_plots'\">\n      <a ngbNavLink>Scatter Plots</a>\n      <ng-template ngbNavContent>\n        <app-d3-plot [plotData]=\"scatterPlotData\"></app-d3-plot>\n      </ng-template>\n    </li>\n  </ul>\n\n  <div [ngbNavOutlet]=\"nav\"></div>\n</div>\n\n<!--Allele Select Modal-->\n<ng-template #alleleModal let-modal2>\n  <div class=\"modal-header\">\n    <h4 class=\"modal-title\" id=\"modal-allele-title\">\n      Number of Selected Alleles: {{modalAlleles.length}}\n    </h4>\n    <button type=\"button\" class=\"btn-close\" aria-label=\"Close\"\n            (click)=\"dismissAlleleModal();\">\n    </button>\n  </div>\n\n  <div class=\"modal-body\">\n    <div class=\"form-group row p-2\">\n      <div class=\"col-sm-3 col-form-label\">\n        <label [className]=\"'font-weight-bold'\">\n          MHC Allele(s)\n        </label>\n      </div>\n      <div class=\"col-sm-7 d-flex flex-row\">\n        <!--        <input class=\"form-control\" formControlName=\"allele\" type=\"text\" placeholder=\"HLA-A*02:01,HLA-A*01:01\">-->\n        <input #alleleSearchModal type=\"text\" class=\"form-control\"\n               [ngbTypeahead]=\"search\"\n               [inputFormatter]=\"inputFormatter\"\n               [resultTemplate]=\"rt\"\n               [editable]=\"false\"\n               [disabled]=\"loading\"\n               (selectItem)=\"onAlleleSelectModal({e : $event, input : alleleSearchModal})\"\n               (blur)=\"onBlurAlleleSelectModal($event, alleleSearchModal)\"\n               (focus)=\"alleleSearchModal.value=''; alleleSearchModal.placeholder=''\"\n               [defaultValue]=\"modalAlleles.length ? selectedModalAlleleLabels : ''\"\n               [placeholder]=\"'Ex: HLA-A*02:01'\"\n               placement=\"bottom-left\"\n        />\n      </div>\n      <div class=\"col-sm-2\">\n        <div *ngIf=\"searching\" class=\"d-flex justify-content-center col\">\n          <div class=\"spinner-border text-primary align-self-center\" role=\"status\">\n            <span class=\"visually-hidden sr-only\">Loading...</span>\n          </div>\n        </div>\n      </div>\n    </div>\n\n    <div *ngIf=\"modalAlleles.length > 0\" class=\"p-2 d-flex flex-column justify-content-start\">\n\n      <ul class=\"list-group\">\n        <!--<li *ngFor=\"let i of selectedAssayProtocols;\" class=\"list-group-item list-group-item-success\">{{i['allele']['allele']}} {{i['assayCondition'] && '+'}} {{i['assayCondition']}}</li>-->\n        <li *ngFor=\"let i of modalAlleles; let j=index;\" class=\"list-group-item list-group-item-primary list-group-item-action\">{{i['label']}}\n          <button class=\"btn-close float-end\" type=\"button\" (click)=\"onAlleleDeselect2(j, alleleSearchModal)\"\n                  [disabled]=\"loading\">\n          </button>\n        </li>\n      </ul>\n    </div>\n    <div class=\"modal-footer\" style=\"overflow-x: auto; overflow-y: auto\">\n      <fieldset class=\"w-100\">\n        <button type=\"button\" class=\"btn btn-secondary\" (click)=\"generate27Alleles(alleleSearchModal)\"\n                ngbTooltip=\"Covers ~97% of the human population\"\n                placement=\"bottom\">27 Allele Panel\n        </button>\n        <button type=\"button\" class=\"btn btn-sm\" placement=\"bottom\"\n                [ngbPopover]=\"popOverContent\"\n                popoverTitle=\"27 Allele Panel Source\">\n          <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\" class=\"bi bi-info-circle\"\n               viewBox=\"0 0 16 16\">\n            <path d=\"M8 15A7 7 0 1 1 8 1a7 7 0 0 1 0 14zm0 1A8 8 0 1 0 8 0a8 8 0 0 0 0 16z\"/>\n            <path\n              d=\"m8.93 6.588-2.29.287-.082.38.45.083c.294.07.352.176.288.469l-.738 3.468c-.194.897.105 1.319.808 1.319.545 0 1.178-.252 1.465-.598l.088-.416c-.2.176-.492.246-.686.246-.275 0-.375-.193-.304-.533L8.93 6.588zM9 4.5a1 1 0 1 1-2 0 1 1 0 0 1 2 0z\"/>\n          </svg>\n        </button>\n        <ng-template #popOverContent>\n          <a target=\"_blank\"\n             href=\"https://help.iedb.org/hc/en-us/articles/114094151851-HLA-allele-frequencies-and-reference-sets-with-maximal-population-coverage\">\n            HLA allele frequencies and reference sets with maximal population coverage\n          </a>\n        </ng-template>\n        <div class=\"float-end\">\n          <button type=\"button\" class=\"btn btn-secondary mx-1\" (click)=\"onAlleleClearModal(alleleSearchModal);\">\n            Clear Selected Allele(s)\n          </button>\n          <button type=\"button\" class=\"btn btn-dark-blue-grey text-white mx-1\" (click)=\"onSubmitModalAlleles();\">\n            Submit\n          </button>\n        </div>\n      </fieldset>\n    </div>\n\n\n  </div>\n</ng-template>\n\n\n<!--Alert Modal -->\n<ng-template #alertModal let-modal4>\n  <div class=\"modal-header\">\n    <h4 class=\"modal-title\" id=\"alert-modal-title\">Validation Error(s)</h4>\n    <button type=\"button\" class=\"btn-close\" aria-label=\"Close\" (click)=\"modal4.dismiss('Cross click'); modalOpen=false;\">\n    </button>\n  </div>\n  <div class=\"modal-body\">\n    <app-alert-component></app-alert-component>\n  </div>\n  <div class=\"modal-footer\">\n    <!--    <button type=\"button\" class=\"btn btn-secondary\" (click)=\"null\">Reset</button>-->\n    <!--    <button type=\"button\" class=\"btn btn-primary\" (click)=\"null\">Display</button>-->\n  </div>\n</ng-template>\n\n<!--Confirm Modal -->\n<ng-template #confirmModal let-confirmModal>\n  <div class=\"modal-header\">\n    <h4 class=\"modal-title\" id=\"modal-title\">Are you sure?</h4>\n    <button type=\"button\" class=\"btn-close\" aria-label=\"Close\" (click)=\"confirmModal.dismiss('Cross click'); modalOpen=false;\">\n    </button>\n  </div>\n  <div class=\"modal-body\">\n    <div *ngIf=\"!saveState; else saveStateConfirmation\">\n      <p><strong>Re-running this step of the pipeline will delete all downstream results, including:</strong></p>\n      <ol>\n        <li *ngFor=\"let tool of tools.slice(this.index+1)\"> {{tool.name}} </li>\n      </ol>\n      <p><strong>To access the current results, you can use this link</strong></p>\n    </div>\n    <ng-template #saveStateConfirmation>\n      <p><strong>Applying these filters for input to the next stage will delete results from all downstream steps in\n        this session, including:</strong></p>\n      <ol>\n        <li *ngFor=\"let tool of tools.slice(this.index+1)\"> {{tool.name}} </li>\n      </ol>\n      <p><strong>To access the current results, you can use this link</strong></p>\n    </ng-template>\n    <!-- pipeline URL input group-->\n    <div class=\"input-group\">\n      <input type=\"text\" class=\"form-control\" id=\"pipeline-url-input\" [value]=\"pipelineUrl\">\n      <button class=\"btn btn-secondary\" [cdkCopyToClipboard]=\"pipelineUrl\" ngbTooltip=\"copy url\" placement=\"top\">\n        <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-clipboard\" viewBox=\"0 0 16 16\">\n          <path\n            d=\"M4 1.5H3a2 2 0 0 0-2 2V14a2 2 0 0 0 2 2h10a2 2 0 0 0 2-2V3.5a2 2 0 0 0-2-2h-1v1h1a1 1 0 0 1 1 1V14a1 1 0 0 1-1 1H3a1 1 0 0 1-1-1V3.5a1 1 0 0 1 1-1h1v-1z\"/>\n          <path\n            d=\"M9.5 1a.5.5 0 0 1 .5.5v1a.5.5 0 0 1-.5.5h-3a.5.5 0 0 1-.5-.5v-1a.5.5 0 0 1 .5-.5h3zm-3-1A1.5 1.5 0 0 0 5 1.5v1A1.5 1.5 0 0 0 6.5 4h3A1.5 1.5 0 0 0 11 2.5v-1A1.5 1.5 0 0 0 9.5 0h-3z\"/>\n        </svg>\n      </button>\n    </div>\n  </div>\n  <div class=\"modal-footer\">\n    <button type=\"button\" class=\"btn btn-outline-secondary\" (click)=\"confirmModal.dismiss('cancel click')\">No\n    </button>\n    <button type=\"button\" class=\"btn btn-danger\" (click)=\"confirmModal.close('Ok click'); onRunConfirm();\">Yes, continue\n      and destroy downstream steps\n    </button>\n  </div>\n</ng-template>\n","import {\n  Component,\n  OnInit,\n  OnDestroy,\n  Input,\n  Output,\n  EventEmitter,\n  ViewChild,\n  ElementRef,\n  OnChanges,\n  SimpleChanges,\n  AfterViewInit,\n  isDevMode\n} from '@angular/core';\nimport {HttpClient} from \"@angular/common/http\";\nimport {UntypedFormBuilder, UntypedFormGroup, FormControl, UntypedFormArray, FormGroupDirective, Validators} from \"@angular/forms\";\n\nimport {CdkDragDrop} from '@angular/cdk/drag-drop';\nimport { Location } from '@angular/common';\nimport {Title} from \"@angular/platform-browser\";\n\nimport {Observable, timer, of, from, Subject, Subscription} from \"rxjs\";\nimport {NgbModal, NgbActiveModal} from '@ng-bootstrap/ng-bootstrap';\n\nimport {catchError, debounce, debounceTime, distinctUntilChanged, tap, switchMap, takeUntil} from 'rxjs/operators';\nimport {environment} from \"../../../environments/environment\";\nimport {AlertServiceService} from \"../../services/alert-service/alert-service.service\";\nimport {AlleleSearchService} from \"../../services/allele-search/allele-search.service\";\nimport {PipelineService} from \"../../services/pipeline-service/pipeline.service\";\nimport {PipelineStateService} from \"../../services/state-services/pipeline-state-service/pipeline-state.service\";\nimport {ActivatedRoute, Router} from \"@angular/router\";\nimport {SequenceParserService} from \"../../services/sequence-parser/sequence-parser.service\";\nimport Stage from \"../../_global/Stage\";\nimport Tool from \"../../_global/Tool\";\nimport PipelineParams from \"../../_global/PipelineParams\";\nimport _ from \"lodash\";\nimport * as sarsSampleData from \"../../services/data/t-cell-sample.json\";\nimport * as pepCompSampleData from \"../../services/data/pepcomp-sample.json\";\nimport * as pipelineData from \"../../services/data/pipeline-example.json\";\nimport Allele from \"../../_global/Allele\";\nimport * as alleleData from \"../../services/data/27-alleles.json\";\n// import {initTCellPredictionTool} from \"../../services/state-services/default-stage-states\";\nimport {\n  initPeptideBindingComparisonTool,\n  initTCellPredictionTool\n} from \"../../services/state-services/default-stage-states\";\nimport {isASCII, IsJsonString} from \"../../util/string-helpers\";\nimport {isMaxLength} from \"../../util/is-max-length\";\nimport Columns from \"../../_global/Columns\";\nimport {columnListToObject} from \"../../util/convert-columns\";\nimport onCsvDownloadAllClickedNew from \"../../util/on-csv-download\";\n\nconst API_URL = `${environment['api_url']}/api/v1/pepcomp`;\n\n@Component({\n  selector: 'app-peptide-variant-comparison',\n  templateUrl: './peptide-variant-comparison.component.html',\n  styleUrls: ['./peptide-variant-comparison.component.scss']\n})\nexport class PeptideVariantComparisonComponent implements OnInit, OnDestroy, AfterViewInit, OnChanges{\n  sequencePlaceHolder = `Ex:\nFLYNPLTRV\\tFLYNLLTRV\nMLGERLFPL\\tMLGEQLFPL\nFLDEFMEAV\\tFLDEFMEGV\nVVLSWAPPV\\tVVMSWAPPV\nLLLDDSLVSI\\tLLLDDLLVSI\nGSFGDIYLA\\tGLFGDIYLA\nALYGSVPVL\\tALYGFVPVL\nILTGLNYEA\\tILTGLNYEV\nSLADEAEVHL\\tSLADEAEVYL\nCQWGRLWQL\\tCMWGRLWQL\n`\n\n  /** Pipeline form */\n  @Input() formGroupName!: string\n  @Input() index!: number;\n  @Input() resultUrl!: string | undefined;\n  @Input() showEmailModal: boolean = false;\n\n  @Input() emailForm!: UntypedFormGroup;\n  @Output() openEmailModal = new EventEmitter<any>();\n\n  active = 'processing_plots'\n\n  @Output() emitIndex = new EventEmitter<number>(); // used for run all\n  @Output() emitOnCancel = new EventEmitter<any>();\n\n  @ViewChild('alleleSearch') alleleSearch!: ElementRef;\n  @ViewChild('alertModal') alertModal!: ElementRef;\n  @ViewChild('confirmModal') confirmModal!: ElementRef;\n  @ViewChild('alleleModal') alleleModal!: ElementRef;\n\n\n  @Input() events: Observable<void> = of();\n  private eventsSubscription: Subscription  = new Subscription();\n\n  @Input() runAllEvent: Observable<void> = of();\n  private runAllSubscription: Subscription  = new Subscription();\n\n  unsubscribe$ = new Subject();\n\n  // plotLoading = false;\n  // processingPlots: {method: string, url: string, thresholdInput: number}[] = []\n\n  // d3-plot variable\n  links: any[] = [\n    {\"Framework\": \"Vue\", \"Stars\": \"166443\", \"Released\": \"2014\"},\n    {\"Framework\": \"React\", \"Stars\": \"150793\", \"Released\": \"2013\"},\n    {\"Framework\": \"Angular\", \"Stars\": \"62342\", \"Released\": \"2016\"},\n    {\"Framework\": \"Backbone\", \"Stars\": \"27647\", \"Released\": \"2010\"},\n    {\"Framework\": \"Ember\", \"Stars\": \"21471\", \"Released\": \"2011\"},\n  ];\n\n  /**\n   {\n     <allele_name>: {\n        <peptidea>: float, <peptideb>: float,\n        <sequenceA>: string, <sequenceB>: string\n     }\n   }\n   * */\n  scatterPlotData: any = []\n  /**\n   There are 63 peptide_table columns (\"results.peptide_table.table_columns\") in\n   https://api-nextgen-tools-dev.iedb.org/api/v1/results/d4b4a399-a0b4-4a88-b07d-03288ab9aef7\n\n\n   Also, consider scales for each column,\n\n   i.e. https://gitlab.lji.org/iedb/tools/tools-redesign/ar-redesign-prototype/-/issues/609#note_35183\n\n   peptideA median binding/elution percentile = 1\n   peptideA netmhcpan_el score =\n   peptideA netmhcpan_el percentile = 1\n   peptideA netmhcpan_ba IC50\n   peptideA netmhcpan_ba percentile = 1\n     ...\n   peptideA comblib_sidney2008 IC50/SCORE = ?\n   peptideA comblib_sidney2008 percentile = 1? such small numbers maybe make it 0.1?\n\n   ************************************************\n\n   DISPLAY_NAME value\n\n   peptideA median binding/elution percentile\n   peptideA netmhcpan_el score\n   peptideA netmhcpan_el percentile\n   peptideA netmhcpan_ba IC50\n   peptideA netmhcpan_ba percentile\n   peptideA ann IC50\n   peptideA ann percentile\n   peptideA smmpmbec IC50\n   peptideA smmpmbec percentile\n   peptideA smm IC50\n   peptideA smm percentile\n   peptideA comblib_sidney2008 IC50\n   peptideA comblib_sidney2008 percentile\n   peptideA mhcflurry IC50\n   peptideA mhcflurry percentile\n   peptideA mhcnp score\n   peptideA mhcnp percentile\n   peptideA immunogenicity score\n   peptideA immunogenicity percentile\n\n   { <display_name>:\n    [\n      {\n       <allele>: string,\n       <peptide-peptidea>: string, <peptide-peptideb>: string,\n       <value-peptidea>: float, <value-peptideb>: float,\n      },\n     {\n       <allele>: string,\n       <peptide-peptidea>: string, <peptide-peptideb>: string,\n       <value-peptidea>: float, <value-peptideb>: float,\n     },\n    ],\n    <display_name>: [collection],\n    <display_name>: [collection],\n   }\n\n   EX:\n   { median binding/elution percentile:\n     [\n       {\n         allele: \"HLA-A*02:01\",\n         <peptidea>: \"FLYNPLTRV\", <peptideb>: \"FLYNLLTRV\",\n         <valuea>: float, <valueb>: float,\n       },\n       {\n         <allele>: string,\n         <peptidea>: \"MLGERLFPL\", <peptideb>: \"MLGEQLFPL\",\n         <valuea>: float, <valueb>: float,\n       },\n     ],\n     netmhcpan_el score: [collection],\n     netmhcpan_el percentile: [collection],\n     netmhcpan_ba IC50: [],\n     netmhcpan_ba percentile: [],\n\n   }\n\n   Note: collection = # of alleles * greatest seq #\n         so if ran w/ 27 alleles and 10 seq # (default), collection has 270 elements\n\n   ************\n\n\n     [\n        {\n          <display_name/method_name>: string,\n          <allele>: string,\n          <peptide-peptidea>: string, <peptide-peptideb>: string,\n          <value-peptidea>: float, <value-peptideb>: float,\n        },\n     ]\n\n   EX:\n\n   [\n     {\n       display_name: \"median binding/elution percentile\",\n       allele: \"HLA-A*02:01\",\n       peptidea: \"FLYNPLTRV\", peptideb: \"FLYNLLTRV\",\n       valuea: float, valueb: float,\n     },\n     {\n       display_name: \"median binding/elution percentile\",\n       allele: \"HLA-A*02:02\",\n       peptidea: \"FLYNPLTRV\", peptideb: \"FLYNLLTRV\",\n       valuea: float, valueb: float,\n     },\n   ]\n   * */\n  scatterPlotData2: any = []\n  scatterPlotAlleles: string[] = []\n  scatterPlotDisplayNames: string[] = []\n\n  selectedSeqNumPlots = '';\n  selectedAllelePlots = '';\n  selectedLengthPlots = ''\n  sequenceNumbers = []\n\n  sequence_table_order: any[] = [];\n  sequence_table_columns: Columns[] | any;\n  sequence_table: [(string | number)[]] = [[]]\n\n  residue_table_order: any[] = [];\n  residue_table_columns: Columns[] | any;\n  residue_table: [(string | number)[]] = [[]]\n\n  allele_distances_table_order: any[] = [];\n  allele_distances_table_columns: Columns[] | any;\n  allele_distances_table: [(string | number)[]] = [[]]\n\n  peptide_table_order: any[] = [];\n  peptide_table_columns: Columns[] | any;\n  peptide_table: [(string | number)[]] = [[]]\n\n  stages$: Observable<Stage[]> = this._stateService.stages$;\n  tools$: Observable<Tool[]> = this._stateService.tools$;\n  pipelineId$: Observable<string> = this._stateService.pipelineId$;\n  params$: Observable<PipelineParams> = this._stateService.params$;\n\n  stages: Stage[] = [];\n  tools: Tool[] = [];\n  pipelineId = '';\n  params!: PipelineParams;\n\n  /** Form variables */\n  pepcompForm!: UntypedFormGroup;\n\n  /** sequence variables */\n  synthesisDownloadLinks = {\n    sequence_list_json_uri: '',\n    sequence_list_fasta_uri: '',\n    download_sequences: ''\n  };\n\n  swaggerUrl = `${environment['api_url']}/apidocs`\n\n  filteredSequences: { name: string, sequences: string }[] = [];\n  numOfAA: number = 0;\n  numOfCharacters: number = 0;\n  seqFormat: string = 'Unknown';\n\n  /** API Call variables */\n  runSetInterval: any;\n  submitted = false;\n  loading = false;\n  getResultsClicked = true;\n  pipelineLoading = false;\n  tableStateSaving = false;\n  saveState = false;\n\n  defaultOrder: any[] = [];\n\n  errorMessages: string[] = [];\n  warningMessages: string[] = [];\n\n  /** Alleles */\n  searching = false;\n  searchFailed = false;\n\n  modalAlleles: Allele[] = [];\n  modalOpen = false;\n\n  /** sequence files */\n  maxCharacters = 1000000;\n  files: any[] = [];\n  fileName = '';\n\n  pipelineUrl: string = ''\n\n  data: any\n\n  inputChange = {\n    /** Keeps track of inputChanges to highlight selected parameter table row*/\n    input_sequence_text: false,\n    alleles: false,\n    predictors: false,\n    table_state: false,\n  }\n\n  predictionOptions: {display_name: string, short_name: string, group: string, source: string, has_ic50: boolean}[] = [];\n  basicProcessingPredictionOption: {display_name: string, short_name: string, group: string, source: string, has_ic50: boolean}[] = []\n  processingOptions: {display_name: string, short_name: string, group: string, source: string, has_ic50: boolean}[] = [];\n\n  mhciLoading: boolean = false;\n  mhciPredictors: any[] = [];\n\n  constructor(\n    public alertService: AlertServiceService,\n    private http: HttpClient,\n    private fb: UntypedFormBuilder,\n    private _alleleSearchService: AlleleSearchService,\n    private _pipelineService: PipelineService,\n    private _stateService: PipelineStateService,\n    private rootFormGroup: FormGroupDirective, // pipeline component\n    private route: ActivatedRoute,\n    private router: Router,\n    private titleService: Title,\n    private location: Location,\n    private sequenceParserService: SequenceParserService,\n    private modalService: NgbModal,\n  ) {\n  }\n\n\n\n  ngOnInit(): void {\n    if (isDevMode()) {\n      console.log('Development!');\n    } else {\n      console.log('Production!');\n    }\n\n    this.getMHCIList();\n    // this.tCellForm = this.fb.group(this.initialControlConfig);\n    this.pepcompForm = this.rootFormGroup.control.get(this.formGroupName) as UntypedFormGroup;\n    // this.peptideLengthSliderOptions = Object.assign({}, this.peptideLengthSliderOptions, {disabled: this.breakPeptides});\n\n    this.pipelineId$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n      console.log(`pipelineId=${value}`);\n      this.pipelineId = value;\n      this.pipelineUrl = `${window.location.origin}/pipeline/${value}`;\n    })\n    this.stages$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n      console.log(value);\n      this.stages = value;\n      this.errorMessages = this.stages[this.index]?.stage_messages!.errors\n      this.warningMessages = this.stages[this.index]?.stage_messages!.warnings\n    })\n    this.tools$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n      console.log('tools$');\n      console.log(value);\n      this.tools = value;\n      this.submitted = this.tools[this.index]?.submitted\n\n      const inputSequenceTextId = this.tools[this.index]?.input_data_uri?.input_sequence_text_id\n\n      this.synthesisDownloadLinks.sequence_list_json_uri = `${environment['api_url']}/api/v1/sequence_list_json/${inputSequenceTextId}`\n      this.synthesisDownloadLinks.sequence_list_fasta_uri = `${environment['api_url']}/api/v1/sequence_list_fasta/${inputSequenceTextId}`\n      this.synthesisDownloadLinks.download_sequences = `${environment['api_url']}/api/v1/download_sequences/${inputSequenceTextId}`\n\n      // this.loading = this.tools[this.index]?.loading\n      if(!this.tools[this.index]?.loading) {\n        this.loading = false;\n        clearInterval(this.runSetInterval)\n      }\n\n      /** pipeline Loading */\n      this.pipelineLoading = _.some(this.tools, {loading: true})\n      // if(this.pipelineLoading) {\n      //   this.disableInputs();\n      // } else {\n      //   this.enableInputs();\n      // }\n      console.log('pipelineLoading')\n      console.log(this.pipelineLoading)\n\n    })\n\n    this.params$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n      console.log(`params`);\n      console.log(value);\n      this.params = value;\n    })\n\n    this.eventsSubscription = this.events.subscribe(() => this.onRunMain());\n    this.runAllSubscription = this.runAllEvent.subscribe(() => this.onRunAll())\n\n    this.onChanges();\n\n    if(this.pepcompForm.get('inputSequenceText')?.value) {\n      this.sequenceParser(this.pepcompForm.get('inputSequenceText')?.value)\n    }\n\n  }\n\n  ngOnDestroy() {\n    clearInterval(this.runSetInterval);\n    clearInterval(this._pipelineService.runSetInterval)\n    this.unsubscribe$.next();\n    this.unsubscribe$.complete();\n\n    this.eventsSubscription.unsubscribe();\n    this.runAllSubscription.unsubscribe();\n  }\n\n  ngAfterViewInit() {\n    setTimeout(() => {\n      const run = history.state?.run;\n      // console.log(run);\n      run && this.onRunMain();\n    }, 0)\n  }\n\n  ngOnChanges(changes: SimpleChanges) {\n    if(changes.resultUrl?.currentValue) {\n      console.log(changes.resultUrl.currentValue);\n      console.log('ngOnChanges t-cell')\n      this.loading = true;\n      this.getResultsSetInterval(changes.resultUrl.currentValue);\n    }\n  }\n\n  get selectedAlleleLabels() {\n    return this.alleles.value.map(((o: { label: string; }) => o.label)).join(', ');\n  }\n\n  get selectedModalAlleleLabels() {\n    return this.modalAlleles.map(((o: { label: string; }) => o.label)).join(', ');\n  }\n\n  get predictionModels() {\n    return this.pepcompForm.get('predictionModels') as UntypedFormArray;\n  }\n\n  get alleles() {\n    return this.pepcompForm.get('alleles') as UntypedFormArray;\n  }\n\n  get breakPeptides() : boolean {\n    return this.pepcompForm.get('breakPeptides')?.value;\n  }\n\n  get inputSequenceText(){\n    return this.pepcompForm.get('inputSequenceText')?.value\n  }\n\n  get peptideLength() {\n    return this.pepcompForm.get('peptideLength')?.value;\n  }\n\n  get styleResultContainer(){\n    return !this.loading && this.submitted ? 'none' : 'dotted';\n  }\n\n  setDefaultFormValues() {\n    /** defaults - use Sars placeholders*/\n    let seq: string = ''\n    let all: string = ''\n    if(environment.production || environment['name'] === 'DEV') { // prod or dev\n      const {input_sequence_text, alleles } = pepCompSampleData; // correct examples\n      seq = input_sequence_text\n      all = alleles\n    } else {\n      const {input_sequence_text, alleles } = pipelineData;\n      seq = input_sequence_text\n      all = alleles\n    }\n    /** Sequences */\n    let sequences = this.pepcompForm.value.inputSequenceText\n    if(!sequences && this.index===0) {\n      this._stateService.setInputSequenceText(seq);\n      this.pepcompForm.controls.inputSequenceText.setValue(seq);\n    }\n\n    /** Alleles */\n    const patchValues = (allele: string, synonym = '', score = null) => {\n      /** patchValues - helper function */\n      return this.fb.group({\n        label: [allele],\n        synonym: [synonym],\n        score: [score]\n      })\n    }\n    if(this.alleles.length===0) {\n      _.forEach(all.split(','), (allele) => {\n        this.alleles.push(patchValues(allele));\n      })\n      // this.alleleSearch!.nativeElement.value = alleles;\n    }\n  }\n\n  onRun() {\n    /**\n     Update pipeline State\n     *\n     * */\n    /** Reset global datatables search ext */\n    $.fn.dataTable.ext.search = [];\n\n    const stage_number = this.index + 1;\n    /** run_stage_range */\n    const run_stage_range: [number, number] = [stage_number, stage_number]\n    /** default formValue */\n    this.setDefaultFormValues()\n    /** Sequences */\n    let sequences = this.pepcompForm.value.inputSequenceText\n\n    /** input parameters */\n    const inputParameters = this._pipelineService.convertPepcompForm(this.pepcompForm)\n\n    /** Table State */\n    const { table_state } = this.stages[this.index];\n\n    const newStage = {\n      \"stage_display_name\": \"Peptide Variant Comparison\",\n      \"stage_number\": stage_number,\n      \"stage_type\": \"prediction\",\n      \"tool_group\": \"peptide_variant_comparison\",\n      \"input_sequence_text\": sequences,\n      \"input_parameters\": inputParameters,\n      \"table_state\": table_state\n    }\n\n    const params = {\n      \"pipeline_id\": '',\n      \"pipeline_title\": this.emailForm.controls['name'].value,\n      \"email\": this.emailForm.controls['email'].value,\n      \"run_stage_range\": run_stage_range,\n      \"stages\": [\n        newStage\n      ]\n    }\n\n    /** set params */\n    const initToolLoading = Object.assign(initPeptideBindingComparisonTool, {\n      loading: true,\n      submitted: false,\n      appliedFilters: !_.isEmpty(table_state?.columns)\n    })\n    this._stateService.setParams(params);\n    this._stateService.insertTool(initToolLoading, this.index);\n    this._stateService.insertInputParametersToStage(inputParameters, this.index);\n\n    // this._stateService.insertTableStateToStage({columns: {}}, this.index);\n\n    this.postPipelineAPI(params);\n  }\n\n  onRun2(){\n    const params = this.params;\n    const stage_number = this.index + 1;\n    const input_stage_number = this.index; // previous index\n\n    /** run_stage_range */\n    const run_stage_range: [number, number] = [stage_number, stage_number]\n    /** default formValue */\n    this.setDefaultFormValues()\n\n    /** input parameters */\n    const inputParameters = this._pipelineService.convertPepcompForm(this.pepcompForm)\n    const initialStage = this.stages[this.index];\n\n    /** Table State */\n    const { table_state } = this.stages[this.index];\n\n    const stage: Stage = {\n      ...initialStage,\n      result_url: undefined,\n      stage_number: stage_number,\n      input_stage_number: input_stage_number,\n      input_parameters: inputParameters,\n      table_state\n    }\n\n    // this.params.stages.push(stage);\n    params.stages[this.index] = stage;\n    params.run_stage_range = run_stage_range;\n    params.pipeline_title = this.emailForm.controls['name'].value;\n    params.email = this.emailForm.controls['email'].value;\n\n    // console.log(params)\n\n    /** set params */\n    const loadingTool = Object.assign(initPeptideBindingComparisonTool, {\n      loading: true,\n      submitted: false,\n      appliedFilters: !_.isEmpty(table_state?.columns)\n    })\n\n    this._stateService.setParams(params);\n    this._stateService.insertTool(loadingTool, this.index);\n    this._stateService.insertInputParametersToStage(inputParameters, this.index);\n\n    this.postPipelineAPI(params);\n  }\n\n  getResultsSetInterval(result_url: string) {\n    /** */\n    this.getResultsClicked = true\n\n    this.residue_table_order = [];\n    this.residue_table_columns = null;\n    this.residue_table = [[]]\n\n    this.sequence_table = [[]]\n    this.allele_distances_table = [[]]\n    this.residue_table = [[]]\n    this.peptide_table = [[]]\n    // this.processingPlots = []\n\n    this.resultUrl = result_url;\n    console.log(result_url)\n    this.inputChange = _.mapValues(this.inputChange, () => false);\n    let increment = 0;\n    const milliseconds = 3000;\n    this.runSetInterval = setInterval(() => {\n      this._pipelineService.getResults(`${result_url}?statusOnly=true`).subscribe(\n        {\n          next: resp => {\n            console.log(resp);\n            if (resp['status'] === 'error' || resp['errors']) {\n              // this.errorMessages = resp['errors'];\n              // this.warningMessages = resp['warnings'];\n              this.submitted = false;\n              this.loading = false;\n              const prevTool = this.tools[this.index];\n              const submittedTool = Object.assign(prevTool, {\n                submitted: this.submitted,\n                loading: this.loading,\n              })\n              this._stateService.insertTool(submittedTool, this.index);\n              clearInterval(this.runSetInterval);\n              this.enableInputs();\n            }\n            if (resp['data']['warnings']?.length) {\n              // console.log(resp['warnings']);\n              this.warningMessages = resp['data']['warnings'];\n            }\n            if (resp['data']['errors']?.length) {\n              // console.log(resp['warnings']);\n              this.errorMessages = resp['data']['errors'];\n            }\n\n            if (resp['status'] === 'done') {\n              clearInterval(this.runSetInterval);\n\n              this._pipelineService.getResults(result_url).subscribe(resp => {\n                // clearInterval(this.runSetInterval);\n                console.log(resp)\n                this.defaultOrder = [[]]\n                /** 1) Create Column */\n                const data = resp['data']['results'];\n                this.active = data[0].type // = 'peptide_table' // this.active = 'scatter_plots'\n                _.forEach(data, table => {\n                  if (table.type === 'residue_table') {\n                    this.residue_table_columns = _.map(table.table_columns, (column, i) => {\n                      if (column.default_order && Number.isFinite(column.row_sort_priority)) { // set defaultOrder\n                        this.residue_table_order[column.row_sort_priority] = [i, column.default_order === \"ascending\" ? 'asc' : 'desc'];\n                      }\n                      column['title'] = `${column['display_name']}`; // required\n                      column['data'] = `${column['name']}`;\n                      let source = column['source'];\n\n                      column['filterKey'] = `${source}.${column.name}`\n\n                      // console.log(`source=${source}`);\n                      let tempSource = source.split('.')\n                      // console.log(tempSource);\n                      source = tempSource[tempSource.length - 1];\n                      // console.log(`source=${source}`);\n                      column['data'] = `${source}_${column['name']}`;\n                      /** remove `core` from name */\n                      // column['name'] = column['display_name'] ? column['display_name'] : column['name']\n                      column['value_limits'] = column['type'] === 'int' ? {\n                        minValue: NaN,\n                        maxValue: NaN,\n                        applied: false\n                      } : {\n                        possibleValues: [],\n                        textValue: null,\n                        selectedValues: [],\n                        applied: false\n                      }\n                      return column\n                    });\n                    // this.currentOrder = [...this.defaultOrder];\n                    if (this.residue_table_columns) {\n                      this.residue_table = table.table_data;\n                    }\n                    // console.log(this.residue_table_order);\n                    // console.log(this.residue_table_columns);\n                    // console.log(this.residue_table);\n                  }\n                  if (table.type === 'netmhcpan_allele_distance') {\n                    this.allele_distances_table_columns = _.map(table.table_columns, (column, i) => {\n                      if (column.default_order && Number.isFinite(column.row_sort_priority)) { // set defaultOrder\n                        this.allele_distances_table[column.row_sort_priority] = [i, column.default_order === \"ascending\" ? 'asc' : 'desc'];\n                      }\n                      column['title'] = `${column['display_name']}`; // required\n                      column['data'] = `${column['name']}`;\n                      let source = column['source'];\n\n                      column['filterKey'] = `${source}.${column.name}`\n\n                      // console.log(`source=${source}`);\n                      let tempSource = source.split('.')\n                      // console.log(tempSource);\n                      source = tempSource[tempSource.length - 1];\n                      // console.log(`source=${source}`);\n                      column['data'] = `${source}_${column['name']}`;\n                      /** remove `core` from name */\n                      // column['name'] = column['display_name'] ? column['display_name'] : column['name']\n                      // column['value_limits'] = column['type'] === 'int' ? {\n                      //   minValue: NaN,\n                      //   maxValue: NaN,\n                      //   applied: false\n                      // } : {\n                      //   possibleValues: [],\n                      //   textValue: null,\n                      //   selectedValues: [],\n                      //   applied: false\n                      // }\n                      column['value_limits'] = column['value_limits'] ? this.setValueLimits(column) : undefined\n                      return column\n                    });\n                    // this.currentOrder = [...this.defaultOrder];\n                    if (this.allele_distances_table_columns) {\n                      this.allele_distances_table = table.table_data;\n                    }\n                  }\n                  if (table.type === 'peptide_table') {\n                    /** peptide_table_columns */\n                    let indexA: number = 0\n                    let indexB: number = 0\n                    this.peptide_table_columns = _.map(table.table_columns, (column, i: number) => {\n                      if (column.default_order && Number.isFinite(column.row_sort_priority)) { // set defaultOrder\n                        this.defaultOrder[column.row_sort_priority] = [i, column.default_order === \"ascending\" ? 'asc' : 'desc'];\n                      }\n                      column['title'] = `${column['display_name']}`; // required\n                      column['data'] = `${column['name']}`;\n                      let source = column['source'];\n\n                      column['filterKey'] = `${source}.${column.name}`\n\n                      // console.log(`source=${source}`);\n                      let tempSource = source.split('.')\n                      // console.log(tempSource);\n                      source = tempSource[tempSource.length - 1];\n                      // console.log(`source=${source}`);\n                      column['data'] = `${source}_${column['name']}`;\n                      /** remove `core` from name */\n                      // column['name'] = column['display_name'] ? column['display_name'] : column['name']\n\n                      column['value_limits'] = column['value_limits'] &&  this.setValueLimits(column)\n\n                      /** Check and find indeces for EL score */\n\n                      /** using name instead of display_name, but name is not unique */\n                      // indexA = column['name'] === 'score-peptidea' ? Number(i) : indexA\n                      // indexB = column['name'] === 'score-peptideb' ? Number(i) : indexB\n\n                      /** netmhcpan_el score */\n                      // indexA = column['display_name'] === 'peptideA netmhcpan_el score' ? Number(i) : indexA\n                      // indexB = column['display_name'] === 'peptideB netmhcpan_el score' ? Number(i) : indexB\n\n                      /** median binding/elution percentile */\n                      indexA = column['display_name'] === 'peptideA median binding/elution percentile' ? Number(i) : indexA\n                      indexB = column['display_name'] === 'peptideB median binding/elution percentile' ? Number(i) : indexB\n\n                      /** immunogenicity score */\n                      // indexA = column['display_name'] === 'peptideA immunogenicity score' ? Number(i) : indexA\n                      // indexB = column['display_name'] === 'peptideB immunogenicity score' ? Number(i) : indexB\n\n                      // /**\n                      //  * 1. Needs to be passed index 5\n                      //  * 2.\n                      //  * */\n                      // if(i > 4) {\n                      //   this.scatterPlotData2[column.display_name]\n                      // }\n\n                      // indexB = column['name'].includes(['score-peptideb']) ? Number(i) : indexB\n                      return column\n                    });\n                    this.peptide_table_order = [...this.defaultOrder];\n                    if (this.peptide_table_columns) {\n                      this.peptide_table = table.table_data;\n                    }\n                    // console.log(this.peptide_table_order);\n                    // console.log(this.peptide_table_columns);\n                    // console.log(this.peptide_table);\n                    /**\n                     scatterPlotData\n                     * <index> = <field>\n                     * 5 = allele\n                     *\n                     * indexA (9) = score-peptidea\n                     * indexB (14) = score-peptideb\n                     * */\n                    // TODO COMMENTED THIS OUT\n                    // _.forEach(table.table_data, (i) => {\n                    //   // console.log(indexA)\n                    //   // console.log(indexB)\n                    //   if(this.scatterPlotData[i[5]]){ // already exists, push\n                    //     this.scatterPlotData[i[5]].push({'peptidea': i[indexA], 'peptideb': i[indexB], 'sequenceA': i[1], 'sequenceB': i[2]})\n                    //   }  else { // else, create data and push alleles\n                    //     this.scatterPlotData[i[5]] = [{'peptidea': i[indexA], 'peptideb': i[indexB], 'sequenceA': i[1], 'sequenceB': i[2]}]\n                    //     this.scatterPlotAlleles.push(i[5])\n                    //   }\n                    // })\n                    // console.error(this.scatterPlotData)\n                  }\n                  if (table.type === 'input_sequence_table') {\n                    this.sequence_table_columns = _.map(table.table_columns, (column, i) => {\n                      // if (column.default_order && Number.isFinite(column.row_sort_priority)) { // set defaultOrder\n                      //   this.defaultOrder[column.row_sort_priority] = [i, column.default_order === \"ascending\" ? 'asc' : 'desc'];\n                      // }\n                      column['title'] = `${column['display_name']}`; // required\n                      column['data'] = `${column['name']}`;\n                      let source = column['source'];\n\n                      column['filterKey'] = `${source}.${column.name}`\n\n                      // console.log(`source=${source}`);\n                      let tempSource = source.split('.')\n                      // console.log(tempSource);\n                      source = tempSource[tempSource.length - 1];\n                      // console.log(`source=${source}`);\n                      column['data'] = `${source}_${column['name']}`;\n                      /** remove `core` from name */\n                      // column['name'] = column['display_name'] ? column['display_name'] : column['name']\n                      // column['value_limits'] = column['type'] === 'int' ? {\n                      //   minValue: NaN,\n                      //   maxValue: NaN,\n                      //   applied: false\n                      // } : {\n                      //   possibleValues: [],\n                      //   textValue: null,\n                      //   selectedValues: [],\n                      //   applied: false\n                      // }\n\n                      column['value_limits'] = column['value_limits'] ? this.setValueLimits(column) : undefined\n                      // column['value_limits'] = column['value_limits'] && this.setValueLimits(column)\n                      return column\n\n\n\n                    });\n                    this.sequence_table_order = []\n                    if (this.sequence_table_columns) {\n\n                      this.sequence_table = table.table_data\n                    }\n                  }\n                  if (table.type === 'processing_plots') {\n                    const all_plots_uri = new URL(table.all_plots_uri)\n\n                    this.selectedSeqNumPlots = all_plots_uri.searchParams.get('sequence_number') || ''\n                    this.selectedLengthPlots = all_plots_uri.searchParams.get('length') || ''\n                    this.selectedAllelePlots = all_plots_uri.searchParams.get('allele') || ''\n\n                    this.sequenceNumbers = table.sequence_numbers\n\n                    // this.processingPlots = _.map(table.urls, (plot) => {\n                    //\n                    //   const url = new URL(plot.url)\n                    //   const thresholdInput = url.searchParams.get('threshold')\n                    //\n                    //   return {\n                    //     thresholdInput,\n                    //     ...plot\n                    //   }\n                    // })\n                    // this.processingPlots = table.urls\n                    // console.log(this.processingPlots)\n                  }\n\n                })\n                this._pipelineService.getResults(`${result_url}/plot_data`).subscribe(resp => {\n                  console.log(resp)\n                  this.scatterPlotData = resp['plot_data']\n                  console.log('HERE')\n                  console.log(this.scatterPlotData)\n                  // added here from TODO below\n                  this.submitted = true; this.loading = false;\n                  const prevTool = this.tools[this.index];\n                  console.log(prevTool)\n                  const submittedTCellPredictionTool = Object.assign(prevTool, {\n                    submitted: this.submitted,\n                    loading: this.loading,\n                  })\n                  this._stateService.insertTool(submittedTCellPredictionTool, this.index);\n                })\n\n                // TODO, added GET Result/plot_data get result because of how Yan implemented it now, not ideal...\n                // this.submitted = true; this.loading = false;\n                // const prevTool = this.tools[this.index];\n                // console.log(prevTool)\n                // const submittedTCellPredictionTool = Object.assign(prevTool, {\n                //   submitted: this.submitted,\n                //   loading: this.loading,\n                // })\n                // this._stateService.insertTool(submittedTCellPredictionTool, this.index);\n\n                this.enableInputs();\n              })\n            }\n            if (resp['status'] === 'canceled') {\n              /** if status is canceled, then just stop loader **/\n              this.submitted = false;\n              this.loading = false;\n              const prevTool = this.tools[this.index];\n              console.log(prevTool)\n              const submittedTCellPredictionTool = Object.assign(prevTool, {\n                submitted: this.submitted,\n                loading: this.loading,\n              })\n              this._stateService.insertTool(submittedTCellPredictionTool, this.index);\n              clearInterval(this.runSetInterval);\n              // console.log(data);\n              this.enableInputs();\n              // set error message\n              // this.errorMessages = [`PIPELINE_ID=${this.pipelineId} w/ STATUS=${resp['status']}`]\n            }\n            else {\n              this.getResultsClicked = false;\n              console.log(`current status: ${resp['status']} - ${increment}`);\n              increment += 1;\n            }\n          },\n          error: error => {\n            console.error(error);\n            this.enableInputs();\n            clearInterval(this.runSetInterval);\n            this.loading = false;\n          }\n        }\n      )\n    }, milliseconds);\n  }\n\n  setValueLimits(column: Columns) : any {\n    /* set value_limits (i.e. filters) for each column based on if type is a number/string */\n    return column['type'] === 'int' || column['type'] === 'float' ? {\n      ...column['value_limits'],\n      minValue: NaN,\n      maxValue: NaN,\n      applied: false\n    } : {\n      // ...column['value_limits'],\n      possibleValues: column['value_limits']['unique_values'],\n      textValue: null,\n      selectedValues: [],\n      applied: false\n    }\n  }\n\n  postPipelineAPI(params: PipelineParams, getResults: boolean = true) {\n    this.disableInputs();\n    if (getResults) {\n      this.errorMessages = [];\n      this.warningMessages = [];\n    }\n    this.loading = getResults; // true - defaults\n    this.submitted = !getResults; // false - defaults\n    this.tableStateSaving = !getResults\n\n    this._pipelineService.postPipeline(params).subscribe(\n      (resp) => {\n        // Errors and Warnings\n        if (resp['errors'] && resp['errors'].length) {\n          console.log(resp);\n          console.error(resp['errors']);\n          this.errorMessages = resp['errors'];\n          if (resp['warnings'].length) {\n            console.log(resp['warnings']);\n            this.warningMessages = resp['warnings'];\n          }\n          this.loading = false;\n          this.submitted = true;\n          const submittedTCellPredictionTool = Object.assign(initPeptideBindingComparisonTool, {\n            submitted: false,\n            loading: false,\n          })\n          this._stateService.insertTool(submittedTCellPredictionTool, this.index);\n          this.enableInputs();\n          return;\n        }\n        // Warnings\n        if (resp['warnings'].length) {\n          console.log(resp['warnings']);\n          this.warningMessages = resp['warnings'];\n        }\n\n        const inputDataUri = {input_sequence_text_id: resp.input_sequence_text_id}\n        this._stateService.insertInputDataUriToTool(inputDataUri, this.index)\n\n        this._stateService.setPipelineId(resp.pipeline_id);\n        this._stateService.setPipelineIdToParams(resp.pipeline_id);\n        this._stateService.setPipelineSpecId(resp.pipeline_spec_id);\n        /** Display email Modal if emailModalShow=true */\n        this.location.replaceState(`pipeline/${resp.pipeline_id}`)\n        // this.titleService.setTitle(`IEDB NG Tools Pipeline`);\n\n        // this.location.replaceState(`pipeline/${resp.pipeline_id}`)\n        // this.router.createUrlTree([`pipeline/${resp.pipeline_id}`])\n        if (getResults) {\n          const result_url = `${resp.results_uri}`;\n          console.log(result_url);\n          this.getResultsSetInterval(result_url);\n        } else {\n          this.inputChange.table_state = false;\n          this.submitted = true;\n          this.loading = false;\n          this.tableStateSaving = false;\n          this.enableInputs();\n        }\n      },\n      (error) => {\n        console.error(error);\n        this.errorMessages.push(error.error);\n        this.submitted = false;\n        this.loading = false;\n        const prevTool = this.tools[this.index];\n        const submittedTool = Object.assign(prevTool, {\n          submitted: this.submitted,\n          loading: this.loading,\n        })\n        this._stateService.insertTool(submittedTool, this.index);\n        clearInterval(this.runSetInterval);\n        this.enableInputs();\n      }\n    )\n\n  }\n\n  onRunConfirm() {\n    let indicies = _.range(this.index + 1, this.stages.length)\n    let initTool: Tool;\n    console.log(indicies);\n    _.forEach(indicies, i => {\n      initTool = this.tools[i];\n      const unSubmittedTool = {\n        ...initTool,\n        loading: false,\n        submitted: false,\n      }\n      this._stateService.insertTool(unSubmittedTool, i);\n    })\n    this.saveState ? this.onSaveTableStateMain() : this.onRun();\n  }\n\n  onRunAll() {\n    this.setDefaultFormValues()\n    this.emitIndex.emit(this.index);\n  }\n\n  onRunMain() {\n    if(this.pepcompForm.invalid){\n\n      this.alertService.add(`Input sequence text is too long. The maximum number of characters allowed is ${this.maxCharacters.toLocaleString()}\\nYour sequence contains ${this.inputSequenceText.length.toLocaleString()}`, 'alert-danger');\n      this.open(this.alertModal)\n      return;\n    }\n\n    const hasResult = _.find(this.tools.slice(this.index+1), (o) => o.submitted || o.loading)\n    if(this.stages.length > 1 && hasResult) {\n      this.open(this.confirmModal);\n    } else {\n      this.getResultsClicked = true;\n      if(this.index===0) {\n        this.onRun();\n      } else {\n        this.onRun2()\n      }// There is no onRun2() because Peptide Variant Comparison can only be the initial tool\n    }\n  }\n\n\n  onChanges(): void {\n    /** PredictionModel sessionStorage */\n    this.pepcompForm.get('predictionModels')?.valueChanges.subscribe(val => {\n      // sessionStorage.setItem('predictionModels', JSON.stringify(val));\n      this.inputChange.predictors = this.submitted\n    });\n\n    const sequenceFieldChange = this.pepcompForm.get('inputSequenceText')?.valueChanges.pipe(\n      debounce(v => timer(1000)),\n    );\n\n    // this.pepcompForm.get('breakPeptides')?.valueChanges.subscribe(val => {\n    //   this.peptideLengthSliderOptions = Object.assign({}, this.peptideLengthSliderOptions, {disabled: val});\n    // })\n\n    sequenceFieldChange?.subscribe(val => {\n      console.log('sequenceFieldChange')\n      // sessionStorage.setItem('sequences', val);\n      this.sequenceParser(val);\n      this.inputChange.input_sequence_text = this.submitted;\n      if (val === '') {  // delete\n        this.filteredSequences = [];\n        this.numOfAA = 0;\n        // this.alertService.clear();\n        // this.myForm.patchValue({\n        //   inputFormat: 0\n        // });\n      }\n    });\n  }\n\n\n  sequenceParser(val: string) {\n\n    const firstChar = val[0];\n    const firstLine = val.split('\\n')[0]\n    console.log(firstLine)\n\n    /** Named white space */\n    let firstLineNumOfElements = 0\n    let separator = ' '\n    if(firstLine.includes(' ')){\n      separator = ' '\n    } else if (firstLine.includes('\\t')){\n      separator = '\\t'\n    } else if (firstLine.includes('\\s')){\n      separator = '\\s'\n    }\n    firstLineNumOfElements = firstLine.split(separator).length\n    console.log(firstLineNumOfElements)\n    console.log(separator)\n\n    const slicedVal = val.slice(0, this.maxCharacters)\n\n    if(val.length > this.maxCharacters) {\n      //  Skip parsing\n    } else if (firstChar === '>' && this.sequenceParserService.fastaValidate(val)) { // fasta\n      this.seqFormat = this.sequenceParserService.seqFormat;\n      this.numOfCharacters = slicedVal.length\n    } else if ((firstChar === '{' || firstChar === '[') && IsJsonString(val)) { // json\n      this.seqFormat = 'JSON'\n      this.numOfCharacters = slicedVal.length\n    } else if (firstLineNumOfElements === 2 && this.sequenceParserService.namedWhiteSpaceValidate(val, separator)) {\n      // named white space\n      this.seqFormat = this.sequenceParserService.seqFormat;\n      this.numOfCharacters = slicedVal.length\n    } else if (val.length > 3 && !val.includes('>') && this.sequenceParserService.unnamedWhiteSpaceValidate(val)) {\n      // Unnamed\n      this.seqFormat = this.sequenceParserService.seqFormat;\n      this.numOfCharacters = slicedVal.length\n    } else if (val === '') {  // delete\n      /**\n       * Takes care of it up top - still need this if statement\n       * */\n      this.seqFormat = 'Unknown';\n      this.numOfCharacters = 0\n    } else { // error\n      this.seqFormat = 'Error';\n      this.numOfCharacters = 0\n    }\n  }\n\n  /** Allele Modal Functions */\n  open(content: any) {\n    this.modalOpen = true;\n    this.modalService.open(content, {\n      ariaLabelledBy: 'modal-basic-title',\n      size: 'lg',\n      animation: true,\n      backdrop: 'static'\n    }).result.then((result) => {\n      // this.closeResult = `Closed with: ${result}`;\n      this.saveState = false;\n      this.modalOpen = false;\n    }, (reason) => {\n      this.saveState = false;\n      this.alleleSearch.nativeElement.focus();\n      // this.closeResult = `Dismissed ${TCellPredictionComponent.getDismissReason(reason)}`;\n    });\n  }\n\n  onOpenAlleleModal() {\n    this.open(this.alleleModal)\n    this.modalAlleles = [...this.alleles.value]\n    console.log(this.modalAlleles)\n  }\n\n  dismissAlleleModal() {\n    this.modalOpen = false;\n    this.modalService.dismissAll()\n  }\n\n  onSubmitModalAlleles() {\n    this.alleles.clear()\n    _.forEach(this.modalAlleles, (selectedAllele) => {\n      this.alleles.push(this.fb.group(selectedAllele));\n    })\n    this.inputChange.alleles = this.submitted;\n    this.modalService.dismissAll()\n    this.modalOpen = false;\n  }\n\n  generate27Alleles(input: any) {\n    this.modalAlleles = []\n    // this.alleles.clear()\n    const { alleles } = alleleData;\n    _.forEach(alleles.split(','), (allele) => {this.modalAlleles.push({label: allele, synonym: null, score: null})})\n    input.value = this.selectedModalAlleleLabels;\n  }\n\n  enableInputs() {\n    // this.tCellForm.enable({emitEvent: false});\n    // this.peptideLengthSliderOptions = Object.assign({}, this.peptideLengthSliderOptions, {disabled: this.breakPeptides});\n  }\n\n  disableInputs() {\n    // this.tCellForm.disable({emitEvent: false});\n    // this.peptideLengthSliderOptions = Object.assign({}, this.peptideLengthSliderOptions, {disabled: true});\n  }\n\n  /** File Download/Upload*/\n  uploadSequenceFile($event: any) {\n    $event.preventDefault();\n    /**\n     * Used for 'Upload' button\n     * */\n    const {files} = $event.target;\n    files && this.onFileDropped(files);\n  }\n\n\n  onCancel() {\n    console.log(this.runSetInterval)\n    clearInterval(this.runSetInterval);\n    this.emitOnCancel.emit()\n\n    this.inputChange.table_state = false;\n    // this.submitted = false;\n    const currentTool = this.tools[this.index];\n    const unSubmittedTool = {\n      ...currentTool,\n      loading: false,\n      submitted: false,\n      appliedFilters: undefined\n    }\n    this._stateService.insertTool(unSubmittedTool, this.index);\n    this.warningMessages = [];\n    this.loading = false;\n    this.tableStateSaving = false;\n    this.enableInputs();\n  }\n\n  onReset() {\n    this.alertService.clear();\n    this.errorMessages = [];\n    this.warningMessages = [];\n\n    const oldSequence = this.stages[this.index].input_sequence_text\n    const input_parameters = this.params.stages[this.index].input_parameters\n\n    console.log(input_parameters)\n\n    // sequences\n    this.filteredSequences = [];\n    this.numOfAA = 0;\n    // order\n    this.peptide_table_order = [];\n    this.defaultOrder = [];\n    // tCellForm values\n    const peptideLength = [9, 10];\n    this.pepcompForm.patchValue({\n      inputSequenceText: '',\n      peptideLength,\n    }, {emitEvent: false});\n\n    // selected alleles\n    this.alleles.clear()\n\n    // predictors\n    const initPredictor = {\n      type: 'binding',\n      method: 'netmhcpan_el',\n    }\n    const pm = this.pepcompForm.controls.predictionModels as UntypedFormArray\n    pm.clear({emitEvent: false})\n    pm.push(this.fb.group(initPredictor), {emitEvent: false});\n\n    this.enableInputs();\n\n    if(this.submitted){\n      this.inputChange =  {\n        ...this.inputChange,\n        /** Keeps track of inputChanges to highlight selected parameter table row*/\n        input_sequence_text: oldSequence !== '',\n        alleles: !_.isEqual([], input_parameters.alleles),\n        // lengths: !_.isEqual(peptideLength, input_parameters.peptide_length_range),\n        predictors: !_.isEqual([initPredictor], input_parameters.predictors),\n      }\n    }\n  }\n\n  onFileDropped($event: any[]) {\n    console.log($event);\n    const file = $event[0];\n    const fileSize = file.size / 1024; // in kB\n    console.log(file.type);\n    if (fileSize > 20000) {\n      this.alertService.add('File Size is too big! (20mB max)', 'alert-danger');\n      this.open(this.alertModal);\n    }\n    else {\n      this.prepareSequenceFileList($event);\n    }\n  }\n\n  prepareSequenceFileList(files: Array<any>) {\n    console.log(files);\n    this.fileName = files[0].name;\n    const reader = new FileReader();\n    const myForm = this.pepcompForm;\n    for (const item of files) {\n      // console.log(item);\n      reader.readAsText(item);\n      reader.onload = () => {\n        const val = reader.result?.toString() || '';\n        console.log(val);\n        const v = isASCII(val);\n        console.log(v);\n        if (v) {\n          // myForm.patchValue({inputSequenceText: val.substring(0, this.maxCharacters)});\n          const w = isMaxLength(val, this.maxCharacters)\n          if (w) {\n            myForm.patchValue({inputSequenceText: val});\n          } else {\n            this.alertService.add(`Sequence is too long - max Sequence length is ${this.maxCharacters.toLocaleString(\"en-US\")} characters`, 'alert-danger');\n            this.open(this.alertModal);\n          }\n          // this.sequenceParser(val);  // auto parser\n        } else {\n          this.alertService.add('Invalid file type.\\nValid file types are .txt, .fa, .fasta, .json, .faa,', 'alert-danger');\n          this.open(this.alertModal);\n        }\n      };\n\n      reader.onerror = () => {\n        console.log(reader.error);\n      };\n      item.progress = 0;\n      this.files.push(item);\n    }\n  }\n\n  onSaveTableStateMain() {\n    const hasResult = _.find(this.tools.slice(this.index+1), {submitted: true})\n    if (hasResult) {\n      this.saveState = true;\n      this.open(this.confirmModal);\n    } else {\n      this.onSaveTableState();\n    }\n  }\n\n  onSaveTableState() {\n    const tool_group = 'mhci'\n\n    const params = this.params\n    // create colObj and params\n    let colObj = columnListToObject(this.peptide_table_columns, tool_group)\n    const stages = params.stages;\n    const stageTemp = stages[this.index];\n    stageTemp.table_state = [{table: 'peptide_table', columns: colObj}];\n    stages[this.index] = stageTemp\n    params.stages = stages;\n    // run_stage_range\n    const stage_number = this.index + 1;\n    params.run_stage_range = [stage_number, stage_number];\n    this._stateService.setParams(params);\n    // appliedFilters\n    let appliedFilters = !_.isEmpty(colObj);\n    this._stateService.setToolAppliedFilters(appliedFilters, this.index)\n    this.postPipelineAPI(params, false);\n    this.saveState = false;\n  }\n\n  onFilterApplied() {\n    this.inputChange.table_state = this.submitted;\n  }\n\n  onClearTableState() {\n    this.peptide_table_columns = _.map(this.peptide_table_columns, (c) => {\n      c.value_limits = c.type === 'int'? {\n          minValue: NaN,\n          maxValue: NaN,\n          applied: false\n        } :\n        {\n          possibleValues: [],\n          textValue: null,\n          selectedValues: [],\n          applied: false\n        }\n      return c\n    })\n    this.inputChange.table_state = this.submitted;\n  }\n\n  /** Predictors Drag and Drop */\n\n  dropPredictionModel(event: CdkDragDrop<string[]>) {\n    const {previousIndex, currentIndex} = event;\n\n    const control = this.predictionModels.at(previousIndex);\n    this.predictionModels.removeAt(previousIndex);\n    this.predictionModels.insert(currentIndex, control);\n\n    if (previousIndex !== currentIndex) {\n      this.inputChange.predictors = this.submitted;\n    }\n  }\n\n  setInputChangePredictors(value: boolean) {\n    this.inputChange.predictors = this.submitted;\n  }\n\n  removePredictorByIndex(index: number) {\n    this.predictionModels.removeAt(index);\n    this.inputChange.predictors = this.submitted;\n  }\n\n  addpredictionModel() {\n    this.predictionModels.push(this.mhcBindingFormGroup());\n    this.inputChange.predictors = this.submitted;\n  }\n\n  addPmhcImmungencityFormGroup() {\n    this.predictionModels.push(this.pmhcImmunogencityFormGroup());\n    this.inputChange.predictors = this.submitted;\n  }\n\n  mhcBindingFormGroup(method = 'netmhcpan_el') {\n    /**\n     * Creates mhcBindingFormGroup using formBuilder\n     *\n     * Currently defaulted to 'netmhcpan_el'\n     * */\n    return this.fb.group({\n      type: 'binding',\n      method: this.fb.control(method),\n    })\n  }\n\n  pmhcImmunogencityFormGroup(mask_choice = 'default', position_to_mask = '2,5,9') {\n    /**\n     * */\n    return this.fb.group({\n      type: 'immunogenicity',\n      mask_choice: mask_choice,\n      position_to_mask: this.fb.control(position_to_mask),\n    })\n  }\n\n  /** Allele Search Functions */\n  onAlleleSelect({e, input}: { e: any, input: any }) {\n    e.preventDefault();\n    const selectedAllele = e.item;\n    let labels = _.map(this.alleles.value, (allele) => allele.label)\n    if (!labels.includes(selectedAllele.label)) {\n      this.alleles.push(this.fb.group(selectedAllele));\n    }\n    // sessionStorage.setItem('selectedAlleles', JSON.stringify(this.selectedAlleles));\n    input.value = '';\n    this.inputChange.alleles = this.submitted;\n  }\n\n  onAlleleSelectModal({e, input}: { e: any, input: any }) {\n    e.preventDefault();\n    const selectedAllele = e.item;\n    let labels = _.map(this.modalAlleles, (allele) => allele.label)\n    if (!labels.includes(selectedAllele.label)) {\n      this.modalAlleles.push(selectedAllele);\n    }\n    input.value = '';\n  }\n\n  onBlurAlleleSelect(e: { preventDefault: () => void; }, input: { value: string; placeholder: string; }) {\n    /**\n     * Displays alleles in the text box when out of focus.\n     * */\n    e.preventDefault();\n    input.value = '';\n    input.placeholder = 'Ex. HLA-A*02:01'\n    if (this.alleles.length) {\n      const labels = _.map(this.alleles.value, (o) => {\n        return o.label;\n      });\n      input.value = labels.join(', ');\n    }\n  }\n\n  onBlurAlleleSelectModal(e: { preventDefault: () => void; }, input: { value: string; placeholder: string; }) {\n    /**\n     * Displays alleles in the text box when out of focus.\n     * */\n    e.preventDefault();\n    input.placeholder = 'Ex. HLA-A*02:01'\n    input.value = this.modalAlleles.length ? this.selectedModalAlleleLabels : ''\n  }\n\n  onAlleleClear(input: { value: string; }) {\n    this.inputChange.alleles = this.submitted;\n    this.alleles.clear()\n    input.value = '';\n  }\n\n  onAlleleClearModal(input: { value: string; }) {\n    this.modalAlleles = []\n    input.value = ''\n  }\n\n  onAlleleDeselect(index: number) {\n    this.alleles.removeAt(index)\n    this.inputChange.alleles = this.submitted;\n    // input.value = '';\n    // if (this.alleles.length) {\n    //   input.value = this.selectedAlleleLabels\n    // }\n  }\n\n\n  onAlleleDeselect2(index: number, input: { value: string }) {\n    console.log(index)\n    _.pullAt(this.modalAlleles, [index])\n    const labels = this.modalAlleles.map(((o: { label: string; }) => o.label)).join(', ')\n    input.value = this.modalAlleles.length ? labels : ''\n  }\n\n  search = (text$: Observable<string>) =>\n    text$.pipe(\n      debounceTime(1000),\n      distinctUntilChanged(),\n      tap(() => this.searching = true),\n      switchMap(term => {\n          // console.log(term);\n          return this._alleleSearchService.search(term).pipe(\n            tap(() => this.searchFailed = false),\n            catchError(() => {\n              this.searchFailed = true;\n              return of([]);\n            }))\n        }\n      ),\n      tap(() => this.searching = false)\n    )\n\n  resultFormatter = (result: any) => {\n    /**\n     *  The function that converts an item from the result list to a string to display in the popup.\n     * */\n    return result.synonyms.length > 0 ? `${result.label} - (${result.synonyms})` : result.label;\n  }\n\n  inputFormatter(value: any): any {\n    /**\n     * The function that converts an item from the result list to a string to display in the <input> field.\n     * */\n    if (value.label) {\n      return `${value.label}`;\n    }\n  }\n\n  onDownloadParameter() {\n    // TODO change convert function\n    const data = this._pipelineService.convertTCellForm(this.pepcompForm)\n\n    const a = document.createElement('a');\n    a.setAttribute('style', 'display:none;');\n    document.body.appendChild(a);\n    // const contentType = 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet;charset=UTF-16';\n    // var blob = new Blob([csvData], { type: contentType });\n    const blob = new Blob([JSON.stringify(data, null, 2)], ); // thx: http://stackoverflow.com/a/18925211\n    a.href = window.URL.createObjectURL(blob);\n    a.download = 'parameter.json';\n\n    a.click();\n  }\n\n\n  /** Download Sequence File API calls\n   * onDownloadJson()\n   * onDownloadFasta() - removed\n   * onDownloadOriginal()\n   * */\n  onDownloadJson() {\n    onCsvDownloadAllClickedNew(this.synthesisDownloadLinks.sequence_list_json_uri, this.http, 'json');\n  }\n\n  // onDownloadFasta() {\n  //   onCsvDownloadAllClickedNew(this.synthesisDownloadLinks.sequence_list_fasta_uri, this.http, 'fasta');\n  // }\n\n  onDownloadOriginal() {\n    onCsvDownloadAllClickedNew(this.synthesisDownloadLinks.download_sequences, this.http, 'txt');\n  }\n\n  getMHCIList() {\n    this.mhciLoading = true;\n    this.http.get<any[]>(API_URL)\n      .pipe().subscribe(\n      resp => {\n        // @ts-ignore\n        this.mhciPredictors = resp['predictors'];\n        // console.log(this.mhciPredictors);\n        this.predictionOptions = _.filter(this.mhciPredictors, {'group': 'binding'});\n        this.basicProcessingPredictionOption = _.filter(this.mhciPredictors, {'group': 'binding', 'has_ic50': true})\n        this.processingOptions = _.filter(this.mhciPredictors, {'group': 'processing'});\n        console.log(this.processingOptions)\n        this.mhciLoading = false;\n      }\n    )\n  }\n}\n","/**\n *\n * Used for vcf file validation\n * limit should be 5000\n * */\n\nexport function isMaxLines(str: string, maxNoLines: number)\n{\n  return (String(str).match(/\\n/g) || '').length + 1 < maxNoLines\n}\n","<form [formGroup]=\"mutgenForm\" (ngSubmit)=\"onRunMain()\" class=\"container\">\n  <div class=\"d-flex flex-row p-2\">\n    <h2 class=\"pe-2 display-5\">{{index + 1}}</h2>\n    <hr class=\"mt-4 flex-grow-1 divider\"/>\n  </div>\n\n  <div class=\"d-flex pb-3\">\n    <h4 class=\"p-2 tool-name\" id=\"mutgen-label\">Mutated Peptide Generator\n      <img class='pb-1' src=\"/assets/symbols/cedar/symbol.svg\" alt=\"cedar\" height=\"24\" width=\"24\">\n    </h4>\n    <div class=\"d-flex flex-row tool-links\" role=\"group\" aria-label=\"tool-links\">\n      <button type=\"button\" class=\"btn btn-link text-dark d-flex flex-column justify-content-center align-items-center\">\n        <a target=\"_blank\" routerLink=\"/docs/tools/mpg/index.html\" class=\"text-dark d-flex flex-column justify-content-center align-items-center\">\n          <svg width=\"1em\" height=\"1em\" viewBox=\"0 0 16 16\" class=\"bi bi-file-earmark-text\" fill=\"currentColor\"\n               xmlns=\"http://www.w3.org/2000/svg\">\n            <path\n              d=\"M4 1h5v1H4a1 1 0 0 0-1 1v10a1 1 0 0 0 1 1h8a1 1 0 0 0 1-1V6h1v7a2 2 0 0 1-2 2H4a2 2 0 0 1-2-2V3a2 2 0 0 1 2-2z\"/>\n            <path d=\"M9 4.5V1l5 5h-3.5A1.5 1.5 0 0 1 9 4.5z\"/>\n            <path fill-rule=\"evenodd\"\n                  d=\"M5 11.5a.5.5 0 0 1 .5-.5h2a.5.5 0 0 1 0 1h-2a.5.5 0 0 1-.5-.5zm0-2a.5.5 0 0 1 .5-.5h5a.5.5 0 0 1 0 1h-5a.5.5 0 0 1-.5-.5zm0-2a.5.5 0 0 1 .5-.5h5a.5.5 0 0 1 0 1h-5a.5.5 0 0 1-.5-.5z\"/>\n          </svg>\n          Docs\n        </a>\n      </button>\n      <button type=\"button\" class=\"btn btn-link\">\n        <a target=\"_blank\" [href]=\"swaggerUrl\" class=\"text-dark d-flex flex-column justify-content-center align-items-center\">\n          <svg width=\"1em\" height=\"1em\" viewBox=\"0 0 16 16\" class=\"bi bi-gear\" fill=\"currentColor\"\n               xmlns=\"http://www.w3.org/2000/svg\">\n            <path fill-rule=\"evenodd\"\n                  d=\"M8.837 1.626c-.246-.835-1.428-.835-1.674 0l-.094.319A1.873 1.873 0 0 1 4.377 3.06l-.292-.16c-.764-.415-1.6.42-1.184 1.185l.159.292a1.873 1.873 0 0 1-1.115 2.692l-.319.094c-.835.246-.835 1.428 0 1.674l.319.094a1.873 1.873 0 0 1 1.115 2.693l-.16.291c-.415.764.42 1.6 1.185 1.184l.292-.159a1.873 1.873 0 0 1 2.692 1.116l.094.318c.246.835 1.428.835 1.674 0l.094-.319a1.873 1.873 0 0 1 2.693-1.115l.291.16c.764.415 1.6-.42 1.184-1.185l-.159-.291a1.873 1.873 0 0 1 1.116-2.693l.318-.094c.835-.246.835-1.428 0-1.674l-.319-.094a1.873 1.873 0 0 1-1.115-2.692l.16-.292c.415-.764-.42-1.6-1.185-1.184l-.291.159A1.873 1.873 0 0 1 8.93 1.945l-.094-.319zm-2.633-.283c.527-1.79 3.065-1.79 3.592 0l.094.319a.873.873 0 0 0 1.255.52l.292-.16c1.64-.892 3.434.901 2.54 2.541l-.159.292a.873.873 0 0 0 .52 1.255l.319.094c1.79.527 1.79 3.065 0 3.592l-.319.094a.873.873 0 0 0-.52 1.255l.16.292c.893 1.64-.902 3.434-2.541 2.54l-.292-.159a.873.873 0 0 0-1.255.52l-.094.319c-.527 1.79-3.065 1.79-3.592 0l-.094-.319a.873.873 0 0 0-1.255-.52l-.292.16c-1.64.893-3.433-.902-2.54-2.541l.159-.292a.873.873 0 0 0-.52-1.255l-.319-.094c-1.79-.527-1.79-3.065 0-3.592l.319-.094a.873.873 0 0 0 .52-1.255l-.16-.292c-.892-1.64.902-3.433 2.541-2.54l.292.159a.873.873 0 0 0 1.255-.52l.094-.319z\"/>\n            <path fill-rule=\"evenodd\"\n                  d=\"M8 5.754a2.246 2.246 0 1 0 0 4.492 2.246 2.246 0 0 0 0-4.492zM4.754 8a3.246 3.246 0 1 1 6.492 0 3.246 3.246 0 0 1-6.492 0z\"/>\n          </svg>\n          API\n        </a>\n      </button>\n      <button type=\"button\" class=\"btn btn-link text-dark d-flex flex-column justify-content-center align-items-center\"\n              routerLink=\"/download-all\"\n              [state]=\"{tool: 'mhc-class-i-binding'}\">\n        <svg width=\"1em\" height=\"1em\" viewBox=\"0 0 16 16\" class=\"bi bi-cloud-arrow-down\" fill=\"currentColor\"\n             xmlns=\"http://www.w3.org/2000/svg\">\n          <path fill-rule=\"evenodd\"\n                d=\"M4.406 3.342A5.53 5.53 0 0 1 8 2c2.69 0 4.923 2 5.166 4.579C14.758 6.804 16 8.137 16 9.773 16 11.569 14.502 13 12.687 13H3.781C1.708 13 0 11.366 0 9.318c0-1.763 1.266-3.223 2.942-3.593.143-.863.698-1.723 1.464-2.383zm.653.757c-.757.653-1.153 1.44-1.153 2.056v.448l-.445.049C2.064 6.805 1 7.952 1 9.318 1 10.785 2.23 12 3.781 12h8.906C13.98 12 15 10.988 15 9.773c0-1.216-1.02-2.228-2.313-2.228h-.5v-.5C12.188 4.825 10.328 3 8 3a4.53 4.53 0 0 0-2.941 1.1z\"/>\n          <path fill-rule=\"evenodd\"\n                d=\"M7.646 10.854a.5.5 0 0 0 .708 0l2-2a.5.5 0 0 0-.708-.708L8.5 9.293V5.5a.5.5 0 0 0-1 0v3.793L6.354 8.146a.5.5 0 1 0-.708.708l2 2z\"/>\n        </svg>\n        Download\n      </button>\n      <button type=\"button\" class=\"btn btn-link text-dark d-flex flex-column justify-content-center align-items-center\"\n              routerLink=\"/citation\">\n        <svg width=\"1em\" height=\"1em\" viewBox=\"0 0 16 16\" class=\"bi bi-chat-square-quote\" fill=\"currentColor\"\n             xmlns=\"http://www.w3.org/2000/svg\">\n          <path fill-rule=\"evenodd\"\n                d=\"M14 1H2a1 1 0 0 0-1 1v8a1 1 0 0 0 1 1h2.5a2 2 0 0 1 1.6.8L8 14.333 9.9 11.8a2 2 0 0 1 1.6-.8H14a1 1 0 0 0 1-1V2a1 1 0 0 0-1-1zM2 0a2 2 0 0 0-2 2v8a2 2 0 0 0 2 2h2.5a1 1 0 0 1 .8.4l1.9 2.533a1 1 0 0 0 1.6 0l1.9-2.533a1 1 0 0 1 .8-.4H14a2 2 0 0 0 2-2V2a2 2 0 0 0-2-2H2z\"/>\n          <path fill-rule=\"evenodd\"\n                d=\"M7.066 4.76A1.665 1.665 0 0 0 4 5.668a1.667 1.667 0 0 0 2.561 1.406c-.131.389-.375.804-.777 1.22a.417.417 0 1 0 .6.58c1.486-1.54 1.293-3.214.682-4.112zm4 0A1.665 1.665 0 0 0 8 5.668a1.667 1.667 0 0 0 2.561 1.406c-.131.389-.375.804-.777 1.22a.417.417 0 1 0 .6.58c1.486-1.54 1.293-3.214.682-4.112z\"/>\n        </svg>\n        Cite\n      </button>\n    </div>\n  </div>\n\n  <!--  Sequence Input-->\n  <ng-container *ngIf=\"index===0\">\n    <div class=\"row p-2\">\n      <h5 class=\"col-3 text-left\">Input Variant Calls (VCF)</h5>\n\n      <div class=\"col-9\">\n        <!--          <div class=\"btn-group btn-group-sm ml-auto\">-->\n        <button type=\"button\" class=\"btn btn-sm btn-dark-blue-grey text-white\" (click)=\"null\"\n                [disabled]=\"!submitted\"\n                data-toggle=\"dropdown\"\n                data-bs-toggle=\"dropdown\" aria-haspopup=\"true\" aria-expanded=\"false\">\n          <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n               class=\"bi bi-download\" viewBox=\"0 0 16 16\">\n            <path\n              d=\"M.5 9.9a.5.5 0 0 1 .5.5v2.5a1 1 0 0 0 1 1h12a1 1 0 0 0 1-1v-2.5a.5.5 0 0 1 1 0v2.5a2 2 0 0 1-2 2H2a2 2 0 0 1-2-2v-2.5a.5.5 0 0 1 .5-.5z\"/>\n            <path\n              d=\"M7.646 11.854a.5.5 0 0 0 .708 0l3-3a.5.5 0 0 0-.708-.708L8.5 10.293V1.5a.5.5 0 0 0-1 0v8.793L5.354 8.146a.5.5 0 1 0-.708.708l3 3z\"/>\n          </svg>\n        </button>\n        <div class=\"dropdown-menu\" aria-labelledby=\"dropdownMenuButton\">\n          <div class=\"dropdown-item\">\n            <label>Download as: </label>\n            &nbsp;\n            <div class=\"btn-group\">\n              <button\n                [className]=\"submitted ? 'btn btn-sky-blue text-white' : 'btn btn-outline-secondary'\"\n                type=\"button\" (click)=\"onDownloadJson()\">\n                JSON\n              </button>\n              <button\n                [className]=\"submitted ? 'btn btn-sky-blue text-white' : 'btn btn-outline-secondary'\"\n                type=\"button\" (click)=\"onDownloadOriginal()\"\n              >VCF\n              </button>\n            </div>\n          </div>\n        </div>\n        &nbsp;\n        <input type=\"file\"\n               #uploader\n               style=\"display: none\"\n               id=\"file\"\n               (change)=\"uploadSequenceFile($event)\">\n\n        <ng-template #uploadSequencesTipContent>\n          <div>\n            Upload sequence file <br> (.vcf)\n          </div>\n\n        </ng-template>\n        <button type=\"button\" class=\"btn btn-dark-blue-grey btn-sm text-white\" (click)=\"uploader.click()\" [disabled]=\"loading\"\n                ngbTooltip='Clear allele(s)'\n                [ngbTooltip]=\"uploadSequencesTipContent\" placement=\"right\">\n          <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\" class=\"bi bi-upload\"\n               viewBox=\"0 0 16 16\">\n            <path\n              d=\"M.5 9.9a.5.5 0 0 1 .5.5v2.5a1 1 0 0 0 1 1h12a1 1 0 0 0 1-1v-2.5a.5.5 0 0 1 1 0v2.5a2 2 0 0 1-2 2H2a2 2 0 0 1-2-2v-2.5a.5.5 0 0 1 .5-.5z\"/>\n            <path\n              d=\"M7.646 1.146a.5.5 0 0 1 .708 0l3 3a.5.5 0 0 1-.708.708L8.5 2.707V11.5a.5.5 0 0 1-1 0V2.707L5.354 4.854a.5.5 0 1 1-.708-.708l3-3z\"/>\n          </svg>\n        </button>\n        &nbsp;\n      </div>\n    </div>\n    <div class=\"d-flex flex-column p-2\" appDnd (fileDropped)=\"onFileDropped($event)\">\n      <textarea class='form-control'\n                [style.border-color]=\"inputChange.input_sequence_text ? '#f0ad4d' : null\"\n                id=\"vcfFormControlTextArea\"\n                rows=\"10\"\n                formControlName=\"inputVcfText\"\n                [readOnly]=\"loading\"\n                [placeholder]=\"sequencePlaceHolder\"></textarea>\n\n<!--      <div class=\"d-flex flex-row-reverse justify-content-between p-2\">-->\n<!--        <small *ngIf=\"inputSequenceText.length >= maxCharacters; else sequenceCounter\" class=\"text-danger\">-->\n<!--          Sequence text is too long -  {{maxCharacters | number}} characters allowed-->\n<!--        </small>-->\n<!--        <ng-template #sequenceCounter>-->\n<!--          <small class=\"text-muted\">-->\n<!--            Format: {{seqFormat}} | {{numOfCharacters | number}} characters-->\n<!--          </small>-->\n<!--        </ng-template>-->\n<!--        <small *ngIf=\"inputChange.input_sequence_text\" class=\"help-block form-text text-warning\">-->\n<!--          Parameter changed since prediction.-->\n<!--        </small>-->\n<!--      </div>-->\n    </div>\n  </ng-container>\n\n  <!--  Prediction parameter -->\n  <div class=\"row p-2\">\n    <h5 class=\"col-3 text-left\">Prediction Parameters</h5>\n    <div class=\"col-9\">\n    </div>\n  </div>\n\n  <!--  Peptide Length -->\n  <div class=\"form-group row p-2\" id=\"peptideLengthRow\">\n    <div class=\"col-sm-3 col-form-label\">\n      <label class=\"text-left\">Peptide Length</label>\n    </div>\n\n    <div class=\"col-sm-8\">\n      <div [className]=\"inputChange.lengths ? 'input-change-slider' : 'custom-ngx-slider'\">\n        <ngx-slider\n          formControlName=\"peptideLength\"\n          (userChangeEnd)=\"onLengthChange($event)\"\n          [options]=\"peptideLengthSliderOptions\"></ngx-slider>\n        <small *ngIf=\"inputChange.lengths\" class=\"help-block form-text text-warning\">\n          Parameter changed since prediction.\n        </small>\n      </div>\n\n    </div>\n  </div>\n\n  <div class=\"form-group row row-cols-4 p-2\" id=\"peptideMutationPositionRow\">\n    <div class=\"col col-form-label\">\n      <label class=\"text-left\">Peptide 1 Mutation Position</label>\n    </div>\n    <div class=\"col\">\n      <input type=\"number\" class=\"form-control w-50\" id=\"peptideMutationPosition1\"\n             formControlName=\"peptideMutationPosition1\"\n             min=\"1\" max=\"40\">\n      <small *ngIf=\"inputChange.peptideMutationPosition1\" class=\"help-block form-text text-warning\">\n        Parameter changed since prediction.\n      </small>\n    </div>\n\n    <div class=\"col col-form-label\">\n      <label class=\"text-left\">Peptide 2 Mutation Position</label>\n    </div>\n    <div class=\"col\">\n      <input type=\"number\" class=\"form-control w-50\" id=\"peptideMutationPosition2\"\n             formControlName=\"peptideMutationPosition2\"\n             min=\"1\" max=\"40\">\n      <small *ngIf=\"inputChange.peptideMutationPosition2\" class=\"help-block form-text text-warning\">\n        Parameter changed since prediction.\n      </small>\n    </div>\n    <div class=\"col col-form-label\">\n      <label class=\"text-left\">Frameshift Overlap</label>\n    </div>\n    <div class=\"col\">\n      <input type=\"number\" class=\"form-control w-50\" id=\"frameShiftOverlapInput\"\n             formControlName=\"frameshiftOverlap\"\n             min=\"1\" max=\"39\">\n      <small *ngIf=\"inputChange.frameshiftOverlap\" class=\"help-block form-text text-warning\">\n        Parameter changed since prediction.\n      </small>\n    </div>\n    <div class=\"col-sm-3 col-form-label\">\n      <label class=\"text-left\">Maximum Peptide Length</label>\n    </div>\n    <div class=\"col-sm-3\">\n      <input type=\"number\" class=\"form-control w-50\" id=\"maxPepLengthInput\"\n             formControlName=\"maximumPeptideLength\"\n             min=\"9\" max=\"100\">\n      <small *ngIf=\"inputChange.maximumPeptideLength\" class=\"help-block form-text text-warning\">\n        Parameter changed since prediction.\n      </small>\n    </div>\n  </div>\n\n  <hr/>\n\n  <div class=\"form-group d-flex flex-row-reverse pt-2\">\n\n    <div class=\"p-2\">\n      <!--        [disabled]=\"filteredSequences.length===0\"-->\n      <button type=\"button\" class=\"reset-button btn btn-secondary btn-lg\" [disabled]=\"loading\"\n              (click)=\"onReset();\">\n        <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-arrow-clockwise\" viewBox=\"0 0 16 16\">\n          <path fill-rule=\"evenodd\" d=\"M8 3a5 5 0 1 0 4.546 2.914.5.5 0 0 1 .908-.417A6 6 0 1 1 8 2v1z\"/>\n          <path\n            d=\"M8 4.466V.534a.25.25 0 0 1 .41-.192l2.36 1.966c.12.1.12.284 0 .384L8.41 4.658A.25.25 0 0 1 8 4.466z\"/>\n        </svg>\n      </button>\n      &nbsp;\n      <span *ngIf=\"loading; else elseBlock\">\n        <button type=\"button\" class=\"btn btn-danger btn-lg\" (click)=\"onCancel()\"> Cancel Run </button>\n      </span>\n      <ng-template #elseBlock>\n        <div *ngIf=\"index!==0; else runButtonBlock\" class=\"btn-group\">\n          <div class=\"btn-group\">\n            <button type=\"submit\" class=\"run-button btn btn-dark-blue-grey btn-lg text-white\"\n                    [disabled]=\"\n                    (index>0 && !tools[index-1].submitted) ||\n                    pipelineLoading\"\n            >\n              <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\" class=\"bi bi-play-fill\" viewBox=\"0 0 16 16\">\n                <path d=\"m11.596 8.697-6.363 3.692c-.54.313-1.233-.066-1.233-.697V4.308c0-.63.692-1.01 1.233-.696l6.363 3.692a.802.802 0 0 1 0 1.393z\"/>\n              </svg>\n            </button>\n            <button type=\"button\" class=\"btn btn-dark-blue-grey text-white dropdown-toggle dropdown-toggle-split\"\n                    data-toggle=\"dropdown\"\n                    data-bs-toggle=\"dropdown\" aria-haspopup=\"true\" aria-expanded=\"false\"\n                    [disabled]=\"pipelineLoading\">\n              <!--              <span class=\"sr-only\">Toggle Dropdown</span>-->\n            </button>\n            <div class=\"dropdown-menu\">\n              <a class=\"dropdown-item\" (click)=\"onRunAll()\">Run All Above</a>\n            </div>\n          </div>\n        </div>\n        <ng-template #runButtonBlock>\n          <button type=\"submit\" class=\"run-button btn btn-dark-blue-grey btn-lg text-white\"\n                  [disabled]=\"\n                    (index>0 && !tools[index-1].submitted) ||\n                    pipelineLoading\"\n          >\n            <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\" class=\"bi bi-play-fill\" viewBox=\"0 0 16 16\">\n              <path d=\"m11.596 8.697-6.363 3.692c-.54.313-1.233-.066-1.233-.697V4.308c0-.63.692-1.01 1.233-.696l6.363 3.692a.802.802 0 0 1 0 1.393z\"/>\n            </svg>\n          </button>\n        </ng-template>\n\n      </ng-template>\n    </div>\n  </div>\n\n</form>\n<!--Errors and Warnings accordion -->\n<div ngbAccordion>\n  <!--  Error -->\n  <div ngbAccordionItem=\"first\" *ngIf=\"errorMessages.length\" #first=\"ngbAccordionItem\" [collapsed]=\"true\">\n    <h2 ngbAccordionHeader>\n      <button ngbAccordionButton class=\"accordion-button justify-content-center\">\n        <span class=\"text-danger m-1\">Errors ({{errorMessages.length}})</span>\n        <!--        <div>-->\n        <svg *ngIf=\"first.collapsed\" xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-arrow-left-circle-fill\" style=\"color: #dc3545;\" viewBox=\"0 0 16 16\">\n          <path\n            d=\"M8 0a8 8 0 1 0 0 16A8 8 0 0 0 8 0zm3.5 7.5a.5.5 0 0 1 0 1H5.707l2.147 2.146a.5.5 0 0 1-.708.708l-3-3a.5.5 0 0 1 0-.708l3-3a.5.5 0 1 1 .708.708L5.707 7.5H11.5z\"/>\n        </svg>\n        <!--        </div>-->\n        <!--        <div>-->\n        <svg *ngIf=\"!first.collapsed\" xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-arrow-down-circle-fill\" style=\"color: #dc3545;\" viewBox=\"0 0 16 16\">\n          <path\n            d=\"M16 8A8 8 0 1 1 0 8a8 8 0 0 1 16 0zM8.5 4.5a.5.5 0 0 0-1 0v5.793L5.354 8.146a.5.5 0 1 0-.708.708l3 3a.5.5 0 0 0 .708 0l3-3a.5.5 0 0 0-.708-.708L8.5 10.293V4.5z\"/>\n        </svg>\n        <!--        </div>-->\n      </button>\n    </h2>\n    <div ngbAccordionCollapse>\n      <div ngbAccordionBody>\n        <ng-template>\n          <ol>\n            <li *ngFor=\"let message of errorMessages; let i=index;\">{{message}}</li>\n          </ol>\n        </ng-template>\n      </div>\n    </div>\n  </div>\n  <!--  Warning -->\n  <div ngbAccordionItem=\"second\" *ngIf=\"warningMessages.length\" #second=\"ngbAccordionItem\" [collapsed]=\"true\">\n    <h2 ngbAccordionHeader>\n      <button ngbAccordionButton class=\"accordion-button justify-content-center\">\n        <span class=\"text-warning m-1\">Warnings ({{warningMessages.length}})</span>\n        <svg *ngIf=\"second.collapsed\"  xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-arrow-left-circle-fill\" style=\"color: #f0ad4d;\" viewBox=\"0 0 16 16\">\n          <path\n            d=\"M8 0a8 8 0 1 0 0 16A8 8 0 0 0 8 0zm3.5 7.5a.5.5 0 0 1 0 1H5.707l2.147 2.146a.5.5 0 0 1-.708.708l-3-3a.5.5 0 0 1 0-.708l3-3a.5.5 0 1 1 .708.708L5.707 7.5H11.5z\"/>\n        </svg>\n        <svg *ngIf=\"!second.collapsed\" xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-arrow-down-circle-fill\" style=\"color: #f0ad4d;\" viewBox=\"0 0 16 16\">\n          <path\n            d=\"M16 8A8 8 0 1 1 0 8a8 8 0 0 1 16 0zM8.5 4.5a.5.5 0 0 0-1 0v5.793L5.354 8.146a.5.5 0 1 0-.708.708l3 3a.5.5 0 0 0 .708 0l3-3a.5.5 0 0 0-.708-.708L8.5 10.293V4.5z\"/>\n        </svg>\n      </button>\n    </h2>\n    <div ngbAccordionCollapse>\n      <div ngbAccordionBody>\n        <ng-template>\n          <ol>\n            <li *ngFor=\"let message of warningMessages; let i=index;\">{{message}}</li>\n          </ol>\n        </ng-template>\n      </div>\n    </div>\n  </div>\n</div>\n\n<div *ngIf=\"!loading && !submitted && !(errorMessages.length && warningMessages.length)\"\n     class=\"p-2 d-flex justify-content-center col\"\n     [style.borderStyle]=\"styleResultContainer\">\n  <label class=\"p-2 font-italic\">\n    Results will load once step is run.\n  </label>\n</div>\n\n<div *ngIf=\"loading\" class=\"p-2 d-flex justify-content-center col\" [style.borderStyle]=\"styleResultContainer\">\n  <div class=\"spinner-border text-primary align-self-center p-3 mb-3\" role=\"status\">\n    <span class=\"visually-hidden sr-only\">Loading...</span>\n  </div>\n  <label *ngIf=\"!getResultsClicked\" class=\"p-2 font-italic\">\n    Calculating results, please wait... Click <a href=\"javascript:void(0)\" (click)=\"openEmailModal.emit()\">here</a> to\n    receive email.\n  </label>\n  <label *ngIf=\"getResultsClicked\" class=\"p-2 font-italic\">\n    Checking job status, please wait...\n  </label>\n</div>\n\n<div class=\"container-fluid p-2\" id=\"table-result-container\"\n     *ngIf=\"!loading && submitted  && !(errorMessages.length && warningMessages.length)\">\n  <ul ngbNav #nav=\"ngbNav\" [(activeId)]=\"active\" [animation]='false' [destroyOnHide]=\"false\" class=\"nav-tabs\">\n    <!--    Peptide Output Table -->\n    <li *ngIf=\"unique_peptide_table[0].length\" [ngbNavItem]=\"'unique_peptide'\">\n      <a ngbNavLink> Unique Peptides </a>\n      <ng-template ngbNavContent>\n        <app-result-table [table_data]=\"unique_peptide_table\"\n                          table_name=\"unique_peptide\"\n                          [order]=\"unique_peptide_table_order\"\n                          [columns]=\"unique_peptide_table_columns\"\n                          [tool_group]=\"formGroupName\"\n                          [index]=\"index\"\n                          [inputChange]=\"inputChange.table_state_1\"\n                          [tableStateSaving]=\"tableStateSaving\"\n                          (emitFilterApplied)=\"onFilterApplied()\"\n                          (emitResetTableState)=\"onClearTableState()\"\n                          (emitSaveTableState)=\"onSaveTableStateMain('unique_peptide')\"\n        ></app-result-table>\n      </ng-template>\n    </li>\n    <!--    Output Table -->\n    <li *ngIf=\"peptide_table[0].length\" [ngbNavItem]=\"'peptide'\">\n      <a ngbNavLink> All Peptides </a>\n      <ng-template ngbNavContent>\n        <app-result-table [table_data]=\"peptide_table\"\n                          table_name=\"peptide\"\n                          [order]=\"peptide_table_order\"\n                          [columns]=\"peptide_table_columns\"\n                          [tool_group]=\"formGroupName\"\n                          [index]=\"index\"\n                          [inputChange]=\"inputChange.table_state_2\"\n                          [tableStateSaving]=\"tableStateSaving\"\n                          (emitFilterApplied)=\"onFilterApplied2()\"\n                          (emitResetTableState)=\"onClearTable2State()\"\n                          (emitSaveTableState)=\"onSaveTableStateMain('peptide')\"\n        ></app-result-table>\n      </ng-template>\n    </li>\n    <!--    SNP Table -->\n    <li *ngIf=\"snp_table[0].length\" [ngbNavItem]=\"'snp'\">\n      <a ngbNavLink>All SNPs</a>\n      <ng-template ngbNavContent>\n        <!--        Result Table -->\n        <app-result-table [table_data]=\"snp_table\"\n                          table_name=\"snp\"\n                          [order]=\"snp_table_order\"\n                          [columns]=\"snp_table_columns\"\n                          [tool_group]=\"formGroupName\"\n        ></app-result-table>\n<!--        [inputChange]=\"inputChange.table_state\"-->\n<!--        [tableStateSaving]=\"tableStateSaving\"-->\n<!--        (emitFilterApplied)=\"onFilterApplied()\"-->\n<!--        (emitResetTableState)=\"onClearTableState()\"-->\n<!--        (emitSaveTableState)=\"onSaveTableStateMain()\"-->\n      </ng-template>\n    </li>\n  </ul>\n\n  <div [ngbNavOutlet]=\"nav\"></div>\n</div>\n\n<!--Alert Modal -->\n<ng-template #alertModal let-modal4>\n  <div class=\"modal-header\">\n    <h4 class=\"modal-title\" id=\"alert-modal-title\">Validation Error(s)</h4>\n    <button type=\"button\" class=\"btn-close\" aria-label=\"Close\" (click)=\"modal4.dismiss('Cross click'); modalOpen=false;\">\n    </button>\n  </div>\n  <div class=\"modal-body\">\n    <app-alert-component></app-alert-component>\n  </div>\n  <div class=\"modal-footer\">\n    <!--    <button type=\"button\" class=\"btn btn-secondary\" (click)=\"null\">Reset</button>-->\n    <!--    <button type=\"button\" class=\"btn btn-dark-blue-grey\" (click)=\"null\">Display</button>-->\n  </div>\n</ng-template>\n\n<!--Confirm Modal -->\n<ng-template #confirmModal let-confirmModal>\n  <div class=\"modal-header\">\n    <h4 class=\"modal-title\" id=\"modal-title\">Are you sure?</h4>\n    <button type=\"button\" class=\"btn-close\" aria-label=\"Close\" (click)=\"confirmModal.dismiss('Cross click'); modalOpen=false;\">\n    </button>\n  </div>\n  <div class=\"modal-body\">\n    <div *ngIf=\"!saveState; else saveStateConfirmation\">\n      <p><strong>Re-running this step of the pipeline will delete all downstream results, including:</strong></p>\n      <ol>\n        <li *ngFor=\"let tool of tools.slice(this.index+1)\"> {{tool.name}} </li>\n      </ol>\n      <p><strong>To access the current results, you can use this link</strong></p>\n    </div>\n    <ng-template #saveStateConfirmation>\n      <p><strong>Applying these filters for input to the next stage will delete results from all downstream steps in\n        this session, including:</strong></p>\n      <ol>\n        <li *ngFor=\"let tool of tools.slice(this.index+1)\"> {{tool.name}} </li>\n      </ol>\n      <p><strong>To access the current results, you can use this link</strong></p>\n    </ng-template>\n    <!-- pipeline URL input group-->\n    <div class=\"input-group\">\n      <input type=\"text\" class=\"form-control\" id=\"pipeline-url-input\" [value]=\"pipelineUrl\">\n      <button class=\"btn btn-secondary\" [cdkCopyToClipboard]=\"pipelineUrl\" ngbTooltip=\"copy url\" placement=\"top\">\n        <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n             class=\"bi bi-clipboard\" viewBox=\"0 0 16 16\">\n          <path\n            d=\"M4 1.5H3a2 2 0 0 0-2 2V14a2 2 0 0 0 2 2h10a2 2 0 0 0 2-2V3.5a2 2 0 0 0-2-2h-1v1h1a1 1 0 0 1 1 1V14a1 1 0 0 1-1 1H3a1 1 0 0 1-1-1V3.5a1 1 0 0 1 1-1h1v-1z\"/>\n          <path\n            d=\"M9.5 1a.5.5 0 0 1 .5.5v1a.5.5 0 0 1-.5.5h-3a.5.5 0 0 1-.5-.5v-1a.5.5 0 0 1 .5-.5h3zm-3-1A1.5 1.5 0 0 0 5 1.5v1A1.5 1.5 0 0 0 6.5 4h3A1.5 1.5 0 0 0 11 2.5v-1A1.5 1.5 0 0 0 9.5 0h-3z\"/>\n        </svg>\n      </button>\n    </div>\n  </div>\n  <div class=\"modal-footer\">\n    <button type=\"button\" class=\"btn btn-outline-secondary\" (click)=\"confirmModal.dismiss('cancel click')\">No\n    </button>\n    <button type=\"button\" class=\"btn btn-danger\" (click)=\"confirmModal.close('Ok click'); onRunConfirm();\">Yes, continue\n      and destroy downstream steps\n    </button>\n  </div>\n</ng-template>\n","import {\n  AfterViewInit,\n  Component,\n  ElementRef,\n  EventEmitter,\n  Input,\n  OnChanges, OnDestroy,\n  OnInit,\n  Output,\n  SimpleChanges,\n  ViewChild\n} from '@angular/core';\nimport {FormGroupDirective, UntypedFormArray, UntypedFormBuilder, UntypedFormGroup} from \"@angular/forms\";\nimport {HttpClient} from \"@angular/common/http\";\nimport {ActivatedRoute, Router} from \"@angular/router\";\nimport {Location} from \"@angular/common\";\nimport {Title} from \"@angular/platform-browser\";\n\nimport {NgbModal} from \"@ng-bootstrap/ng-bootstrap\";\nimport {Observable, of, Subject, Subscription} from \"rxjs\";\nimport {takeUntil} from \"rxjs/operators\";\nimport _ from \"lodash\";\nimport * as pako from 'pako';\n\nimport {ChangeContext, Options, CustomStepDefinition} from \"ngx-slider-v2\";\n\nimport Columns from \"../_global/Columns\";\nimport Stage from \"../_global/Stage\";\nimport Tool from \"../_global/Tool\";\nimport PipelineParams from \"../_global/PipelineParams\";\n\nimport {AlertServiceService} from \"../services/alert-service/alert-service.service\";\nimport {PipelineService} from \"../services/pipeline-service/pipeline.service\";\nimport {PipelineStateService} from \"../services/state-services/pipeline-state-service/pipeline-state.service\";\nimport {SequenceParserService} from \"../services/sequence-parser/sequence-parser.service\";\nimport {\n  initMutatedPeptideGeneratorTool\n} from \"../services/state-services/default-stage-states\";\n\nimport {isASCII} from \"../util/string-helpers\";\nimport {isMaxLines} from \"../util/is-max-lines\";\nimport {columnListToObject} from \"../util/convert-columns\";\nimport onCsvDownloadAllClickedNew from \"../util/on-csv-download\";\n\nimport {environment} from \"../../environments/environment\";\n\n@Component({\n  selector: 'app-mutated-peptide-generator',\n  templateUrl: './mutated-peptide-generator.component.html',\n  styleUrls: ['./mutated-peptide-generator.component.scss']\n})\nexport class MutatedPeptideGeneratorComponent implements OnInit, OnDestroy, AfterViewInit, OnChanges{\n\n  /** Pipeline form */\n  @Input() formGroupName!: string\n  @Input() index!: number;\n  @Input() resultUrl!: string | undefined;\n  @Input() showEmailModal: boolean = false;\n\n  @Input() emailForm!: UntypedFormGroup;\n  @Output() openEmailModal = new EventEmitter<any>();\n\n  active = 'unique_peptide'\n\n  @Output() emitIndex = new EventEmitter<number>(); // used for run all\n  @Output() emitOnCancel = new EventEmitter<any>();\n\n  // @ViewChild('alleleSearch') alleleSearch!: ElementRef;\n  @ViewChild('alertModal') alertModal!: ElementRef;\n  @ViewChild('confirmModal') confirmModal!: ElementRef;\n  @ViewChild('alleleModal') alleleModal!: ElementRef;\n\n  @Input() events: Observable<void> = of();\n  private eventsSubscription: Subscription  = new Subscription();\n\n  @Input() runAllEvent: Observable<void> = of();\n  private runAllSubscription: Subscription  = new Subscription();\n\n  unsubscribe$ = new Subject();\n\n  modalOpen = false;\n\n  /** API Call variables */\n  runSetInterval: any;\n  submitted = false;\n  loading = false;\n  getResultsClicked = true;\n  pipelineLoading = false;\n  tableStateSaving = false;\n  saveState = false;\n\n  defaultOrder: any[] = [];\n\n  errorMessages: string[] = [];\n  warningMessages: string[] = [];\n\n  snp_table_order: any[] = []\n  snp_table_columns: Columns[] | any;\n  snp_table: [(string | number)[]] = [[]]\n\n  unique_peptide_table_order: any[] = [];\n  unique_peptide_table_columns: Columns[] | any;\n  unique_peptide_table: [(string | number)[]] = [[]]\n\n  peptide_table_order: any[] = [];\n  peptide_table_columns: Columns[] | any;\n  peptide_table: [(string | number)[]] = [[]]\n\n  stages$: Observable<Stage[]> = this._stateService.stages$;\n  tools$: Observable<Tool[]> = this._stateService.tools$;\n  pipelineId$: Observable<string> = this._stateService.pipelineId$;\n  params$: Observable<PipelineParams> = this._stateService.params$;\n\n  stages: Stage[] = [];\n  tools: Tool[] = [];\n  pipelineId = '';\n  params!: PipelineParams;\n\n  /** Form variables */\n  mutgenForm!: UntypedFormGroup;\n  defaultInputVcfText: string = ''\n\n  sequencePlaceHolder = `Drag a SNPeff-annotated VCF file (max: 5,000 lines) into this box or click 'Run' to use this example:\n##fileformat=VCFv4.1\n##fileDate=20240220\n##source=freeBayes v0.9.21\n##reference=Homo_sapiens.GRCh38.dna.primary_assembly.fa\n##phasing=none\n##commandline=\"freebayes -f Homo_sapiens.GRCh38.dna.primary_assembly.fa --pooled-discrete --genotype-qualities --min-repeat-entropy 1 --min-alternate-fraction 0.02 --min-alternate-count 2 --region 1:0..248956422 output/syntheticX/syntheticX/syntheticX_normal.bam output/syntheticX/syntheticX_tumor.bam\"\n##INFO=<ID=NS,Number=1,Type=Integer,Description=\"Number of samples with data\">\n##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth at the locus\">\n##INFO=<ID=DPB,Number=1,Type=Float,Description=\"Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype\">\n##INFO=<ID=AC,Number=A,Type=Integer,Description=\"Total number of alternate alleles in called genotypes\">\n##INFO=<ID=AN,Number=1,Type=Integer,Description=\"Total number of alleles in called genotypes\">\n##INFO=<ID=AF,Number=A,Type=Float,Description=\"Estimated allele frequency in the range (0,1]\">\n##INFO=<ID=RO,Number=1,Type=Integer,Description=\"Reference allele observation count, with partial observations recorded fractionally\">\n##INFO=<ID=AO,Number=A,Type=Integer,Description=\"Alternate allele observations, with partial observations recorded fractionally\">\n##INFO=<ID=PRO,Number=1,Type=Float,Description=\"Reference allele observation count, with partial observations recorded fractionally\">\n##INFO=<ID=PAO,Number=A,Type=Float,Description=\"Alternate allele observations, with partial observations recorded fractionally\">\n##INFO=<ID=QR,Number=1,Type=Integer,Description=\"Reference allele quality sum in phred\">\n##INFO=<ID=QA,Number=A,Type=Integer,Description=\"Alternate allele quality sum in phred\">\n##INFO=<ID=PQR,Number=1,Type=Float,Description=\"Reference allele quality sum in phred for partial observations\">\n##INFO=<ID=PQA,Number=A,Type=Float,Description=\"Alternate allele quality sum in phred for partial observations\">\n##INFO=<ID=SRF,Number=1,Type=Integer,Description=\"Number of reference observations on the forward strand\">\n##INFO=<ID=SRR,Number=1,Type=Integer,Description=\"Number of reference observations on the reverse strand\">\n##INFO=<ID=SAF,Number=A,Type=Integer,Description=\"Number of alternate observations on the forward strand\">\n##INFO=<ID=SAR,Number=A,Type=Integer,Description=\"Number of alternate observations on the reverse strand\">\n##INFO=<ID=SRP,Number=1,Type=Float,Description=\"Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality\">\n##INFO=<ID=SAP,Number=A,Type=Float,Description=\"Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality\">\n##INFO=<ID=AB,Number=A,Type=Float,Description=\"Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous\">\n##INFO=<ID=ABP,Number=A,Type=Float,Description=\"Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality\">\n##INFO=<ID=RUN,Number=A,Type=Integer,Description=\"Run length: the number of consecutive repeats of the alternate allele in the reference genome\">\n##INFO=<ID=RPP,Number=A,Type=Float,Description=\"Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality\">\n##INFO=<ID=RPPR,Number=1,Type=Float,Description=\"Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality\">\n##INFO=<ID=RPL,Number=A,Type=Float,Description=\"Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele\">\n##INFO=<ID=RPR,Number=A,Type=Float,Description=\"Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele\">\n##INFO=<ID=EPP,Number=A,Type=Float,Description=\"End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality\">\n##INFO=<ID=EPPR,Number=1,Type=Float,Description=\"End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality\">\n##INFO=<ID=DPRA,Number=A,Type=Float,Description=\"Alternate allele depth ratio.  Ratio between depth in samples with each called alternate allele and those without.\">\n##INFO=<ID=ODDS,Number=1,Type=Float,Description=\"The log odds ratio of the best genotype combination to the second-best.\">\n##INFO=<ID=GTI,Number=1,Type=Integer,Description=\"Number of genotyping iterations required to reach convergence or bailout.\">\n##INFO=<ID=TYPE,Number=A,Type=String,Description=\"The type of allele, either snp, mnp, ins, del, or complex.\">\n##INFO=<ID=CIGAR,Number=A,Type=String,Description=\"The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing.  Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.\">\n##INFO=<ID=NUMALT,Number=1,Type=Integer,Description=\"Number of unique non-reference alleles in called genotypes at this position.\">\n##INFO=<ID=MEANALT,Number=A,Type=Float,Description=\"Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles.\">\n##INFO=<ID=LEN,Number=A,Type=Integer,Description=\"allele length\">\n##INFO=<ID=MQM,Number=A,Type=Float,Description=\"Mean mapping quality of observed alternate alleles\">\n##INFO=<ID=MQMR,Number=1,Type=Float,Description=\"Mean mapping quality of observed reference alleles\">\n##INFO=<ID=PAIRED,Number=A,Type=Float,Description=\"Proportion of observed alternate alleles which are supported by properly paired read fragments\">\n##INFO=<ID=PAIREDR,Number=1,Type=Float,Description=\"Proportion of observed reference alleles which are supported by properly paired read fragments\">\n##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n##FORMAT=<ID=GQ,Number=1,Type=Float,Description=\"Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype\">\n##FORMAT=<ID=GL,Number=G,Type=Float,Description=\"Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy\">\n##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\n##FORMAT=<ID=RO,Number=1,Type=Integer,Description=\"Reference allele observation count\">\n##FORMAT=<ID=QR,Number=1,Type=Integer,Description=\"Sum of quality of the reference observations\">\n##FORMAT=<ID=AO,Number=A,Type=Integer,Description=\"Alternate allele observation count\">\n##FORMAT=<ID=QA,Number=A,Type=Integer,Description=\"Sum of quality of the alternate observations\">\n##INFO=<ID=SSC,Number=1,Type=Float,Description=\"Somatic score\">\n##SnpEffVersion=\"5.2c (build 2024-04-09 12:24), by Pablo Cingolani\"\n##SnpEffCmd=\"SnpEff  -noStats -cancer -cancerSamples in.samples GRCh38.86 \"\n##INFO=<ID=ANN,Number=.,Type=String,Description=\"Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' \">\n##INFO=<ID=LOF,Number=.,Type=String,Description=\"Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'\">\n##INFO=<ID=NMD,Number=.,Type=String,Description=\"Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'\">\n#CHROM\\tPOS\\tID\\tREF\\tALT\\tQUAL\\tFILTER\\tINFO\\tFORMAT\\tsyntheticX_normal\\tsyntheticX_tumor\n19\\t36007191\\t.\\tC\\tA\\t24.8697\\tPASS\\tSSC=8.6069;TYPE=snp;ANN=A|synonymous_variant|LOW|SYNE4|ENSG00000181392|transcript|ENST00000490730.1|protein_coding|3/8|c.357G>T|p.Arg119Arg|469/1175|357/1063|119/353||WARNING_TRANSCRIPT_INCOMPLETE,A|synonymous_variant|LOW|SYNE4|ENSG00000181392|transcript|ENST00000324444.7|protein_coding|3/8|c.357G>T|p.Arg119Arg|469/1354|357/1215|119/404||,A|downstream_gene_variant|MODIFIER|ALKBH6|ENSG00000239382|transcript|ENST00000378875.7|protein_coding||c.*2099G>T|||||1933|,A|downstream_gene_variant|MODIFIER|ALKBH6|ENSG00000239382|transcript|ENST00000490986.5|nonsense_mediated_decay||n.*2509G>T|||||1930|,A|downstream_gene_variant|MODIFIER|ALKBH6|ENSG00000239382|transcript|ENST00000252984.11|protein_coding||c.*2099G>T|||||2014|,A|downstream_gene_variant|MODIFIER|ALKBH6|ENSG00000239382|transcript|ENST00000392183.7|retained_intron||n.*3099G>T|||||3099|,A|downstream_gene_variant|MODIFIER|ALKBH6|ENSG00000239382|transcript|ENST00000466196.5|retained_intron||n.*3547G>T|||||3547|,A|downstream_gene_variant|MODIFIER|AC002116.8|ENSG00000248101|transcript|ENST00000473572.2|retained_intron||n.*1447G>T|||||1447|,A|downstream_gene_variant|MODIFIER|ALKBH6|ENSG00000239382|transcript|ENST00000495116.6|processed_transcript||n.*1929G>T|||||1929|,A|downstream_gene_variant|MODIFIER|ALKBH6|ENSG00000239382|transcript|ENST00000471323.1|retained_intron||n.*1931G>T|||||1931|,A|downstream_gene_variant|MODIFIER|ALKBH6|ENSG00000239382|transcript|ENST00000475223.5|retained_intron||n.*3547G>T|||||3547|,A|downstream_gene_variant|MODIFIER|ALKBH6|ENSG00000239382|transcript|ENST00000486389.5|protein_coding||c.*2376G>T|||||1933|,A|downstream_gene_variant|MODIFIER|ALKBH6|ENSG00000239382|transcript|ENST00000462793.5|retained_intron||n.*2270G>T|||||2270|,A|downstream_gene_variant|MODIFIER|ALKBH6|ENSG00000239382|transcript|ENST00000590666.5|retained_intron||n.*3989G>T|||||3989|,A|downstream_gene_variant|MODIFIER|ALKBH6|ENSG00000239382|transcript|ENST00000461668.5|nonsense_mediated_decay||n.*2581G>T|||||1930|,A|downstream_gene_variant|MODIFIER|ALKBH6|ENSG00000239382|transcript|ENST00000490483.5|nonsense_mediated_decay||n.*2509G>T|||||1930|,A|downstream_gene_variant|MODIFIER|ALKBH6|ENSG00000239382|transcript|ENST00000485128.5|protein_coding||c.*2376G>T|||||1984|,A|downstream_gene_variant|MODIFIER|ALKBH6|ENSG00000239382|transcript|ENST00000497999.1|nonsense_mediated_decay||n.*2598G>T|||||2091|,A|downstream_gene_variant|MODIFIER|ALKBH6|ENSG00000239382|transcript|ENST00000468004.5|retained_intron||n.*3353G>T|||||3353|,A|downstream_gene_variant|MODIFIER|ALKBH6|ENSG00000239382|transcript|ENST00000481257.5|nonsense_mediated_decay||n.*3846G>T|||||3445|,A|downstream_gene_variant|MODIFIER|ALKBH6|ENSG00000239382|transcript|ENST00000592353.1|retained_intron||n.*3847G>T|||||3847|,A|intron_variant|MODIFIER|SYNE4|ENSG00000181392|transcript|ENST00000340477.9|protein_coding|2/5|c.280-520G>T||||||,A|intron_variant|MODIFIER|SYNE4|ENSG00000181392|transcript|ENST00000505054.2|retained_intron|1/2|n.394+1026G>T||||||,A|intron_variant|MODIFIER|SYNE4|ENSG00000181392|transcript|ENST00000397428.7|protein_coding|1/2|c.39+1363G>T||||||WARNING_TRANSCRIPT_INCOMPLETE,A|intron_variant|MODIFIER|SYNE4|ENSG00000181392|transcript|ENST00000503121.5|protein_coding|2/2|c.240+1026G>T||||||WARNING_TRANSCRIPT_INCOMPLETE,A|non_coding_transcript_exon_variant|MODIFIER|SYNE4|ENSG00000181392|transcript|ENST00000465425.1|retained_intron|3/7|n.469G>T||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:39.9452:8:8:320:0:0:0,-2.40824,-29.1663\\t0/1:24.8697:4:2:82:2:78:-6.19866,0,-6.57556\n10\\t101131861\\t.\\tT\\tC\\t0.0\\tPASS\\tSSC=176.441;TYPE=snp;ANN=C|missense_variant|MODERATE|TLX1|ENSG00000107807|transcript|ENST00000370196.10|protein_coding|1/3|c.320T>C|p.Leu107Ser|1357/2906|320/993|107/330||,C|missense_variant|MODERATE|TLX1|ENSG00000107807|transcript|ENST00000467928.2|protein_coding|1/3|c.320T>C|p.Leu107Ser|558/1838|320/774|107/257||,C|missense_variant|MODERATE|TLX1|ENSG00000107807|transcript|ENST00000463716.3|protein_coding|1/2|c.134T>C|p.Leu45Ser|134/469|134/469|45/155||WARNING_TRANSCRIPT_INCOMPLETE,C|upstream_gene_variant|MODIFIER|TLX1NB|ENSG00000236311|transcript|ENST00000445873.5|processed_transcript||n.-735A>G|||||735|,C|upstream_gene_variant|MODIFIER|TLX1NB|ENSG00000236311|transcript|ENST00000425505.1|processed_transcript||n.-735A>G|||||735|,C|upstream_gene_variant|MODIFIER|TLX1|ENSG00000107807|transcript|ENST00000533319.1|processed_transcript||n.-921T>C|||||921|,C|upstream_gene_variant|MODIFIER|TLX1|ENSG00000107807|transcript|ENST00000525019.1|processed_transcript||n.-2453T>C|||||2453|\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:658:657:25828:1:12:0,-196.878,-2320.96\\t0/0:99:97:94:3642:3:94:0,-20.4367,-319.031\n22\\t25351843\\t.\\tTG\\tT\\t0.0\\tPASS\\tSSC=153.764;TYPE=del;OLD_VARIANT=22:25351843:TGGGGCGT/TGGGCGT;ANN=T|frameshift_variant|HIGH|LRP5L|ENSG00000100068|transcript|ENST00000402785.2|protein_coding|4/4|c.714delC|p.Thr239fs|811/1193|714/759|238/252||,T|frameshift_variant|HIGH|LRP5L|ENSG00000100068|transcript|ENST00000610821.4|protein_coding|4/4|c.714delC|p.Thr239fs|3179/3602|714/759|238/252||,T|frameshift_variant|HIGH|LRP5L|ENSG00000100068|transcript|ENST00000402859.6|protein_coding|6/6|c.714delC|p.Thr239fs|1238/1661|714/759|238/252||,T|3_prime_UTR_variant|MODIFIER|LRP5L|ENSG00000100068|transcript|ENST00000474163.1|nonsense_mediated_decay|4/4|n.*412delC|||||5547|,T|upstream_gene_variant|MODIFIER|CTA-246H3.11|ENSG00000231466|transcript|ENST00000434827.1|processed_pseudogene||n.-1522delC|||||1522|,T|downstream_gene_variant|MODIFIER|LRP5L|ENSG00000100068|transcript|ENST00000484509.1|retained_intron||n.*2913delC|||||2913|,T|intron_variant|MODIFIER|LRP5L|ENSG00000100068|transcript|ENST00000444995.7|protein_coding|6/6|c.656-30delC||||||,T|non_coding_transcript_exon_variant|MODIFIER|LRP5L|ENSG00000100068|transcript|ENST00000467672.5|retained_intron|4/4|n.3179delC||||||,T|non_coding_transcript_exon_variant|MODIFIER|LRP5L|ENSG00000100068|transcript|ENST00000474163.1|nonsense_mediated_decay|4/4|n.*412delC||||||;LOF=(LRP5L|ENSG00000100068|8|0.38)\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:504:501:19784:0:0:0,-178.21,-1896.78\\t0/0:99:84:81:3200:2:82:0,-24.446,-284.026\n17\\t7024470\\t.\\tACCA\\tCCCC\\t1.78519E-4\\tPASS\\tSSC=0.42928;TYPE=complex;ANN=CCCC|synonymous_variant|LOW|BCL6B|ENSG00000161940|transcript|ENST00000293805.9|protein_coding|4/9|c.471_474delACCAinsCCCC|p.159|563/3555|471/1440|157/479||,CCCC|upstream_gene_variant|MODIFIER|BCL6B|ENSG00000161940|transcript|ENST00000571729.1|retained_intron||n.-2321_-2318delACCAinsCCCC|||||2321|,CCCC|upstream_gene_variant|MODIFIER|MIR497HG|ENSG00000267532|transcript|ENST00000443997.1|antisense||n.-4843_-4840delTGGTinsGGGG|||||4840|,CCCC|upstream_gene_variant|MODIFIER|BCL6B|ENSG00000161940|transcript|ENST00000537931.2|protein_coding||c.-2031_-2028delACCAinsCCCC|||||2031|WARNING_TRANSCRIPT_NO_START_CODON,CCCC|upstream_gene_variant|MODIFIER|MIR497HG|ENSG00000267532|transcript|ENST00000572453.1|antisense||n.-4814_-4811delTGGTinsGGGG|||||4811|,CCCC|downstream_gene_variant|MODIFIER|BCL6B|ENSG00000161940|transcript|ENST00000573503.1|protein_coding||c.*233_*236delACCAinsCCCC|||||233|WARNING_TRANSCRIPT_INCOMPLETE,CCCC|downstream_gene_variant|MODIFIER|BCL6B|ENSG00000161940|transcript|ENST00000576705.1|protein_coding||c.*166_*169delACCAinsCCCC|||||166|WARNING_TRANSCRIPT_INCOMPLETE,CCCC|non_coding_transcript_exon_variant|MODIFIER|BCL6B|ENSG00000161940|transcript|ENST00000572216.1|processed_transcript|4/4|n.379_382delACCAinsCCCC||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:58.2077:12:10:324:2:24:0,-1.33237,-27.1817\\t0/0:44.0237:3:3:119:0:0:0,-0.90309,-11.095\n22\\t42128903\\t.\\tT\\tA\\t9.57029E-16\\tPASS\\tSSC=171.425;TYPE=snp;ANN=A|missense_variant|MODERATE|CYP2D6|ENSG00000100197|transcript|ENST00000360608.9|protein_coding|4/9|c.547A>T|p.Ser183Cys|662/1684|547/1494|183/497||,A|missense_variant|MODERATE|CYP2D6|ENSG00000100197|transcript|ENST00000359033.4|protein_coding|3/8|c.394A>T|p.Ser132Cys|468/1433|394/1341|132/446||,A|missense_variant|MODERATE|CYP2D6|ENSG00000100197|transcript|ENST00000389970.7|protein_coding|4/10|c.481A>T|p.Ser161Cys|637/1714|481/1485|161/494||,A|upstream_gene_variant|MODIFIER|NDUFA6-AS1|ENSG00000237037|transcript|ENST00000617009.4|antisense||n.-3128T>A|||||3128|,A|upstream_gene_variant|MODIFIER|NDUFA6-AS1|ENSG00000237037|transcript|ENST00000621190.1|antisense||n.-3128T>A|||||3128|,A|upstream_gene_variant|MODIFIER|RP4-669P10.19|ENSG00000227370|transcript|ENST00000417586.1|processed_pseudogene||n.-3640T>A|||||3640|,A|downstream_gene_variant|MODIFIER|NDUFA6-AS1|ENSG00000237037|transcript|ENST00000451451.1|antisense||n.*3875T>A|||||3875|,A|downstream_gene_variant|MODIFIER|NDUFA6-AS1|ENSG00000237037|transcript|ENST00000417327.5|antisense||n.*3554T>A|||||3554|,A|downstream_gene_variant|MODIFIER|NDUFA6-AS1|ENSG00000237037|transcript|ENST00000536447.6|antisense||n.*3944T>A|||||3944|,A|downstream_gene_variant|MODIFIER|NDUFA6-AS1|ENSG00000237037|transcript|ENST00000595777.5|antisense||n.*3944T>A|||||3944|,A|downstream_gene_variant|MODIFIER|NDUFA6-AS1|ENSG00000237037|transcript|ENST00000600968.5|antisense||n.*3944T>A|||||3944|,A|downstream_gene_variant|MODIFIER|NDUFA6-AS1|ENSG00000237037|transcript|ENST00000434834.5|antisense||n.*3901T>A|||||3901|,A|downstream_gene_variant|MODIFIER|NDUFA6-AS1|ENSG00000237037|transcript|ENST00000610250.5|antisense||n.*4004T>A|||||4004|,A|downstream_gene_variant|MODIFIER|NDUFA6-AS1|ENSG00000237037|transcript|ENST00000547929.6|retained_intron||n.*4004T>A|||||4004|,A|downstream_gene_variant|MODIFIER|NDUFA6-AS1|ENSG00000237037|transcript|ENST00000617396.4|antisense||n.*4341T>A|||||4341|,A|downstream_gene_variant|MODIFIER|NDUFA6-AS1|ENSG00000237037|transcript|ENST00000609499.5|retained_intron||n.*4004T>A|||||4004|,A|downstream_gene_variant|MODIFIER|NDUFA6-AS1|ENSG00000237037|transcript|ENST00000609833.5|retained_intron||n.*4004T>A|||||4004|,A|downstream_gene_variant|MODIFIER|NDUFA6-AS1|ENSG00000237037|transcript|ENST00000608643.5|retained_intron||n.*4019T>A|||||4019|,A|intron_variant|MODIFIER|NDUFA6-AS1|ENSG00000237037|transcript|ENST00000439129.5|antisense|5/6|n.1718+3496T>A||||||,A|non_coding_transcript_exon_variant|MODIFIER|CYP2D6|ENSG00000100197|transcript|ENST00000360124.9|nonsense_mediated_decay|2/7|n.214A>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|CYP2D6|ENSG00000100197|transcript|ENST00000488442.1|retained_intron|3/8|n.1271A>T||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:646:646:24929:0:0:0,-194.465,-2195.25\\t0/0:99:92:90:3541:2:49:0,-23.04,-304.263\n6\\t160064455\\t.\\tC\\tCG\\t1.09451E-13\\tPASS\\tSSC=226.209;TYPE=ins;OLD_VARIANT=6:160064455:CGGGGGGGGACA/CGGGGGGGGGACA;ANN=CG|frameshift_variant|HIGH|IGF2R|ENSG00000197081|transcript|ENST00000356956.5|protein_coding|28/48|c.3949dupG|p.Asp1317fs|4098/14044|3950/7476|1317/2491||INFO_REALIGN_3_PRIME;LOF=(IGF2R|ENSG00000197081|5|0.20)\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:1057:1004:39425:21:778:0,-326.753,-3525.51\\t0/0:99:352:327:12912:11:406:0,-100.544,-1130.26\n9\\t70286221\\t.\\tT\\tC\\t0.0\\tPASS\\tSSC=160.285;TYPE=snp;ANN=C|missense_variant|MODERATE|SMC5|ENSG00000198887|transcript|ENST00000361138.6|protein_coding|8/25|c.1003T>C|p.Ser335Pro|1120/5980|1003/3306|335/1101||,C|non_coding_transcript_exon_variant|MODIFIER|SMC5|ENSG00000198887|transcript|ENST00000618375.1|processed_transcript|2/3|n.134T>C||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:1133:1089:36523:24:308:0,-307.33,-3255.79\\t0/0:99:537:514:17203:10:120:0,-147.045,-1535.38\n1\\t227732408\\t.\\tG\\tT\\t0.0\\tPASS\\tSSC=135.632;TYPE=snp;ANN=T|missense_variant|MODERATE|JMJD4|ENSG00000081692|transcript|ENST00000366758.7|protein_coding|6/6|c.1376C>A|p.Ala459Asp|1376/2595|1376/1392|459/463||,T|missense_variant|MODERATE|JMJD4|ENSG00000081692|transcript|ENST00000615711.4|protein_coding|6/6|c.1376C>A|p.Ala459Asp|1376/2591|1376/1392|459/463||,T|missense_variant|MODERATE|JMJD4|ENSG00000081692|transcript|ENST00000620518.4|protein_coding|6/6|c.1238C>A|p.Ala413Asp|1248/2432|1238/1254|413/417||,T|missense_variant|MODERATE|JMJD4|ENSG00000081692|transcript|ENST00000438896.2|protein_coding|6/6|c.1328C>A|p.Ala443Asp|1328/2502|1328/1344|443/447||,T|upstream_gene_variant|MODIFIER|SNAP47|ENSG00000143740|transcript|ENST00000315781.9|protein_coding||c.-3002G>T|||||2588|,T|upstream_gene_variant|MODIFIER|SNAP47|ENSG00000143740|transcript|ENST00000366759.8|protein_coding||c.-3002G>T|||||2588|,T|upstream_gene_variant|MODIFIER|SNAP47|ENSG00000143740|transcript|ENST00000418653.5|protein_coding||c.-3024G>T|||||3023|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|SNAP47|ENSG00000143740|transcript|ENST00000617596.4|protein_coding||c.-3137G>T|||||3045|,T|upstream_gene_variant|MODIFIER|SNAP47|ENSG00000143740|transcript|ENST00000426344.5|protein_coding||c.-3029G>T|||||3028|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|SNAP47|ENSG00000143740|transcript|ENST00000470038.1|processed_transcript||n.-3765G>T|||||3765|,T|downstream_gene_variant|MODIFIER|JMJD4|ENSG00000081692|transcript|ENST00000480590.1|retained_intron||n.*740C>A|||||740|,T|downstream_gene_variant|MODIFIER|JMJD4|ENSG00000081692|transcript|ENST00000465251.1|retained_intron||n.*1211C>A|||||1211|,T|intron_variant|MODIFIER|SNAP47|ENSG00000143740|transcript|ENST00000366760.5|protein_coding|1/3|c.-95+3622G>T||||||,T|intron_variant|MODIFIER|SNAP47|ENSG00000143740|transcript|ENST00000475930.1|processed_transcript|2/2|n.297+696G>T||||||,T|intron_variant|MODIFIER|SNAP47|ENSG00000143740|transcript|ENST00000491439.1|processed_transcript|2/2|n.243+661G>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|SNAP47|ENSG00000143740|transcript|ENST00000480897.5|processed_transcript|3/3|n.431G>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|SNAP47|ENSG00000143740|transcript|ENST00000480265.1|processed_transcript|2/2|n.258G>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|JMJD4|ENSG00000081692|transcript|ENST00000485807.1|retained_intron|2/2|n.1766C>A||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:527:526:20653:1:37:0,-154.945,-1853.29\\t0/0:99:90:88:3530:2:82:0,-19.313,-309.931\n3\\t123722214\\t.\\tG\\tC\\t5.93688E-15\\tPASS\\tSSC=149.583;TYPE=snp;ANN=C|missense_variant|MODERATE|MYLK|ENSG00000065534|transcript|ENST00000475616.5|protein_coding|10/31|c.1718C>G|p.Ala573Gly|1718/5745|1718/5745|573/1914||,C|missense_variant|MODERATE|MYLK|ENSG00000065534|transcript|ENST00000360304.7|protein_coding|12/33|c.1718C>G|p.Ala573Gly|1904/7738|1718/5745|573/1914||,C|missense_variant|MODERATE|MYLK|ENSG00000065534|transcript|ENST00000360772.7|protein_coding|14/34|c.1718C>G|p.Ala573Gly|2097/10027|1718/5592|573/1863||,C|missense_variant|MODERATE|MYLK|ENSG00000065534|transcript|ENST00000354792.9|protein_coding|11/32|c.1511C>G|p.Ala504Gly|1697/7531|1511/5538|504/1845||,C|missense_variant|MODERATE|MYLK|ENSG00000065534|transcript|ENST00000359169.5|protein_coding|12/32|c.1718C>G|p.Ala573Gly|1904/7585|1718/5592|573/1863||,C|missense_variant|MODERATE|MYLK|ENSG00000065534|transcript|ENST00000346322.9|protein_coding|12/33|c.1511C>G|p.Ala504Gly|1805/5892|1511/5538|504/1845||,C|3_prime_UTR_variant|MODIFIER|MYLK|ENSG00000065534|transcript|ENST00000464489.5|nonsense_mediated_decay|12/33|n.*1297C>G|||||17740|,C|non_coding_transcript_exon_variant|MODIFIER|MYLK|ENSG00000065534|transcript|ENST00000464489.5|nonsense_mediated_decay|12/33|n.*1297C>G||||||,C|non_coding_transcript_exon_variant|MODIFIER|MYLK|ENSG00000065534|transcript|ENST00000514623.1|retained_intron|3/4|n.2286C>G||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:554:553:22058:0:0:0,-166.47,-1971.73\\t0/0:99:82:79:3198:2:82:0,-16.8869,-279.96\n19\\t643332\\t.\\tC\\tG\\t3.4716E-14\\tPASS\\tSSC=183.092;TYPE=snp;ANN=G|stop_gained|HIGH|FGF22|ENSG00000070388|transcript|ENST00000215530.6|protein_coding|2/3|c.312C>G|p.Tyr104*|343/1311|312/513|104/170||,G|stop_gained|HIGH|FGF22|ENSG00000070388|transcript|ENST00000586042.6|protein_coding|2/3|c.312C>G|p.Tyr104*|343/1288|312/498|104/165||,G|downstream_gene_variant|MODIFIER|RNF126|ENSG00000070423|transcript|ENST00000292363.9|protein_coding||c.*4796G>C|||||4194|,G|downstream_gene_variant|MODIFIER|RNF126|ENSG00000070423|transcript|ENST00000586749.1|retained_intron||n.*4198G>C|||||4198|,G|downstream_gene_variant|MODIFIER|RNF126|ENSG00000070423|transcript|ENST00000589762.5|protein_coding||c.*4800G>C|||||4800|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|RNF126|ENSG00000070423|transcript|ENST00000605891.5|nonsense_mediated_decay||n.*5567G>C|||||4194|,G|downstream_gene_variant|MODIFIER|RNF126|ENSG00000070423|transcript|ENST00000590885.6|processed_transcript||n.*4197G>C|||||4197|,G|downstream_gene_variant|MODIFIER|FGF22|ENSG00000070388|transcript|ENST00000591390.1|retained_intron||n.*1742C>G|||||1742|\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:855:815:29588:39:478:0,-214.057,-2617.14\\t0/0:99:121:115:4120:5:60:0,-30.9648,-365.175\n3\\t160425010\\t.\\tA\\tC\\t0.0\\tPASS\\tSSC=162.974;TYPE=snp;ANN=C|synonymous_variant|LOW|SMC4|ENSG00000113810|transcript|ENST00000344722.5|protein_coding|15/23|c.2469A>C|p.Ala823Ala|2814/5356|2469/3867|823/1288||,C|synonymous_variant|LOW|SMC4|ENSG00000113810|transcript|ENST00000357388.7|protein_coding|16/24|c.2469A>C|p.Ala823Ala|2920/5471|2469/3867|823/1288||,C|synonymous_variant|LOW|SMC4|ENSG00000113810|transcript|ENST00000469762.5|protein_coding|16/24|c.2394A>C|p.Ala798Ala|2499/3998|2394/3792|798/1263||,C|synonymous_variant|LOW|SMC4|ENSG00000113810|transcript|ENST00000462787.5|protein_coding|15/22|c.2469A>C|p.Ala823Ala|3628/5033|2469/3693|823/1230||,C|upstream_gene_variant|MODIFIER|SMC4|ENSG00000113810|transcript|ENST00000488017.1|retained_intron||n.-3786A>C|||||3786|,C|downstream_gene_variant|MODIFIER|SMC4|ENSG00000113810|transcript|ENST00000469858.5|nonsense_mediated_decay||n.*1777A>C|||||63|,C|downstream_gene_variant|MODIFIER|SMC4|ENSG00000113810|transcript|ENST00000497203.1|retained_intron||n.*1416A>C|||||1416|,C|intron_variant|MODIFIER|RP11-432B6.3|ENSG00000248710|transcript|ENST00000483754.1|nonsense_mediated_decay|3/18|n.952+13222T>G||||||,C|non_coding_transcript_exon_variant|MODIFIER|SMC4|ENSG00000113810|transcript|ENST00000462668.5|retained_intron|8/16|n.1692A>C||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:1620:1579:56755:40:495:0,-443.125,-5044.11\\t0/0:99:1001:982:36062:17:229:0,-280.151,-3212.6\n19\\t9757955\\t.\\tA\\tT\\t2.43962E-7\\tPASS\\tSSC=1.89386;TYPE=snp;ANN=T|synonymous_variant|LOW|ZNF846|ENSG00000196605|transcript|ENST00000397902.6|protein_coding|6/6|c.1122T>A|p.Ala374Ala|1536/2016|1122/1602|374/533||,T|3_prime_UTR_variant|MODIFIER|ZNF846|ENSG00000196605|transcript|ENST00000586293.5|protein_coding|5/5|c.*778T>A|||||778|,T|upstream_gene_variant|MODIFIER|CTD-2623N2.3|ENSG00000267370|transcript|ENST00000588113.1|unprocessed_pseudogene||n.-1092T>A|||||1092|,T|downstream_gene_variant|MODIFIER|ZNF846|ENSG00000196605|transcript|ENST00000591377.1|retained_intron||n.*519T>A|||||519|,T|downstream_gene_variant|MODIFIER|ZNF846|ENSG00000196605|transcript|ENST00000590471.1|processed_transcript||n.*4433T>A|||||4433|,T|downstream_gene_variant|MODIFIER|ZNF846|ENSG00000196605|transcript|ENST00000587650.1|processed_transcript||n.*4145T>A|||||4145|,T|downstream_gene_variant|MODIFIER|ZNF846|ENSG00000196605|transcript|ENST00000589412.5|protein_coding||c.*592T>A|||||592|WARNING_TRANSCRIPT_INCOMPLETE,T|downstream_gene_variant|MODIFIER|ZNF846|ENSG00000196605|transcript|ENST00000586814.5|protein_coding||c.*794T>A|||||794|WARNING_TRANSCRIPT_INCOMPLETE,T|downstream_gene_variant|MODIFIER|ZNF846|ENSG00000196605|transcript|ENST00000592587.1|protein_coding||c.*1918T>A|||||1918|WARNING_TRANSCRIPT_INCOMPLETE,T|intron_variant|MODIFIER|ZNF846|ENSG00000196605|transcript|ENST00000589453.5|nonsense_mediated_decay|5/7|n.*674+104T>A||||||,T|intron_variant|MODIFIER|ZNF846|ENSG00000196605|transcript|ENST00000588267.5|protein_coding|5/5|c.631+104T>A||||||,T|intron_variant|MODIFIER|ZNF846|ENSG00000196605|transcript|ENST00000592859.1|protein_coding|2/2|c.631+104T>A||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:94.3483:28:26:1049:2:53:0,-3.39901,-89.6661\\t0/0:72.5331:6:5:205:0:0:0,-1.50515,-18.4586\n22\\t17548233\\t.\\tA\\tG\\t4.2069E-14\\tPASS\\tSSC=328.198;TYPE=snp;ANN=G|synonymous_variant|LOW|CECR2|ENSG00000099954|transcript|ENST00000400585.6|protein_coding|17/19|c.2454A>G|p.Thr818Thr|2892/4833|2454/3903|818/1300||,G|synonymous_variant|LOW|CECR2|ENSG00000099954|transcript|ENST00000262608.12|protein_coding|17/19|c.2457A>G|p.Thr819Thr|2842/4783|2457/3906|819/1301||,G|synonymous_variant|LOW|CECR2|ENSG00000099954|transcript|ENST00000342247.9|protein_coding|18/20|c.3006A>G|p.Thr1002Thr|3424/6178|3006/4455|1002/1484||,G|synonymous_variant|LOW|CECR2|ENSG00000099954|transcript|ENST00000612582.1|protein_coding|17/19|c.2880A>G|p.Thr960Thr|2887/9645|2880/4329|960/1442||,G|upstream_gene_variant|MODIFIER|CECR2|ENSG00000099954|transcript|ENST00000355219.3|nonsense_mediated_decay||n.-766A>G|||||766|\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:1473:1421:47573:36:437:0,-399.278,-4238.46\\t0/0:99:274:262:8853:10:120:0,-71.0802,-785.455\n6\\t35452666\\t.\\tC\\tT\\t0.0\\tPASS\\tSSC=132.932;TYPE=snp;ANN=T|missense_variant|MODERATE|FANCE|ENSG00000112039|transcript|ENST00000229769.2|protein_coding|1/10|c.121C>T|p.Arg41Trp|306/2554|121/1611|41/536||,T|downstream_gene_variant|MODIFIER|MKRNP2|ENSG00000227154|transcript|ENST00000436521.1|unprocessed_pseudogene||n.*2800C>T|||||2800|\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:503:503:19998:0:0:0,-151.418,-1798.06\\t0/0:99:86:84:3354:2:78:0,-18.4858,-294.497\n11\\t108250705\\t.\\tC\\tT\\t0.0\\tPASS\\tSSC=111.591;TYPE=snp;OLD_MULTIALLELIC=11:108250705:C/G/T;ANN=T|stop_gained|HIGH|ATM|ENSG00000149311|transcript|ENST00000527805.5|protein_coding|10/27|c.1240C>T|p.Gln414*|1973/4841|1240/4108|414/1368||WARNING_TRANSCRIPT_INCOMPLETE,T|stop_gained|HIGH|ATM|ENSG00000149311|transcript|ENST00000452508.6|protein_coding|11/64|c.1240C>T|p.Gln414*|1429/12954|1240/9171|414/3056||,T|stop_gained|HIGH|ATM|ENSG00000149311|transcript|ENST00000278616.8|protein_coding|10/63|c.1240C>T|p.Gln414*|1625/13147|1240/9171|414/3056||,T|upstream_gene_variant|MODIFIER|ATM|ENSG00000149311|transcript|ENST00000525012.5|processed_transcript||n.-2116C>T|||||2116|,T|upstream_gene_variant|MODIFIER|ATM|ENSG00000149311|transcript|ENST00000533526.1|processed_transcript||n.-2116C>T|||||2116|;LOF=(ATM|ENSG00000149311|25|0.12);NMD=(ATM|ENSG00000149311|25|0.12)\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:683:659:22302:15:190:0,-185.787,-1988.09\\t0/0:99:303:291:9534:5:70:0,-82.8026,-851.246\n2\\t39035228\\t.\\tT\\tC\\t1.30189E-14\\tPASS\\tSSC=261.19;TYPE=snp;ANN=C|missense_variant|MODERATE|SOS1|ENSG00000115904|transcript|ENST00000402219.6|protein_coding|8/23|c.1058A>G|p.Tyr353Cys|1099/8314|1058/4002|353/1333||,C|missense_variant|MODERATE|SOS1|ENSG00000115904|transcript|ENST00000426016.5|protein_coding|9/24|c.1058A>G|p.Tyr353Cys|1145/8517|1058/4002|353/1333||,C|missense_variant|MODERATE|SOS1|ENSG00000115904|transcript|ENST00000395038.6|protein_coding|8/22|c.1058A>G|p.Tyr353Cys|1086/4123|1058/3957|353/1318||,C|non_coding_transcript_exon_variant|MODIFIER|SOS1|ENSG00000115904|transcript|ENST00000461545.1|retained_intron|3/4|n.408A>G||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:1743:1665:60732:50:630:0,-459.576,-5403.2\\t0/0:99:735:706:25542:17:214:0,-198.386,-2277.24\n9\\t94320516\\t.\\tT\\tC\\t4.3455E-14\\tPASS\\tSSC=483.276;TYPE=snp;ANN=C|missense_variant|MODERATE|NUTM2F|ENSG00000130950|transcript|ENST00000253262.8|protein_coding|5/7|c.1060A>G|p.Thr354Ala|1081/2561|1060/2271|354/756||,C|missense_variant|MODERATE|NUTM2F|ENSG00000130950|transcript|ENST00000341207.5|protein_coding|5/8|c.1060A>G|p.Thr354Ala|1081/2516|1060/2226|354/741||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:1982:1933:70604:42:529:0,-546.925,-6030.86\\t0/0:99:237:230:8640:6:82:0,-63.6489,-725.973\n10\\t102504189\\t.\\tACCG\\tCCCC\\t0.0\\tPASS\\tSSC=158.978;TYPE=complex;OLD_MULTIALLELIC=10:102504189:ACCG/CCCC/CCCG/ACCC;ANN=CCCC|missense_variant|MODERATE|SUFU|ENSG00000107882|transcript|ENST00000369902.7|protein_coding|1/12|c.37_40delACCGinsCCCC|p.ThrAla13ProPro|203/5001|37/1455|13/484||,CCCC|missense_variant|MODERATE|SUFU|ENSG00000107882|transcript|ENST00000369899.6|protein_coding|1/11|c.37_40delACCGinsCCCC|p.ThrAla13ProPro|183/1839|37/1302|13/433||,CCCC|missense_variant|MODERATE|SUFU|ENSG00000107882|transcript|ENST00000423559.2|protein_coding|1/10|c.37_40delACCGinsCCCC|p.ThrAla13ProPro|111/2601|37/1446|13/481||,CCCC|upstream_gene_variant|MODIFIER|ACTR1A|ENSG00000138107|transcript|ENST00000369905.8|protein_coding||c.-1545_-1542delCGGTinsGGGG|||||1478|,CCCC|upstream_gene_variant|MODIFIER|ACTR1A|ENSG00000138107|transcript|ENST00000481044.6|processed_transcript||n.-1538_-1535delCGGTinsGGGG|||||1535|,CCCC|upstream_gene_variant|MODIFIER|ACTR1A|ENSG00000138107|transcript|ENST00000487599.1|protein_coding||c.-1545_-1542delCGGTinsGGGG|||||1511|,CCCC|upstream_gene_variant|MODIFIER|ACTR1A|ENSG00000138107|transcript|ENST00000636707.1|nonsense_mediated_decay||n.-1545_-1542delCGGTinsGGGG|||||1480|\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:832:682:23916:38:472:0,-197.548,-2101.91\\t0/0:99:156:126:4526:8:120:0,-38.5703,-394.886\n17\\t41586597\\t.\\tAGCT\\tA\\t22.2524\\tPASS\\tSSC=6.40064;TYPE=del;OLD_VARIANT=17:41586597:AGCTGCTGCTGCTGCTGCTG/AGCTGCTGCTGCTGCTG;ANN=A|conservative_inframe_deletion|MODERATE|KRT14|ENSG00000186847|transcript|ENST00000167586.6|protein_coding|1/8|c.235_237delAGC|p.Ser79del|324/1662|235/1419|79/472||,A|upstream_gene_variant|MODIFIER|KRT14|ENSG00000186847|transcript|ENST00000441550.2|retained_intron||n.-3145_-3143delAGC|||||3143|,A|upstream_gene_variant|MODIFIER|KRT14|ENSG00000186847|transcript|ENST00000476662.1|retained_intron||n.-2129_-2127delAGC|||||2127|\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:11.6396:2:2:81:0:0:0,-0.60206,-7.68573\\t0/1:22.2521:4:2:81:2:74:-5.79858,0,-6.48161\n12\\t389017\\t.\\tA\\tC\\t0.0\\tPASS\\tSSC=183.031;TYPE=snp;ANN=C|missense_variant|MODERATE|KDM5A|ENSG00000073614|transcript|ENST00000399788.6|protein_coding|1/28|c.75T>G|p.Ser25Arg|438/10763|75/5073|25/1690||,C|missense_variant|MODERATE|KDM5A|ENSG00000073614|transcript|ENST00000544760.1|protein_coding|1/13|c.75T>G|p.Ser25Arg|266/2338|75/2147|25/714||WARNING_TRANSCRIPT_INCOMPLETE,C|missense_variant|MODERATE|KDM5A|ENSG00000073614|transcript|ENST00000535014.5|protein_coding|1/3|c.75T>G|p.Ser25Arg|248/551|75/378|25/125||WARNING_TRANSCRIPT_NO_STOP_CODON,C|missense_variant|MODERATE|KDM5A|ENSG00000073614|transcript|ENST00000543507.1|protein_coding|1/4|c.75T>G|p.Ser25Arg|257/575|75/393|25/130||WARNING_TRANSCRIPT_NO_STOP_CODON,C|upstream_gene_variant|MODIFIER|CCDC77|ENSG00000120647|transcript|ENST00000543504.5|protein_coding||c.-582A>C|||||378|WARNING_TRANSCRIPT_NO_STOP_CODON,C|upstream_gene_variant|MODIFIER|CCDC77|ENSG00000120647|transcript|ENST00000540180.5|protein_coding||c.-528A>C|||||331|,C|upstream_gene_variant|MODIFIER|CCDC77|ENSG00000120647|transcript|ENST00000537453.1|processed_transcript||n.-256A>C|||||256|,C|upstream_gene_variant|MODIFIER|KDM5A|ENSG00000073614|transcript|ENST00000536014.5|protein_coding||c.-677T>G|||||487|WARNING_TRANSCRIPT_INCOMPLETE,C|upstream_gene_variant|MODIFIER|CCDC77|ENSG00000120647|transcript|ENST00000422000.5|protein_coding||c.-582A>C|||||333|,C|upstream_gene_variant|MODIFIER|CCDC77|ENSG00000120647|transcript|ENST00000535052.5|protein_coding||c.-625A>C|||||345|WARNING_TRANSCRIPT_NO_STOP_CODON,C|upstream_gene_variant|MODIFIER|CCDC77|ENSG00000120647|transcript|ENST00000540344.5|processed_transcript||n.-402A>C|||||402|\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:1137:1114:40658:23:296:0,-315.503,-3629.07\\t0/0:99:460:453:16529:5:60:0,-132.472,-1480.89\n21\\t41473484\\t.\\tT\\tA\\t2.97738E-14\\tPASS\\tSSC=97.0928;TYPE=snp;ANN=A|missense_variant|MODERATE|TMPRSS2|ENSG00000184012|transcript|ENST00000332149.9|protein_coding|9/14|c.740A>T|p.Asn247Ile|875/3205|740/1479|247/492||,A|missense_variant|MODERATE|TMPRSS2|ENSG00000184012|transcript|ENST00000454499.5|protein_coding|10/14|c.740A>T|p.Asn247Ile|1174/1901|740/1467|247/488||WARNING_TRANSCRIPT_NO_STOP_CODON,A|missense_variant|MODERATE|TMPRSS2|ENSG00000184012|transcript|ENST00000398585.7|protein_coding|9/14|c.851A>T|p.Asn284Ile|912/3240|851/1590|284/529||,A|missense_variant|MODERATE|TMPRSS2|ENSG00000184012|transcript|ENST00000458356.5|protein_coding|9/14|c.740A>T|p.Asn247Ile|829/1701|740/1479|247/492||,A|missense_variant|MODERATE|TMPRSS2|ENSG00000184012|transcript|ENST00000424093.5|protein_coding|8/8|c.620A>T|p.Asn207Ile|688/726|620/658|207/218||WARNING_TRANSCRIPT_INCOMPLETE,A|upstream_gene_variant|MODIFIER|TMPRSS2|ENSG00000184012|transcript|ENST00000469395.1|retained_intron||n.-4647A>T|||||4647|\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:400:399:15720:1:22:0,-118.212,-1411.29\\t0/0:99:96:94:3652:2:82:0,-21.1192,-320.899\n2\\t39278433\\t.\\tC\\tG\\t3.85729E-14\\tPASS\\tSSC=207.86;TYPE=snp;ANN=G|missense_variant|MODERATE|MAP4K3|ENSG00000011566|transcript|ENST00000263881.7|protein_coding|24/34|c.1768G>C|p.Glu590Gln|2093/4362|1768/2685|590/894||,G|missense_variant|MODERATE|MAP4K3|ENSG00000011566|transcript|ENST00000341681.9|protein_coding|23/33|c.1705G>C|p.Glu569Gln|2019/4271|1705/2622|569/873||,G|missense_variant|MODERATE|MAP4K3|ENSG00000011566|transcript|ENST00000437545.5|protein_coding|23/33|c.1516G>C|p.Glu506Gln|1667/3924|1516/2433|506/810||,G|upstream_gene_variant|MODIFIER|MAP4K3|ENSG00000011566|transcript|ENST00000495648.3|retained_intron||n.-14G>C|||||14|\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:1220:1186:43554:26:330:0,-335.143,-3885.88\\t0/0:99:433:428:15911:2:24:0,-127.283,-1428.41\n19\\t48498789\\t.\\tA\\tG\\t0.0\\tPASS\\tSSC=45.7104;TYPE=snp;OLD_MULTIALLELIC=19:48498789:AGGAGGTGGCGGC/GGGGGGGGGGGGG/GGGGGGGGGCGGG/GGGGGGGGGCGGC/GGGGGGTGGCGGG/GGGGGGTGGCGGC/GGGAGGGGGGGGG/AGGGGGTGGGGGC/GGGAGGTGGCGGC/AGGGGGTGGCGGC/AGGAGGGGGCGGC;OLD_VARIANT=19:48498789:AGGAGGTGGCGGC/GGGAGGTGGCGGC;ANN=G|synonymous_variant|LOW|LMTK3|ENSG00000142235|transcript|ENST00000270238.3|protein_coding|12/16|c.2367T>C|p.Pro789Pro|2367/4972|2367/4470|789/1489||,G|synonymous_variant|LOW|LMTK3|ENSG00000142235|transcript|ENST00000600059.5|protein_coding|11/15|c.2280T>C|p.Pro760Pro|2508/5113|2280/4383|760/1460||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:147:81:3015:7:94:0,-52.6494,-348.753\\t0/0:99:29:18:647:1:12:0,-6.44703,-77.6863\n19\\t50415746\\t.\\tA\\tG\\t0.0\\tPASS\\tSSC=135.077;TYPE=snp;ANN=G|missense_variant|MODERATE|POLD1|ENSG00000062822|transcript|ENST00000595904.5|protein_coding|21/26|c.2818A>G|p.Ser940Gly|2818/3402|2818/3402|940/1133||,G|missense_variant|MODERATE|POLD1|ENSG00000062822|transcript|ENST00000440232.6|protein_coding|22/27|c.2740A>G|p.Ser914Gly|2793/3444|2740/3324|914/1107||,G|missense_variant|MODERATE|POLD1|ENSG00000062822|transcript|ENST00000599857.5|protein_coding|22/27|c.2740A>G|p.Ser914Gly|2784/3435|2740/3324|914/1107||,G|missense_variant|MODERATE|POLD1|ENSG00000062822|transcript|ENST00000613923.4|protein_coding|22/27|c.2818A>G|p.Ser940Gly|2887/3542|2818/3402|940/1133||,G|missense_variant|MODERATE|POLD1|ENSG00000062822|transcript|ENST00000593407.5|protein_coding|5/8|c.520A>G|p.Ser174Gly|521/867|520/866|174/287||WARNING_TRANSCRIPT_INCOMPLETE,G|missense_variant|MODERATE|POLD1|ENSG00000062822|transcript|ENST00000593981.1|protein_coding|4/8|c.364A>G|p.Ser122Gly|366/873|364/871|122/289||WARNING_TRANSCRIPT_INCOMPLETE,G|upstream_gene_variant|MODIFIER|SPIB|ENSG00000269404|transcript|ENST00000595883.5|protein_coding||c.-3217A>G|||||3192|,G|upstream_gene_variant|MODIFIER|SPIB|ENSG00000269404|transcript|ENST00000270632.7|protein_coding||c.-3217A>G|||||3212|,G|upstream_gene_variant|MODIFIER|POLD1|ENSG00000062822|transcript|ENST00000597963.5|retained_intron||n.-567A>G|||||567|,G|upstream_gene_variant|MODIFIER|POLD1|ENSG00000062822|transcript|ENST00000596221.1|retained_intron||n.-1207A>G|||||1207|,G|upstream_gene_variant|MODIFIER|SPIB|ENSG00000269404|transcript|ENST00000439922.6|protein_coding||c.-3275A>G|||||3192|,G|upstream_gene_variant|MODIFIER|SPIB|ENSG00000269404|transcript|ENST00000596074.5|protein_coding||c.-3217A>G|||||3195|,G|upstream_gene_variant|MODIFIER|SPIB|ENSG00000269404|transcript|ENST00000594685.1|protein_coding||c.-3217A>G|||||3208|WARNING_TRANSCRIPT_INCOMPLETE,G|upstream_gene_variant|MODIFIER|SPIB|ENSG00000269404|transcript|ENST00000599923.5|retained_intron||n.-3193A>G|||||3193|,G|upstream_gene_variant|MODIFIER|SPIB|ENSG00000269404|transcript|ENST00000594188.1|retained_intron||n.-3195A>G|||||3195|,G|upstream_gene_variant|MODIFIER|SPIB|ENSG00000269404|transcript|ENST00000597855.5|protein_coding||c.-3217A>G|||||3195|,G|upstream_gene_variant|MODIFIER|CTD-2545M3.6|ENSG00000142539|transcript|ENST00000599632.1|protein_coding||c.-54A>G|||||53|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|POLD1|ENSG00000062822|transcript|ENST00000596425.1|protein_coding||c.*2245A>G|||||2245|WARNING_TRANSCRIPT_INCOMPLETE,G|intron_variant|MODIFIER|POLD1|ENSG00000062822|transcript|ENST00000600859.5|nonsense_mediated_decay|21/25|n.2717+156A>G||||||,G|non_coding_transcript_exon_variant|MODIFIER|POLD1|ENSG00000062822|transcript|ENST00000596648.1|retained_intron|2/4|n.105A>G||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:578:573:22174:5:80:0,-166.637,-1986.42\\t0/0:99:116:113:4261:3:36:0,-31.5595,-380.086\n17\\t31940471\\t.\\tG\\tT\\t0.0\\tPASS\\tSSC=78.2338;TYPE=snp;ANN=T|missense_variant|MODERATE|SUZ12|ENSG00000178691|transcript|ENST00000322652.9|protein_coding|3/16|c.371G>T|p.Arg124Ile|600/4491|371/2220|124/739||,T|missense_variant|MODERATE|SUZ12|ENSG00000178691|transcript|ENST00000580398.1|protein_coding|3/15|c.371G>T|p.Arg124Ile|551/3977|371/2151|124/716||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:501:489:17464:11:138:0,-138.237,-1244.84\\t0/0:99:214:210:7495:2:59:0,-60.0032,-553.172\n14\\t24375678\\t.\\tA\\tC\\t0.0\\tPASS\\tSSC=150.353;TYPE=snp;ANN=C|missense_variant|MODERATE|NFATC4|ENSG00000100968|transcript|ENST00000413692.6|protein_coding|8/10|c.2081A>C|p.Glu694Ala|2225/5700|2081/2895|694/964||,C|missense_variant|MODERATE|NFATC4|ENSG00000100968|transcript|ENST00000554591.5|protein_coding|8/11|c.2081A>C|p.Glu694Ala|2197/2893|2081/2574|694/857||,C|missense_variant|MODERATE|NFATC4|ENSG00000100968|transcript|ENST00000554966.5|protein_coding|8/11|c.1931A>C|p.Glu644Ala|2013/2506|1931/2424|644/807||,C|missense_variant|MODERATE|NFATC4|ENSG00000100968|transcript|ENST00000555590.5|protein_coding|8/11|c.1931A>C|p.Glu644Ala|2013/2830|1931/2748|644/915||,C|missense_variant|MODERATE|NFATC4|ENSG00000100968|transcript|ENST00000424781.6|protein_coding|8/10|c.1931A>C|p.Glu644Ala|2013/5488|1931/2745|644/914||,C|missense_variant|MODERATE|NFATC4|ENSG00000100968|transcript|ENST00000539237.6|protein_coding|8/10|c.1988A>C|p.Glu663Ala|2211/5686|1988/2802|663/933||,C|missense_variant|MODERATE|NFATC4|ENSG00000100968|transcript|ENST00000556279.5|protein_coding|8/11|c.1988A>C|p.Glu663Ala|2107/2924|1988/2805|663/934||,C|missense_variant|MODERATE|NFATC4|ENSG00000100968|transcript|ENST00000553469.5|protein_coding|8/11|c.1988A>C|p.Glu663Ala|2073/2566|1988/2481|663/826||,C|missense_variant|MODERATE|NFATC4|ENSG00000100968|transcript|ENST00000554050.5|protein_coding|7/10|c.1892A>C|p.Glu631Ala|2213/3057|1892/2385|631/794||,C|missense_variant|MODERATE|NFATC4|ENSG00000100968|transcript|ENST00000250373.8|protein_coding|7/10|c.1892A>C|p.Glu631Ala|2033/4749|1892/2709|631/902||,C|missense_variant|MODERATE|NFATC4|ENSG00000100968|transcript|ENST00000553708.5|protein_coding|7/9|c.1892A>C|p.Glu631Ala|1892/5367|1892/2706|631/901||,C|missense_variant|MODERATE|NFATC4|ENSG00000100968|transcript|ENST00000554344.5|protein_coding|6/9|c.1682A>C|p.Glu561Ala|2138/2955|1682/2499|561/832||,C|missense_variant|MODERATE|NFATC4|ENSG00000100968|transcript|ENST00000554661.5|protein_coding|6/9|c.1682A>C|p.Glu561Ala|2138/2631|1682/2175|561/724||,C|missense_variant|MODERATE|NFATC4|ENSG00000100968|transcript|ENST00000556169.5|protein_coding|7/10|c.1856A>C|p.Glu619Ala|2016/2509|1856/2349|619/782||,C|missense_variant|MODERATE|NFATC4|ENSG00000100968|transcript|ENST00000422617.7|protein_coding|7/9|c.1856A>C|p.Glu619Ala|2016/5491|1856/2670|619/889||,C|missense_variant|MODERATE|NFATC4|ENSG00000100968|transcript|ENST00000557451.5|protein_coding|6/8|c.1682A>C|p.Glu561Ala|2138/5613|1682/2496|561/831||,C|missense_variant|MODERATE|NFATC4|ENSG00000100968|transcript|ENST00000555453.5|protein_coding|7/10|c.1856A>C|p.Glu619Ala|2002/3169|1856/2673|619/890||,C|missense_variant|MODERATE|NFATC4|ENSG00000100968|transcript|ENST00000554473.5|protein_coding|4/7|c.497A>C|p.Glu166Ala|889/1382|497/990|166/329||,C|missense_variant|MODERATE|NFATC4|ENSG00000100968|transcript|ENST00000556759.5|protein_coding|4/7|c.497A>C|p.Glu166Ala|889/2025|497/1314|166/437||,C|missense_variant|MODERATE|NFATC4|ENSG00000100968|transcript|ENST00000555167.1|protein_coding|4/6|c.497A>C|p.Glu166Ala|889/4364|497/1311|166/436||,C|missense_variant|MODERATE|NFATC4|ENSG00000100968|transcript|ENST00000553879.5|protein_coding|7/10|c.1682A>C|p.Glu561Ala|1867/2707|1682/2499|561/832||,C|5_prime_UTR_variant|MODIFIER|NFATC4|ENSG00000100968|transcript|ENST00000555393.5|protein_coding|2/4|c.-245A>C|||||696|,C|5_prime_UTR_variant|MODIFIER|NFATC4|ENSG00000100968|transcript|ENST00000555802.1|protein_coding|2/5|c.-245A>C|||||696|,C|5_prime_UTR_variant|MODIFIER|NFATC4|ENSG00000100968|transcript|ENST00000557767.5|protein_coding|2/5|c.-245A>C|||||696|,C|upstream_gene_variant|MODIFIER|NFATC4|ENSG00000100968|transcript|ENST00000555821.1|processed_transcript||n.-396A>C|||||396|,C|downstream_gene_variant|MODIFIER|NFATC4|ENSG00000100968|transcript|ENST00000440487.6|processed_transcript||n.*3862A>C|||||3862|,C|downstream_gene_variant|MODIFIER|NFATC4|ENSG00000100968|transcript|ENST00000556957.5|retained_intron||n.*1533A>C|||||1533|,C|downstream_gene_variant|MODIFIER|NFATC4|ENSG00000100968|transcript|ENST00000557028.5|retained_intron||n.*971A>C|||||971|,C|downstream_gene_variant|MODIFIER|NFATC4|ENSG00000100968|transcript|ENST00000554779.1|protein_coding||c.*3092A>C|||||3092|WARNING_TRANSCRIPT_INCOMPLETE,C|non_coding_transcript_exon_variant|MODIFIER|NFATC4|ENSG00000100968|transcript|ENST00000556302.5|retained_intron|6/7|n.2349A>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|NFATC4|ENSG00000100968|transcript|ENST00000554655.5|retained_intron|7/10|n.2548A>C||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:852:818:30252:32:434:0,-217.063,-2680.52\\t0/0:99:243:238:8969:5:70:0,-66.7104,-800.255\n2\\t105089049\\t.\\tC\\tT\\t39.442\\tPASS\\tSSC=7.70381;TYPE=snp;ANN=T|synonymous_variant|LOW|MRPS9|ENSG00000135972|transcript|ENST00000258455.7|protein_coding|6/11|c.555C>T|p.Leu185Leu|665/1500|555/1191|185/396||,T|upstream_gene_variant|MODIFIER|MRPS9|ENSG00000135972|transcript|ENST00000472220.1|retained_intron||n.-3049C>T|||||3049|,T|non_coding_transcript_exon_variant|MODIFIER|MRPS9|ENSG00000135972|transcript|ENST00000413583.5|nonsense_mediated_decay|1/6|n.30C>T||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:1.78475:1:1:41:0:0:0,-0.30103,-4.09457\\t1/1:13.7445:2:0:0:2:78:-7.40278,-0.60206,0\n16\\t30980043\\t.\\tT\\tC\\t1.42238E-14\\tPASS\\tSSC=221.913;TYPE=snp;ANN=C|synonymous_variant|LOW|SETD1A|ENSG00000099381|transcript|ENST00000262519.12|protein_coding|14/19|c.4257T>C|p.Ser1419Ser|4943/6903|4257/5124|1419/1707||,C|downstream_gene_variant|MODIFIER|RP11-1072A3.3|ENSG00000279196|transcript|ENST00000624286.1|TEC||n.*4587A>G|||||4587|\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:911:886:32097:19:229:0,-252.087,-2864.89\\t0/0:99:112:108:3976:3:36:0,-30.1743,-354.449\n7\\t102277952\\t.\\tA\\tC\\t2.05223E-14\\tPASS\\tSSC=129.744;TYPE=snp;ANN=C|missense_variant|MODERATE|CUX1|ENSG00000257923|transcript|ENST00000437600.8|protein_coding|18/23|c.1567A>C|p.Asn523His|1694/3031|1567/2037|523/678||,C|missense_variant|MODERATE|CUX1|ENSG00000257923|transcript|ENST00000622516.4|protein_coding|18/23|c.1561A>C|p.Asn521His|1653/2990|1561/2031|521/676||,C|missense_variant|MODERATE|CUX1|ENSG00000257923|transcript|ENST00000292538.8|protein_coding|18/23|c.1567A>C|p.Asn523His|1593/2930|1567/2037|523/678||,C|missense_variant|MODERATE|CUX1|ENSG00000257923|transcript|ENST00000393824.7|protein_coding|17/22|c.1450A>C|p.Asn484His|1473/2331|1450/1920|484/639||,C|missense_variant|MODERATE|CUX1|ENSG00000257923|transcript|ENST00000547394.6|protein_coding|17/22|c.1519A>C|p.Asn507His|1541/2878|1519/1989|507/662||,C|missense_variant|MODERATE|CUX1|ENSG00000257923|transcript|ENST00000425244.6|protein_coding|17/22|c.1429A>C|p.Asn477His|1439/2776|1429/1899|477/632||,C|non_coding_transcript_exon_variant|MODIFIER|CUX1|ENSG00000257923|transcript|ENST00000487284.2|retained_intron|3/8|n.254A>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|CUX1|ENSG00000257923|transcript|ENST00000560541.5|processed_transcript|18/23|n.1839A>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|CUX1|ENSG00000257923|transcript|ENST00000558836.5|processed_transcript|17/22|n.1673A>C||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:593:587:18985:4:48:0,-173.589,-1702.86\\t0/0:99:162:156:5061:4:48:0,-43.8448,-450.919\n17\\t37731789\\t.\\tT\\tC\\t0.0\\tPASS\\tSSC=290.046;TYPE=snp;ANN=C|missense_variant|MODERATE|HNF1B|ENSG00000275410|transcript|ENST00000617811.4|protein_coding|4/9|c.851A>G|p.His284Arg|1214/2977|851/1674|284/557||,C|missense_variant|MODERATE|HNF1B|ENSG00000275410|transcript|ENST00000621123.4|protein_coding|4/9|c.773A>G|p.His258Arg|948/1971|773/1596|258/531||,C|missense_variant|MODERATE|HNF1B|ENSG00000275410|transcript|ENST00000613727.4|protein_coding|4/7|c.773A>G|p.His258Arg|907/1546|773/1374|258/457||,C|missense_variant|MODERATE|HNF1B|ENSG00000275410|transcript|ENST00000617272.4|protein_coding|4/8|c.851A>G|p.His284Arg|985/1820|851/1278|284/425||,C|missense_variant|MODERATE|HNF1B|ENSG00000275410|transcript|ENST00000614313.4|protein_coding|4/8|c.851A>G|p.His284Arg|985/1819|851/1647|284/548||,C|missense_variant|MODERATE|HNF1B|ENSG00000275410|transcript|ENST00000620125.1|protein_coding|6/6|c.754A>G|p.Thr252Ala|975/1103|754/882|252/293||,C|non_coding_transcript_exon_variant|MODIFIER|HNF1B|ENSG00000275410|transcript|ENST00000618894.1|retained_intron|2/2|n.303A>G||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:1461:1420:52449:36:527:0,-390.901,-4668.11\\t0/0:99:359:355:13371:4:78:0,-100.855,-1195.18\n6\\t31355560\\t.\\tTGGGG\\tCGGGA\\t0.0\\tPASS\\tSSC=92.3602;TYPE=complex;ANN=CGGGA|missense_variant|MODERATE|HLA-B|ENSG00000234745|transcript|ENST00000412585.6|protein_coding|4/8|c.648_652delCCCCAinsTCCCG|p.Ile218Val|681/1547|648/1089|216/362||,CGGGA|missense_variant|MODERATE|HLA-B|ENSG00000234745|transcript|ENST00000434333.1|protein_coding|3/3|c.681_685delCCCCAinsTCCCG|p.Ile229Val|810/863|681/738|227/245||WARNING_TRANSCRIPT_NO_STOP_CODON,CGGGA|upstream_gene_variant|MODIFIER|MIR6891|ENSG00000277402|transcript|ENST00000618788.1|miRNA||n.-248_-244delCCCCAinsTCCCG|||||244|,CGGGA|upstream_gene_variant|MODIFIER|XXbac-BPG248L24.12|ENSG00000271581|transcript|ENST00000603274.1|unprocessed_pseudogene||n.-1087_-1083delTGGGGinsCGGGA|||||1087|,CGGGA|upstream_gene_variant|MODIFIER|HLA-B|ENSG00000234745|transcript|ENST00000481849.5|retained_intron||n.-758_-754delCCCCAinsTCCCG|||||754|,CGGGA|upstream_gene_variant|MODIFIER|HLA-B|ENSG00000234745|transcript|ENST00000497377.5|retained_intron||n.-488_-484delCCCCAinsTCCCG|||||484|,CGGGA|non_coding_transcript_exon_variant|MODIFIER|HLA-B|ENSG00000234745|transcript|ENST00000463574.1|retained_intron|1/2|n.239_243delCCCCAinsTCCCG||||||,CGGGA|non_coding_transcript_exon_variant|MODIFIER|HLA-B|ENSG00000234745|transcript|ENST00000498007.1|retained_intron|3/3|n.914_918delCCCCAinsTCCCG||||||,CGGGA|non_coding_transcript_exon_variant|MODIFIER|HLA-B|ENSG00000234745|transcript|ENST00000474381.1|retained_intron|2/2|n.1097_1101delCCCCAinsTCCCG||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:968:902:35747:55:2195:0,-156.895,-3176.54\\t0/0:99:266:259:10300:6:242:0,-64.5348,-943.326\n19\\t5135358\\t.\\tA\\tT\\t0.0\\tPASS\\tSSC=248.905;TYPE=snp;ANN=T|missense_variant|MODERATE|KDM4B|ENSG00000127663|transcript|ENST00000536461.5|protein_coding|15/23|c.2207A>T|p.Glu736Val|2247/5027|2207/3393|736/1130||,T|missense_variant|MODERATE|KDM4B|ENSG00000127663|transcript|ENST00000159111.8|protein_coding|15/23|c.2105A>T|p.Glu702Val|2323/5593|2105/3291|702/1096||,T|missense_variant|MODERATE|KDM4B|ENSG00000127663|transcript|ENST00000588361.1|protein_coding|8/12|c.1340A>T|p.Glu447Val|1342/3039|1340/1869|447/622||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|KDM4B|ENSG00000127663|transcript|ENST00000611640.4|protein_coding|16/24|c.2207A>T|p.Glu736Val|2433/5703|2207/3393|736/1130||,T|upstream_gene_variant|MODIFIER|KDM4B|ENSG00000127663|transcript|ENST00000588166.1|processed_transcript||n.-178A>T|||||178|,T|non_coding_transcript_exon_variant|MODIFIER|KDM4B|ENSG00000127663|transcript|ENST00000589104.5|retained_intron|9/17|n.1871A>T||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:899:897:34686:0:0:0,-270.024,-3118.27\\t0/0:99:96:94:3644:2:82:0,-21.1192,-320.199\n7\\t7969419\\t.\\tG\\tA\\t0.0\\tPASS\\tSSC=43.9033;TYPE=snp;ANN=A|missense_variant|MODERATE|GLCCI1|ENSG00000106415|transcript|ENST00000223145.9|protein_coding|1/8|c.69G>A|p.Met23Ile|626/4743|69/1644|23/547||,A|upstream_gene_variant|MODIFIER|GLCCI1|ENSG00000106415|transcript|ENST00000492797.5|retained_intron||n.-288G>A|||||288|,A|upstream_gene_variant|MODIFIER|GLCCI1|ENSG00000106415|transcript|ENST00000460897.1|retained_intron||n.-317G>A|||||317|,A|upstream_gene_variant|MODIFIER|GLCCI1|ENSG00000106415|transcript|ENST00000414914.5|protein_coding||c.-268G>A|||||268|WARNING_TRANSCRIPT_INCOMPLETE,A|upstream_gene_variant|MODIFIER|GLCCI1|ENSG00000106415|transcript|ENST00000430798.1|protein_coding||c.-268G>A|||||268|WARNING_TRANSCRIPT_INCOMPLETE,A|upstream_gene_variant|MODIFIER|GLCCI1|ENSG00000106415|transcript|ENST00000470583.5|processed_transcript||n.-1022G>A|||||1022|,A|upstream_gene_variant|MODIFIER|GLCCI1|ENSG00000106415|transcript|ENST00000474269.5|processed_transcript||n.-1033G>A|||||1033|,A|downstream_gene_variant|MODIFIER|UMAD1|ENSG00000219545|transcript|ENST00000482067.3|protein_coding||c.*1646G>A|||||1399|,A|intron_variant|MODIFIER|AC006042.7|ENSG00000233108|transcript|ENST00000428660.1|antisense|1/1|n.132+353C>T||||||,A|intron_variant|MODIFIER|RP11-505D17.1|ENSG00000283549|transcript|ENST00000469183.5|processed_transcript|4/4|n.492-34489G>A||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:204:204:8080:0:0:0,-61.4101,-726.729\\t0/0:99:84:82:3281:2:82:0,-17.5068,-287.543\n13\\t87677763\\t.\\tTGCA\\tT\\t3.50176E-14\\tPASS\\tSSC=31.1978;TYPE=del;OLD_VARIANT=13:87677763:TGCAGCAGCAGCAGCAG/TGCAGCAGCAGCAG;ANN=T|disruptive_inframe_deletion|MODERATE|SLITRK5|ENSG00000165300|transcript|ENST00000325089.7|protein_coding|2/2|c.2390_2392delAGC|p.Gln797del|2609/21103|2390/2877|797/958||INFO_REALIGN_3_PRIME\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:148:137:5428:4:155:0,-50.1627,-500.181\\t0/0:99:44:42:1657:0:0:0,-18.9649,-152.513\n2\\t74101995\\t.\\tA\\tG\\t1.3531E-14\\tPASS\\tSSC=169.858;TYPE=snp;ANN=G|missense_variant|MODERATE|TET3|ENSG00000187605|transcript|ENST00000409262.7|protein_coding|11/11|c.5207A>G|p.Glu1736Gly|5207/11388|5207/5388|1736/1795||,G|missense_variant|MODERATE|TET3|ENSG00000187605|transcript|ENST00000305799.8|protein_coding|11/11|c.4928A>G|p.Glu1643Gly|4993/5174|4928/5109|1643/1702||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:639:637:24904:1:12:0,-190.977,-2237.96\\t0/0:99:96:94:3701:2:82:0,-21.1192,-325.324\n17\\t31236017\\t.\\tA\\tC\\t0.0\\tPASS\\tSSC=169.999;TYPE=snp;ANN=C|missense_variant|MODERATE|NF1|ENSG00000196712|transcript|ENST00000358273.8|protein_coding|29/58|c.3970A>C|p.Thr1324Pro|4353/12425|3970/8520|1324/2839||,C|missense_variant|MODERATE|NF1|ENSG00000196712|transcript|ENST00000356175.7|protein_coding|29/57|c.3970A>C|p.Thr1324Pro|4353/12362|3970/8457|1324/2818||,C|missense_variant|MODERATE|NF1|ENSG00000196712|transcript|ENST00000456735.6|protein_coding|21/50|c.2968A>C|p.Thr990Pro|2968/7787|2968/7509|990/2502||WARNING_TRANSCRIPT_NO_START_CODON,C|3_prime_UTR_variant|MODIFIER|NF1|ENSG00000196712|transcript|ENST00000495910.6|nonsense_mediated_decay|27/29|n.*3371A>C|||||54583|,C|non_coding_transcript_exon_variant|MODIFIER|NF1|ENSG00000196712|transcript|ENST00000579081.5|nonsense_mediated_decay|29/58|n.4072A>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|NF1|ENSG00000196712|transcript|ENST00000495910.6|nonsense_mediated_decay|27/29|n.*3371A>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|NF1|ENSG00000196712|transcript|ENST00000493220.5|retained_intron|12/21|n.2506A>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|NF1|ENSG00000196712|transcript|ENST00000466819.5|nonsense_mediated_decay|3/10|n.445A>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|NF1|ENSG00000196712|transcript|ENST00000479614.1|nonsense_mediated_decay|3/9|n.445A>C||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:1152:1079:39413:52:668:0,-280.346,-3483.25\\t0/0:99:457:429:15688:23:286:0,-110.347,-1384.79\n1\\t76868591\\t.\\tCGCA\\tC\\t5.82463E-5\\tPASS\\tSSC=20.1327;TYPE=del;OLD_VARIANT=1:76868591:CGCAGCAGCAGCAGCAGCAGCAGCAA/CGCAGCAGCAGCAGCAGCAGCAA;ANN=C|disruptive_inframe_deletion|MODERATE|ST6GALNAC5|ENSG00000117069|transcript|ENST00000477717.5|protein_coding|2/5|c.132_134delGCA|p.Gln45del|367/3751|132/1011|44/336||INFO_REALIGN_3_PRIME,C|non_coding_transcript_exon_variant|MODIFIER|ST6GALNAC5|ENSG00000117069|transcript|ENST00000496845.1|processed_transcript|2/2|n.326_328delGCA||||||INFO_REALIGN_3_PRIME,C|non_coding_transcript_exon_variant|MODIFIER|ST6GALNAC5|ENSG00000117069|transcript|ENST00000480428.1|processed_transcript|2/3|n.328_330delGCA||||||INFO_REALIGN_3_PRIME,C|non_coding_transcript_exon_variant|MODIFIER|ST6GALNAC5|ENSG00000117069|transcript|ENST00000318803.6|nonsense_mediated_decay|2/5|n.132_134delGCA||||||INFO_REALIGN_3_PRIME\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:56:52:2094:2:82:0,-16.8685,-184.324\\t0/1:5.82463e-05:11:9:366:2:82:-3.26423,0,-28.7895\n2\\t85303979\\t.\\tT\\tG\\t6.58156E-14\\tPASS\\tSSC=294.911;TYPE=snp;ANN=G|missense_variant|MODERATE|TCF7L1|ENSG00000152284|transcript|ENST00000282111.3|protein_coding|6/12|c.743T>G|p.Leu248Arg|1018/2968|743/1767|248/588||,G|downstream_gene_variant|MODIFIER|TCF7L1|ENSG00000152284|transcript|ENST00000442813.1|protein_coding||c.*1485T>G|||||1485|WARNING_TRANSCRIPT_INCOMPLETE,G|non_coding_transcript_exon_variant|MODIFIER|TCF7L1|ENSG00000152284|transcript|ENST00000490744.1|retained_intron|1/2|n.587T>G||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:1675:1587:52933:81:1166:0,-397.205,-4655.24\\t0/0:99:398:384:13209:13:191:0,-102.294,-1170.74\n3\\t128101645\\t.\\tC\\tG\\t0.0\\tPASS\\tSSC=195.793;TYPE=snp;ANN=G|missense_variant|MODERATE|RUVBL1|ENSG00000175792|transcript|ENST00000322623.9|protein_coding|5/11|c.517G>C|p.Asp173His|617/1761|517/1371|173/456||,G|missense_variant|MODERATE|RUVBL1|ENSG00000175792|transcript|ENST00000464873.5|protein_coding|5/10|c.337G>C|p.Asp113His|1088/2126|337/948|113/315||,G|upstream_gene_variant|MODIFIER|RUVBL1|ENSG00000175792|transcript|ENST00000585057.5|nonsense_mediated_decay||n.-4149G>C|||||4149|,G|upstream_gene_variant|MODIFIER|RUVBL1|ENSG00000175792|transcript|ENST00000472125.5|protein_coding||c.-27G>C|||||26|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|RUVBL1|ENSG00000175792|transcript|ENST00000478892.1|protein_coding||c.-901G>C|||||901|WARNING_TRANSCRIPT_NO_START_CODON\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:1016:989:34913:27:423:0,-267.633,-3101.28\\t0/0:99:262:258:8926:4:76:0,-71.8402,-795.744\n22\\t40266750\\t.\\tG\\tA\\t0.0\\tPASS\\tSSC=41.2466;TYPE=snp;ANN=A|stop_gained|HIGH|TNRC6B|ENSG00000100354|transcript|ENST00000335727.13|protein_coding|5/21|c.2520G>A|p.Trp840*|2714/17933|2520/5172|840/1723||,A|stop_gained|HIGH|TNRC6B|ENSG00000100354|transcript|ENST00000446273.1|protein_coding|1/17|c.1746G>A|p.Trp582*|1748/4741|1746/4173|582/1390||WARNING_TRANSCRIPT_NO_START_CODON,A|stop_gained|HIGH|TNRC6B|ENSG00000100354|transcript|ENST00000454349.6|protein_coding|5/23|c.2520G>A|p.Trp840*|2731/18279|2520/5502|840/1833||,A|intron_variant|MODIFIER|TNRC6B|ENSG00000100354|transcript|ENST00000402203.5|protein_coding|7/23|c.566-3372G>A||||||,A|intron_variant|MODIFIER|TNRC6B|ENSG00000100354|transcript|ENST00000301923.13|protein_coding|7/23|c.566-3372G>A||||||;LOF=(TNRC6B|ENSG00000100354|9|0.33);NMD=(TNRC6B|ENSG00000100354|9|0.33)\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:133:133:5314:0:0:0,-40.037,-478.067\\t0/1:7.76924e-18:19:17:669:2:73:-1.20962,0,-54.8095\n22\\t37983649\\t.\\tG\\tA\\t0.0\\tPASS\\tSSC=251.666;TYPE=snp;ANN=A|missense_variant|MODERATE|SOX10|ENSG00000100146|transcript|ENST00000360880.6|protein_coding|3/5|c.136C>T|p.Pro46Ser|401/2861|136/1401|46/466||,A|missense_variant|MODERATE|SOX10|ENSG00000100146|transcript|ENST00000396884.6|protein_coding|2/4|c.136C>T|p.Pro46Ser|419/2879|136/1401|46/466||,A|missense_variant|MODERATE|SOX10|ENSG00000100146|transcript|ENST00000427770.1|protein_coding|2/3|c.136C>T|p.Pro46Ser|368/873|136/641|46/212||WARNING_TRANSCRIPT_INCOMPLETE,A|upstream_gene_variant|MODIFIER|SOX10|ENSG00000100146|transcript|ENST00000446929.5|protein_coding||c.-237C>T|||||235|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|POLR2F|ENSG00000100142|transcript|ENST00000333418.4|protein_coding||c.-2545G>A|||||2544|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|POLR2F|ENSG00000100142|transcript|ENST00000427034.1|protein_coding||c.-2552G>A|||||2550|WARNING_TRANSCRIPT_NO_START_CODON,A|intron_variant|MODIFIER|POLR2F|ENSG00000100142|transcript|ENST00000443002.5|nonsense_mediated_decay|5/7|n.*39-1403G>A||||||,A|intron_variant|MODIFIER|POLR2F|ENSG00000100142|transcript|ENST00000407936.5|protein_coding|4/5|c.294-2505G>A||||||,A|intron_variant|MODIFIER|POLR2F|ENSG00000100142|transcript|ENST00000405557.5|protein_coding|4/4|c.293+16479G>A||||||,A|intron_variant|MODIFIER|SOX10|ENSG00000100146|transcript|ENST00000470555.1|processed_transcript|1/1|n.70+690C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|MIR4534|ENSG00000279010|transcript|ENST00000623111.1|sense_overlapping|1/1|n.35298G>A||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:906:906:35931:0:0:0,-272.733,-3230.15\\t0/0:99:93:91:3544:2:73:0,-21.0666,-312.046\n7\\t99493944\\t.\\tC\\tT\\t5.07465E-12\\tPASS\\tSSC=8.07507;TYPE=snp;ANN=T|missense_variant|MODERATE|ZNF394|ENSG00000160908|transcript|ENST00000337673.6|protein_coding|3/3|c.1271G>A|p.Arg424Lys|1475/2179|1271/1686|424/561||,T|3_prime_UTR_variant|MODIFIER|ZNF394|ENSG00000160908|transcript|ENST00000426306.2|protein_coding|2/2|c.*655G>A|||||655|,T|downstream_gene_variant|MODIFIER|ZNF394|ENSG00000160908|transcript|ENST00000481881.1|retained_intron||n.*3918G>A|||||3918|,T|downstream_gene_variant|MODIFIER|ZNF394|ENSG00000160908|transcript|ENST00000485576.1|retained_intron||n.*4540G>A|||||4540|,T|downstream_gene_variant|MODIFIER|ZNF394|ENSG00000160908|transcript|ENST00000464401.1|retained_intron||n.*4641G>A|||||4641|,T|downstream_gene_variant|MODIFIER|ZNF394|ENSG00000160908|transcript|ENST00000394177.3|processed_transcript||n.*635G>A|||||635|,T|intron_variant|MODIFIER|ZNF789|ENSG00000198556|transcript|ENST00000494186.1|processed_transcript|1/1|n.115-6779C>T||||||,T|intron_variant|MODIFIER|ZNF394|ENSG00000160908|transcript|ENST00000462024.1|processed_transcript|1/1|n.83+4772G>A||||||,T|intron_variant|MODIFIER|ZNF789|ENSG00000198556|transcript|ENST00000493485.5|protein_coding|4/4|c.131-9603C>T||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:46:43:1737:2:24:0,-11.3864,-154.251\\t0/0:99:11:11:424:0:0:0,-3.31133,-38.5031\n17\\t82830857\\t.\\tT\\tG\\t5.85226E-14\\tPASS\\tSSC=197.44;TYPE=snp;ANN=G|missense_variant|MODERATE|ZNF750|ENSG00000141579|transcript|ENST00000269394.3|protein_coding|3/3|c.1457A>C|p.Asp486Ala|2291/3713|1457/2172|486/723||,G|missense_variant|MODERATE|ZNF750|ENSG00000141579|transcript|ENST00000572562.1|protein_coding|3/3|c.260A>C|p.Asp87Ala|585/1513|260/975|87/324||,G|intron_variant|MODIFIER|TBCD|ENSG00000141556|transcript|ENST00000355528.8|protein_coding|13/38|c.1318+15923T>G||||||,G|intron_variant|MODIFIER|TBCD|ENSG00000141556|transcript|ENST00000539345.6|protein_coding|13/39|c.1318+15923T>G||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:854:842:31570:5:60:0,-249.572,-2833.07\\t0/0:99:191:187:6837:4:58:0,-52.1318,-609.71\n4\\t87114595\\t.\\tGGA\\tCGG\\t7.47356E-14\\tPASS\\tSSC=220.86;TYPE=complex;OLD_MULTIALLELIC=4:87114595:GGA/CGG/CGA/GGG;ANN=CGG|missense_variant|MODERATE|AFF1|ENSG00000172493|transcript|ENST00000307808.10|protein_coding|11/20|c.1741_1743delGGAinsCGG|p.Gly581Arg|2161/9390|1741/3633|581/1210||,CGG|missense_variant|MODERATE|AFF1|ENSG00000172493|transcript|ENST00000395146.8|protein_coding|12/21|c.1762_1764delGGAinsCGG|p.Gly588Arg|2037/9285|1762/3657|588/1218||,CGG|missense_variant|MODERATE|AFF1|ENSG00000172493|transcript|ENST00000544085.5|protein_coding|11/23|c.1741_1743delGGAinsCGG|p.Gly581Arg|1753/3644|1741/3618|581/1205||,CGG|upstream_gene_variant|MODIFIER|AFF1|ENSG00000172493|transcript|ENST00000503369.1|retained_intron||n.-348_-346delGGAinsCGG|||||348|\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:1341:1066:39163:72:925:0,-296.629,-3429.05\\t0/0:99:345:270:9885:18:223:0,-75.7695,-864.765\n16\\t72795165\\t.\\tT\\tA\\t4.82166E-14\\tPASS\\tSSC=526.717;TYPE=snp;ANN=A|missense_variant|MODERATE|ZFHX3|ENSG00000140836|transcript|ENST00000268489.9|protein_coding|9/10|c.7517A>T|p.His2506Leu|8190/16064|7517/11112|2506/3703||,A|missense_variant|MODERATE|ZFHX3|ENSG00000140836|transcript|ENST00000397992.5|protein_coding|8/9|c.4775A>T|p.His1592Leu|5967/13841|4775/8370|1592/2789||,A|downstream_gene_variant|MODIFIER|RP5-991G20.1|ENSG00000259768|transcript|ENST00000563328.4|antisense||n.*3541T>A|||||3541|\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:2418:2334:79409:77:1019:0,-634.117,-7048.95\\t0/0:99:414:399:13698:15:190:0,-107.4,-1214.83\n19\\t49601523\\t.\\tACT\\tCCC\\t0.00243228\\tPASS\\tSSC=3.25855;TYPE=complex;OLD_MULTIALLELIC=19:49601523:ACT/CCC/ACC;ANN=CCC|missense_variant|MODERATE|PRR12|ENSG00000126464|transcript|ENST00000418929.6|protein_coding|6/14|c.4378_4380delACTinsCCC|p.Thr1460Pro|4390/6955|4378/6111|1460/2036||,CCC|missense_variant|MODERATE|PRR12|ENSG00000126464|transcript|ENST00000615927.1|protein_coding|4/12|c.1915_1917delACTinsCCC|p.Thr639Pro|1915/4479|1915/3648|639/1215||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:84.6254:24:18:602:2:24:0,-3.86061,-52.1599\\t0/.:0.00238636:3:2:62:0:0:-1.29684,-1.8989,-6.93536\n7\\t154968982\\t.\\tCCTG\\tC\\t1.78401E-13\\tPASS\\tSSC=183.705;TYPE=del;OLD_VARIANT=7:154968982:CCTGCTGCTGCTGCTGT/CCTGCTGCTGCTGT;ANN=C|conservative_inframe_deletion|MODERATE|PAXIP1|ENSG00000157212|transcript|ENST00000397192.5|protein_coding|7/21|c.1216_1218delCAG|p.Gln406del|1261/3711|1216/3210|406/1069||,C|conservative_inframe_deletion|MODERATE|PAXIP1|ENSG00000157212|transcript|ENST00000404141.5|protein_coding|7/21|c.1216_1218delCAG|p.Gln406del|1373/3827|1216/3210|406/1069||,C|3_prime_UTR_variant|MODIFIER|PAXIP1|ENSG00000157212|transcript|ENST00000457196.5|nonsense_mediated_decay|8/22|n.*935_*937delCAG|||||17075|,C|upstream_gene_variant|MODIFIER|PAXIP1|ENSG00000157212|transcript|ENST00000464717.5|retained_intron||n.-3275_-3273delCAG|||||3273|,C|downstream_gene_variant|MODIFIER|PAXIP1|ENSG00000157212|transcript|ENST00000494182.1|processed_transcript||n.*64_*66delCAG|||||66|,C|non_coding_transcript_exon_variant|MODIFIER|PAXIP1|ENSG00000157212|transcript|ENST00000475066.1|retained_intron|3/4|n.1304_1306delCAG||||||,C|non_coding_transcript_exon_variant|MODIFIER|PAXIP1|ENSG00000157212|transcript|ENST00000457196.5|nonsense_mediated_decay|8/22|n.*935_*937delCAG||||||,C|non_coding_transcript_exon_variant|MODIFIER|PAXIP1|ENSG00000157212|transcript|ENST00000473219.5|processed_transcript|7/21|n.3156_3158delCAG||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:788:736:29188:33:1248:0,-263.694,-2702.74\\t0/0:99:244:230:9186:8:315:0,-79.9888,-832.854\n17\\t7848045\\t.\\tG\\tA\\t0.0\\tPASS\\tSSC=452.635;TYPE=snp;ANN=A|missense_variant|MODERATE|KDM6B|ENSG00000132510|transcript|ENST00000254846.9|protein_coding|11/22|c.1757G>A|p.Arg586Gln|2146/6713|1757/5049|586/1682||,A|missense_variant|MODERATE|KDM6B|ENSG00000132510|transcript|ENST00000448097.6|protein_coding|11/23|c.1757G>A|p.Arg586Gln|2088/5422|1757/4932|586/1643||,A|downstream_gene_variant|MODIFIER|KDM6B|ENSG00000132510|transcript|ENST00000571047.5|processed_transcript||n.*2698G>A|||||2698|,A|downstream_gene_variant|MODIFIER|KDM6B|ENSG00000132510|transcript|ENST00000575521.1|processed_transcript||n.*3073G>A|||||3073|,A|downstream_gene_variant|MODIFIER|KDM6B|ENSG00000132510|transcript|ENST00000570632.1|protein_coding||c.*474G>A|||||474|WARNING_TRANSCRIPT_INCOMPLETE\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:2497:2409:83668:78:1176:0,-642.874,-7417.09\\t0/0:99:679:666:24333:13:156:0,-190.239,-2173.91\n17\\t4894305\\t.\\tT\\tC\\t7.47356E-14\\tPASS\\tSSC=267.869;TYPE=snp;OLD_MULTIALLELIC=17:4894305:T/G/C;ANN=C|synonymous_variant|LOW|MINK1|ENSG00000141503|transcript|ENST00000355280.10|protein_coding|23/32|c.2802T>C|p.Ser934Ser|2998/4961|2802/3999|934/1332||,C|synonymous_variant|LOW|MINK1|ENSG00000141503|transcript|ENST00000347992.11|protein_coding|23/32|c.2715T>C|p.Ser905Ser|2899/4863|2715/3912|905/1303||,C|synonymous_variant|LOW|MINK1|ENSG00000141503|transcript|ENST00000453408.7|protein_coding|23/32|c.2742T>C|p.Ser914Ser|2742/3939|2742/3939|914/1312||,C|3_prime_UTR_variant|MODIFIER|MINK1|ENSG00000141503|transcript|ENST00000574453.5|nonsense_mediated_decay|23/32|n.*2471T>C|||||13134|,C|3_prime_UTR_variant|MODIFIER|MINK1|ENSG00000141503|transcript|ENST00000571207.5|nonsense_mediated_decay|19/28|n.*1453T>C|||||3874|,C|upstream_gene_variant|MODIFIER|MINK1|ENSG00000141503|transcript|ENST00000574871.1|retained_intron||n.-239T>C|||||239|,C|upstream_gene_variant|MODIFIER|MINK1|ENSG00000141503|transcript|ENST00000575511.1|retained_intron||n.-553T>C|||||553|,C|upstream_gene_variant|MODIFIER|MINK1|ENSG00000141503|transcript|ENST00000576037.1|protein_coding||c.-1900T>C|||||1900|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|CHRNE|ENSG00000108556|transcript|ENST00000293780.4|protein_coding||c.*4431A>G|||||3469|,C|downstream_gene_variant|MODIFIER|MINK1|ENSG00000141503|transcript|ENST00000572629.1|retained_intron||n.*655T>C|||||655|,C|downstream_gene_variant|MODIFIER|MINK1|ENSG00000141503|transcript|ENST00000571526.1|retained_intron||n.*434T>C|||||434|,C|downstream_gene_variant|MODIFIER|MINK1|ENSG00000141503|transcript|ENST00000572304.1|retained_intron||n.*89T>C|||||89|,C|downstream_gene_variant|MODIFIER|CHRNE|ENSG00000108556|transcript|ENST00000572438.1|retained_intron||n.*3752A>G|||||3752|,C|non_coding_transcript_exon_variant|MODIFIER|MINK1|ENSG00000141503|transcript|ENST00000574453.5|nonsense_mediated_decay|23/32|n.*2471T>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|MINK1|ENSG00000141503|transcript|ENST00000572330.5|retained_intron|22/31|n.3584T>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|MINK1|ENSG00000141503|transcript|ENST00000571207.5|nonsense_mediated_decay|19/28|n.*1453T>C||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:1159:1110:39728:30:410:0,-306.28,-3535.13\\t0/0:99:213:201:7501:5:70:0,-55.7099,-668.273\n22\\t17505004\\t.\\tG\\tA\\t0.0\\tPASS\\tSSC=233.422;TYPE=snp;ANN=A|missense_variant|MODERATE|CECR2|ENSG00000099954|transcript|ENST00000400585.6|protein_coding|7/19|c.369G>A|p.Met123Ile|807/4833|369/3903|123/1300||,A|missense_variant|MODERATE|CECR2|ENSG00000099954|transcript|ENST00000262608.12|protein_coding|7/19|c.369G>A|p.Met123Ile|754/4783|369/3906|123/1301||,A|missense_variant|MODERATE|CECR2|ENSG00000099954|transcript|ENST00000342247.9|protein_coding|7/20|c.858G>A|p.Met286Ile|1276/6178|858/4455|286/1484||,A|missense_variant|MODERATE|CECR2|ENSG00000099954|transcript|ENST00000612582.1|protein_coding|7/19|c.792G>A|p.Met264Ile|799/9645|792/4329|264/1442||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:943:941:36337:2:24:0,-281.591,-3264.69\\t0/0:99:213:207:8203:5:172:0,-48.1686,-722.01\n19\\t35633777\\t.\\tC\\tT\\t0.0\\tPASS\\tSSC=20.2972;TYPE=snp;ANN=T|synonymous_variant|LOW|RBM42|ENSG00000126254|transcript|ENST00000262633.8|protein_coding|7/10|c.775C>T|p.Leu259Leu|880/1680|775/1443|259/480||,T|synonymous_variant|LOW|RBM42|ENSG00000126254|transcript|ENST00000588161.5|protein_coding|6/9|c.685C>T|p.Leu229Leu|809/1609|685/1353|229/450||,T|synonymous_variant|LOW|RBM42|ENSG00000126254|transcript|ENST00000592202.5|protein_coding|5/8|c.613C>T|p.Leu205Leu|700/1469|613/1281|205/426||,T|synonymous_variant|LOW|RBM42|ENSG00000126254|transcript|ENST00000589559.5|protein_coding|6/8|c.688C>T|p.Leu230Leu|765/1328|688/1161|230/386||,T|synonymous_variant|LOW|RBM42|ENSG00000126254|transcript|ENST00000589871.1|protein_coding|6/9|c.709C>T|p.Leu237Leu|732/1487|709/1377|237/458||,T|downstream_gene_variant|MODIFIER|RBM42|ENSG00000126254|transcript|ENST00000592526.1|retained_intron||n.*1865C>T|||||1865|,T|intron_variant|MODIFIER|RBM42|ENSG00000126254|transcript|ENST00000586618.5|protein_coding|3/4|c.339+2581C>T||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:91:89:3533:2:24:0,-25.1137,-315.702\\t0/0:99:16:16:639:0:0:0,-4.81648,-57.8408\n6\\t99613712\\t.\\tC\\tG\\t0.0\\tPASS\\tSSC=62.8682;TYPE=snp;ANN=G|missense_variant|MODERATE|PRDM13|ENSG00000112238|transcript|ENST00000369215.4|protein_coding|4/4|c.1077C>G|p.His359Gln|1382/2429|1077/2124|359/707||,G|3_prime_UTR_variant|MODIFIER|PRDM13|ENSG00000112238|transcript|ENST00000369214.2|nonsense_mediated_decay|4/4|n.*739C>G|||||4464|,G|non_coding_transcript_exon_variant|MODIFIER|PRDM13|ENSG00000112238|transcript|ENST00000369214.2|nonsense_mediated_decay|4/4|n.*739C>G||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:217:217:8622:0:0:0,-65.3235,-775.43\\t0/0:99:34:32:1260:2:82:0,-2.45534,-105.884\n9\\t65737394\\t.\\tT\\tA\\t0.0\\tPASS\\tSSC=38.2653;TYPE=snp;ANN=A|synonymous_variant|LOW|FOXD4L4|ENSG00000184659|transcript|ENST00000377413.2|protein_coding|1/1|c.249T>A|p.Pro83Pro|840/2230|249/1251|83/416||,A|downstream_gene_variant|MODIFIER|CBWD5|ENSG00000147996|transcript|ENST00000382405.7|protein_coding||c.*3778T>A|||||3353|,A|downstream_gene_variant|MODIFIER|CBWD5|ENSG00000147996|transcript|ENST00000377389.5|nonsense_mediated_decay||n.*4887T>A|||||3721|,A|downstream_gene_variant|MODIFIER|CBWD5|ENSG00000147996|transcript|ENST00000497250.5|nonsense_mediated_decay||n.*4511T>A|||||3724|,A|downstream_gene_variant|MODIFIER|CBWD5|ENSG00000147996|transcript|ENST00000430059.6|protein_coding||c.*3778T>A|||||3720|,A|downstream_gene_variant|MODIFIER|CBWD5|ENSG00000147996|transcript|ENST00000486221.5|nonsense_mediated_decay||n.*4562T>A|||||3722|,A|downstream_gene_variant|MODIFIER|CBWD5|ENSG00000147996|transcript|ENST00000377395.8|protein_coding||c.*3778T>A|||||3718|,A|downstream_gene_variant|MODIFIER|CBWD5|ENSG00000147996|transcript|ENST00000461932.5|retained_intron||n.*3400T>A|||||3400|,A|downstream_gene_variant|MODIFIER|CBWD5|ENSG00000147996|transcript|ENST00000377392.9|protein_coding||c.*3778T>A|||||3354|,A|downstream_gene_variant|MODIFIER|CBWD5|ENSG00000147996|transcript|ENST00000480229.5|nonsense_mediated_decay||n.*4564T>A|||||3535|,A|downstream_gene_variant|MODIFIER|CBWD5|ENSG00000147996|transcript|ENST00000429800.6|protein_coding||c.*3778T>A|||||3721|,A|downstream_gene_variant|MODIFIER|CBWD5|ENSG00000147996|transcript|ENST00000476797.5|processed_transcript||n.*3721T>A|||||3721|,A|downstream_gene_variant|MODIFIER|CBWD5|ENSG00000147996|transcript|ENST00000485088.5|retained_intron||n.*3402T>A|||||3402|,A|downstream_gene_variant|MODIFIER|CBWD5|ENSG00000147996|transcript|ENST00000463075.1|retained_intron||n.*3722T>A|||||3722|,A|downstream_gene_variant|MODIFIER|CBWD5|ENSG00000147996|transcript|ENST00000491485.1|retained_intron||n.*3720T>A|||||3720|,A|downstream_gene_variant|MODIFIER|CBWD5|ENSG00000147996|transcript|ENST00000489273.1|protein_coding||c.*3778T>A|||||3723|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|CBWD5|ENSG00000147996|transcript|ENST00000468066.5|processed_transcript||n.*3814T>A|||||3814|,A|downstream_gene_variant|MODIFIER|CBWD5|ENSG00000147996|transcript|ENST00000480819.6|retained_intron||n.*3723T>A|||||3723|,A|downstream_gene_variant|MODIFIER|CBWD5|ENSG00000147996|transcript|ENST00000486191.5|processed_transcript||n.*3747T>A|||||3747|\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:175:170:6441:5:139:0,-45.7911,-422.912\\t0/0:99:25:25:934:0:0:0,-7.52575,-65.7374\n7\\t105041014\\t.\\tC\\tA\\t3.82117E-14\\tPASS\\tSSC=44.903;TYPE=snp;ANN=A|missense_variant|MODERATE|KMT2E|ENSG00000005483|transcript|ENST00000257745.8|protein_coding|2/26|c.62C>A|p.Ala21Glu|448/6714|62/5577|21/1858||,A|missense_variant|MODERATE|KMT2E|ENSG00000005483|transcript|ENST00000311117.7|protein_coding|3/27|c.62C>A|p.Ala21Glu|607/6874|62/5577|21/1858||,A|missense_variant|MODERATE|KMT2E|ENSG00000005483|transcript|ENST00000495267.5|protein_coding|2/7|c.62C>A|p.Ala21Glu|504/1133|62/691|21/229||WARNING_TRANSCRIPT_INCOMPLETE,A|missense_variant|MODERATE|KMT2E|ENSG00000005483|transcript|ENST00000476671.5|protein_coding|3/15|c.62C>A|p.Ala21Glu|568/2523|62/1830|21/609||,A|missense_variant|MODERATE|KMT2E|ENSG00000005483|transcript|ENST00000474203.5|protein_coding|4/6|c.62C>A|p.Ala21Glu|466/617|62/213|21/70||WARNING_TRANSCRIPT_NO_STOP_CODON,A|missense_variant|MODERATE|KMT2E|ENSG00000005483|transcript|ENST00000478990.5|protein_coding|2/10|c.62C>A|p.Ala21Glu|506/1500|62/1056|21/351||WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|KMT2E|ENSG00000005483|transcript|ENST00000480368.5|processed_transcript||n.*158C>A|||||158|,A|non_coding_transcript_exon_variant|MODIFIER|KMT2E|ENSG00000005483|transcript|ENST00000334884.9|nonsense_mediated_decay|3/26|n.62C>A||||||,A|non_coding_transcript_exon_variant|MODIFIER|KMT2E|ENSG00000005483|transcript|ENST00000482560.6|nonsense_mediated_decay|2/14|n.62C>A||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:850:823:27658:23:286:0,-228.929,-2459.83\\t0/0:99:672:653:21767:15:190:0,-184.026,-1940.17\n3\\t9447999\\t.\\tC\\tG\\t0.0\\tPASS\\tSSC=381.417;TYPE=snp;ANN=G|missense_variant|MODERATE|SETD5|ENSG00000168137|transcript|ENST00000302463.10|protein_coding|14/22|c.1802C>G|p.Thr601Ser|2166/4786|1802/4035|601/1344||,G|missense_variant|MODERATE|SETD5|ENSG00000168137|transcript|ENST00000407969.5|protein_coding|13/21|c.2153C>G|p.Thr718Ser|2167/6463|2153/4386|718/1461||,G|missense_variant|MODERATE|SETD5|ENSG00000168137|transcript|ENST00000402198.5|protein_coding|15/23|c.2096C>G|p.Thr699Ser|2531/6827|2096/4329|699/1442||,G|missense_variant|MODERATE|SETD5|ENSG00000168137|transcript|ENST00000406341.5|protein_coding|14/22|c.2096C>G|p.Thr699Ser|2286/6582|2096/4329|699/1442||,G|missense_variant|MODERATE|SETD5|ENSG00000168137|transcript|ENST00000399686.6|protein_coding|6/14|c.1097C>G|p.Thr366Ser|1098/3362|1097/2733|366/910||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|SETD5|ENSG00000168137|transcript|ENST00000421188.1|protein_coding|1/7|c.29C>G|p.Thr10Ser|30/1323|29/1322|10/439||WARNING_TRANSCRIPT_INCOMPLETE,G|3_prime_UTR_variant|MODIFIER|SETD5|ENSG00000168137|transcript|ENST00000443339.5|nonsense_mediated_decay|17/20|n.*2356C>G|||||18085|,G|3_prime_UTR_variant|MODIFIER|SETD5|ENSG00000168137|transcript|ENST00000413704.5|nonsense_mediated_decay|6/14|n.*600C>G|||||2287|,G|upstream_gene_variant|MODIFIER|SETD5|ENSG00000168137|transcript|ENST00000478961.5|processed_transcript||n.-476C>G|||||476|,G|upstream_gene_variant|MODIFIER|SETD5|ENSG00000168137|transcript|ENST00000476740.1|processed_transcript||n.-560C>G|||||560|,G|downstream_gene_variant|MODIFIER|SETD5|ENSG00000168137|transcript|ENST00000497213.5|processed_transcript||n.*2267C>G|||||2267|,G|downstream_gene_variant|MODIFIER|SETD5|ENSG00000168137|transcript|ENST00000464410.1|retained_intron||n.*281C>G|||||281|,G|non_coding_transcript_exon_variant|MODIFIER|SETD5|ENSG00000168137|transcript|ENST00000493918.5|retained_intron|11/19|n.2260C>G||||||,G|non_coding_transcript_exon_variant|MODIFIER|SETD5|ENSG00000168137|transcript|ENST00000443339.5|nonsense_mediated_decay|17/20|n.*2356C>G||||||,G|non_coding_transcript_exon_variant|MODIFIER|SETD5|ENSG00000168137|transcript|ENST00000413704.5|nonsense_mediated_decay|6/14|n.*600C>G||||||,G|non_coding_transcript_exon_variant|MODIFIER|SETD5|ENSG00000168137|transcript|ENST00000466242.5|retained_intron|5/13|n.1437C>G||||||,G|non_coding_transcript_exon_variant|MODIFIER|SETD5|ENSG00000168137|transcript|ENST00000488236.5|processed_transcript|1/5|n.313C>G||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:2206:2158:85723:45:732:0,-597.376,-7639.94\\t0/0:99:811:795:31645:16:311:0,-215.959,-2816.74\n11\\t64810090\\t.\\tT\\tG\\t0.0\\tPASS\\tSSC=121.879;TYPE=snp;ANN=G|missense_variant|MODERATE|MEN1|ENSG00000133895|transcript|ENST00000377321.5|protein_coding|2/10|c.20A>C|p.Gln7Pro|88/2614|20/1728|7/575||,G|missense_variant|MODERATE|MEN1|ENSG00000133895|transcript|ENST00000312049.10|protein_coding|2/10|c.20A>C|p.Gln7Pro|130/2761|20/1833|7/610||,G|missense_variant|MODERATE|MEN1|ENSG00000133895|transcript|ENST00000424912.1|protein_coding|3/3|c.20A>C|p.Gln7Pro|396/816|20/440|7/145||WARNING_TRANSCRIPT_INCOMPLETE,G|missense_variant|MODERATE|MEN1|ENSG00000133895|transcript|ENST00000429702.5|protein_coding|2/2|c.20A>C|p.Gln7Pro|524/944|20/440|7/145||WARNING_TRANSCRIPT_INCOMPLETE,G|missense_variant|MODERATE|MEN1|ENSG00000133895|transcript|ENST00000377313.5|protein_coding|1/9|c.20A>C|p.Gln7Pro|43/1871|20/1848|7/615||,G|missense_variant|MODERATE|MEN1|ENSG00000133895|transcript|ENST00000413626.1|protein_coding|2/4|c.20A>C|p.Gln7Pro|107/870|20/783|7/260||WARNING_TRANSCRIPT_NO_STOP_CODON,G|missense_variant|MODERATE|MEN1|ENSG00000133895|transcript|ENST00000337652.5|protein_coding|2/10|c.20A>C|p.Gln7Pro|524/3162|20/1848|7/615||,G|missense_variant|MODERATE|MEN1|ENSG00000133895|transcript|ENST00000377316.6|protein_coding|1/8|c.20A>C|p.Gln7Pro|396/2868|20/1668|7/555||,G|missense_variant|MODERATE|MEN1|ENSG00000133895|transcript|ENST00000377326.7|protein_coding|1/9|c.20A>C|p.Gln7Pro|519/3150|20/1833|7/610||,G|missense_variant|MODERATE|MEN1|ENSG00000133895|transcript|ENST00000315422.8|protein_coding|2/10|c.20A>C|p.Gln7Pro|517/3148|20/1833|7/610||,G|missense_variant|MODERATE|MEN1|ENSG00000133895|transcript|ENST00000394374.6|protein_coding|2/10|c.20A>C|p.Gln7Pro|517/3155|20/1848|7/615||,G|missense_variant|MODERATE|MEN1|ENSG00000133895|transcript|ENST00000394376.5|protein_coding|3/11|c.20A>C|p.Gln7Pro|396/3034|20/1848|7/615||,G|missense_variant|MODERATE|MEN1|ENSG00000133895|transcript|ENST00000440873.5|protein_coding|2/7|c.20A>C|p.Gln7Pro|88/1107|20/1039|7/345||WARNING_TRANSCRIPT_INCOMPLETE,G|missense_variant|MODERATE|MEN1|ENSG00000133895|transcript|ENST00000450708.5|protein_coding|2/6|c.20A>C|p.Gln7Pro|99/922|20/843|7/280||WARNING_TRANSCRIPT_NO_STOP_CODON,G|upstream_gene_variant|MODIFIER|MEN1|ENSG00000133895|transcript|ENST00000478548.1|retained_intron||n.-3722A>C|||||3722|,G|upstream_gene_variant|MODIFIER|MEN1|ENSG00000133895|transcript|ENST00000487019.1|processed_transcript||n.-4098A>C|||||4098|\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:747:701:26219:44:584:0,-171.696,-2304.7\\t0/0:99:191:184:6864:7:84:0,-49.8168,-609.737\n1\\t22593326\\t.\\tC\\tT\\t0.0\\tPASS\\tSSC=130.137;TYPE=snp;ANN=T|missense_variant&splice_region_variant|MODERATE|EPHA8|ENSG00000070886|transcript|ENST00000166244.7|protein_coding|6/17|c.1316C>T|p.Ala439Val|1388/4943|1316/3018|439/1005||,T|downstream_gene_variant|MODIFIER|EPHA8|ENSG00000070886|transcript|ENST00000374644.8|protein_coding||c.*3947C>T|||||3705|\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:466:466:18718:0:0:0,-140.28,-1682.94\\t0/0:99:46:44:1756:2:39:0,-10.1426,-154.542\n7\\t151570202\\t.\\tT\\tA\\t1.45857E-14\\tPASS\\tSSC=111.852;TYPE=snp;ANN=A|stop_gained|HIGH|PRKAG2|ENSG00000106617|transcript|ENST00000287878.8|protein_coding|10/16|c.1075A>T|p.Lys359*|1580/3305|1075/1710|359/569||,A|stop_gained|HIGH|PRKAG2|ENSG00000106617|transcript|ENST00000418337.6|protein_coding|6/12|c.352A>T|p.Lys118*|606/2318|352/987|118/328||,A|stop_gained|HIGH|PRKAG2|ENSG00000106617|transcript|ENST00000392801.6|protein_coding|10/16|c.943A>T|p.Lys315*|1386/2281|943/1578|315/525||,A|stop_gained|HIGH|PRKAG2|ENSG00000106617|transcript|ENST00000476632.1|protein_coding|7/8|c.352A>T|p.Lys118*|986/1123|352/489|118/162||WARNING_TRANSCRIPT_NO_STOP_CODON,A|stop_gained|HIGH|PRKAG2|ENSG00000106617|transcript|ENST00000492843.5|protein_coding|8/14|c.703A>T|p.Lys235*|1024/2699|703/1338|235/445||,A|3_prime_UTR_variant|MODIFIER|PRKAG2|ENSG00000106617|transcript|ENST00000488258.5|nonsense_mediated_decay|9/10|n.*315A>T|||||25247|,A|3_prime_UTR_variant|MODIFIER|PRKAG2|ENSG00000106617|transcript|ENST00000493872.5|nonsense_mediated_decay|7/7|n.*324A>T|||||61439|,A|downstream_gene_variant|MODIFIER|PRKAG2|ENSG00000106617|transcript|ENST00000491938.5|retained_intron||n.*2206A>T|||||2206|,A|non_coding_transcript_exon_variant|MODIFIER|PRKAG2|ENSG00000106617|transcript|ENST00000488258.5|nonsense_mediated_decay|9/10|n.*315A>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|PRKAG2|ENSG00000106617|transcript|ENST00000478989.5|nonsense_mediated_decay|3/8|n.127A>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|PRKAG2|ENSG00000106617|transcript|ENST00000493872.5|nonsense_mediated_decay|7/7|n.*324A>T||||||;LOF=(PRKAG2|ENSG00000106617|16|0.25);NMD=(PRKAG2|ENSG00000106617|16|0.25)\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:764:741:26773:17:229:0,-207.573,-2386.51\\t0/0:99:345:337:12050:7:87:0,-95.7206,-1075.69\n18\\t55403662\\t.\\tG\\tA\\t0.0\\tPASS\\tSSC=17.3356;TYPE=snp;ANN=A|missense_variant|MODERATE|TCF4|ENSG00000196628|transcript|ENST00000564228.5|protein_coding|1/16|c.53C>T|p.Ser18Phe|53/1915|53/1791|18/596||,A|missense_variant|MODERATE|TCF4|ENSG00000196628|transcript|ENST00000544241.6|protein_coding|1/16|c.53C>T|p.Ser18Phe|334/2264|53/1803|18/600||,A|missense_variant|MODERATE|TCF4|ENSG00000196628|transcript|ENST00000630828.2|protein_coding|1/7|c.53C>T|p.Ser18Phe|103/735|53/685|18/227||WARNING_TRANSCRIPT_INCOMPLETE,A|5_prime_UTR_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000628078.2|protein_coding|1/8|c.-230C>T|||||52680|WARNING_TRANSCRIPT_INCOMPLETE,A|upstream_gene_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000562680.5|retained_intron||n.-1623C>T|||||1623|,A|upstream_gene_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000562638.5|protein_coding||c.-1995C>T|||||1950|WARNING_TRANSCRIPT_INCOMPLETE,A|upstream_gene_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000537856.7|protein_coding||c.-2101C>T|||||1905|,A|upstream_gene_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000570177.6|protein_coding||c.-1629C>T|||||1422|,A|upstream_gene_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000568186.5|protein_coding||c.-227C>T|||||2|WARNING_TRANSCRIPT_INCOMPLETE,A|upstream_gene_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000569012.5|protein_coding||c.-2184C>T|||||2111|WARNING_TRANSCRIPT_INCOMPLETE,A|upstream_gene_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000630268.2|protein_coding||c.-1626C>T|||||1456|WARNING_TRANSCRIPT_NO_STOP_CODON,A|upstream_gene_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000562030.3|protein_coding||c.-2683C>T|||||2137|WARNING_TRANSCRIPT_INCOMPLETE,A|upstream_gene_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000562607.5|protein_coding||c.-2680C>T|||||2569|WARNING_TRANSCRIPT_INCOMPLETE,A|upstream_gene_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000566376.3|processed_transcript||n.-157C>T|||||157|,A|upstream_gene_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000590810.5|protein_coding||c.-1790C>T|||||1623|WARNING_TRANSCRIPT_NO_STOP_CODON,A|upstream_gene_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000637250.1|processed_transcript||n.-2745C>T|||||2745|,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000398339.5|protein_coding|6/20|c.611-144C>T||||||,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000356073.8|protein_coding|5/19|c.305-144C>T||||||,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000543082.5|protein_coding|3/17|c.179-144C>T||||||,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000567880.5|protein_coding|4/16|c.305-144C>T||||||,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000566286.5|protein_coding|4/18|c.299-144C>T||||||,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000625716.2|processed_transcript|3/4|n.235-144C>T||||||,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000562543.5|protein_coding|5/6|c.305-144C>T||||||WARNING_TRANSCRIPT_INCOMPLETE,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000540999.5|protein_coding|4/18|c.233-144C>T||||||,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000537578.5|protein_coding|4/18|c.233-144C>T||||||,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000561992.5|protein_coding|1/15|c.-86-144C>T||||||,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000563686.5|retained_intron|2/7|n.160-144C>T||||||,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000566514.5|protein_coding|4/9|c.266-144C>T||||||WARNING_TRANSCRIPT_INCOMPLETE,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000630712.2|protein_coding|1/5|c.-86-144C>T||||||WARNING_TRANSCRIPT_INCOMPLETE,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000565908.6|protein_coding|4/8|c.233-144C>T||||||WARNING_TRANSCRIPT_INCOMPLETE,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000562847.5|protein_coding|5/6|c.68-144C>T||||||WARNING_TRANSCRIPT_INCOMPLETE,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000565580.3|processed_transcript|3/5|n.234-144C>T||||||,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000626425.2|protein_coding|4/7|c.233-144C>T||||||WARNING_TRANSCRIPT_NO_STOP_CODON,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000563824.5|protein_coding|3/5|c.233-144C>T||||||WARNING_TRANSCRIPT_INCOMPLETE,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000568147.5|protein_coding|4/6|c.269-144C>T||||||WARNING_TRANSCRIPT_INCOMPLETE,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000563888.6|protein_coding|4/6|c.233-144C>T||||||WARNING_TRANSCRIPT_NO_STOP_CODON,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000564343.5|protein_coding|4/5|c.233-144C>T||||||WARNING_TRANSCRIPT_NO_STOP_CODON,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000627784.2|protein_coding|5/6|c.305-144C>T||||||WARNING_TRANSCRIPT_NO_STOP_CODON,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000616053.4|protein_coding|5/17|c.233-144C>T||||||,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000564999.5|protein_coding|5/19|c.305-144C>T||||||,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000354452.7|protein_coding|5/19|c.305-144C>T||||||,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000629387.2|protein_coding|5/19|c.305-144C>T||||||,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000568673.5|protein_coding|4/18|c.233-144C>T||||||,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000568740.5|protein_coding|4/18|c.233-144C>T||||||,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000566279.5|protein_coding|5/17|c.305-144C>T||||||,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000565018.6|protein_coding|4/16|c.233-144C>T||||||,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000564403.6|protein_coding|5/19|c.305-144C>T||||||,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000626584.2|protein_coding|1/12|c.-164-144C>T||||||,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000629343.2|protein_coding|1/8|c.-22+18530C>T||||||WARNING_TRANSCRIPT_INCOMPLETE,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000628636.2|protein_coding|1/8|c.-86-144C>T||||||WARNING_TRANSCRIPT_INCOMPLETE,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000627136.2|processed_transcript|4/8|n.279-144C>T||||||,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000630319.2|protein_coding|1/6|c.74-144C>T||||||WARNING_TRANSCRIPT_INCOMPLETE,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000568169.5|protein_coding|4/9|c.317-144C>T||||||WARNING_TRANSCRIPT_INCOMPLETE,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000625925.2|protein_coding|1/6|c.-83-144C>T||||||WARNING_TRANSCRIPT_NO_STOP_CODON,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000566777.5|protein_coding|1/6|c.-86-144C>T||||||WARNING_TRANSCRIPT_INCOMPLETE,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000631043.2|processed_transcript|1/5|n.104-144C>T||||||,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000627685.2|protein_coding|4/8|c.233-144C>T||||||WARNING_TRANSCRIPT_NO_STOP_CODON,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000626595.2|protein_coding|5/9|c.305-144C>T||||||WARNING_TRANSCRIPT_NO_STOP_CODON,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000569357.4|nonsense_mediated_decay|5/6|n.*141-144C>T||||||,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000637239.1|processed_transcript|3/17|n.372-144C>T||||||,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000638154.1|protein_coding|4/18|c.305-144C>T||||||,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000637115.1|nonsense_mediated_decay|6/20|n.*195-144C>T||||||,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000635822.1|protein_coding|5/19|c.305-144C>T||||||,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000636400.1|protein_coding|5/19|c.233-144C>T||||||,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000636751.1|nonsense_mediated_decay|4/19|n.233-144C>T||||||,A|intron_variant|MODIFIER|TCF4|ENSG00000196628|transcript|ENST00000637500.1|processed_transcript|1/1|n.94-144C>T||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:110:109:4309:1:12:0,-31.9133,-386.542\\t0/0:99:56:54:2157:2:24:0,-14.5777,-192.014\n19\\t7911277\\t.\\tA\\tG\\t4.68907E-14\\tPASS\\tSSC=318.745;TYPE=snp;ANN=G|missense_variant|MODERATE|MAP2K7|ENSG00000076984|transcript|ENST00000397983.7|protein_coding|9/12|c.931A>G|p.Thr311Ala|991/3396|931/1308|311/435||,G|missense_variant|MODERATE|MAP2K7|ENSG00000076984|transcript|ENST00000397981.7|protein_coding|8/11|c.883A>G|p.Thr295Ala|985/3430|883/1281|295/426||,G|missense_variant|MODERATE|MAP2K7|ENSG00000076984|transcript|ENST00000397979.3|protein_coding|8/11|c.883A>G|p.Thr295Ala|937/3361|883/1260|295/419||,G|upstream_gene_variant|MODIFIER|TGFBR3L|ENSG00000260001|transcript|ENST00000565886.1|protein_coding||c.-4991A>G|||||4868|,G|downstream_gene_variant|MODIFIER|MAP2K7|ENSG00000076984|transcript|ENST00000475022.1|retained_intron||n.*4211A>G|||||4211|,G|downstream_gene_variant|MODIFIER|CTD-3193O13.13|ENSG00000268149|transcript|ENST00000595655.1|antisense||n.*1371T>C|||||1371|,G|downstream_gene_variant|MODIFIER|MAP2K7|ENSG00000076984|transcript|ENST00000494348.1|retained_intron||n.*172A>G|||||172|,G|downstream_gene_variant|MODIFIER|MAP2K7|ENSG00000076984|transcript|ENST00000465324.1|retained_intron||n.*542A>G|||||542|,G|non_coding_transcript_exon_variant|MODIFIER|MAP2K7|ENSG00000076984|transcript|ENST00000468058.1|retained_intron|7/10|n.1078A>G||||||,G|non_coding_transcript_exon_variant|MODIFIER|MAP2K7|ENSG00000076984|transcript|ENST00000498118.1|retained_intron|2/2|n.89A>G||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:1374:1338:45283:28:386:0,-376.47,-4037.32\\t0/0:99:226:217:7534:8:111:0,-57.7253,-667.65\n4\\t13544317\\t.\\tC\\tT\\t0.0\\tPASS\\tSSC=157.392;TYPE=snp;ANN=T|missense_variant|MODERATE|NKX3-2|ENSG00000109705|transcript|ENST00000382438.5|protein_coding|1/2|c.98G>A|p.Arg33His|734/2801|98/1002|33/333||,T|downstream_gene_variant|MODIFIER|LINC01096|ENSG00000246095|transcript|ENST00000501050.1|lincRNA||n.*1759G>A|||||1759|,T|downstream_gene_variant|MODIFIER|LINC01096|ENSG00000246095|transcript|ENST00000503938.1|lincRNA||n.*1758G>A|||||1758|\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:560:560:22471:0:0:0,-168.577,-2020.3\\t0/0:99:63:61:2461:2:82:0,-11.1852,-213.834\n7\\t151570191\\t.\\tC\\tA\\t4.55042E-14\\tPASS\\tSSC=108.562;TYPE=snp;ANN=A|splice_region_variant&non_coding_transcript_exon_variant|LOW|PRKAG2|ENSG00000106617|transcript|ENST00000493872.5|nonsense_mediated_decay|7/7|n.*335G>T||||||,A|synonymous_variant|LOW|PRKAG2|ENSG00000106617|transcript|ENST00000287878.8|protein_coding|10/16|c.1086G>T|p.Val362Val|1591/3305|1086/1710|362/569||,A|synonymous_variant|LOW|PRKAG2|ENSG00000106617|transcript|ENST00000418337.6|protein_coding|6/12|c.363G>T|p.Val121Val|617/2318|363/987|121/328||,A|synonymous_variant|LOW|PRKAG2|ENSG00000106617|transcript|ENST00000392801.6|protein_coding|10/16|c.954G>T|p.Val318Val|1397/2281|954/1578|318/525||,A|synonymous_variant|LOW|PRKAG2|ENSG00000106617|transcript|ENST00000476632.1|protein_coding|7/8|c.363G>T|p.Val121Val|997/1123|363/489|121/162||WARNING_TRANSCRIPT_NO_STOP_CODON,A|synonymous_variant|LOW|PRKAG2|ENSG00000106617|transcript|ENST00000492843.5|protein_coding|8/14|c.714G>T|p.Val238Val|1035/2699|714/1338|238/445||,A|3_prime_UTR_variant|MODIFIER|PRKAG2|ENSG00000106617|transcript|ENST00000488258.5|nonsense_mediated_decay|9/10|n.*326G>T|||||25258|,A|3_prime_UTR_variant|MODIFIER|PRKAG2|ENSG00000106617|transcript|ENST00000493872.5|nonsense_mediated_decay|7/7|n.*335G>T|||||61450|,A|downstream_gene_variant|MODIFIER|PRKAG2|ENSG00000106617|transcript|ENST00000491938.5|retained_intron||n.*2217G>T|||||2217|,A|non_coding_transcript_exon_variant|MODIFIER|PRKAG2|ENSG00000106617|transcript|ENST00000488258.5|nonsense_mediated_decay|9/10|n.*326G>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|PRKAG2|ENSG00000106617|transcript|ENST00000478989.5|nonsense_mediated_decay|3/8|n.138G>T||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:754:726:24946:20:265:0,-200.714,-2219.11\\t0/0:99:345:332:11540:10:120:0,-92.1523,-1026.9\n3\\t44721521\\t.\\tG\\tT\\t32.7588\\tPASS\\tSSC=8.68277;TYPE=snp;ANN=T|missense_variant|MODERATE|ZNF502|ENSG00000196653|transcript|ENST00000296091.8|protein_coding|4/4|c.704G>T|p.Gly235Val|960/3270|704/1635|235/544||,T|missense_variant|MODERATE|ZNF502|ENSG00000196653|transcript|ENST00000436624.6|protein_coding|3/3|c.704G>T|p.Gly235Val|858/2314|704/1635|235/544||,T|missense_variant|MODERATE|ZNF502|ENSG00000196653|transcript|ENST00000449836.5|protein_coding|3/3|c.704G>T|p.Gly235Val|865/3173|704/1635|235/544||,T|downstream_gene_variant|MODIFIER|ZNF502|ENSG00000196653|transcript|ENST00000411443.1|protein_coding||c.*239G>T|||||239|WARNING_TRANSCRIPT_NO_STOP_CODON\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:28.6358:6:6:204:0:0:0,-1.80618,-18.6824\\t0/1:32.1936:3:1:41:2:82:-6.87659,0,-3.19148\n5\\t57482408\\t.\\tATCTGGT\\tCTCGGGA\\t0.0\\tPASS\\tSSC=51.3288;TYPE=complex;ANN=CTCGGGA|missense_variant|MODERATE|ACTBL2|ENSG00000169067|transcript|ENST00000423391.2|protein_coding|1/1|c.294_300delACCAGATinsTCCCGAG|p.Asp100Glu|402/2794|294/1131|98/376||,CTCGGGA|intron_variant|MODIFIER|CTD-2023N9.1|ENSG00000250961|transcript|ENST00000506106.1|antisense|1/3|n.120-11667_120-11661delATCTGGTinsCTCGGGA||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:197:196:7835:0:0:0,-63.8184,-758.476\\t0/0:99:61:58:2274:2:80:0,-12.4896,-217.738\n1\\t53594360\\t.\\tG\\tT\\t0.0\\tPASS\\tSSC=177.655;TYPE=snp;ANN=T|synonymous_variant|LOW|GLIS1|ENSG00000174332|transcript|ENST00000312233.4|protein_coding|3/10|c.543C>A|p.Gly181Gly|1110/2812|543/1863|181/620||,T|synonymous_variant|LOW|GLIS1|ENSG00000174332|transcript|ENST00000628545.1|protein_coding|3/10|c.1068C>A|p.Gly356Gly|1110/2807|1068/2388|356/795||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:665:663:26240:1:41:0,-196.054,-2355.23\\t0/0:99:89:86:3430:3:90:0,-18.3988,-300.336\n10\\t112950777\\t.\\tT\\tA\\t5.71366E-14\\tPASS\\tSSC=173.418;TYPE=snp;ANN=A|synonymous_variant|LOW|TCF7L2|ENSG00000148737|transcript|ENST00000355995.8|protein_coding|1/15|c.21T>A|p.Gly7Gly|528/4073|21/1860|7/619||,A|synonymous_variant|LOW|TCF7L2|ENSG00000148737|transcript|ENST00000534894.5|protein_coding|1/11|c.21T>A|p.Gly7Gly|528/3778|21/1227|7/408||,A|synonymous_variant|LOW|TCF7L2|ENSG00000148737|transcript|ENST00000536810.5|protein_coding|1/13|c.21T>A|p.Gly7Gly|528/3953|21/1740|7/579||,A|synonymous_variant|LOW|TCF7L2|ENSG00000148737|transcript|ENST00000538897.5|protein_coding|1/14|c.21T>A|p.Gly7Gly|528/4000|21/1449|7/482||,A|synonymous_variant|LOW|TCF7L2|ENSG00000148737|transcript|ENST00000543371.5|protein_coding|1/14|c.21T>A|p.Gly7Gly|528/4037|21/1824|7/607||,A|synonymous_variant|LOW|TCF7L2|ENSG00000148737|transcript|ENST00000627217.2|protein_coding|1/14|c.21T>A|p.Gly7Gly|371/3680|21/1809|7/602||,A|synonymous_variant|LOW|TCF7L2|ENSG00000148737|transcript|ENST00000369397.8|protein_coding|1/14|c.21T>A|p.Gly7Gly|326/3802|21/1791|7/596||,A|synonymous_variant|LOW|TCF7L2|ENSG00000148737|transcript|ENST00000355717.9|protein_coding|1/13|c.21T>A|p.Gly7Gly|192/1979|21/1470|7/489||,A|synonymous_variant|LOW|TCF7L2|ENSG00000148737|transcript|ENST00000352065.10|protein_coding|1/15|c.21T>A|p.Gly7Gly|118/1553|21/1380|7/459||,A|synonymous_variant|LOW|TCF7L2|ENSG00000148737|transcript|ENST00000545257.6|protein_coding|1/15|c.21T>A|p.Gly7Gly|114/2160|21/1431|7/476||,A|synonymous_variant|LOW|TCF7L2|ENSG00000148737|transcript|ENST00000629706.2|protein_coding|1/13|c.21T>A|p.Gly7Gly|21/1755|21/1755|7/584||,A|synonymous_variant|LOW|TCF7L2|ENSG00000148737|transcript|ENST00000369395.6|protein_coding|1/15|c.21T>A|p.Gly7Gly|118/1541|21/1368|7/455||,A|5_prime_UTR_variant|MODIFIER|TCF7L2|ENSG00000148737|transcript|ENST00000542695.5|protein_coding|1/15|c.-298T>A|||||768|,A|upstream_gene_variant|MODIFIER|TCF7L2|ENSG00000148737|transcript|ENST00000346198.5|protein_coding||c.-139T>A|||||139|WARNING_TRANSCRIPT_INCOMPLETE,A|non_coding_transcript_exon_variant|MODIFIER|RP11-57H14.2|ENSG00000233547|transcript|ENST00000369391.3|antisense|2/2|n.329A>T||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:1483:1392:45103:61:912:0,-355.306,-3973.74\\t0/0:99:760:708:24073:29:444:0,-181.888,-2124.43\n14\\t50428753\\t.\\tT\\tC\\t2.001E-14\\tPASS\\tSSC=155.498;TYPE=snp;ANN=C|splice_region_variant&synonymous_variant|LOW|MAP4K5|ENSG00000012983|transcript|ENST00000013125.8|protein_coding|29/32|c.2235A>G|p.Lys745Lys|2554/4354|2235/2541|745/846||,C|splice_region_variant&non_coding_transcript_exon_variant|LOW|MAP4K5|ENSG00000012983|transcript|ENST00000554990.5|retained_intron|15/18|n.2988A>G||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:935:913:31825:22:289:0,-255.322,-2835.73\\t0/0:99:376:365:12759:11:147:0,-99.8239,-1134.2\n19\\t50416471\\t.\\tC\\tT\\t0.0\\tPASS\\tSSC=124.579;TYPE=snp;ANN=T|missense_variant|MODERATE|POLD1|ENSG00000062822|transcript|ENST00000595904.5|protein_coding|22/26|c.2974C>T|p.Leu992Phe|2974/3402|2974/3402|992/1133||,T|missense_variant|MODERATE|POLD1|ENSG00000062822|transcript|ENST00000440232.6|protein_coding|23/27|c.2896C>T|p.Leu966Phe|2949/3444|2896/3324|966/1107||,T|missense_variant|MODERATE|POLD1|ENSG00000062822|transcript|ENST00000599857.5|protein_coding|23/27|c.2896C>T|p.Leu966Phe|2940/3435|2896/3324|966/1107||,T|missense_variant|MODERATE|CTD-2545M3.6|ENSG00000142539|transcript|ENST00000599632.1|protein_coding|2/10|c.103C>T|p.Leu35Phe|104/1265|103/1191|35/396||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|POLD1|ENSG00000062822|transcript|ENST00000613923.4|protein_coding|23/27|c.2974C>T|p.Leu992Phe|3043/3542|2974/3402|992/1133||,T|missense_variant|MODERATE|POLD1|ENSG00000062822|transcript|ENST00000593407.5|protein_coding|6/8|c.676C>T|p.Leu226Phe|677/867|676/866|226/287||WARNING_TRANSCRIPT_INCOMPLETE,T|missense_variant|MODERATE|POLD1|ENSG00000062822|transcript|ENST00000593981.1|protein_coding|5/8|c.520C>T|p.Leu174Phe|522/873|520/871|174/289||WARNING_TRANSCRIPT_INCOMPLETE,T|upstream_gene_variant|MODIFIER|SPIB|ENSG00000269404|transcript|ENST00000595883.5|protein_coding||c.-2492C>T|||||2467|,T|upstream_gene_variant|MODIFIER|SPIB|ENSG00000269404|transcript|ENST00000270632.7|protein_coding||c.-2492C>T|||||2487|,T|upstream_gene_variant|MODIFIER|POLD1|ENSG00000062822|transcript|ENST00000596221.1|retained_intron||n.-482C>T|||||482|,T|upstream_gene_variant|MODIFIER|SPIB|ENSG00000269404|transcript|ENST00000439922.6|protein_coding||c.-2550C>T|||||2467|,T|upstream_gene_variant|MODIFIER|SPIB|ENSG00000269404|transcript|ENST00000596074.5|protein_coding||c.-2492C>T|||||2470|,T|upstream_gene_variant|MODIFIER|SPIB|ENSG00000269404|transcript|ENST00000594685.1|protein_coding||c.-2492C>T|||||2483|WARNING_TRANSCRIPT_INCOMPLETE,T|upstream_gene_variant|MODIFIER|SPIB|ENSG00000269404|transcript|ENST00000599923.5|retained_intron||n.-2468C>T|||||2468|,T|upstream_gene_variant|MODIFIER|SPIB|ENSG00000269404|transcript|ENST00000594188.1|retained_intron||n.-2470C>T|||||2470|,T|upstream_gene_variant|MODIFIER|SPIB|ENSG00000269404|transcript|ENST00000597855.5|protein_coding||c.-2492C>T|||||2470|,T|downstream_gene_variant|MODIFIER|POLD1|ENSG00000062822|transcript|ENST00000596425.1|protein_coding||c.*2970C>T|||||2970|WARNING_TRANSCRIPT_INCOMPLETE,T|non_coding_transcript_exon_variant|MODIFIER|POLD1|ENSG00000062822|transcript|ENST00000600859.5|nonsense_mediated_decay|22/26|n.2793C>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|POLD1|ENSG00000062822|transcript|ENST00000597963.5|retained_intron|1/4|n.159C>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|POLD1|ENSG00000062822|transcript|ENST00000596648.1|retained_intron|2/4|n.830C>T||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:476:476:18787:0:0:0,-143.29,-1689.23\\t0/0:99:88:86:3411:2:82:0,-18.711,-299.241\n16\\t4337131\\t.\\tT\\tTG\\t0.0\\tPASS\\tSSC=283.339;TYPE=ins;OLD_MULTIALLELIC=16:4337131:TGGGGGGGGCAT/TGGGGGGGGGCAT/GGGGGGGGGCAT;OLD_VARIANT=16:4337131:TGGGGGGGGCAT/TGGGGGGGGGCAT;ANN=TG|frameshift_variant|HIGH|GLIS2|ENSG00000126603|transcript|ENST00000433375.1|protein_coding|6/6|c.1190dupG|p.Met398fs|1248/3705|1191/1575|397/524||INFO_REALIGN_3_PRIME,TG|frameshift_variant|HIGH|GLIS2|ENSG00000126603|transcript|ENST00000262366.7|protein_coding|8/8|c.1190dupG|p.Met398fs|2012/4469|1191/1575|397/524||INFO_REALIGN_3_PRIME,TG|downstream_gene_variant|MODIFIER|PAM16|ENSG00000217930|transcript|ENST00000318059.7|protein_coding||c.*3187dupC|||||3116|,TG|downstream_gene_variant|MODIFIER|PAM16|ENSG00000217930|transcript|ENST00000573236.5|retained_intron||n.*3117dupC|||||3117|,TG|downstream_gene_variant|MODIFIER|CORO7-PAM16|ENSG00000103426|transcript|ENST00000572467.5|protein_coding||c.*3187dupC|||||3119|,TG|downstream_gene_variant|MODIFIER|PAM16|ENSG00000217930|transcript|ENST00000573450.5|processed_transcript||n.*3119dupC|||||3119|,TG|downstream_gene_variant|MODIFIER|PAM16|ENSG00000217930|transcript|ENST00000573553.5|protein_coding||c.*3187dupC|||||3119|,TG|downstream_gene_variant|MODIFIER|CORO7-PAM16|ENSG00000103426|transcript|ENST00000575334.5|nonsense_mediated_decay||n.*4860dupC|||||3119|,TG|downstream_gene_variant|MODIFIER|PAM16|ENSG00000217930|transcript|ENST00000571941.5|protein_coding||c.*3187dupC|||||3119|,TG|downstream_gene_variant|MODIFIER|PAM16|ENSG00000217930|transcript|ENST00000575848.5|protein_coding||c.*3187dupC|||||3119|,TG|downstream_gene_variant|MODIFIER|PAM16|ENSG00000217930|transcript|ENST00000575636.5|nonsense_mediated_decay||n.*3458dupC|||||3119|,TG|downstream_gene_variant|MODIFIER|PAM16|ENSG00000217930|transcript|ENST00000571986.5|nonsense_mediated_decay||n.*3458dupC|||||3119|,TG|downstream_gene_variant|MODIFIER|PAM16|ENSG00000217930|transcript|ENST00000571178.1|nonsense_mediated_decay||n.*3360dupC|||||3186|,TG|downstream_gene_variant|MODIFIER|PAM16|ENSG00000217930|transcript|ENST00000573614.5|processed_transcript||n.*3119dupC|||||3119|,TG|downstream_gene_variant|MODIFIER|PAM16|ENSG00000217930|transcript|ENST00000576217.1|protein_coding||c.*3187dupC|||||3119|,TG|downstream_gene_variant|MODIFIER|CORO7-PAM16|ENSG00000103426|transcript|ENST00000572274.1|processed_transcript||n.*3809dupC|||||3809|,TG|downstream_gene_variant|MODIFIER|PAM16|ENSG00000217930|transcript|ENST00000571819.1|processed_transcript||n.*4520dupC|||||4520|,TG|intron_variant|MODIFIER|PAM16|ENSG00000217930|transcript|ENST00000577031.5|protein_coding|4/4|c.291+3788dupC||||||,TG|non_coding_transcript_exon_variant|MODIFIER|RP11-295D4.1|ENSG00000262712|transcript|ENST00000574705.1|sense_intronic|1/1|n.687dupC||||||;LOF=(GLIS2|ENSG00000126603|2|1.00)\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:994:923:36342:33:1111:0,-322.811,-3219.44\\t0/0:99:105:93:3665:3:123:0,-39.4717,-325.383\n12\\t49051739\\t.\\tA\\tT\\t1.16443E-13\\tPASS\\tSSC=411.947;TYPE=snp;ANN=T|synonymous_variant|LOW|KMT2D|ENSG00000167548|transcript|ENST00000301067.11|protein_coding|10/54|c.1944T>A|p.Pro648Pro|1944/19419|1944/16614|648/5537||,T|downstream_gene_variant|MODIFIER|KMT2D|ENSG00000167548|transcript|ENST00000547610.1|protein_coding||c.*2641T>A|||||2641|WARNING_TRANSCRIPT_INCOMPLETE\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:2176:2063:71414:100:1355:0,-529.173,-6298.78\\t0/0:99:442:428:14910:12:169:0,-117.226,-1325.59\n9\\t21971181\\t.\\tC\\tT\\t2.57703E-15\\tPASS\\tSSC=81.231;TYPE=snp;ANN=T|missense_variant|MODERATE|CDKN2A|ENSG00000147889|transcript|ENST00000498124.1|protein_coding|2/4|c.178G>A|p.Ala60Thr|217/880|178/504|60/167||,T|missense_variant|MODERATE|CDKN2A|ENSG00000147889|transcript|ENST00000304494.9|protein_coding|2/3|c.178G>A|p.Ala60Thr|449/1218|178/471|60/156||,T|missense_variant|MODERATE|CDKN2A|ENSG00000147889|transcript|ENST00000579755.1|protein_coding|2/3|c.221G>A|p.Gly74Asp|514/1283|221/399|74/132||,T|missense_variant|MODERATE|CDKN2A|ENSG00000147889|transcript|ENST00000578845.2|protein_coding|1/2|c.25G>A|p.Ala9Thr|152/678|25/318|9/105||,T|missense_variant|MODERATE|CDKN2A|ENSG00000147889|transcript|ENST00000498628.6|protein_coding|2/3|c.25G>A|p.Ala9Thr|509/926|25/318|9/105||,T|missense_variant|MODERATE|CDKN2A|ENSG00000147889|transcript|ENST00000579122.1|protein_coding|2/3|c.178G>A|p.Ala60Thr|209/666|178/417|60/138||,T|missense_variant|MODERATE|CDKN2A|ENSG00000147889|transcript|ENST00000494262.5|protein_coding|3/4|c.25G>A|p.Ala9Thr|649/989|25/318|9/105||,T|missense_variant|MODERATE|CDKN2A|ENSG00000147889|transcript|ENST00000497750.1|protein_coding|2/2|c.25G>A|p.Ala9Thr|100/565|25/315|9/104||,T|missense_variant|MODERATE|CDKN2A|ENSG00000147889|transcript|ENST00000530628.2|protein_coding|2/3|c.221G>A|p.Gly74Asp|301/748|221/399|74/132||,T|missense_variant|MODERATE|CDKN2A|ENSG00000147889|transcript|ENST00000479692.2|protein_coding|2/3|c.25G>A|p.Ala9Thr|40/544|25/366|9/121||,T|3_prime_UTR_variant|MODIFIER|CDKN2A|ENSG00000147889|transcript|ENST00000380151.3|nonsense_mediated_decay|2/3|n.*101G>A|||||3296|,T|upstream_gene_variant|MODIFIER|CDKN2A|ENSG00000147889|transcript|ENST00000577854.1|processed_transcript||n.-714G>A|||||714|,T|downstream_gene_variant|MODIFIER|CDKN2A-AS1|ENSG00000224854|transcript|ENST00000441769.3|lincRNA||n.*3430C>T|||||3430|,T|intron_variant|MODIFIER|RP11-145E5.5|ENSG00000264545|transcript|ENST00000404796.2|nonsense_mediated_decay|4/5|n.348-58252C>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|CDKN2A|ENSG00000147889|transcript|ENST00000380151.3|nonsense_mediated_decay|2/3|n.*101G>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|CDKN2A|ENSG00000147889|transcript|ENST00000380150.2|processed_transcript|1/2|n.152G>A||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:307:306:12215:0:0:0,-92.1152,-1098.27\\t0/0:99:62:60:2387:2:82:0,-10.8842,-207.182\n5\\t87383752\\t.\\tG\\tC\\t6.08732E-15\\tPASS\\tSSC=53.614;TYPE=snp;ANN=C|synonymous_variant|LOW|RASA1|ENSG00000145715|transcript|ENST00000274376.10|protein_coding|21/25|c.2730G>C|p.Leu910Leu|3294/3752|2730/3144|910/1047||,C|synonymous_variant|LOW|RASA1|ENSG00000145715|transcript|ENST00000456692.6|protein_coding|21/25|c.2199G>C|p.Leu733Leu|2314/3776|2199/2613|733/870||,C|synonymous_variant|LOW|RASA1|ENSG00000145715|transcript|ENST00000512763.5|protein_coding|22/26|c.2229G>C|p.Leu743Leu|2430/3060|2229/2643|743/880||,C|synonymous_variant|LOW|RASA1|ENSG00000145715|transcript|ENST00000506290.1|protein_coding|22/26|c.2232G>C|p.Leu744Leu|2349/3009|2232/2646|744/881||,C|3_prime_UTR_variant|MODIFIER|RASA1|ENSG00000145715|transcript|ENST00000515800.6|nonsense_mediated_decay|22/26|n.*1255G>C|||||17392|,C|non_coding_transcript_exon_variant|MODIFIER|RASA1|ENSG00000145715|transcript|ENST00000515800.6|nonsense_mediated_decay|22/26|n.*1255G>C||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:742:719:26782:17:204:0,-203.198,-2389.48\\t0/0:99:552:536:20533:14:178:0,-149.584,-1829.98\n19\\t38395985\\t.\\tC\\tG\\t3.49569E-14\\tPASS\\tSSC=101.701;TYPE=snp;ANN=G|missense_variant|MODERATE|SPRED3|ENSG00000188766|transcript|ENST00000338502.8|protein_coding|5/5|c.1073C>G|p.Pro358Arg|1176/4778|1073/1233|358/410||,G|missense_variant|MODERATE|SPRED3|ENSG00000188766|transcript|ENST00000587013.5|protein_coding|5/5|c.1205C>G|p.Pro402Arg|1283/1539|1205/1365|402/454||,G|missense_variant|MODERATE|SPRED3|ENSG00000188766|transcript|ENST00000586301.5|protein_coding|6/6|c.1073C>G|p.Pro358Arg|1203/1366|1073/1233|358/410||,G|downstream_gene_variant|MODIFIER|SPRED3|ENSG00000188766|transcript|ENST00000587564.2|processed_transcript||n.*1509C>G|||||1509|,G|downstream_gene_variant|MODIFIER|SPRED3|ENSG00000188766|transcript|ENST00000586958.1|nonsense_mediated_decay||n.*1423C>G|||||1315|,G|downstream_gene_variant|MODIFIER|SPRED3|ENSG00000188766|transcript|ENST00000587947.5|protein_coding||c.*1222C>G|||||1222|WARNING_TRANSCRIPT_INCOMPLETE,G|downstream_gene_variant|MODIFIER|SPRED3|ENSG00000188766|transcript|ENST00000590962.1|retained_intron||n.*3338C>G|||||3338|\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:369:369:14689:0:0:0,-111.08,-1320.79\\t0/0:99:57:55:2167:2:82:0,-9.37903,-187.417\n11\\t65599516\\t.\\tAGC\\tGGG\\t9.52344E-15\\tPASS\\tSSC=163.894;TYPE=complex;OLD_MULTIALLELIC=11:65599516:AGC/GGG/GGC;ANN=GGG|missense_variant|MODERATE|MAP3K11|ENSG00000173327|transcript|ENST00000309100.7|protein_coding|9/10|c.2082_2084delGCTinsCCC|p.Leu695Pro|2570/3566|2082/2544|694/847||,GGG|missense_variant|MODERATE|MAP3K11|ENSG00000173327|transcript|ENST00000532507.5|protein_coding|4/5|c.330_332delGCTinsCCC|p.Leu111Pro|817/1812|330/792|110/263||,GGG|missense_variant|MODERATE|MAP3K11|ENSG00000173327|transcript|ENST00000530153.5|protein_coding|9/10|c.1311_1313delGCTinsCCC|p.Leu438Pro|1835/2830|1311/1773|437/590||,GGG|3_prime_UTR_variant|MODIFIER|MAP3K11|ENSG00000173327|transcript|ENST00000524848.5|nonsense_mediated_decay|8/9|n.*550_*552delGCTinsCCC|||||7244|,GGG|upstream_gene_variant|MODIFIER|KCNK7|ENSG00000173338|transcript|ENST00000340313.4|protein_coding||c.-3746_-3744delGCTinsCCC|||||3520|,GGG|upstream_gene_variant|MODIFIER|KCNK7|ENSG00000173338|transcript|ENST00000342202.8|protein_coding||c.-3746_-3744delGCTinsCCC|||||3708|,GGG|upstream_gene_variant|MODIFIER|KCNK7|ENSG00000173338|transcript|ENST00000394216.6|protein_coding||c.-3746_-3744delGCTinsCCC|||||3520|,GGG|upstream_gene_variant|MODIFIER|KCNK7|ENSG00000173338|transcript|ENST00000394217.6|protein_coding||c.-3746_-3744delGCTinsCCC|||||3520|,GGG|non_coding_transcript_exon_variant|MODIFIER|MAP3K11|ENSG00000173327|transcript|ENST00000524848.5|nonsense_mediated_decay|8/9|n.*550_*552delGCTinsCCC||||||,GGG|non_coding_transcript_exon_variant|MODIFIER|MAP3K11|ENSG00000173327|transcript|ENST00000534432.1|processed_transcript|5/5|n.597_599delGCTinsCCC||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:803:745:27288:17:236:0,-213.21,-2457.46\\t0/0:99:171:163:6033:2:24:0,-49.3161,-552.777\n17\\t39530715\\t.\\tA\\tT\\t0.0\\tPASS\\tSSC=450.606;TYPE=snp;ANN=T|missense_variant|MODERATE|CDK12|ENSG00000167258|transcript|ENST00000447079.4|protein_coding|14/14|c.3872A>T|p.Gln1291Leu|3905/8336|3872/4473|1291/1490||,T|missense_variant|MODERATE|CDK12|ENSG00000167258|transcript|ENST00000430627.6|protein_coding|14/14|c.3845A>T|p.Gln1282Leu|4156/5918|3845/4446|1282/1481||,T|downstream_gene_variant|MODIFIER|CDK12|ENSG00000167258|transcript|ENST00000584632.5|protein_coding||c.*4552A>T|||||4552|WARNING_TRANSCRIPT_INCOMPLETE,T|intron_variant|MODIFIER|CDK12|ENSG00000167258|transcript|ENST00000559663.1|nonsense_mediated_decay|1/4|n.448+4399A>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|CDK12|ENSG00000167258|transcript|ENST00000584336.1|retained_intron|1/1|n.834A>T||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:2289:2218:80248:70:880:0,-609.552,-7135.65\\t0/0:99:579:567:21001:12:169:0,-158.946,-1873.01\n19\\t18768684\\t.\\tT\\tA\\t0.0\\tPASS\\tSSC=168.819;TYPE=snp;ANN=A|missense_variant|MODERATE|CRTC1|ENSG00000105662|transcript|ENST00000338797.10|protein_coding|11/15|c.1259T>A|p.Leu420Gln|1284/6929|1259/1953|420/650||,A|missense_variant|MODERATE|CRTC1|ENSG00000105662|transcript|ENST00000321949.12|protein_coding|10/14|c.1211T>A|p.Leu404Gln|1237/2501|1211/1905|404/634||,A|missense_variant|MODERATE|CRTC1|ENSG00000105662|transcript|ENST00000594658.5|protein_coding|10/14|c.1088T>A|p.Leu363Gln|1120/2384|1088/1782|363/593||,A|intron_variant|MODIFIER|CRTC1|ENSG00000105662|transcript|ENST00000601916.1|protein_coding|8/9|c.786+3156T>A||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:805:771:28444:34:488:0,-198.271,-2513.49\\t0/0:99:109:106:4015:3:36:0,-29.4523,-357.979\n9\\t93308569\\t.\\tT\\tG\\t3.0256E-14\\tPASS\\tSSC=79.0426;TYPE=snp;ANN=G|synonymous_variant|LOW|WNK2|ENSG00000165238|transcript|ENST00000297954.8|protein_coding|28/30|c.6612T>G|p.Pro2204Pro|6612/7138|6612/6894|2204/2297||,G|synonymous_variant|LOW|WNK2|ENSG00000165238|transcript|ENST00000432730.5|protein_coding|27/29|c.6486T>G|p.Pro2162Pro|6488/7792|6486/6660|2162/2219||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|WNK2|ENSG00000165238|transcript|ENST00000411624.5|protein_coding|21/22|c.4974T>G|p.Pro1658Pro|4975/6679|4974/5319|1658/1772||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|WNK2|ENSG00000165238|transcript|ENST00000448251.5|protein_coding|13/15|c.2889T>G|p.Pro963Pro|2891/3224|2889/3042|963/1013||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|WNK2|ENSG00000165238|transcript|ENST00000395477.6|protein_coding|27/29|c.6501T>G|p.Pro2167Pro|6501/6834|6501/6654|2167/2217||,G|synonymous_variant|LOW|WNK2|ENSG00000165238|transcript|ENST00000453718.2|protein_coding|7/7|c.1920T>G|p.Pro640Pro|1922/1937|1920/1935|640/644||WARNING_TRANSCRIPT_NO_START_CODON,G|non_coding_transcript_exon_variant|MODIFIER|WNK2|ENSG00000165238|transcript|ENST00000467401.1|retained_intron|1/3|n.1933T>G||||||,G|non_coding_transcript_exon_variant|MODIFIER|WNK2|ENSG00000165238|transcript|ENST00000474009.5|processed_transcript|3/3|n.542T>G||||||,G|non_coding_transcript_exon_variant|MODIFIER|WNK2|ENSG00000165238|transcript|ENST00000460335.1|processed_transcript|1/2|n.69T>G||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:409:392:14685:17:234:0,-101.925,-1299.31\\t0/0:99:80:79:3079:1:12:0,-22.8824,-275.97\n19\\t38483504\\t.\\tC\\tT\\t0.0\\tPASS\\tSSC=83.6393;TYPE=snp;ANN=T|missense_variant|MODERATE|RYR1|ENSG00000196218|transcript|ENST00000355481.8|protein_coding|33/105|c.4922C>T|p.Pro1641Leu|5053/15377|4922/15102|1641/5033||,T|missense_variant|MODERATE|RYR1|ENSG00000196218|transcript|ENST00000359596.7|protein_coding|33/106|c.4922C>T|p.Pro1641Leu|4922/15117|4922/15117|1641/5038||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:296:296:11759:0:0:0,-89.1049,-1057.44\\t0/0:99:44:42:1608:2:82:0,-5.46564,-137.159\n6\\t42268688\\t.\\tC\\tA\\t0.00281751\\tPASS\\tSSC=17.1642;TYPE=snp;ANN=A|missense_variant|MODERATE|TRERF1|ENSG00000124496|transcript|ENST00000541110.5|protein_coding|5/18|c.903G>T|p.Gln301His|1472/7646|903/3663|301/1220||,A|missense_variant|MODERATE|TRERF1|ENSG00000124496|transcript|ENST00000372922.8|protein_coding|5/18|c.903G>T|p.Gln301His|1466/7286|903/3603|301/1200||,A|missense_variant|MODERATE|TRERF1|ENSG00000124496|transcript|ENST00000372917.8|protein_coding|5/17|c.420G>T|p.Gln140His|1244/3914|420/2871|140/956||,A|missense_variant|MODERATE|TRERF1|ENSG00000124496|transcript|ENST00000340840.6|protein_coding|4/16|c.903G>T|p.Gln301His|1491/4174|903/3390|301/1129||,A|missense_variant|MODERATE|TRERF1|ENSG00000124496|transcript|ENST00000354325.2|protein_coding|4/16|c.903G>T|p.Gln301His|1491/4138|903/3354|301/1117||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:43:43:1702:0:0:0,-12.9443,-153.397\\t0/1:0.00281751:9:7:273:2:73:-4.21992,0,-22.2207\n2\\t131264040\\t.\\tC\\tT\\t0.0\\tPASS\\tSSC=64.5985;TYPE=snp;ANN=T|missense_variant|MODERATE|POTEE|ENSG00000188219|transcript|ENST00000356920.9|protein_coding|15/15|c.2585C>T|p.Thr862Ile|2921/4159|2585/3228|862/1075||,T|downstream_gene_variant|MODIFIER|POTEE|ENSG00000188219|transcript|ENST00000358087.9|nonsense_mediated_decay||n.*1359C>T|||||449|,T|downstream_gene_variant|MODIFIER|POTEE|ENSG00000188219|transcript|ENST00000514256.5|nonsense_mediated_decay||n.*1338C>T|||||449|,T|downstream_gene_variant|MODIFIER|POTEE|ENSG00000188219|transcript|ENST00000626191.1|protein_coding||c.*1293C>T|||||449|,T|downstream_gene_variant|MODIFIER|POTEE|ENSG00000188219|transcript|ENST00000613282.3|protein_coding||c.*687C>T|||||340|,T|intron_variant|MODIFIER|PLEKHB2|ENSG00000115762|transcript|ENST00000404460.5|protein_coding|6/6|c.424-88980C>T||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:226:224:8976:0:0:0,-67.4307,-723.002\\t0/0:99:34:32:1286:2:78:0,-2.83224,-99.6752\n3\\t65379364\\t.\\tG\\tT\\t1.23661E-6\\tPASS\\tSSC=19.5198;TYPE=snp;ANN=T|synonymous_variant|LOW|MAGI1|ENSG00000151276|transcript|ENST00000402939.6|protein_coding|17/23|c.2892C>A|p.Thr964Thr|2892/4389|2892/4389|964/1462||,T|synonymous_variant|LOW|MAGI1|ENSG00000151276|transcript|ENST00000330909.12|protein_coding|18/25|c.2976C>A|p.Thr992Thr|2976/7415|2976/3864|992/1287||,T|synonymous_variant|LOW|MAGI1|ENSG00000151276|transcript|ENST00000611645.4|protein_coding|17/24|c.2055C>A|p.Thr685Thr|2665/6398|2055/2943|685/980||,T|synonymous_variant|LOW|MAGI1|ENSG00000151276|transcript|ENST00000621418.4|protein_coding|16/22|c.1971C>A|p.Thr657Thr|2581/6225|1971/3468|657/1155||,T|synonymous_variant|LOW|MAGI1|ENSG00000151276|transcript|ENST00000483466.5|protein_coding|18/23|c.2976C>A|p.Thr992Thr|3218/4791|2976/3771|992/1256||,T|synonymous_variant|LOW|MAGI1|ENSG00000151276|transcript|ENST00000463103.6|protein_coding|17/22|c.2601C>A|p.Thr867Thr|2601/4193|2601/3396|867/1131||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|MAGI1|ENSG00000151276|transcript|ENST00000460329.6|protein_coding|17/22|c.2616C>A|p.Thr872Thr|2618/3694|2616/3408|872/1135||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|MAGI1|ENSG00000151276|transcript|ENST00000497477.6|protein_coding|17/21|c.2892C>A|p.Thr964Thr|2892/3555|2892/3483|964/1160||,T|synonymous_variant|LOW|MAGI1|ENSG00000151276|transcript|ENST00000472257.5|protein_coding|14/19|c.2250C>A|p.Thr750Thr|2250/3045|2250/3045|750/1014||WARNING_TRANSCRIPT_NO_START_CODON,T|non_coding_transcript_exon_variant|MODIFIER|MAGI1|ENSG00000151276|transcript|ENST00000468159.1|retained_intron|6/6|n.952C>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|MAGI1|ENSG00000151276|transcript|ENST00000480729.1|processed_transcript|2/3|n.281C>A||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:55:55:2178:0:0:0,-16.5566,-196.178\\t0/1:1.23661e-06:16:14:566:2:82:-2.9632,0,-46.4647\n11\\t64766958\\t.\\tC\\tT\\t1.20541E-16\\tPASS\\tSSC=114.106;TYPE=snp;ANN=T|missense_variant|MODERATE|SF1|ENSG00000168066|transcript|ENST00000377394.7|protein_coding|12/13|c.1528G>A|p.Ala510Thr|1883/2854|1528/1716|510/571||,T|missense_variant|MODERATE|SF1|ENSG00000168066|transcript|ENST00000413725.5|protein_coding|3/4|c.232G>A|p.Ala78Thr|233/843|232/540|78/179||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|SF1|ENSG00000168066|transcript|ENST00000486867.1|protein_coding|5/6|c.682G>A|p.Ala228Thr|682/875|682/875|228/290||WARNING_TRANSCRIPT_INCOMPLETE,T|synonymous_variant|LOW|SF1|ENSG00000168066|transcript|ENST00000377387.5|protein_coding|12/13|c.1899G>A|p.Pro633Pro|1976/2947|1899/2022|633/673||,T|synonymous_variant|LOW|SF1|ENSG00000168066|transcript|ENST00000377390.7|protein_coding|12/13|c.1524G>A|p.Pro508Pro|1862/3470|1524/1920|508/639||,T|synonymous_variant|LOW|SF1|ENSG00000168066|transcript|ENST00000227503.13|protein_coding|12/13|c.1524G>A|p.Pro508Pro|1879/2850|1524/1647|508/548||,T|synonymous_variant|LOW|SF1|ENSG00000168066|transcript|ENST00000334944.9|protein_coding|12/14|c.1524G>A|p.Pro508Pro|1918/3094|1524/1917|508/638||,T|synonymous_variant|LOW|SF1|ENSG00000168066|transcript|ENST00000433274.6|protein_coding|12/13|c.1446G>A|p.Pro482Pro|1755/2317|1446/1842|482/613||,T|synonymous_variant|LOW|SF1|ENSG00000168066|transcript|ENST00000443908.5|protein_coding|3/4|c.480G>A|p.Pro160Pro|480/767|480/603|160/200||WARNING_TRANSCRIPT_NO_START_CODON,T|3_prime_UTR_variant|MODIFIER|SF1|ENSG00000168066|transcript|ENST00000448404.5|nonsense_mediated_decay|11/12|n.*1119G>A|||||3076|,T|downstream_gene_variant|MODIFIER|SF1|ENSG00000168066|transcript|ENST00000489544.1|processed_transcript||n.*1213G>A|||||1213|,T|downstream_gene_variant|MODIFIER|SF1|ENSG00000168066|transcript|ENST00000486960.5|retained_intron||n.*2320G>A|||||2320|,T|downstream_gene_variant|MODIFIER|SF1|ENSG00000168066|transcript|ENST00000626028.1|protein_coding||c.*3076G>A|||||3076|,T|downstream_gene_variant|MODIFIER|SF1|ENSG00000168066|transcript|ENST00000413951.5|nonsense_mediated_decay||n.*3691G>A|||||3339|,T|downstream_gene_variant|MODIFIER|SF1|ENSG00000168066|transcript|ENST00000496969.1|processed_transcript||n.*2584G>A|||||2584|,T|downstream_gene_variant|MODIFIER|SF1|ENSG00000168066|transcript|ENST00000633899.1|processed_transcript||n.*3320G>A|||||3320|,T|downstream_gene_variant|MODIFIER|SF1|ENSG00000168066|transcript|ENST00000432725.1|protein_coding||c.*3422G>A|||||3422|WARNING_TRANSCRIPT_INCOMPLETE,T|non_coding_transcript_exon_variant|MODIFIER|SF1|ENSG00000168066|transcript|ENST00000448404.5|nonsense_mediated_decay|11/12|n.*1119G>A||||||,T|non_coding_transcript_exon_variant|MODIFIER|SF1|ENSG00000168066|transcript|ENST00000477596.1|retained_intron|3/3|n.258G>A||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:566:556:20885:10:130:0,-158.553,-1866.07\\t0/0:99:163:158:6152:4:48:0,-44.4469,-548.983\n21\\t10567752\\t.\\tAT\\tA\\t5.09165E-13\\tPASS\\tSSC=574.304;TYPE=del;OLD_VARIANT=21:10567752:ATTTTTTTTGAC/ATTTTTTTGAC;ANN=A|frameshift_variant|HIGH|TPTE|ENSG00000274391|transcript|ENST00000618007.4|protein_coding|11/24|c.537delT|p.Phe179fs|867/2150|537/1656|179/551||INFO_REALIGN_3_PRIME,A|frameshift_variant|HIGH|TPTE|ENSG00000274391|transcript|ENST00000622113.4|protein_coding|10/23|c.483delT|p.Phe161fs|835/2542|483/1602|161/533||INFO_REALIGN_3_PRIME,A|frameshift_variant|HIGH|TPTE|ENSG00000274391|transcript|ENST00000427445.6|protein_coding|9/22|c.423delT|p.Phe141fs|753/2036|423/1542|141/513||INFO_REALIGN_3_PRIME,A|frameshift_variant|HIGH|TPTE|ENSG00000274391|transcript|ENST00000612746.1|protein_coding|6/19|c.123delT|p.Phe41fs|591/1874|123/1242|41/413||INFO_REALIGN_3_PRIME,A|downstream_gene_variant|MODIFIER|TPTE|ENSG00000274391|transcript|ENST00000612957.4|protein_coding||c.*54delT|||||54|WARNING_TRANSCRIPT_INCOMPLETE,A|non_coding_transcript_exon_variant|MODIFIER|AL078471.5|ENSG00000273840|transcript|ENST00000612267.1|processed_transcript|20/32|n.2159delT||||||INFO_REALIGN_3_PRIME;LOF=(TPTE|ENSG00000274391|5|0.80)\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:3276:3076:122177:72:2867:0,-935.792,-11021.9\\t0/0:99:1256:1177:46810:26:1058:0,-361.488,-4223.02\n15\\t90890431\\t.\\tA\\tT\\t1.1542E-14\\tPASS\\tSSC=200.781;TYPE=snp;ANN=T|missense_variant|MODERATE|FES|ENSG00000182511|transcript|ENST00000328850.7|protein_coding|10/19|c.1267A>T|p.Thr423Ser|1409/2829|1267/2469|423/822||,T|missense_variant|MODERATE|FES|ENSG00000182511|transcript|ENST00000394300.7|protein_coding|8/17|c.1093A>T|p.Thr365Ser|1093/2302|1093/2295|365/764||,T|missense_variant|MODERATE|FES|ENSG00000182511|transcript|ENST00000444422.2|protein_coding|9/17|c.1267A>T|p.Thr423Ser|1267/2266|1267/2259|423/752||,T|missense_variant|MODERATE|FES|ENSG00000182511|transcript|ENST00000414248.6|protein_coding|9/17|c.1093A>T|p.Thr365Ser|1200/2327|1093/2085|365/694||,T|missense_variant|MODERATE|FES|ENSG00000182511|transcript|ENST00000394302.5|protein_coding|9/17|c.1093A>T|p.Thr365Ser|1178/2133|1093/2046|365/681||,T|downstream_gene_variant|MODIFIER|FES|ENSG00000182511|transcript|ENST00000470152.6|nonsense_mediated_decay||n.*1581A>T|||||1053|,T|downstream_gene_variant|MODIFIER|FES|ENSG00000182511|transcript|ENST00000481665.5|retained_intron||n.*4902A>T|||||4902|,T|downstream_gene_variant|MODIFIER|FES|ENSG00000182511|transcript|ENST00000452243.5|protein_coding||c.*3416A>T|||||3416|WARNING_TRANSCRIPT_INCOMPLETE,T|downstream_gene_variant|MODIFIER|FES|ENSG00000182511|transcript|ENST00000559355.5|protein_coding||c.*3222A>T|||||3222|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|FES|ENSG00000182511|transcript|ENST00000443697.1|protein_coding||c.*4889A>T|||||4889|WARNING_TRANSCRIPT_INCOMPLETE,T|downstream_gene_variant|MODIFIER|FES|ENSG00000182511|transcript|ENST00000494259.1|retained_intron||n.*492A>T|||||492|,T|downstream_gene_variant|MODIFIER|FES|ENSG00000182511|transcript|ENST00000497945.2|retained_intron||n.*1106A>T|||||1106|,T|non_coding_transcript_exon_variant|MODIFIER|FES|ENSG00000182511|transcript|ENST00000448367.5|processed_transcript|4/5|n.463A>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|FES|ENSG00000182511|transcript|ENST00000496379.5|retained_intron|3/5|n.341A>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|FES|ENSG00000182511|transcript|ENST00000462476.1|retained_intron|3/3|n.367A>T||||||,T|non_coding_transcript_exon_variant|MODIFIER|FES|ENSG00000182511|transcript|ENST00000464684.5|nonsense_mediated_decay|10/18|n.1267A>T||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:904:880:32880:17:227:0,-249.58,-2935.73\\t0/0:99:183:179:6954:4:68:0,-48.7986,-619.223\n9\\t130664844\\t.\\tC\\tG\\t0.0\\tPASS\\tSSC=108.925;TYPE=snp;ANN=G|missense_variant|MODERATE|PRDM12|ENSG00000130711|transcript|ENST00000253008.2|protein_coding|1/5|c.191C>G|p.Thr64Ser|251/2476|191/1104|64/367||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:381:381:15151:0:0:0,-114.692,-1362.33\\t0/0:99:45:43:1741:2:82:0,-5.76667,-149.116\n15\\t67827863\\t.\\tG\\tA\\t1.507E-15\\tPASS\\tSSC=298.045;TYPE=snp;ANN=A|missense_variant|MODERATE|SKOR1|ENSG00000188779|transcript|ENST00000341418.9|protein_coding|7/15|c.1855G>A|p.Glu619Lys|1855/3332|1855/2607|619/868||,A|missense_variant|MODERATE|SKOR1|ENSG00000188779|transcript|ENST00000380035.2|protein_coding|2/9|c.2035G>A|p.Glu679Lys|2093/3675|2035/2898|679/965||,A|missense_variant|MODERATE|SKOR1|ENSG00000188779|transcript|ENST00000554240.5|protein_coding|2/9|c.1918G>A|p.Glu640Lys|2032/3597|1918/2781|640/926||,A|missense_variant|MODERATE|SKOR1|ENSG00000188779|transcript|ENST00000554054.5|protein_coding|2/9|c.1951G>A|p.Glu651Lys|2038/3620|1951/2814|651/937||,A|upstream_gene_variant|MODIFIER|RP11-34F13.3|ENSG00000259410|transcript|ENST00000558889.5|lincRNA||n.-4862G>A|||||4862|\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:1076:1076:42423:0:0:0,-323.908,-3813.94\\t0/0:99:124:121:4901:3:123:0,-25.8629,-429.472\n14\\t95711797\\t.\\tG\\tA\\t3.05875E-14\\tPASS\\tSSC=107.617;TYPE=snp;ANN=A|synonymous_variant|LOW|TCL1A|ENSG00000100721|transcript|ENST00000402399.5|protein_coding|3/4|c.303C>T|p.Asp101Asp|433/1395|303/345|101/114||,A|synonymous_variant|LOW|TCL1A|ENSG00000100721|transcript|ENST00000554012.5|protein_coding|3/4|c.303C>T|p.Asp101Asp|433/1391|303/345|101/114||,A|synonymous_variant|LOW|TCL1A|ENSG00000100721|transcript|ENST00000555202.1|protein_coding|3/3|c.303C>T|p.Asp101Asp|367/717|303/345|101/114||,A|synonymous_variant|LOW|TCL1A|ENSG00000100721|transcript|ENST00000556450.5|protein_coding|3/4|c.303C>T|p.Asp101Asp|335/872|303/345|101/114||,A|synonymous_variant|LOW|TCL1A|ENSG00000100721|transcript|ENST00000557043.4|protein_coding|3/4|c.120C>T|p.Asp40Asp|226/980|120/162|40/53||,A|3_prime_UTR_variant|MODIFIER|TCL1A|ENSG00000100721|transcript|ENST00000555886.5|nonsense_mediated_decay|4/5|n.*386C>T|||||957|,A|3_prime_UTR_variant|MODIFIER|TCL1A|ENSG00000100721|transcript|ENST00000556156.1|nonsense_mediated_decay|3/4|n.*540C>T|||||957|,A|upstream_gene_variant|MODIFIER|RP11-164H13.1|ENSG00000257275|transcript|ENST00000556386.1|antisense||n.-3683G>A|||||3683|,A|intron_variant|MODIFIER|TCL1A|ENSG00000100721|transcript|ENST00000554119.5|nonsense_mediated_decay|2/2|n.*534+423C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|RP11-164H13.1|ENSG00000257275|transcript|ENST00000547644.6|antisense|1/3|n.51G>A||||||,A|non_coding_transcript_exon_variant|MODIFIER|TCL1A|ENSG00000100721|transcript|ENST00000555886.5|nonsense_mediated_decay|4/5|n.*386C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|TCL1A|ENSG00000100721|transcript|ENST00000553467.1|retained_intron|1/2|n.166C>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|RP11-164H13.1|ENSG00000257275|transcript|ENST00000553445.5|antisense|1/3|n.41G>A||||||,A|non_coding_transcript_exon_variant|MODIFIER|TCL1A|ENSG00000100721|transcript|ENST00000556156.1|nonsense_mediated_decay|3/4|n.*540C>T||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:451:449:17679:2:78:0,-128.362,-1582.21\\t0/0:99:107:104:4135:3:123:0,-20.7454,-360.63\n12\\t52428367\\t.\\tT\\tC\\t1.65146E-14\\tPASS\\tSSC=9.68008;TYPE=snp;ANN=C|missense_variant|MODERATE|KRT75|ENSG00000170454|transcript|ENST00000252245.5|protein_coding|7/9|c.1271A>G|p.Lys424Arg|1492/2324|1271/1656|424/551||,C|non_coding_transcript_exon_variant|MODIFIER|RP11-1020M18.10|ENSG00000257500|transcript|ENST00000548135.1|antisense|3/3|n.502T>C||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:72:70:2817:2:82:0,-13.8945,-245.835\\t0/0:99:14:14:555:0:0:0,-4.21442,-50.2823\n17\\t7890682\\t.\\tG\\tA\\t0.0\\tPASS\\tSSC=162.369;TYPE=snp;OLD_VARIANT=17:7890681:AG/AA;ANN=A|missense_variant|MODERATE|CHD3|ENSG00000170004|transcript|ENST00000358181.8|protein_coding|3/39|c.325G>A|p.Glu109Lys|535/7286|325/5901|109/1966||,A|missense_variant|MODERATE|CHD3|ENSG00000170004|transcript|ENST00000330494.11|protein_coding|3/40|c.325G>A|p.Glu109Lys|475/7328|325/6003|109/2000||,A|missense_variant|MODERATE|CHD3|ENSG00000170004|transcript|ENST00000380358.8|protein_coding|3/40|c.502G>A|p.Glu168Lys|503/7356|502/6180|168/2059||,A|upstream_gene_variant|MODIFIER|CHD3|ENSG00000170004|transcript|ENST00000572579.1|retained_intron||n.-2604G>A|||||2604|,A|upstream_gene_variant|MODIFIER|CHD3|ENSG00000170004|transcript|ENST00000571249.1|protein_coding||c.-3149G>A|||||3147|WARNING_TRANSCRIPT_INCOMPLETE,A|upstream_gene_variant|MODIFIER|CHD3|ENSG00000170004|transcript|ENST00000452447.1|protein_coding||c.-54G>A|||||53|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|CHD3|ENSG00000170004|transcript|ENST00000479080.1|retained_intron||n.-3872G>A|||||3872|,A|downstream_gene_variant|MODIFIER|CHD3|ENSG00000170004|transcript|ENST00000574022.1|processed_transcript||n.*77G>A|||||77|,A|non_coding_transcript_exon_variant|MODIFIER|CHD3|ENSG00000170004|transcript|ENST00000570758.1|processed_transcript|2/2|n.166G>A||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:1115:1081:38357:31:604:0,-285.873,-3393.65\\t0/0:99:493:477:17187:13:275:0,-123.504,-1519.68\n22\\t50249162\\t.\\tT\\tA\\t1.6876E-14\\tPASS\\tSSC=299;TYPE=snp;ANN=A|missense_variant|MODERATE|HDAC10|ENSG00000100429|transcript|ENST00000216271.9|protein_coding|8/20|c.697A>T|p.Met233Leu|1050/2687|697/2010|233/669||,A|missense_variant|MODERATE|HDAC10|ENSG00000100429|transcript|ENST00000349505.4|protein_coding|8/19|c.697A>T|p.Met233Leu|697/1950|697/1950|233/649||,A|missense_variant|MODERATE|HDAC10|ENSG00000100429|transcript|ENST00000448072.5|protein_coding|8/18|c.697A>T|p.Met233Leu|905/2133|697/1860|233/619||,A|3_prime_UTR_variant|MODIFIER|HDAC10|ENSG00000100429|transcript|ENST00000415993.5|nonsense_mediated_decay|7/18|n.*325A>T|||||902|,A|3_prime_UTR_variant|MODIFIER|HDAC10|ENSG00000100429|transcript|ENST00000626012.2|protein_coding|7/19|c.*309A>T|||||902|,A|upstream_gene_variant|MODIFIER|TUBGCP6|ENSG00000128159|transcript|ENST00000248846.9|protein_coding||c.-4703A>T|||||4598|,A|upstream_gene_variant|MODIFIER|TUBGCP6|ENSG00000128159|transcript|ENST00000439308.6|protein_coding||c.-4703A>T|||||4191|,A|upstream_gene_variant|MODIFIER|TUBGCP6|ENSG00000128159|transcript|ENST00000498611.5|retained_intron||n.-4170A>T|||||4170|,A|upstream_gene_variant|MODIFIER|HDAC10|ENSG00000100429|transcript|ENST00000475965.1|retained_intron||n.-707A>T|||||707|,A|upstream_gene_variant|MODIFIER|HDAC10|ENSG00000100429|transcript|ENST00000476310.5|retained_intron||n.-87A>T|||||87|,A|upstream_gene_variant|MODIFIER|HDAC10|ENSG00000100429|transcript|ENST00000497952.5|retained_intron||n.-1214A>T|||||1214|,A|upstream_gene_variant|MODIFIER|HDAC10|ENSG00000100429|transcript|ENST00000496235.5|retained_intron||n.-790A>T|||||790|,A|upstream_gene_variant|MODIFIER|HDAC10|ENSG00000100429|transcript|ENST00000471375.5|retained_intron||n.-122A>T|||||122|,A|downstream_gene_variant|MODIFIER|MAPK12|ENSG00000188130|transcript|ENST00000215659.12|protein_coding||c.*4239A>T|||||3741|,A|downstream_gene_variant|MODIFIER|MAPK12|ENSG00000188130|transcript|ENST00000395780.5|protein_coding||c.*4239A>T|||||3741|,A|downstream_gene_variant|MODIFIER|MAPK12|ENSG00000188130|transcript|ENST00000622558.4|protein_coding||c.*4239A>T|||||3741|,A|downstream_gene_variant|MODIFIER|MAPK12|ENSG00000188130|transcript|ENST00000497738.1|retained_intron||n.*4691A>T|||||4691|,A|downstream_gene_variant|MODIFIER|HDAC10|ENSG00000100429|transcript|ENST00000497483.1|processed_transcript||n.*957A>T|||||957|,A|downstream_gene_variant|MODIFIER|MAPK12|ENSG00000188130|transcript|ENST00000496942.5|retained_intron||n.*4619A>T|||||4619|,A|downstream_gene_variant|MODIFIER|MAPK12|ENSG00000188130|transcript|ENST00000482969.5|retained_intron||n.*4626A>T|||||4626|,A|downstream_gene_variant|MODIFIER|HDAC10|ENSG00000100429|transcript|ENST00000488270.1|retained_intron||n.*125A>T|||||125|,A|downstream_gene_variant|MODIFIER|HDAC10|ENSG00000100429|transcript|ENST00000482213.1|retained_intron||n.*1095A>T|||||1095|,A|downstream_gene_variant|MODIFIER|HDAC10|ENSG00000100429|transcript|ENST00000489424.5|processed_transcript||n.*697A>T|||||697|,A|downstream_gene_variant|MODIFIER|HDAC10|ENSG00000100429|transcript|ENST00000470965.1|processed_transcript||n.*706A>T|||||706|,A|downstream_gene_variant|MODIFIER|MAPK12|ENSG00000188130|transcript|ENST00000488504.5|retained_intron||n.*3741A>T|||||3741|,A|downstream_gene_variant|MODIFIER|MAPK12|ENSG00000188130|transcript|ENST00000467891.5|retained_intron||n.*3758A>T|||||3758|,A|intron_variant|MODIFIER|HDAC10|ENSG00000100429|transcript|ENST00000429374.5|nonsense_mediated_decay|5/13|n.*175+473A>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|HDAC10|ENSG00000100429|transcript|ENST00000415993.5|nonsense_mediated_decay|7/18|n.*325A>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|HDAC10|ENSG00000100429|transcript|ENST00000454936.5|nonsense_mediated_decay|8/16|n.697A>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|HDAC10|ENSG00000100429|transcript|ENST00000477814.5|retained_intron|1/10|n.47A>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|MAPK12|ENSG00000188130|transcript|ENST00000497036.5|processed_transcript|14/26|n.4969A>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|HDAC10|ENSG00000100429|transcript|ENST00000470378.1|retained_intron|1/3|n.42A>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|HDAC10|ENSG00000100429|transcript|ENST00000496909.5|processed_transcript|6/8|n.556A>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|HDAC10|ENSG00000100429|transcript|ENST00000483222.5|processed_transcript|7/19|n.744A>T||||||,A|non_coding_transcript_exon_variant|MODIFIER|HDAC10|ENSG00000100429|transcript|ENST00000498366.5|processed_transcript|7/19|n.806A>T||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:1398:1358:51345:37:603:0,-368.432,-4564.43\\t0/0:99:247:241:9044:4:48:0,-69.4324,-808.981\n4\\t87127027\\t.\\tG\\tT\\t1.20541E-13\\tPASS\\tSSC=198.588;TYPE=snp;ANN=T|missense_variant&splice_region_variant|MODERATE|AFF1|ENSG00000172493|transcript|ENST00000307808.10|protein_coding|14/20|c.2792G>T|p.Gly931Val|3212/9390|2792/3633|931/1210||,T|missense_variant&splice_region_variant|MODERATE|AFF1|ENSG00000172493|transcript|ENST00000395146.8|protein_coding|15/21|c.2813G>T|p.Gly938Val|3088/9285|2813/3657|938/1218||,T|missense_variant&splice_region_variant|MODERATE|AFF1|ENSG00000172493|transcript|ENST00000544085.5|protein_coding|16/23|c.2789G>T|p.Gly930Val|2801/3644|2789/3618|930/1205||,T|downstream_gene_variant|MODIFIER|AFF1|ENSG00000172493|transcript|ENST00000503369.1|retained_intron||n.*1750G>T|||||1750|\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:1300:1267:44359:33:516:0,-344.749,-3942.2\\t0/0:99:526:514:18264:11:132:0,-146.161,-1630.48\n2\\t37228986\\t.\\tA\\tG\\t0.0\\tPASS\\tSSC=220.397;TYPE=snp;ANN=G|synonymous_variant|LOW|CEBPZ|ENSG00000115816|transcript|ENST00000234170.9|protein_coding|2/16|c.207T>C|p.Asp69Asp|353/3463|207/3165|69/1054||,G|synonymous_variant|LOW|CEBPZ|ENSG00000115816|transcript|ENST00000446769.1|protein_coding|2/2|c.60T>C|p.Asp20Asp|148/526|60/438|20/145||WARNING_TRANSCRIPT_NO_STOP_CODON,G|upstream_gene_variant|MODIFIER|NDUFAF7|ENSG00000003509|transcript|ENST00000002125.8|protein_coding||c.-2720A>G|||||2680|,G|upstream_gene_variant|MODIFIER|NDUFAF7|ENSG00000003509|transcript|ENST00000336237.10|protein_coding||c.-2720A>G|||||2693|,G|upstream_gene_variant|MODIFIER|NDUFAF7|ENSG00000003509|transcript|ENST00000474154.5|retained_intron||n.-2677A>G|||||2677|,G|upstream_gene_variant|MODIFIER|NDUFAF7|ENSG00000003509|transcript|ENST00000469831.1|retained_intron||n.-2781A>G|||||2781|,G|upstream_gene_variant|MODIFIER|NDUFAF7|ENSG00000003509|transcript|ENST00000416653.5|protein_coding||c.-2921A>G|||||2781|WARNING_TRANSCRIPT_NO_STOP_CODON,G|upstream_gene_variant|MODIFIER|NDUFAF7|ENSG00000003509|transcript|ENST00000439218.5|protein_coding||c.-2965A>G|||||2834|WARNING_TRANSCRIPT_INCOMPLETE,G|upstream_gene_variant|MODIFIER|NDUFAF7|ENSG00000003509|transcript|ENST00000431821.5|protein_coding||c.-2796A>G|||||2703|WARNING_TRANSCRIPT_NO_STOP_CODON,G|upstream_gene_variant|MODIFIER|NDUFAF7|ENSG00000003509|transcript|ENST00000455230.5|nonsense_mediated_decay||n.-2720A>G|||||2645|,G|upstream_gene_variant|MODIFIER|NDUFAF7|ENSG00000003509|transcript|ENST00000483999.5|processed_transcript||n.-2790A>G|||||2790|,G|upstream_gene_variant|MODIFIER|NDUFAF7|ENSG00000003509|transcript|ENST00000432075.1|protein_coding||c.-3075A>G|||||2856|WARNING_TRANSCRIPT_NO_STOP_CODON\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:1561:1519:59283:41:591:0,-416.639,-5276.18\\t0/0:99:705:692:27124:12:174:0,-196.242,-2422.79\n19\\t18768666\\t.\\tT\\tA\\t0.0\\tPASS\\tSSC=95.7259;TYPE=snp;ANN=A|missense_variant|MODERATE|CRTC1|ENSG00000105662|transcript|ENST00000338797.10|protein_coding|11/15|c.1241T>A|p.Leu414Gln|1266/6929|1241/1953|414/650||,A|missense_variant|MODERATE|CRTC1|ENSG00000105662|transcript|ENST00000321949.12|protein_coding|10/14|c.1193T>A|p.Leu398Gln|1219/2501|1193/1905|398/634||,A|missense_variant|MODERATE|CRTC1|ENSG00000105662|transcript|ENST00000594658.5|protein_coding|10/14|c.1070T>A|p.Leu357Gln|1102/2384|1070/1782|357/593||,A|intron_variant|MODIFIER|CRTC1|ENSG00000105662|transcript|ENST00000601916.1|protein_coding|8/9|c.786+3138T>A||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:743:673:25017:67:1139:0,-120.21,-2146.77\\t0/0:99:101:97:3442:4:64:0,-24.4841,-303.882\n3\\t187725066\\t.\\tG\\tC\\t3.50176E-14\\tPASS\\tSSC=251.531;TYPE=snp;ANN=C|missense_variant|MODERATE|BCL6|ENSG00000113916|transcript|ENST00000232014.8|protein_coding|9/10|c.1852C>G|p.Arg618Gly|2381/2710|1852/2121|618/706||,C|missense_variant|MODERATE|BCL6|ENSG00000113916|transcript|ENST00000406870.6|protein_coding|9/10|c.1852C>G|p.Arg618Gly|2219/3569|1852/2121|618/706||,C|missense_variant|MODERATE|BCL6|ENSG00000113916|transcript|ENST00000450123.6|protein_coding|7/8|c.1684C>G|p.Arg562Gly|1708/2003|1684/1953|562/650||,C|missense_variant|MODERATE|BCL6|ENSG00000113916|transcript|ENST00000621333.4|protein_coding|8/9|c.1684C>G|p.Arg562Gly|2049/3399|1684/1953|562/650||,C|3_prime_UTR_variant|MODIFIER|BCL6|ENSG00000113916|transcript|ENST00000419510.6|nonsense_mediated_decay|9/10|n.*1622C>G|||||6796|,C|intron_variant|MODIFIER|RP11-211G3.3|ENSG00000228804|transcript|ENST00000449623.5|antisense|2/2|n.347-8458G>C||||||,C|intron_variant|MODIFIER|RP11-211G3.3|ENSG00000228804|transcript|ENST00000437407.1|antisense|2/2|n.294-7305G>C||||||,C|non_coding_transcript_exon_variant|MODIFIER|BCL6|ENSG00000113916|transcript|ENST00000419510.6|nonsense_mediated_decay|9/10|n.*1622C>G||||||,C|non_coding_transcript_exon_variant|MODIFIER|BCL6|ENSG00000113916|transcript|ENST00000479110.1|retained_intron|2/2|n.138C>G||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:1004:1002:39973:0:0:0,-301.632,-3593.14\\t0/0:99:229:224:8891:5:205:0,-50.1009,-780.789\n17\\t7847274\\t.\\tT\\tA\\t0.0\\tPASS\\tSSC=231.21;TYPE=snp;ANN=A|missense_variant|MODERATE|KDM6B|ENSG00000132510|transcript|ENST00000254846.9|protein_coding|10/22|c.1079T>A|p.Leu360His|1468/6713|1079/5049|360/1682||,A|missense_variant|MODERATE|KDM6B|ENSG00000132510|transcript|ENST00000448097.6|protein_coding|10/23|c.1079T>A|p.Leu360His|1410/5422|1079/4932|360/1643||,A|missense_variant|MODERATE|KDM6B|ENSG00000132510|transcript|ENST00000570632.1|protein_coding|8/9|c.881T>A|p.Leu294His|1135/1339|881/1085|294/360||WARNING_TRANSCRIPT_INCOMPLETE,A|downstream_gene_variant|MODIFIER|KDM6B|ENSG00000132510|transcript|ENST00000571047.5|processed_transcript||n.*1927T>A|||||1927|,A|downstream_gene_variant|MODIFIER|KDM6B|ENSG00000132510|transcript|ENST00000575521.1|processed_transcript||n.*2302T>A|||||2302|\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:1448:1359:49260:87:1196:0,-327.635,-4321.17\\t0/0:99:381:366:13261:13:196:0,-96.4245,-1174.77\n19\\t1615670\\t.\\tA\\tG\\t0.0\\tPASS\\tSSC=174.592;TYPE=snp;ANN=G|synonymous_variant|LOW|TCF3|ENSG00000071564|transcript|ENST00000395423.7|protein_coding|15/16|c.1449T>C|p.Pro483Pro|1793/2779|1449/1977|483/658||,G|downstream_gene_variant|MODIFIER|TCF3|ENSG00000071564|transcript|ENST00000590605.2|retained_intron||n.*121T>C|||||121|,G|downstream_gene_variant|MODIFIER|TCF3|ENSG00000071564|transcript|ENST00000586410.2|protein_coding||c.*141T>C|||||141|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|RNU6-1223P|ENSG00000252933|transcript|ENST00000517124.1|snRNA||n.*822T>C|||||822|,G|intron_variant|MODIFIER|TCF3|ENSG00000071564|transcript|ENST00000262965.9|protein_coding|17/18|c.1586+16T>C||||||,G|intron_variant|MODIFIER|TCF3|ENSG00000071564|transcript|ENST00000611869.4|protein_coding|16/17|c.1586+16T>C||||||,G|intron_variant|MODIFIER|TCF3|ENSG00000071564|transcript|ENST00000610756.4|retained_intron|8/9|n.944+16T>C||||||,G|intron_variant|MODIFIER|TCF3|ENSG00000071564|transcript|ENST00000593064.5|protein_coding|2/4|c.233+16T>C||||||WARNING_TRANSCRIPT_NO_START_CODON,G|intron_variant|MODIFIER|TCF3|ENSG00000071564|transcript|ENST00000587425.5|protein_coding|1/3|c.119+16T>C||||||WARNING_TRANSCRIPT_NO_START_CODON,G|intron_variant|MODIFIER|TCF3|ENSG00000071564|transcript|ENST00000585731.5|protein_coding|1/2|c.113+16T>C||||||WARNING_TRANSCRIPT_NO_START_CODON,G|intron_variant|MODIFIER|TCF3|ENSG00000071564|transcript|ENST00000588136.5|protein_coding|16/18|c.1586+16T>C||||||,G|intron_variant|MODIFIER|TCF3|ENSG00000071564|transcript|ENST00000590684.5|protein_coding|3/4|c.290+16T>C||||||,G|intron_variant|MODIFIER|TCF3|ENSG00000071564|transcript|ENST00000585855.2|nonsense_mediated_decay|2/4|n.176+16T>C||||||,G|intron_variant|MODIFIER|TCF3|ENSG00000071564|transcript|ENST00000586164.1|nonsense_mediated_decay|1/2|n.113+16T>C||||||,G|intron_variant|MODIFIER|TCF3|ENSG00000071564|transcript|ENST00000453954.6|protein_coding|17/19|c.1673+16T>C||||||,G|intron_variant|MODIFIER|TCF3|ENSG00000071564|transcript|ENST00000344749.9|protein_coding|15/16|c.1433+16T>C||||||,G|intron_variant|MODIFIER|TCF3|ENSG00000071564|transcript|ENST00000592395.5|nonsense_mediated_decay|1/4|n.113+16T>C||||||,G|intron_variant|MODIFIER|TCF3|ENSG00000071564|transcript|ENST00000592628.5|protein_coding|2/4|c.161+16T>C||||||WARNING_TRANSCRIPT_NO_START_CODON,G|intron_variant|MODIFIER|TCF3|ENSG00000071564|transcript|ENST00000590436.5|protein_coding|3/5|c.572+16T>C||||||WARNING_TRANSCRIPT_NO_START_CODON\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:942:888:29718:52:709:0,-219.144,-2608.64\\t0/0:99:148:148:5063:0:0:0,-44.5524,-455.574\n16\\t30979221\\t.\\tACG\\tCCC\\t4.31541E-14\\tPASS\\tSSC=316.342;TYPE=complex;OLD_MULTIALLELIC=16:30979221:ACG/CCC/CCG;ANN=CCC|missense_variant|MODERATE|SETD1A|ENSG00000099381|transcript|ENST00000262519.12|protein_coding|14/19|c.3435_3437delACGinsCCC|p.Arg1146Pro|4121/6903|3435/5124|1145/1707||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:1470:1264:45150:34:455:0,-382.387,-4069.26\\t0/0:99:248:213:7749:2:24:0,-66.0449,-699.417\n11\\t32435204\\t.\\tC\\tT\\t0.0\\tPASS\\tSSC=114.344;TYPE=snp;ANN=T|missense_variant|MODERATE|WT1|ENSG00000184937|transcript|ENST00000332351.7|protein_coding|1/10|c.142G>A|p.Ala48Thr|427/3122|142/1554|48/517||,T|missense_variant|MODERATE|WT1|ENSG00000184937|transcript|ENST00000452863.7|protein_coding|1/9|c.142G>A|p.Ala48Thr|142/2768|142/1494|48/497||,T|missense_variant|MODERATE|WT1|ENSG00000184937|transcript|ENST00000448076.7|protein_coding|1/10|c.142G>A|p.Ala48Thr|332/2114|142/1545|48/514||,T|upstream_gene_variant|MODIFIER|WT1|ENSG00000184937|transcript|ENST00000379079.6|protein_coding||c.-4665G>A|||||4391|,T|upstream_gene_variant|MODIFIER|WT1-AS|ENSG00000183242|transcript|ENST00000395900.1|antisense||n.-375C>T|||||375|,T|upstream_gene_variant|MODIFIER|WT1|ENSG00000184937|transcript|ENST00000530998.5|protein_coding||c.-4665G>A|||||4391|,T|upstream_gene_variant|MODIFIER|WT1-AS|ENSG00000183242|transcript|ENST00000459866.1|antisense||n.-572C>T|||||572|,T|upstream_gene_variant|MODIFIER|WT1-AS|ENSG00000183242|transcript|ENST00000442957.1|antisense||n.-3166C>T|||||3166|,T|upstream_gene_variant|MODIFIER|WT1-AS|ENSG00000183242|transcript|ENST00000494911.5|antisense||n.-314C>T|||||314|,T|upstream_gene_variant|MODIFIER|WT1-AS|ENSG00000183242|transcript|ENST00000478367.5|antisense||n.-2419C>T|||||2419|,T|upstream_gene_variant|MODIFIER|WT1-AS|ENSG00000183242|transcript|ENST00000525436.1|antisense||n.-597C>T|||||597|,T|upstream_gene_variant|MODIFIER|WT1-AS_1|ENSG00000278822|transcript|ENST00000619639.1|misc_RNA||n.-534C>T|||||534|,T|upstream_gene_variant|MODIFIER|WT1-AS_2|ENSG00000273677|transcript|ENST00000613208.1|misc_RNA||n.-1107C>T|||||1107|,T|upstream_gene_variant|MODIFIER|WT1-AS_3|ENSG00000278045|transcript|ENST00000613262.1|misc_RNA||n.-1593C>T|||||1593|,T|upstream_gene_variant|MODIFIER|WT1-AS_6|ENSG00000276530|transcript|ENST00000614919.1|misc_RNA||n.-3882C>T|||||3882|,T|upstream_gene_variant|MODIFIER|WT1-AS_7|ENSG00000273908|transcript|ENST00000426618.3|misc_RNA||n.-4512C>T|||||4512|,T|upstream_gene_variant|MODIFIER|WT1-AS_8|ENSG00000277119|transcript|ENST00000615200.1|misc_RNA||n.-4905C>T|||||4905|,T|upstream_gene_variant|MODIFIER|WT1-AS|ENSG00000183242|transcript|ENST00000612620.1|misc_RNA||n.-1866C>T|||||1866|,T|upstream_gene_variant|MODIFIER|WT1-AS|ENSG00000183242|transcript|ENST00000615677.1|misc_RNA||n.-2419C>T|||||2419|,T|non_coding_transcript_exon_variant|MODIFIER|WT1|ENSG00000184937|transcript|ENST00000379077.7|nonsense_mediated_decay|1/10|n.142G>A||||||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:407:407:16227:0:0:0,-122.519,-1459.02\\t0/0:99:53:51:2047:2:82:0,-8.17491,-176.625\n16\\t3729155\\t.\\tA\\tT\\t0.0\\tPASS\\tSSC=200.889;TYPE=snp;ANN=T|synonymous_variant|LOW|CREBBP|ENSG00000005339|transcript|ENST00000262367.9|protein_coding|31/31|c.5892T>A|p.Arg1964Arg|6702/10803|5892/7329|1964/2442||,T|synonymous_variant|LOW|CREBBP|ENSG00000005339|transcript|ENST00000382070.7|protein_coding|30/30|c.5778T>A|p.Arg1926Arg|5982/7598|5778/7215|1926/2404||,T|downstream_gene_variant|MODIFIER|CREBBP|ENSG00000005339|transcript|ENST00000571763.5|retained_intron||n.*2753T>A|||||2753|,T|downstream_gene_variant|MODIFIER|CREBBP|ENSG00000005339|transcript|ENST00000576720.1|retained_intron||n.*2756T>A|||||2756|,T|downstream_gene_variant|MODIFIER|CREBBP|ENSG00000005339|transcript|ENST00000637492.1|protein_coding||c.*1357T>A|||||1357|WARNING_TRANSCRIPT_INCOMPLETE\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:99:839:804:27986:26:312:0,-221.796,-2488.24\\t0/0:99:98:91:3314:7:94:0,-20.9068,-289.701\n19\\t49596858\\t.\\tG\\tA\\t23.8449\\tPASS\\tSSC=11.1436;TYPE=snp;ANN=A|synonymous_variant|LOW|PRR12|ENSG00000126464|transcript|ENST00000418929.6|protein_coding|4/14|c.2523G>A|p.Pro841Pro|2535/6955|2523/6111|841/2036||,A|synonymous_variant|LOW|PRR12|ENSG00000126464|transcript|ENST00000615927.1|protein_coding|2/12|c.60G>A|p.Pro20Pro|60/4479|60/3648|20/1215||\\tGT:GQ:DP:RO:QR:AO:QA:GL\\t0/0:65.1424:14:14:520:0:0:0,-4.21442,-47.1235\\t1/1:0.087987:2:0:0:2:73:-6.92919,-0.60206,0\n`\n\n  inputChange = {\n    /** Keeps track of inputChanges to highlight selected parameter table row*/\n    input_sequence_text: false,\n    lengths: false,\n    peptideMutationPosition1: false,\n    peptideMutationPosition2: false,\n    frameshiftOverlap: false,\n    maximumPeptideLength: false,\n    table_state_1: false,\n    table_state_2: false,\n  }\n  /**\n   input_vcf_text: string\n   peptide_length: int range(9-40, default=20)\n   peptide_mutation_position1 number field: range(1-peptide_length)\n   peptide_mutation_position2 number field: range(1-peptide_length)\n      by default, this should be null\n   frameshift_overlap: int range(1-20, default=9)\n   min_length_near_start_stop: int range(5-peptide_lenth)\n   maximum_peptide_length: int range(peptide_length +1 - peptide_length+10, default=peptide_length+3)\n   reference_genome: text\n   * */\n\n  peptideLengthSliderOptions: Options = { // ngx-slider option\n    showTicks: true,\n    disabled: false,\n    stepsArray: _.map(_.range(9, 41), (num): CustomStepDefinition => {return {value: num, legend: num % 5 === 0 ? `${num}` : undefined}}),\n    minRange: 1,\n    noSwitching: true,\n    hideLimitLabels: true\n  };\n  /** Peptide Length slider: The '9' and '40' above the control aren't necessary and don't seem to be aligned with the notches.  I would suggest to remove them altogether.  Also, to be more consistent with TC1, can we move all of the labels above the line?  Potentially move the selected length to below the line.*/\n  // peptideLengthSliderOptions: Options = {\n  //   floor: 9,\n  //   ceil: 40,\n  //   showTicksValues: true,\n  //   translate: (value) => {\n  //     if (value === 9) return '';\n  //     if (value === 40) return '';\n  //     else return `${value}`;\n  //   },\n  //   // @ts-ignore\n  //   stepsArray: _.map(_.range(9, 41), (num) => {\n  //     return {value: num, legend: num % 5 === 0 ? num : null}\n  //   }),\n  // }\n\n  /** sequence files */\n  // maxCharacters = 1000000;\n  maxLines = 5000;\n  files: any[] = [];\n  fileName = '';\n\n  pipelineUrl: string = ''\n\n  /** sequence variables */\n  synthesisDownloadLinks = {\n    sequence_list_json_uri: '',\n    vcf_download_uri: ''\n  };\n\n  swaggerUrl = `${environment['api_url']}/apidocs`\n\n  constructor(\n    public alertService: AlertServiceService,\n    private http: HttpClient,\n    private fb: UntypedFormBuilder,\n    private _pipelineService: PipelineService,\n    private _stateService: PipelineStateService,\n    private rootFormGroup: FormGroupDirective, // pipeline component\n    private route: ActivatedRoute,\n    private router: Router,\n    private location: Location,\n    private titleService: Title,\n    private sequenceParserService: SequenceParserService,\n    private modalService: NgbModal,\n  ) {\n  }\n\n  ngOnInit(): void {\n\n    /** Load default vcf file*/\n    this.http.get(\"assets/vcf-files/syntheticX.rand.speedseq.nrm.decomp.ann.100.vcf\", {responseType: 'text'}).subscribe(data =>{\n      console.log(data);\n      this.defaultInputVcfText = data;\n    })\n\n    this.mutgenForm = this.rootFormGroup.control.get(this.formGroupName) as UntypedFormGroup;\n\n    this.pipelineId$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n      this.pipelineId = value;\n      this.pipelineUrl = `${window.location.origin}/pipeline/${value}`;\n    })\n    this.stages$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n      this.stages = value;\n      this.errorMessages = this.stages[this.index]?.stage_messages!.errors\n      this.warningMessages = this.stages[this.index]?.stage_messages!.warnings\n    })\n    this.tools$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n      console.log('tools$');\n      console.log(value);\n      this.tools = value;\n      this.submitted = this.tools[this.index]?.submitted\n\n      // input_vcf_text_id INSTEAD OF inputSequenceTextURIs\n      const inputSequenceTextId = this.tools[this.index]?.input_data_uri?.input_vcf_text_id\n\n      this.synthesisDownloadLinks.sequence_list_json_uri = `${environment['api_url']}/api/v1/sequence_list_json/${inputSequenceTextId}`\n      this.synthesisDownloadLinks.vcf_download_uri = `${environment['api_url']}/api/v1/download_sequences/${inputSequenceTextId}`\n\n      /** pipeline Loading */\n      this.pipelineLoading = _.some(this.tools, {loading: true})\n\n      /** cancel run all  */\n      if(!this.tools[this.index]?.loading) {\n        this.loading = false;\n        clearInterval(this.runSetInterval)\n      }\n      // this.loading = this.tools[this.index]?.loading\n      // if (this.tools[this.index]?.submitted){this.submitted = true}\n      // if (this.tools[this.index].appliedFilters){this.submitted = true}\n      // this.componentDisabled = value[this.index].disabled;\n    })\n\n    this.params$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n      console.log(`params`);\n      console.log(value);\n      this.params = value;\n    })\n\n    this.eventsSubscription = this.events.subscribe(() => this.onRunMain());\n    this.runAllSubscription = this.runAllEvent.subscribe(() => this.onRunAll())\n\n    this.onChanges() // TODO uncomment\n\n  }\n\n  ngOnDestroy() {\n    clearInterval(this.runSetInterval);\n    clearInterval(this._pipelineService.runSetInterval)\n    this.unsubscribe$.next();\n    this.unsubscribe$.complete();\n\n    this.eventsSubscription.unsubscribe();\n    this.runAllSubscription.unsubscribe();\n  }\n\n  ngAfterViewInit() {\n    setTimeout(() => {\n      const run = history.state?.run;\n      // console.log(run);\n      run && this.onRunMain();\n    }, 0)\n  }\n\n  ngOnChanges(changes: SimpleChanges) {\n    if(changes.resultUrl?.currentValue) {\n      console.log(changes.resultUrl.currentValue);\n      console.log('ngOnChanges t-cell')\n      this.loading = true;\n      this.getResultsSetInterval(changes.resultUrl.currentValue);\n    }\n  }\n\n  get styleResultContainer(){\n    return !this.loading && this.submitted ? 'none' : 'dotted';\n  }\n\n  get inputSequenceText(){\n    return this.mutgenForm.get('inputVcfText')?.value\n  }\n\n  get peptideMutationPosition1() {\n    return this.mutgenForm.get('peptideMutationPosition1')?.value;\n  }\n\n  get peptideMutationPosition2() {\n    return this.mutgenForm.get('peptideMutationPosition2')?.value;\n  }\n\n  onChanges(): void {\n    this.mutgenForm.get('peptideMutationPosition1')?.valueChanges.subscribe(() => {\n      this.inputChange.peptideMutationPosition1 = this.submitted\n    });\n    this.mutgenForm.get('peptideMutationPosition2')?.valueChanges.subscribe(() => {\n      this.inputChange.peptideMutationPosition2 = this.submitted\n    });\n    this.mutgenForm.get('frameshiftOverlap')?.valueChanges.subscribe(() => {\n      this.inputChange.frameshiftOverlap = this.submitted\n    });\n    this.mutgenForm.get('maximumPeptideLength')?.valueChanges.subscribe(() => {\n      this.inputChange.maximumPeptideLength = this.submitted\n    });\n  }\n\n  onRunMain() {\n    // if(this.mutgenForm.invalid){\n    //   this.alertService.add(`Input sequence text is too long. The maximum number of characters allowed is ${this.maxCharacters.toLocaleString()}\\nYour sequence contains ${this.inputSequenceText.length.toLocaleString()}`, 'alert-danger');\n    //   this.open(this.alertModal)\n    //   return;\n    // }\n\n    const hasResult = _.find(this.tools.slice(this.index+1), (o) => o.submitted || o.loading)\n    if(this.stages.length > 1 && hasResult) {\n      this.open(this.confirmModal);\n    } else {\n      this.getResultsClicked = true;\n      if(this.index===0) {\n        this.onRun();\n      } else {\n        // this.onRun2()\n      }\n    }\n  }\n\n  onRun() {\n    /**\n     Update pipeline State\n     *\n     * */\n    /** Reset global datatables search ext */\n    $.fn.dataTable.ext.search = [];\n\n    const stage_number = this.index + 1;\n    /** run_stage_range */\n    const run_stage_range: [number, number] = [stage_number, stage_number]\n    /** default formValue */\n    this.setDefaultFormValues()\n    /** Sequences */\n    let sequences = this.mutgenForm.value.inputVcfText\n\n    /** input parameters */\n    const inputParameters = this._pipelineService.convertMutgenForm(this.mutgenForm)\n\n    /** Table State */\n    const { table_state } = this.stages[this.index];\n\n    const newStage = {\n      \"stage_display_name\": \"Mutated Peptide Generator\",\n      \"stage_number\": stage_number,\n      \"stage_type\": \"prediction\",\n      \"tool_group\": \"mutgen\",\n      \"input_vcf_text\": sequences,\n      \"input_parameters\": inputParameters,\n      \"table_state\": table_state\n    }\n\n    const params = {\n      \"pipeline_id\": '',\n      \"pipeline_title\": this.emailForm.controls['name'].value,\n      \"email\": this.emailForm.controls['email'].value,\n      \"run_stage_range\": run_stage_range,\n      \"stages\": [\n        newStage\n      ]\n    }\n\n    /** set params */\n    const initToolLoading = Object.assign(initMutatedPeptideGeneratorTool, {\n      loading: true,\n      submitted: false,\n      appliedFilters: !_.isEmpty(table_state?.columns)\n    })\n    this._stateService.setParams(params);\n    this._stateService.insertTool(initToolLoading, this.index);\n    this._stateService.insertInputParametersToStage(inputParameters, this.index);\n\n    // this._stateService.insertTableStateToStage({columns: {}}, this.index);\n\n    this.postPipelineAPI(params);\n  }\n\n  // onRun2() {\n  //\n  // }\n\n  /** File Download/Upload*/\n  uploadSequenceFile($event: any) {\n    $event.preventDefault();\n    /**\n     * Used for 'Upload' button\n     * */\n    const {files} = $event.target;\n    files && this.onFileDropped(files);\n  }\n\n  onFileDropped($event: any[]) {\n    console.log($event);\n    const file = $event[0];\n    const fileSize = file.size / 1024; // in kB\n    console.log(file.type);\n    if (fileSize > 20000) {\n      this.alertService.add('File Size is too big! (20mB max)', 'alert-danger');\n      this.open(this.alertModal);\n    } else if(file.type==='application/x-gzip') {\n      console.log('GZIPPED')\n      this.prepareGzipFileList($event)\n    } else {\n      this.prepareSequenceFileList($event);\n    }\n  }\n\n  /** Modal Functions */\n  open(content: any) {\n    this.modalOpen = true;\n    this.modalService.open(content, {\n      ariaLabelledBy: 'modal-basic-title',\n      size: 'lg',\n      animation: true,\n      backdrop: 'static'\n    }).result.then((result) => {\n      // this.closeResult = `Closed with: ${result}`;\n      this.saveState = false;\n      this.modalOpen = false;\n    }, (reason) => {\n      this.saveState = false;\n      // this.alleleSearch.nativeElement.focus();\n      // this.closeResult = `Dismissed ${TCellPredictionComponent.getDismissReason(reason)}`;\n    });\n  }\n\n  prepareSequenceFileList(files: Array<any>) {\n    /**\n     * Reads vcf file and enters it via myForm.patchValue({inputVcfText: val});\n     * */\n    console.log(files);\n    this.fileName = files[0].name;\n    console.log(this.fileName)\n    const reader = new FileReader();\n    const myForm = this.mutgenForm;\n    for (const item of files) {\n      // console.log(item);\n      reader.readAsText(item);\n      reader.onload = () => {\n        const val = reader.result?.toString() || '';\n        console.log(val);\n        const v = isASCII(val);\n        console.log(v);\n        if (v) {\n          const w = isMaxLines(val, this.maxLines)\n          if (w) {\n            myForm.patchValue({inputVcfText: val});\n          } else {\n            this.alertService.add(`VCF is too long - ${this.maxLines.toLocaleString(\"en-US\")} lines max`, 'alert-danger');\n            this.open(this.alertModal);\n          }\n        } else {\n          this.alertService.add('Invalid file type.\\nValid file types are .vcf.gz, .vcf,', 'alert-danger');\n          this.open(this.alertModal);\n        }\n      };\n\n      reader.onerror = () => {\n        console.log(reader.error);\n      };\n      item.progress = 0;\n      this.files.push(item);\n    }\n  }\n\n  prepareGzipFileList(files: Array<any>) {\n    /**\n     * Reads vcf.gz file and enters it via myForm.patchValue({inputVcfText: val});\n     * */\n    console.log(files);\n    this.fileName = files[0].name;\n    console.log(this.fileName)\n    const reader = new FileReader();\n    const myForm = this.mutgenForm;\n    for (const item of files) {\n      // console.log(item);\n      reader.readAsArrayBuffer(item);\n      reader.onload = () => {\n        console.log(reader.result)\n        // const val = 'asdfads'\n        let val = ''\n        try {\n          val = pako.inflate(reader.result as pako.Data, { to: 'string' });\n        } catch (error) {\n          this.alertService.add(`Error reading file ${this.fileName}.\\nIf this file was compressed with bgzip, try recompressing with gzip.\\nOtherwise, contact support (help@iedb.org) for assistance.`, 'alert-danger');\n          this.open(this.alertModal);\n          console.log(error);\n        }\n\n        // console.log(val);\n        const v = isASCII(val);\n\n        if (v) {\n          const w = isMaxLines(val, this.maxLines)\n          if (w) {\n            myForm.patchValue({inputVcfText: val});\n          } else {\n            this.alertService.add(`VCF is too long - ${this.maxLines.toLocaleString(\"en-US\")} lines max`, 'alert-danger');\n            this.open(this.alertModal);\n          }\n        } else {\n          this.alertService.add('Invalid file type.\\nValid file types are .vcf.gz, .vcf,', 'alert-danger');\n          this.open(this.alertModal);\n        }\n      };\n\n      reader.onerror = () => {\n        console.log(reader.error);\n      };\n      item.progress = 0;\n      this.files.push(item);\n    }\n  }\n\n  onLengthChange(changeContext: ChangeContext): void {\n    /**\n     * used in (userChangeEnd)\n     * */\n    this.inputChange.lengths = this.submitted;\n  }\n  onFrameshiftOverlapChange(changeContext: ChangeContext): void {\n    /**\n     * used in (userChangeEnd)\n     * */\n    this.inputChange.frameshiftOverlap = this.submitted;\n  }\n\n  onMaximumPeptideLengthChange(changeContext: ChangeContext): void {\n    /**\n     * used in (userChangeEnd)\n     * */\n    this.inputChange.maximumPeptideLength = this.submitted;\n  }\n  onPeptideMutationPosition1Change(changeContext: ChangeContext): void {\n    /**\n     * used in (userChangeEnd)\n     * */\n    this.inputChange.peptideMutationPosition1 = this.submitted;\n  }\n  onPeptideMutationPosition2Change(changeContext: ChangeContext): void {\n    /**\n     * used in (userChangeEnd)\n     * */\n    this.inputChange.peptideMutationPosition2 = this.submitted;\n  }\n\n  setValueLimits(column: Columns) : any {\n    /* set value_limits (i.e. filters) for each column based on if type is a number/string */\n    return column['type'] === 'int' || column['type'] === 'float' ? {\n      ...column['value_limits'],\n      minValue: NaN,\n      maxValue: NaN,\n      applied: false\n    } : {\n      // ...column['value_limits'],\n      possibleValues: column['value_limits']['unique_values'],\n      textValue: null,\n      selectedValues: [],\n      applied: false\n    }\n  }\n\n  postPipelineAPI(params: PipelineParams, getResults: boolean = true) {\n    /**\n     * params\n     * getResults: boolean\n     *  false - used in 'Save Table State'\n     * */\n    /** initial set up */\n    this.disableInputs(); // TODO uncomment this\n    this.loading = getResults; // true - defaults\n    this.submitted = !getResults; // false - defaults\n    this.tableStateSaving = !getResults\n    if (getResults) {\n      this.errorMessages = [];\n      this.warningMessages = [];\n    }\n    this._pipelineService.postPipeline(params).subscribe(\n      (resp) => {\n        // Errors and Warnings\n        if (resp['errors'] && resp['errors'].length) {\n          console.log(resp);\n          console.error(resp['errors']);\n          this.errorMessages = resp['errors'];\n          if (resp['warnings'].length) {\n            console.log(resp['warnings']);\n            this.warningMessages = resp['warnings'];\n          }\n          this.loading = false;\n          this.submitted = true;\n          const submittedTool = Object.assign(initMutatedPeptideGeneratorTool, {\n            submitted: false,\n            loading: false,\n          })\n          this._stateService.insertTool(submittedTool, this.index);\n          this.enableInputs();\n          return;\n        }\n        // Warnings\n        if (resp['warnings'].length) {\n          console.log(resp['warnings']);\n          this.warningMessages = resp['warnings'];\n        }\n\n        console.log(resp.pipeline_id);\n\n        const inputDataUri = {input_sequence_text_id: resp.input_sequence_text_id}\n        this._stateService.insertInputDataUriToTool(inputDataUri, this.index)\n\n        this._stateService.setPipelineId(resp.pipeline_id);\n        this._stateService.setPipelineIdToParams(resp.pipeline_id);\n        this._stateService.setPipelineSpecId(resp.pipeline_spec_id);\n        /** Display email Modal if emailModalShow=true */\n        if (this.showEmailModal) {\n          // this.open(this.emailModal);\n        }\n        this.location.replaceState(`pipeline/${resp.pipeline_id}`)\n        // this.titleService.setTitle(`IEDB NG Tools Pipeline`);\n\n        if (getResults) {\n          const result_url = `${resp.results_uri}`;\n          console.log(result_url);\n          this.getResultsSetInterval(result_url);\n        } else {\n          this.submitted = true;\n          this.loading = false;\n          this.tableStateSaving = false;\n          this.enableInputs();\n        }\n      },\n      error => {\n        console.error(error);\n        this.errorMessages.push(error.error);\n        this.submitted = false;\n        this.loading = false;\n        const prevTool = this.tools[this.index];\n        const submittedTool = Object.assign(prevTool, {\n          submitted: this.submitted,\n          loading: this.loading,\n        })\n        this._stateService.insertTool(submittedTool, this.index);\n        clearInterval(this.runSetInterval);\n        this.enableInputs();\n      })\n  }\n\n  getResultsSetInterval(result_url: string) {\n    /** */\n    this.getResultsClicked = true\n\n    // this.residue_table_order = [];\n    // this.residue_table_columns = null;\n    // this.residue_table = [[]]\n    //\n    // this.sequence_table = [[]]\n    // this.allele_distances_table = [[]]\n    // this.residue_table = [[]]\n    this.snp_table = [[]]\n    // this.processingPlots = []\n\n    this.resultUrl = result_url;\n    console.log(result_url)\n    this.inputChange = _.mapValues(this.inputChange, () => false);\n    let increment = 0;\n    const milliseconds = 3000;\n    this.runSetInterval = setInterval(() => {\n      this._pipelineService.getResults(`${result_url}?statusOnly=true`).subscribe(\n        {\n          next: resp => {\n            console.log(resp);\n            if (resp['status'] === 'error' || resp['errors']) {\n              // this.errorMessages = resp['errors'];\n              // this.warningMessages = resp['warnings'];\n              this.submitted = false;\n              this.loading = false;\n              const prevTool = this.tools[this.index];\n              const submittedTool = Object.assign(prevTool, {\n                submitted: this.submitted,\n                loading: this.loading,\n              })\n              this._stateService.insertTool(submittedTool, this.index);\n              clearInterval(this.runSetInterval);\n              this.enableInputs();\n            }\n            if (resp['data']['warnings']?.length) {\n              // console.log(resp['warnings']);\n              this.warningMessages = resp['data']['warnings'];\n            }\n            if (resp['data']['errors']?.length) {\n              // console.log(resp['warnings']);\n              this.errorMessages = resp['data']['errors'];\n            }\n\n            if (resp['status'] === 'done') {\n              clearInterval(this.runSetInterval);\n\n              this._pipelineService.getResults(result_url).subscribe(resp => {\n                // clearInterval(this.runSetInterval);\n                console.log(resp)\n                this.defaultOrder = [[]]\n                /** 1) Create Column */\n                const data = resp['data']['results'];\n                this.active = data[0].type // = 'unique_table' // this.active = 'scatter_plots'\n                console.log(this.active)\n                _.forEach(data, table => {\n                  if (table.type === 'snp') {\n                    /** snp_table_columns */\n                    this.snp_table_columns = _.map(table.table_columns, (column, i: number) => {\n                      if (column.default_order && Number.isFinite(column.row_sort_priority)) { // set defaultOrder\n                        this.defaultOrder[column.row_sort_priority] = [i, column.default_order === \"ascending\" ? 'asc' : 'desc'];\n                      }\n                      column['title'] = `${column['display_name']}`; // required\n                      column['data'] = `${column['name']}`;\n                      let source = column['source'];\n\n                      column['filterKey'] = `${source}.${column.name}`\n\n                      // console.log(`source=${source}`);\n                      let tempSource = source.split('.')\n                      // console.log(tempSource);\n                      source = tempSource[tempSource.length - 1];\n                      // console.log(`source=${source}`);\n                      column['data'] = `${source}_${column['name']}`;\n                      /** remove `core` from name */\n                      // column['name'] = column['display_name'] ? column['display_name'] : column['name']\n\n                      column['value_limits'] = column['value_limits'] &&  this.setValueLimits(column)\n\n                      return column\n                    });\n                    this.snp_table_order = [...this.defaultOrder];\n                    if (this.snp_table_columns) {\n                      this.snp_table = table.table_data;\n                    }\n                    // console.log(this.peptide_table_order);\n                    // console.log(this.peptide_table_columns);\n                    // console.log(this.peptide_table);\n                    /**\n                     scatterPlotData\n                     * <index> = <field>\n                     * 5 = allele\n                     *\n                     * indexA (9) = score-peptidea\n                     * indexB (14) = score-peptideb\n                     * */\n                    // TODO COMMENTED THIS OUT\n                    // _.forEach(table.table_data, (i) => {\n                    //   // console.log(indexA)\n                    //   // console.log(indexB)\n                    //   if(this.scatterPlotData[i[5]]){ // already exists, push\n                    //     this.scatterPlotData[i[5]].push({'peptidea': i[indexA], 'peptideb': i[indexB], 'sequenceA': i[1], 'sequenceB': i[2]})\n                    //   }  else { // else, create data and push alleles\n                    //     this.scatterPlotData[i[5]] = [{'peptidea': i[indexA], 'peptideb': i[indexB], 'sequenceA': i[1], 'sequenceB': i[2]}]\n                    //     this.scatterPlotAlleles.push(i[5])\n                    //   }\n                    // })\n                    // console.error(this.scatterPlotData)\n                  }\n                  if (table.type === 'unique_peptide') {\n                    /** peptide_output_columns */\n                    this.unique_peptide_table_columns = _.map(table.table_columns, (column, i: number) => {\n                      if (column.default_order && Number.isFinite(column.row_sort_priority)) { // set defaultOrder\n                        this.defaultOrder[column.row_sort_priority] = [i, column.default_order === \"ascending\" ? 'asc' : 'desc'];\n                      }\n                      column['title'] = `${column['display_name']}`; // required\n                      column['data'] = `${column['name']}`;\n                      let source = column['source'];\n\n                      column['filterKey'] = `${source}.${column.name}`\n\n                      // console.log(`source=${source}`);\n                      let tempSource = source.split('.')\n                      // console.log(tempSource);\n                      source = tempSource[tempSource.length - 1];\n                      // console.log(`source=${source}`);\n                      column['data'] = `${source}_${column['name']}`;\n                      /** remove `core` from name */\n                      // column['name'] = column['display_name'] ? column['display_name'] : column['name']\n\n                      column['value_limits'] = column['value_limits'] &&  this.setValueLimits(column)\n\n                      return column\n                    });\n                    this.unique_peptide_table_order = [...this.defaultOrder];\n                    if (this.unique_peptide_table_columns) {\n                      this.unique_peptide_table = table.table_data;\n                    }\n                  }\n                  if (table.type === 'peptide') {\n                    /** output_columns */\n                    this.peptide_table_columns = _.map(table.table_columns, (column, i: number) => {\n                      if (column.default_order && Number.isFinite(column.row_sort_priority)) { // set defaultOrder\n                        this.defaultOrder[column.row_sort_priority] = [i, column.default_order === \"ascending\" ? 'asc' : 'desc'];\n                      }\n                      column['title'] = `${column['display_name']}`; // required\n                      column['data'] = `${column['name']}`;\n                      let source = column['source'];\n\n                      column['filterKey'] = `${source}.${column.name}`\n\n                      // console.log(`source=${source}`);\n                      let tempSource = source.split('.')\n                      // console.log(tempSource);\n                      source = tempSource[tempSource.length - 1];\n                      // console.log(`source=${source}`);\n                      column['data'] = `${source}_${column['name']}`;\n                      /** remove `core` from name */\n                      // column['name'] = column['display_name'] ? column['display_name'] : column['name']\n\n                      column['value_limits'] = column['value_limits'] &&  this.setValueLimits(column)\n\n                      return column\n                    });\n                    this.peptide_table_order = [...this.defaultOrder];\n                    if (this.peptide_table_columns) {\n                      this.peptide_table = table.table_data;\n                    }\n                  }\n                })\n                this.submitted = true; this.loading = false;\n                const prevTool = this.tools[this.index];\n                console.log(prevTool)\n                const submittedTCellPredictionTool = Object.assign(prevTool, {\n                  submitted: this.submitted,\n                  loading: this.loading,\n                })\n                this._stateService.insertTool(submittedTCellPredictionTool, this.index);\n\n                this.enableInputs();\n              })\n            }\n            if (resp['status'] === 'canceled') {\n              /** if status is canceled, then just stop loader **/\n              this.submitted = false;\n              this.loading = false;\n              const prevTool = this.tools[this.index];\n              console.log(prevTool)\n              const submittedTCellPredictionTool = Object.assign(prevTool, {\n                submitted: this.submitted,\n                loading: this.loading,\n              })\n              this._stateService.insertTool(submittedTCellPredictionTool, this.index);\n              clearInterval(this.runSetInterval);\n              // console.log(data);\n              this.enableInputs();\n              // set error message\n              // this.errorMessages = [`PIPELINE_ID=${this.pipelineId} w/ STATUS=${resp['status']}`]\n            }\n            else {\n              this.getResultsClicked = false;\n              console.log(`current status: ${resp['status']} - ${increment}`);\n              increment += 1;\n            }\n          },\n          error: error => {\n            console.error(error);\n            this.enableInputs();\n            clearInterval(this.runSetInterval);\n            this.loading = false;\n          }\n        }\n      )\n    }, milliseconds);\n  }\n\n  onReset() {\n    this.alertService.clear();\n    this.errorMessages = [];\n    this.warningMessages = [];\n\n    // input parameters\n    const peptideLength: number = 21;\n    const peptideMutationPosition1: number = 11;\n    const peptideMutationPosition2: number | null = null;\n    const frameshiftOverlap: number = 9\n    const minLengthNearStartStop = 16\n    const maximumPeptideLength = 24\n\n    this.mutgenForm.patchValue({\n      inputVcfText: '',\n      peptideLength,\n      peptideMutationPosition1,\n      peptideMutationPosition2,\n      frameshiftOverlap,\n      minLengthNearStartStop,\n      maximumPeptideLength\n    }, {emitEvent: false});\n  }\n\n  onCancel(){\n    console.log(this.runSetInterval)\n    clearInterval(this.runSetInterval);\n    this.emitOnCancel.emit()\n\n    this.inputChange.table_state_1 = false; this.inputChange.table_state_2 = false;\n    // this.submitted = false;\n    const currentTool = this.tools[this.index];\n    const unSubmittedTool = {\n      ...currentTool,\n      loading: false,\n      submitted: false,\n      appliedFilters: undefined\n    }\n    this._stateService.insertTool(unSubmittedTool, this.index);\n    this.warningMessages = [];\n    this.loading = false;\n    this.tableStateSaving = false;\n    this.enableInputs();\n  }\n\n  onFilterApplied() {\n    this.inputChange.table_state_1 = this.submitted;\n  }\n  onFilterApplied2() {\n    this.inputChange.table_state_2 = this.submitted;\n  }\n\n  onClearTableState() {\n    this.unique_peptide_table_columns = _.map(this.unique_peptide_table_columns, (c) => {\n      c.filters = ['int', 'float'].includes(c.type) ? {\n          minValue: NaN,\n          maxValue: NaN,\n          applied: false\n        } :\n        {\n          possibleValues: [],\n          textValue: null,\n          selectedValues: [],\n          applied: false\n        }\n      return c\n    })\n    this.inputChange.table_state_1 = this.submitted;\n  }\n\n  onClearTable2State() {\n    this.peptide_table_columns = _.map(this.peptide_table_columns, (c) => {\n      c.value_limits = c.type === 'int'? {\n          minValue: NaN,\n          maxValue: NaN,\n          applied: false\n        } :\n        {\n          possibleValues: [],\n          textValue: null,\n          selectedValues: [],\n          applied: false\n        }\n      return c\n    })\n    this.inputChange.table_state_2 = this.submitted;\n  }\n\n  onSaveTableStateMain(table_name: string) {\n    console.log(table_name)\n    const hasResult = _.find(this.tools.slice(this.index+1), {submitted: true})\n    if (hasResult) {\n      this.saveState = true;\n      this.open(this.confirmModal);\n    } else {\n      switch (table_name) {\n        case 'unique_peptide':\n          this.onSaveTable1State();\n          break;\n        case 'peptide':\n          this.onSaveTable2State();\n          break;\n      }\n    }\n  }\n  onSaveTable1State() {\n    const tool_group = 'mutgen'\n\n    const params = this.params\n    // create colObj and params\n    console.log(this.unique_peptide_table_columns)\n    console.log(this.peptide_table_columns)\n\n    let colObj = columnListToObject(this.unique_peptide_table_columns, tool_group)\n    let colObj2 = columnListToObject(this.peptide_table_columns, tool_group)\n\n    const table_state = [\n      {table: 'unique_peptide', columns: colObj},\n      {table: 'peptide', columns: colObj2}\n    ]\n    this._stateService.insertTableStateToStage(table_state, this.index)\n    // this._stateService.insertTableStateToStage({columns: colObj}, this.index)\n\n    const stages = params.stages;\n    const stageTemp = stages[this.index];\n\n\n    stageTemp.table_state[0].columns = colObj\n\n    stages[this.index] = stageTemp\n    params.stages = stages;\n    // run_stage_range\n    const stage_number = this.index + 1;\n    params.run_stage_range = [stage_number, stage_number];\n    this._stateService.setParams(params);\n    // appliedFilters\n    let appliedFilters = !_.isEmpty(colObj);\n    this._stateService.setToolAppliedFilters(appliedFilters, this.index)\n    this.postPipelineAPI(params, false);\n    this.inputChange.table_state_1 = false;\n\n    this.saveState = false;\n  }\n\n  onSaveTable2State() {\n    const tool_group = 'mutgen'\n\n    const params = this.params\n    /** create colObj and params */\n    let colObj = columnListToObject(this.unique_peptide_table_columns, tool_group)\n    let colObj2 = columnListToObject(this.peptide_table_columns, tool_group)\n\n    const table_state = [\n      {table: 'unique_peptide', columns: colObj},\n      {table: 'peptide', columns: colObj2 }\n    ]\n    this._stateService.insertTableStateToStage(table_state, this.index)\n\n    const stages = params.stages;\n    const stageTemp = stages[this.index];\n    console.log(this.peptide_table_columns)\n    console.log(stageTemp)\n\n    stageTemp.table_state[1].columns = colObj2\n\n    stages[this.index] = stageTemp\n    params.stages = stages;\n    /** run_stage_range */\n    const stage_number = this.index + 1;\n    params.run_stage_range = [stage_number, stage_number];\n    this._stateService.setParams(params);\n    /** appliedFilters */\n    let appliedFilters = !_.isEmpty(colObj2);\n    this._stateService.setToolAppliedFilters(appliedFilters, this.index)\n    this.postPipelineAPI(params, false);\n    this.inputChange.table_state_2 = false;\n\n    this.saveState = false;\n  }\n\n  onRunConfirm() {\n    let indicies = _.range(this.index + 1, this.stages.length)\n    let initTool: Tool;\n    console.log(indicies);\n    _.forEach(indicies, i => {\n      initTool = this.tools[i];\n      const unSubmittedTool = {\n        ...initTool,\n        loading: false,\n        submitted: false,\n      }\n      this._stateService.insertTool(unSubmittedTool, i);\n    })\n    // TODO - need to have a way to save table on confirm modal based on what table was saved - created a variable to keep track of what table is selected\n    this.saveState ? this.onSaveTableStateMain('unique_peptide') : this.onRun();\n  }\n\n  onRunAll() {\n    this.setDefaultFormValues()\n    this.emitIndex.emit(this.index);\n  }\n\n  setDefaultFormValues() {\n    /** defaults - use Sars placeholders*/\n    const input_vcf_text: string  = this.defaultInputVcfText;\n    /** Sequences */\n    let sequences = this.mutgenForm.value.inputVcfText\n    if(!sequences && this.index===0) {\n      this._stateService.setInputVcfText(input_vcf_text);\n      this.mutgenForm.controls.inputVcfText.setValue(input_vcf_text);\n    }\n  }\n\n  enableInputs() {\n    this.mutgenForm.controls['peptideMutationPosition1'].enable({emitEvent: false})\n    this.mutgenForm.controls['peptideMutationPosition2'].enable({emitEvent: false})\n    this.mutgenForm.controls['frameshiftOverlap'].enable({emitEvent: false})\n    this.mutgenForm.controls['maximumPeptideLength'].enable({emitEvent: false})\n    // this.mutgenForm.enable({emitEvent: false});\n    this.peptideLengthSliderOptions = Object.assign({}, this.peptideLengthSliderOptions, {disabled: false});\n  }\n\n  disableInputs() {\n    this.mutgenForm.controls['peptideMutationPosition1'].disable({emitEvent: false})\n    this.mutgenForm.controls['peptideMutationPosition2'].disable({emitEvent: false})\n    this.mutgenForm.controls['frameshiftOverlap'].disable({emitEvent: false})\n    this.mutgenForm.controls['maximumPeptideLength'].disable({emitEvent: false})\n    // this.mutgenForm.disable({emitEvent: false}); // this enables the slider for some reason, so disable the controls individually\n    this.peptideLengthSliderOptions = Object.assign({}, this.peptideLengthSliderOptions, {disabled: true});\n  }\n\n  onDownloadJson() {\n    onCsvDownloadAllClickedNew(this.synthesisDownloadLinks.sequence_list_json_uri, this.http, 'json');\n  }\n\n  onDownloadOriginal() {\n    /** download vcf file */\n    onCsvDownloadAllClickedNew(this.synthesisDownloadLinks.vcf_download_uri, this.http, 'vcf');\n  }\n}\n\n\n","<div *ngIf=\"loading\" class=\"d-flex justify-content-center col\" style=\"margin-top: 81px\">\n  <div class=\"spinner-border text-primary align-self-center\" role=\"status\">\n    <span class=\"visually-hidden\">Loading...</span>\n  </div>\n</div>\n\n<mat-drawer-container *ngIf=\"!loading\" class=\"pipeline-container\">\n  <mat-drawer mode=\"side\" [(opened)]=\"sidebarOpened\">\n    <div class=\"d-flex flex-row p-2 align-content-center\">\n      <button class=\"btn btn-dark-blue-grey text-white\" (click)=\"sidebarOpened=!sidebarOpened\"> <<</button>\n      <h3 class=\"px-2\">Pipeline Map</h3>\n      <!--Dropdown Links-->\n      <div class=\"dropdown text-center\">\n        <button\n          [disabled]=\"!pipelineId\"\n          [ngbTooltip]=\"!pipelineId ? 'Available after `Run`' : null\"\n          placement=\"bottom\"\n          class=\"btn btn-secondary dropdown-toggle\" type=\"button\" id=\"dropdownMenuButton-pipeline-input-links\"\n          data-bs-toggle=\"dropdown\"\n          data-toggle=\"dropdown\"\n          aria-expanded=\"false\">\n          <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\" class=\"bi bi-clipboard\"\n               viewBox=\"0 0 16 16\">\n            <path\n              d=\"M4 1.5H3a2 2 0 0 0-2 2V14a2 2 0 0 0 2 2h10a2 2 0 0 0 2-2V3.5a2 2 0 0 0-2-2h-1v1h1a1 1 0 0 1 1 1V14a1 1 0 0 1-1 1H3a1 1 0 0 1-1-1V3.5a1 1 0 0 1 1-1h1v-1z\"/>\n            <path\n              d=\"M9.5 1a.5.5 0 0 1 .5.5v1a.5.5 0 0 1-.5.5h-3a.5.5 0 0 1-.5-.5v-1a.5.5 0 0 1 .5-.5h3zm-3-1A1.5 1.5 0 0 0 5 1.5v1A1.5 1.5 0 0 0 6.5 4h3A1.5 1.5 0 0 0 11 2.5v-1A1.5 1.5 0 0 0 9.5 0h-3z\"/>\n          </svg>\n        </button>\n        <!--      Available tools will be listed here, depending on what the previous tool is.-->\n        <ul class=\"dropdown-menu dropdown-menu-right\">\n          <li class=\"dropdown-item\">\n            <div class=\"form-group\">\n              <label for=\"pipeline-url-input\">Link to this pipeline</label>\n              <div class=\"input-group\">\n                <input type=\"text\" class=\"form-control\" id=\"pipeline-url-input\" [value]=\"pipelineUrl\">\n                <button class=\"btn btn-secondary\" [cdkCopyToClipboard]=\"pipelineUrl\" ngbTooltip=\"copy url\"\n                        placement=\"top\">\n                  <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n                       class=\"bi bi-clipboard\" viewBox=\"0 0 16 16\">\n                    <path\n                      d=\"M4 1.5H3a2 2 0 0 0-2 2V14a2 2 0 0 0 2 2h10a2 2 0 0 0 2-2V3.5a2 2 0 0 0-2-2h-1v1h1a1 1 0 0 1 1 1V14a1 1 0 0 1-1 1H3a1 1 0 0 1-1-1V3.5a1 1 0 0 1 1-1h1v-1z\"/>\n                    <path\n                      d=\"M9.5 1a.5.5 0 0 1 .5.5v1a.5.5 0 0 1-.5.5h-3a.5.5 0 0 1-.5-.5v-1a.5.5 0 0 1 .5-.5h3zm-3-1A1.5 1.5 0 0 0 5 1.5v1A1.5 1.5 0 0 0 6.5 4h3A1.5 1.5 0 0 0 11 2.5v-1A1.5 1.5 0 0 0 9.5 0h-3z\"/>\n                  </svg>\n                </button>\n              </div>\n            </div>\n          </li>\n          <li class=\"dropdown-item\">\n            <div class=\"form-group\">\n              <label for=\"pipeline-spec-url-inpput\">Link to pipeline configuration</label>\n              <div class=\"input-group\">\n                <input type=\"text\" class=\"form-control\" id=\"pipeline-spec-url-inpput\" [value]=\"pipelineSpecUrl\">\n                <button class=\"btn btn-secondary\" [cdkCopyToClipboard]=\"pipelineSpecUrl\" ngbTooltip=\"copy url\"\n                        placement=\"top\">\n                  <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n                       class=\"bi bi-clipboard\" viewBox=\"0 0 16 16\">\n                    <path\n                      d=\"M4 1.5H3a2 2 0 0 0-2 2V14a2 2 0 0 0 2 2h10a2 2 0 0 0 2-2V3.5a2 2 0 0 0-2-2h-1v1h1a1 1 0 0 1 1 1V14a1 1 0 0 1-1 1H3a1 1 0 0 1-1-1V3.5a1 1 0 0 1 1-1h1v-1z\"/>\n                    <path\n                      d=\"M9.5 1a.5.5 0 0 1 .5.5v1a.5.5 0 0 1-.5.5h-3a.5.5 0 0 1-.5-.5v-1a.5.5 0 0 1 .5-.5h3zm-3-1A1.5 1.5 0 0 0 5 1.5v1A1.5 1.5 0 0 0 6.5 4h3A1.5 1.5 0 0 0 11 2.5v-1A1.5 1.5 0 0 0 9.5 0h-3z\"/>\n                  </svg>\n                </button>\n              </div>\n\n            </div>\n          </li>\n          <li class=\"dropdown-item d-flex justify-content-center\">\n            <button class=\"btn btn-secondary\" [cdkCopyToClipboard]=\"paramsString\" ngbTooltip=\"copy json\"\n                    placement=\"top\"> Copy API POST request\n            </button>\n          </li>\n        </ul>\n      </div>\n    </div>\n\n    <!--   Pipeline Map Accordions -->\n    <div ngbAccordion>\n      <!--      Info -->\n      <div ngbAccordionItem [collapsed]=\"true\">\n        <h2 ngbAccordionHeader>\n          <button ngbAccordionButton>\n            <h5 class=\"d-flex flex-row\">\n            <span class=\"stage-name-link me-2\">\n              Info\n            </span>\n            </h5>\n          </button>\n        </h2>\n        <div ngbAccordionCollapse>\n          <div ngbAccordionBody>\n            <ng-template>\n              <table class=\"table table-bordered tools-parameter-table\">\n                <tr>\n                  <td><a href=\"javascript:void(0)\" (click)=\"open(emailModal)\" ngbTooltip=\"Click to edit Pipeline Name\"\n                         placement=\"right\">Pipeline Name</a></td>\n                  <td>\n                    {{ submittedEmailForm['name'] }}\n                  </td>\n                </tr>\n                <tr>\n                  <td><a href=\"javascript:void(0)\" (click)=\"open(emailModal)\" ngbTooltip=\"Click to edit Email\"\n                         placement=\"right\">Email</a></td>\n                  <td>\n                    {{ submittedEmailForm['email'] }}\n                  </td>\n                </tr>\n              </table>\n            </ng-template>\n          </div>\n        </div>\n      </div>\n      <!-- Steps -->\n      <div ngbAccordionItem [collapsed]=\"false\">\n\n        <h2 ngbAccordionHeader>\n          <button ngbAccordionButton>\n            <h5 class=\"d-flex flex-row\">\n            <span class=\"stage-name-link me-2\">\n              Steps\n            </span>\n            </h5>\n          </button>\n        </h2>\n        <div ngbAccordionCollapse>\n          <div ngbAccordionBody>\n            <ng-template>\n              <!-- Nested Accordion -->\n              <div ngbAccordion>\n                <ng-container *ngFor=\"let stage of stages$ | async; let idx=index;\">\n                  <div ngbAccordionItem [collapsed]=\"true\">\n\n                    <div ngbAccordionHeader class=\"accordion-button custom-accordion-header d-flex flex-row\">\n                      <div class=\"flex-grow-1 d-flex flex-row\">\n                        <h5 class=\"stage-name-link me-2\" (click)=\"onGoToStage(stage.tool_group)\">\n                      {{ stage.stage_display_name }}\n                      </h5>\n                        <!--      loader      -->\n                        <div *ngIf=\"tools[idx].loading && !tools[idx].submitted\"\n                             class=\"spinner-border spinner-border-sm text-primary\" role=\"status\">\n                          <span class=\"visually-hidden\">Loading...</span>\n                        </div>\n                        <!--    applied Filters        -->\n                        <div *ngIf=\"tools[idx].appliedFilters\" class=\"float-right px-2\" role=\"status\">\n                          <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n                               class=\"bi bi-funnel-fill\" viewBox=\"0 0 16 16\">\n                            <path\n                              d=\"M1.5 1.5A.5.5 0 0 1 2 1h12a.5.5 0 0 1 .5.5v2a.5.5 0 0 1-.128.334L10 8.692V13.5a.5.5 0 0 1-.342.474l-3 1A.5.5 0 0 1 6 14.5V8.692L1.628 3.834A.5.5 0 0 1 1.5 3.5v-2z\"/>\n                          </svg>\n                        </div>\n                        <!--    table        -->\n                        <div *ngIf=\"!tools[idx].loading && tools[idx].submitted\" class=\"float-right px-2\" role=\"status\">\n                          <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n                               class=\"bi bi-table\" viewBox=\"0 0 16 16\">\n                            <path\n                              d=\"M0 2a2 2 0 0 1 2-2h12a2 2 0 0 1 2 2v12a2 2 0 0 1-2 2H2a2 2 0 0 1-2-2V2zm15 2h-4v3h4V4zm0 4h-4v3h4V8zm0 4h-4v3h3a1 1 0 0 0 1-1v-2zm-5 3v-3H6v3h4zm-5 0v-3H1v2a1 1 0 0 0 1 1h3zm-4-4h4V8H1v3zm0-4h4V4H1v3zm5-3v3h4V4H6zm4 4H6v3h4V8z\"/>\n                          </svg>\n                        </div>\n\n                      </div>\n                      <!--Toggle Button -->\n                      <button ngbAccordionToggle class=\"accordion-button-toggle btn btn-link p-0\"></button>\n                      <!--Remove tool (X) Button -->\n                      <button type=\"button\" class=\"btn-close ms-1\" aria-label=\"Close\"\n                              (click)=\"removeToolFromPipeline(stage.tool_group)\"\n                              [hidden]=\"stages[stages.length-1]!==stage || stages.length === 1\">\n                      </button>\n                    </div>\n                    <div ngbAccordionCollapse>\n                      <div ngbAccordionBody>\n                        <ng-template>\n                          <!-- MHCI -->\n                          <div *ngIf=\"stage.tool_group==='mhci'\" class=\"d-flex flex-column justify-content-start\">\n\n                            <table class=\"table-sm table-bordered tools-parameter-table\">\n                              <thead>\n                              <tr>\n                                <th class=\"text-center\" colspan=\"2\">\n                                  Tool Parameters\n                                </th>\n                              </tr>\n                              </thead>\n                              <tr>\n                                <td> Predictors</td>\n                                <td>\n                                  <div *ngFor=\"let o of predictionModels; let i=index;\">\n                                    {{ i + 1 }}\n                                    . {{ o.type }} {{ ['binding', 'processing'].includes(o.type) ? '(' + o.method + ')' : null }}\n                                    <!--                  {{i + 1}}. {{o.type}}{{o.method && '.'}}{{o.method}}-->\n                                  </div>\n                                </td>\n                              </tr>\n                              <tr>\n                                <td> length(s)</td>\n                                <td>\n                          <span *ngIf=\"tCellForm.controls['breakPeptides'].value; else asIsTrue\">\n                            None\n                          </span>\n                                  <ng-template #asIsTrue>\n                            <span\n                              *ngIf=\"tCellForm.controls['peptideLength'].value[0] !== tCellForm.controls['peptideLength'].value[1]; else singlePeptideLength\">\n                              {{ tCellForm.controls['peptideLength'].value[0] }}\n                              - {{ tCellForm.controls['peptideLength'].value[1] }}\n                            </span>\n                                    <ng-template #singlePeptideLength>\n                              <span>\n                                  {{ tCellForm.controls['peptideLength'].value[0] }}\n                              </span>\n                                    </ng-template>\n                                  </ng-template>\n                                </td>\n                              </tr>\n                              <tr>\n                                <td> Alleles</td>\n                                <td>\n                  <span *ngIf=\"selectedAlleles.length===1\">\n                   ({{ selectedAlleles[0].label }})\n                  </span>\n                                  <span *ngIf=\"selectedAlleles.length===2\">\n                     ({{ selectedAlleles[0].label }}, {{ selectedAlleles[1].label }})\n                  </span>\n                                  <span *ngIf=\"selectedAlleles.length > 2\">\n                    ({{ selectedAlleles[0].label }},... {{ selectedAlleles[selectedAlleles.length - 1].label }})\n                  </span>\n                                </td>\n                              </tr>\n                            </table>\n                          </div>\n                          <!-- Cluster -->\n                          <div *ngIf=\"stage.tool_group==='cluster'\" class=\"d-flex flex-column justify-content-start\">\n\n                            <table class=\"table-sm table-bordered tools-parameter-table\">\n                              <thead>\n                              <tr>\n                                <th class=\"text-center\" colspan=\"2\">\n                                  Tool Parameters\n                                </th>\n                              </tr>\n                              </thead>\n                              <tr>\n                                <td> Threshold</td>\n                                <td>\n                                  {{ clusterForm.controls['threshold'].value * 100 }}%\n                                </td>\n                              </tr>\n                              <tr>\n                                <td> length(s)</td>\n                                <td>\n                  <span>\n                  {{ clusterMinPeptideLength }}-{{ clusterMaxPeptideLength }}\n                  </span>\n                                </td>\n                              </tr>\n                              <tr>\n                                <td> Method</td>\n                                <td>\n                  <span>\n                    {{ clusterForm.controls['method'].value }}\n                  </span>\n                                </td>\n                              </tr>\n                            </table>\n                          </div>\n                          <!-- Pepmatch -->\n                          <div *ngIf=\"stage.tool_group==='pepmatch'\" class=\"d-flex flex-column justify-content-start\">\n\n                            <table class=\"table-sm table-bordered tools-parameter-table\">\n                              <thead>\n                              <tr>\n                                <th class=\"text-center\" colspan=\"2\">\n                                  Tool Parameters\n                                </th>\n                              </tr>\n                              </thead>\n                              <tr>\n                                <td> Proteome</td>\n                                <td>\n                                  {{ pepmatchForm.controls['proteome'].value }}\n                                </td>\n                              </tr>\n                              <tr>\n                                <td> Max mismatches</td>\n                                <td>\n                  <span>\n                  {{ pepmatchForm.controls['mismatch'].value }}\n                  </span>\n                                </td>\n                              </tr>\n                              <tr>\n                                <td> Best match per peptide</td>\n                                <td>\n                  <span>\n                    {{ pepmatchForm.controls['bestMatch'].value }}\n                  </span>\n                                </td>\n                              </tr>\n                            </table>\n\n                          </div>\n                          <!-- Pepx -->\n                          <div *ngIf=\"stage.tool_group==='pepx'\" class=\"d-flex flex-column justify-content-start\">\n\n                            <table class=\"table-sm table-bordered tools-parameter-table\">\n                              <thead>\n                              <tr>\n                                <th class=\"text-center\" colspan=\"2\">\n                                  Tool Parameters\n                                </th>\n                              </tr>\n                              </thead>\n                              <tr>\n                                <td> Quantitation Level</td>\n                                <td>\n                                  {{ pepxForm.controls['qlevel'].value }}\n                                </td>\n                              </tr>\n                              <tr>\n                                <td> Data Source</td>\n                                <td>\n                                  {{ pepxForm.controls['datasource'].value }}\n                                </td>\n                              </tr>\n                              <tr>\n                                <td> Dataset ID</td>\n                                <td>\n                  <span>\n                  {{ pepxForm.controls['dataset_id'].value }}\n                  </span>\n                                </td>\n                              </tr>\n\n                            </table>\n                            <!--              <table *ngIf=\"!tools[idx/2].loading && tools[idx/2].submitted\" class=\"table table-bordered filters-table\">-->\n                            <!--                <thead>-->\n                            <!--                <tr>-->\n                            <!--                  <th class=\"text-center\" colspan=\"2\">-->\n                            <!--                    Column Filters-->\n                            <!--                  </th>-->\n                            <!--                </tr>-->\n                            <!--                </thead>-->\n                            <!--                <tbody>-->\n                            <!--                <tr>-->\n                            <!--                  <td> Col A</td>-->\n                            <!--                  <td>-->\n                            <!--                    Min: x-->\n                            <!--                    Max: y-->\n                            <!--                  </td>-->\n                            <!--                </tr>-->\n                            <!--                <tr>-->\n                            <!--                  <td> Col C</td>-->\n                            <!--                  <td>-->\n                            <!--                  <span>-->\n                            <!--                  FVEHIHVLENSLAFK, FVEHIHVLENSLAFK, ...-->\n                            <!--                  </span>-->\n                            <!--                  </td>-->\n                            <!--                </tr>-->\n                            <!--                <tr>-->\n                            <!--                  <td> Col B</td>-->\n                            <!--                  <td>-->\n                            <!--                  <span>-->\n                            <!--                    Selected x value(s)-->\n                            <!--                  </span>-->\n                            <!--                  </td>-->\n                            <!--                </tr>-->\n                            <!--                </tbody>-->\n                            <!--              </table>-->\n                          </div>\n                          <!-- Prediction Binding Comparison -->\n                          <div *ngIf=\"stage.tool_group==='peptide_variant_comparison'\"\n                               class=\"d-flex flex-column justify-content-start\">\n\n                            <table class=\"table-sm table-bordered tools-parameter-table\">\n                              <thead>\n                              <tr>\n                                <th class=\"text-center\" colspan=\"2\">\n                                  Tool Parameters\n                                </th>\n                              </tr>\n                              </thead>\n                              <tr>\n                                <td> Alleles</td>\n                                <td>\n                  <span *ngIf=\"selectedAlleles2.length===1\">\n                   ({{ selectedAlleles2[0].label }})\n                  </span>\n                                  <span *ngIf=\"selectedAlleles2.length===2\">\n                     ({{ selectedAlleles2[0].label }}, {{ selectedAlleles2[1].label }})\n                  </span>\n                                  <span *ngIf=\"selectedAlleles2.length > 2\">\n                    ({{ selectedAlleles2[0].label }},... {{ selectedAlleles2[selectedAlleles2.length - 1].label }})\n                  </span>\n                                </td>\n                              </tr>\n                              <tr>\n                                <td> Predictors</td>\n                                <td>\n                                  <div *ngFor=\"let o of predictionModels2; let i=index;\">\n                                    {{ i + 1 }}\n                                    . {{ o.type }} {{ ['binding', 'processing'].includes(o.type) ? '(' + o.method + ')' : null }}\n                                    <!--                  {{i + 1}}. {{o.type}}{{o.method && '.'}}{{o.method}}-->\n                                  </div>\n                                </td>\n                              </tr>\n                            </table>\n                          </div>\n                          <!-- Mut Gen -->\n                          <div *ngIf=\"stage.tool_group==='mutgen'\" class=\"d-flex flex-column justify-content-start\">\n\n                            <table class=\"table-sm table-bordered tools-parameter-table\">\n                              <thead>\n                              <tr>\n                                <th class=\"text-center\" colspan=\"2\">\n                                  Tool Parameters\n                                </th>\n                              </tr>\n                              </thead>\n                              <tr>\n                                <td> Peptide Length</td>\n                                <td>\n                                <span>\n                                {{ mutgenForm.controls['peptideLength'].value }}\n                                </span>\n                                </td>\n                              </tr>\n                              <tr>\n                                <td> Peptide Mutation Position 1</td>\n                                <td>\n                                <span>\n                                {{ mutgenForm.controls['peptideMutationPosition1'].value }}\n                                </span>\n                                </td>\n                              </tr>\n                              <tr>\n                                <td> Peptide Mutation Position 2</td>\n                                <td>\n                                <span>\n                                {{ mutgenForm.controls['peptideMutationPosition2'].value }}\n                                </span>\n                                </td>\n                              </tr>\n                              <tr>\n                                <td> Frameshift Overlap</td>\n                                <td>\n                                <span>\n                                {{ mutgenForm.controls['frameshiftOverlap'].value }}\n                                </span>\n                                </td>\n                              </tr>\n                              <tr>\n                                <td> Minimum Peptide Length</td>\n                                <td>\n                                <span>\n                                {{ mutgenForm.controls['minLengthNearStartStop'].value }}\n                                </span>\n                                </td>\n                              </tr>\n<!--                              TODO took this out when taking out max peptide length input-->\n<!--                              <tr>-->\n<!--                                <td> Maximum Peptide Length</td>-->\n<!--                                <td>-->\n<!--                                <span>-->\n<!--                                {{ mutgenForm.controls['maximumPeptideLength'].value }}-->\n<!--                                </span>-->\n<!--                                </td>-->\n<!--                              </tr>-->\n                            </table>\n                          </div>\n                        </ng-template>\n                      </div>\n                    </div>\n                  </div>\n                </ng-container>\n              </div>\n\n\n              <!-- + Button -->\n              <div id=\"add-tools-button\" class=\"pt-2 dropdown d-flex justify-content-between\">\n                <div>\n                  <!--  MHCI    -->\n                  <button *ngIf=\"stages[stages.length-1].tool_group === 'mhci'\" class='btn btn-lg btn-dark-blue-grey text-white'\n                          [disabled]=\"!tools[tools.length-1].submitted\"\n                          [matMenuTriggerFor]=\"mhci_valid_steps\">\n                    +\n                  </button>\n                  <!-- # sub-menu -->\n                  <mat-menu #mhci_valid_steps=\"matMenu\">\n                    <button mat-menu-item [matMenuTriggerFor]=\"mhci_cluster_inputs\"\n                            [disabled]=\"addedToolGroups.includes('cluster')\">Cluster\n                    </button>\n                    <button mat-menu-item [matMenuTriggerFor]=\"mhci_pepmatch_inputs\"\n                            [disabled]=\"addedToolGroups.includes('pepmatch')\">Pepmatch\n                    </button>\n                    <button mat-menu-item [matMenuTriggerFor]=\"mhci_pepx_inputs\"\n                            [disabled]=\"addedToolGroups.includes('pepx')\">PepX\n                    </button>\n                  </mat-menu>\n                  <mat-menu #mhci_cluster_inputs=\"matMenu\">\n                    <button mat-menu-item (click)=\"addCluster(this.tools.length)\">Peptide Table - Peptide</button>\n                  </mat-menu>\n                  <mat-menu #mhci_pepmatch_inputs=\"matMenu\">\n                    <button mat-menu-item (click)=\"addPepmatch(this.tools.length)\">Peptide Table - Peptide</button>\n                  </mat-menu>\n                  <mat-menu #mhci_pepx_inputs=\"matMenu\">\n                    <button mat-menu-item (click)=\"addPepX(this.tools.length)\">Peptide Table - Peptide</button>\n                  </mat-menu>\n\n                  <!--  Cluster -->\n                  <button *ngIf=\"stages[stages.length-1].tool_group === 'cluster'\" class='btn btn-lg btn-dark-blue-grey text-white'\n                          [disabled]=\"!tools[tools.length-1].submitted\" [matMenuTriggerFor]=\"cluster_valid_steps\"\n                          ngbTooltip=\"add a step to the pipeline\">\n                    +\n                  </button>\n                  <!-- # sub-menu -->\n                  <mat-menu #cluster_valid_steps=\"matMenu\">\n                    <button mat-menu-item [matMenuTriggerFor]=\"cluster_mhci_inputs\"\n                            [disabled]=\"addedToolGroups.includes('mhci')\">T Cell Prediction - Class I\n                    </button>\n                    <button mat-menu-item [matMenuTriggerFor]=\"cluster_pepmatch_inputs\"\n                            [disabled]=\"addedToolGroups.includes('pepmatch')\">Pepmatch\n                    </button>\n                    <button mat-menu-item [matMenuTriggerFor]=\"cluster_pepx_inputs\"\n                            [disabled]=\"addedToolGroups.includes('pepx')\">PepX\n                    </button>\n                  </mat-menu>\n                  <mat-menu #cluster_mhci_inputs=\"matMenu\">\n                    <button mat-menu-item (click)=\"addTCellPrediction(this.tools.length, 'peptide')\">Peptide Table -\n                      Peptide\n                    </button>\n                    <button mat-menu-item (click)=\"addTCellPrediction(this.tools.length, 'cluster_consensus')\">Peptide\n                      Table - Cluster Consensus\n                    </button>\n                  </mat-menu>\n                  <mat-menu #cluster_pepmatch_inputs=\"matMenu\">\n                    <button mat-menu-item (click)=\"addPepmatch(this.tools.length)\">Peptide Table - Peptide</button>\n                    <button mat-menu-item (click)=\"addPepmatch(this.tools.length, 'cluster_consensus')\">Peptide Table -\n                      Cluster Consensus\n                    </button>\n                  </mat-menu>\n                  <mat-menu #cluster_pepx_inputs=\"matMenu\">\n                    <button mat-menu-item (click)=\"addPepX(this.tools.length)\">Peptide Table - Peptide</button>\n                    <button mat-menu-item (click)=\"addPepX(this.tools.length, 'cluster_consensus')\">Peptide Table -\n                      Cluster Consensus\n                    </button>\n                  </mat-menu>\n\n                  <!--  Pepmatch -->\n                  <button *ngIf=\"stages[stages.length-1].tool_group === 'pepmatch'\" class='btn btn-lg btn-dark-blue-grey text-white'\n                          [disabled]=\"!tools[tools.length-1].submitted\" [matMenuTriggerFor]=\"pepmatch_valid_steps\"\n                          ngbTooltip=\"add a step to the pipeline\">\n                    +\n                  </button>\n                  <mat-menu #pepmatch_valid_steps=\"matMenu\">\n                    <button mat-menu-item [matMenuTriggerFor]=\"pepmatch_mhci_inputs\"\n                            [disabled]=\"addedToolGroups.includes('mhci')\">T Cell Prediction - Class I\n                    </button>\n                    <button mat-menu-item [matMenuTriggerFor]=\"pepmatch_cluster_inputs\"\n                            [disabled]=\"addedToolGroups.includes('cluster')\">Cluster\n                    </button>\n                    <button mat-menu-item [matMenuTriggerFor]=\"pepmatch_pepx_inputs\"\n                            [disabled]=\"addedToolGroups.includes('pepx')\">PepX\n                    </button>\n                  </mat-menu>\n                  <mat-menu #pepmatch_mhci_inputs=\"matMenu\">\n                    <button mat-menu-item (click)=\"addTCellPrediction(this.tools.length, 'peptide')\">Peptide Table -\n                      Peptide\n                    </button>\n                    <button mat-menu-item (click)=\"addTCellPrediction(this.tools.length, 'matched_sequence')\">Peptide\n                      Table - Matched\n                      Sequence\n                    </button>\n                  </mat-menu>\n                  <mat-menu #pepmatch_cluster_inputs=\"matMenu\">\n                    <button mat-menu-item (click)=\"addCluster(this.tools.length, 'peptide')\">Peptide Table - Peptide\n                    </button>\n                    <button mat-menu-item (click)=\"addCluster(this.tools.length, 'matched_sequence')\">Peptide Table -\n                      Matched Sequence\n                    </button>\n                  </mat-menu>\n                  <mat-menu #pepmatch_pepx_inputs=\"matMenu\">\n                    <button mat-menu-item (click)=\"addPepX(this.tools.length, 'peptide')\">Peptide Table - Peptide\n                    </button>\n                    <button mat-menu-item (click)=\"addPepX(this.tools.length, 'matched_sequence')\">Peptide Table -\n                      Matched Sequence\n                    </button>\n                  </mat-menu>\n\n                  <!--  Pepx -->\n                  <button *ngIf=\"stages[stages.length-1].tool_group === 'pepx'\" class='btn btn-lg btn-dark-blue-grey text-white'\n                          [disabled]=\"!tools[tools.length-1].submitted\"\n                          [matMenuTriggerFor]=\"pepx_valid_steps\">\n                    +\n                  </button>\n                  <!-- # sub-menu -->\n                  <mat-menu #pepx_valid_steps=\"matMenu\">\n                    <button mat-menu-item [matMenuTriggerFor]=\"pepx_mhci_inputs\"\n                            [disabled]=\"addedToolGroups.includes('mhci')\">T Cell Prediction - Class I\n                    </button>\n                    <button mat-menu-item [matMenuTriggerFor]=\"pepx_cluster_inputs\"\n                            [disabled]=\"addedToolGroups.includes('cluster')\">Cluster\n                    </button>\n                    <button mat-menu-item [matMenuTriggerFor]=\"pepx_pepmatch_inputs\"\n                            [disabled]=\"addedToolGroups.includes('pepmatch')\">Pepmatch\n                    </button>\n                  </mat-menu>\n                  <mat-menu #pepx_mhci_inputs=\"matMenu\">\n                    <button mat-menu-item (click)=\"addTCellPrediction(this.tools.length, 'peptide', 'peptide_table')\">\n                      Peptide Table - Peptide\n                    </button>\n                    <button mat-menu-item\n                            (click)=\"addTCellPrediction(this.tools.length, 'peptide', 'peptide_gene_summary_table')\">\n                      Peptide Gene Summary Table - Peptide\n                    </button>\n                  </mat-menu>\n                  <mat-menu #pepx_cluster_inputs=\"matMenu\">\n                    <button mat-menu-item (click)=\"addCluster(this.tools.length)\">Peptide Table - Peptide</button>\n                    <button mat-menu-item (click)=\"addCluster(this.tools.length, 'peptide', 'peptide_gene_summary_table')\">Peptide Gene Summary\n                      Table - Peptide\n                    </button>\n                  </mat-menu>\n                  <mat-menu #pepx_pepmatch_inputs=\"matMenu\">\n                    <button mat-menu-item (click)=\"addPepmatch(this.tools.length)\">Peptide Table - Peptide</button>\n                    <button mat-menu-item (click)=\"addPepmatch(this.tools.length, 'peptide', 'peptide_gene_summary_table')\">Peptide Gene\n                      Summary Table - Peptide\n                    </button>\n                  </mat-menu>\n\n                  <!--  pepcomp    -->\n                  <button *ngIf=\"stages[stages.length-1].tool_group === 'peptide_variant_comparison'\" class='btn btn-lg btn-dark-blue-grey text-white'\n                          [disabled]=\"!tools[tools.length-1].submitted\"\n                          [matMenuTriggerFor]=\"pepcomp_valid_steps\">\n                    +\n                  </button>\n                  <!-- # sub-menu -->\n                  <mat-menu #pepcomp_valid_steps=\"matMenu\">\n                    <button mat-menu-item [matMenuTriggerFor]=\"pepcomp_mhci_inputs\"\n                            [disabled]=\"addedToolGroups.includes('mhci')\">T Cell Prediction - Class I\n                    </button>\n                    <button mat-menu-item [matMenuTriggerFor]=\"pepcomp_cluster_inputs\"\n                            [disabled]=\"addedToolGroups.includes('cluster')\">Cluster\n                    </button>\n                    <button mat-menu-item [matMenuTriggerFor]=\"pepcomp_pepmatch_inputs\"\n                            [disabled]=\"addedToolGroups.includes('pepmatch')\">Pepmatch\n                    </button>\n                    <button mat-menu-item [matMenuTriggerFor]=\"pepcomp_pepx_inputs\"\n                            [disabled]=\"addedToolGroups.includes('pepx')\">PepX\n                    </button>\n                  </mat-menu>\n\n                  <mat-menu #pepcomp_mhci_inputs=\"matMenu\">\n                    <button mat-menu-item (click)=\"addTCellPrediction(this.tools.length, 'peptide-peptidea')\">Peptide Table - Peptide A</button>\n                    <button mat-menu-item (click)=\"addTCellPrediction(this.tools.length, 'peptide-peptideb')\">Peptide Table - Peptide B</button>\n                  </mat-menu>\n                  <mat-menu #pepcomp_cluster_inputs=\"matMenu\">\n                    <button mat-menu-item (click)=\"addCluster(this.tools.length, 'peptide-peptidea')\">Peptide Table - Peptide A</button>\n                    <button mat-menu-item (click)=\"addCluster(this.tools.length, 'peptide-peptideb')\">Peptide Table - Peptide B</button>\n                  </mat-menu>\n                  <mat-menu #pepcomp_pepmatch_inputs=\"matMenu\">\n                    <button mat-menu-item (click)=\"addPepmatch(this.tools.length, 'peptide-peptidea')\">Peptide Table - Peptide A</button>\n                    <button mat-menu-item (click)=\"addPepmatch(this.tools.length, 'peptide-peptideb')\">Peptide Table - Peptide B</button>\n                  </mat-menu>\n                  <mat-menu #pepcomp_pepx_inputs=\"matMenu\">\n                    <button mat-menu-item (click)=\"addPepX(this.tools.length, 'peptide-peptidea')\">Peptide Table - Peptide A</button>\n                    <button mat-menu-item (click)=\"addPepX(this.tools.length, 'peptide-peptideb')\">Peptide Table - Peptide B</button>\n                  </mat-menu>\n\n                  <!--  mutgen    -->\n                  <button *ngIf=\"stages[stages.length-1].tool_group === 'mutgen'\" class='btn btn-lg btn-dark-blue-grey text-white'\n                          [disabled]=\"!tools[tools.length-1].submitted\"\n                          [matMenuTriggerFor]=\"mutgen_valid_steps\">\n                    +\n                  </button>\n                  <!-- # sub-menu -->\n                  <mat-menu #mutgen_valid_steps=\"matMenu\">\n                    <button mat-menu-item [matMenuTriggerFor]=\"mutgen_mhci_inputs\"\n                            [disabled]=\"addedToolGroups.includes('mhci')\">T Cell Prediction - Class I\n                    </button>\n                    <button mat-menu-item [matMenuTriggerFor]=\"mutgen_cluster_inputs\"\n                            [disabled]=\"addedToolGroups.includes('cluster')\">Cluster\n                    </button>\n                    <button mat-menu-item [matMenuTriggerFor]=\"mutgen_pepmatch_inputs\"\n                            [disabled]=\"addedToolGroups.includes('pepmatch')\">Pepmatch\n                    </button>\n                    <button mat-menu-item [matMenuTriggerFor]=\"mutgen_pepx_inputs\"\n                            [disabled]=\"addedToolGroups.includes('pepx')\">PepX\n                    </button>\n                    <button mat-menu-item [matMenuTriggerFor]=\"mutgen_peptide_variant_comparison_inputs\"\n                            [disabled]=\"addedToolGroups.includes('pepx')\">Peptide Variant Comparison\n                    </button>\n                  </mat-menu>\n\n                  <mat-menu #mutgen_mhci_inputs=\"matMenu\">\n                    <button mat-menu-item (click)=\"addTCellPrediction(this.tools.length, 'reference_peptide', 'unique_peptide')\">Unique Peptides - Reference Peptide</button>\n                    <button mat-menu-item (click)=\"addTCellPrediction(this.tools.length, 'mutant_peptide', 'unique_peptide')\">Unique Peptides - Mutant Peptide</button>\n                    <button mat-menu-item (click)=\"addTCellPrediction(this.tools.length, 'reference_peptide', 'peptide')\">All Peptide Table - Reference Peptide</button>\n                    <button mat-menu-item (click)=\"addTCellPrediction(this.tools.length, 'mutant_peptide', 'peptide')\">All Peptide Table - Mutant Peptide</button>\n                  </mat-menu>\n                  <mat-menu #mutgen_cluster_inputs=\"matMenu\">\n                    <button mat-menu-item (click)=\"addCluster(this.tools.length, 'reference_peptide', 'unique_peptide')\">Unique Peptides - Reference Peptide</button>\n                    <button mat-menu-item (click)=\"addCluster(this.tools.length, 'mutant_peptide', 'unique_peptide')\">Unique Peptides - Mutant Peptide</button>\n                    <button mat-menu-item (click)=\"addCluster(this.tools.length, 'reference_peptide', 'peptide')\">All Peptide Table - Reference Peptide</button>\n                    <button mat-menu-item (click)=\"addCluster(this.tools.length, 'mutant_peptide', 'peptide')\">All Peptide Table - Mutant Peptide</button>\n                  </mat-menu>\n                  <mat-menu #mutgen_pepmatch_inputs=\"matMenu\">\n                    <button mat-menu-item (click)=\"addPepmatch(this.tools.length, 'reference_peptide', 'unique_peptide')\">Unique Peptides - Reference Peptide</button>\n                    <button mat-menu-item (click)=\"addPepmatch(this.tools.length, 'mutant_peptide', 'unique_peptide')\">Unique Peptides - Mutant Peptide</button>\n                    <button mat-menu-item (click)=\"addPepmatch(this.tools.length, 'reference_peptide', 'peptide')\">All Peptide Table - Reference Peptide</button>\n                    <button mat-menu-item (click)=\"addPepmatch(this.tools.length, 'mutant_peptide', 'peptide')\">All Peptide Table - Mutant Peptide</button>\n                  </mat-menu>\n                  <mat-menu #mutgen_pepx_inputs=\"matMenu\">\n                    <button mat-menu-item (click)=\"addPepX(this.tools.length, 'reference_peptide', 'unique_peptide')\">Unique Peptides - Reference Peptide</button>\n                    <button mat-menu-item (click)=\"addPepX(this.tools.length, 'mutant_peptide', 'unique_peptide')\">Unique Peptides - Mutant Peptide</button>\n                    <button mat-menu-item (click)=\"addPepX(this.tools.length, 'reference_peptide', 'peptide')\">All Peptide Table - Reference Peptide</button>\n                    <button mat-menu-item (click)=\"addPepX(this.tools.length, 'mutant_peptide', 'peptide')\">All Peptide Table - Mutant Peptide</button>\n                  </mat-menu>\n                  <mat-menu #mutgen_peptide_variant_comparison_inputs=\"matMenu\">\n                    <button mat-menu-item (click)=\"addPepComp(this.tools.length, 'unique_peptide', 'reference_peptide', 'mutant_peptide')\">Unique Peptides - Reference Peptide + Mutant Peptide</button>\n                    <button mat-menu-item (click)=\"addPepComp(this.tools.length, 'peptide', 'reference_peptide', 'mutant_peptide')\">All Peptide Table - Reference Peptide + Mutant Peptide</button>\n                  </mat-menu>\n\n                  <button type=\"button\" class=\"btn btn-sm\" placement=\"bottom-left\"\n                          [ngbPopover]=\"popOverContent\"\n                          popoverTitle=\"add a step to the pipeline\">\n                    <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n                         class=\"bi bi-info-circle\"\n                         viewBox=\"0 0 16 16\">\n                      <path d=\"M8 15A7 7 0 1 1 8 1a7 7 0 0 1 0 14zm0 1A8 8 0 1 0 8 0a8 8 0 0 0 0 16z\"/>\n                      <path\n                        d=\"m8.93 6.588-2.29.287-.082.38.45.083c.294.07.352.176.288.469l-.738 3.468c-.194.897.105 1.319.808 1.319.545 0 1.178-.252 1.465-.598l.088-.416c-.2.176-.492.246-.686.246-.275 0-.375-.193-.304-.533L8.93 6.588zM9 4.5a1 1 0 1 1-2 0 1 1 0 0 1 2 0z\"/>\n                    </svg>\n                  </button>\n                  <ng-template #popOverContent>\n                    <a target=\"_blank\"\n                       href=\"https://nextgen-tools.iedb.org/docs/pipelines/index.html#building-a-pipeline\">\n                      Documentation\n                    </a>\n                  </ng-template>\n                </div>\n                <!--Run Button -->\n                <!--            tools[tools.length-1].-->\n                <span *ngIf=\"pipelineLoading; else elseBlock\">\n                <button type=\"button\" class=\"btn btn-danger btn-lg\" (click)=\"onCancelRuns()\"> Cancel Run </button>\n            </span>\n                <ng-template #elseBlock>\n                  <div *ngIf=\"tools.length-1 !==0 ; else runButtonBlock\" class=\"btn-group\">\n                    <div class=\"btn-group\">\n                      <!--                <button type=\"submit\" class=\"run-button btn btn-primary btn-lg text-white\"-->\n                      <!--                        [disabled]=\"tools[tools.length-1].loading\"-->\n                      <!--                  >-->\n                      <!--                  &lt;!&ndash;                        (index>0 && !tools[index-1].submitted)&ndash;&gt;-->\n                      <!--                  <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\" class=\"bi bi-play-fill\" viewBox=\"0 0 16 16\">-->\n                      <!--                    <path d=\"m11.596 8.697-6.363 3.692c-.54.313-1.233-.066-1.233-.697V4.308c0-.63.692-1.01 1.233-.696l6.363 3.692a.802.802 0 0 1 0 1.393z\"/>-->\n                      <!--                  </svg>-->\n                      <!--                </button>-->\n\n                      <button class=\"btn btn-lg btn-dark-blue-grey text-white\" (click)=\"emitEventToChild()\">\n                        <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n                             class=\"bi bi-play-fill\" viewBox=\"0 0 16 16\">\n                          <path\n                            d=\"m11.596 8.697-6.363 3.692c-.54.313-1.233-.066-1.233-.697V4.308c0-.63.692-1.01 1.233-.696l6.363 3.692a.802.802 0 0 1 0 1.393z\"/>\n                        </svg>\n                      </button>\n\n                      <button type=\"button\" class=\"btn btn-dark-blue-grey text-white dropdown-toggle dropdown-toggle-split\"\n                              data-toggle=\"dropdown\"\n                              data-bs-toggle=\"dropdown\"\n                              aria-haspopup=\"true\" aria-expanded=\"false\">\n                      </button>\n                      <div class=\"dropdown-menu\">\n                        <a class=\"dropdown-item text-black\" (click)=\"emitRunAllToChild()\">Run All Above</a>\n                      </div>\n                    </div>\n                  </div>\n                  <ng-template #runButtonBlock>\n                    <!--              (index>0 && !tools[index-1].submitted) ||-->\n                    <!--              <button type=\"submit\" class=\"run-button btn btn-primary btn-lg text-white\"-->\n                    <!--                      [disabled]=\"tools[tools.length-1].loading\"-->\n                    <!--              >-->\n                    <!--                <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\" class=\"bi bi-play-fill\" viewBox=\"0 0 16 16\">-->\n                    <!--                  <path d=\"m11.596 8.697-6.363 3.692c-.54.313-1.233-.066-1.233-.697V4.308c0-.63.692-1.01 1.233-.696l6.363 3.692a.802.802 0 0 1 0 1.393z\"/>-->\n                    <!--                </svg>-->\n                    <!--              </button>-->\n\n                    <button class=\"btn btn-lg btn-dark-blue-grey text-white\" [disabled]=\"tools[tools.length-1].loading\"\n                            (click)=\"emitEventToChild()\">\n                      <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n                           class=\"bi bi-play-fill\" viewBox=\"0 0 16 16\">\n                        <path\n                          d=\"m11.596 8.697-6.363 3.692c-.54.313-1.233-.066-1.233-.697V4.308c0-.63.692-1.01 1.233-.696l6.363 3.692a.802.802 0 0 1 0 1.393z\"/>\n                      </svg>\n                    </button>\n                  </ng-template>\n                </ng-template>\n              </div>\n\n            </ng-template>\n          </div>\n        </div>\n      </div>\n    </div>\n\n    <!--    <div> &lt;!&ndash; onRun()&ndash;&gt;-->\n    <!--      <button class=\"btn btn-danger\" (click)=\"debug()\"> Debug</button>-->\n    <!--    </div>-->\n\n  </mat-drawer>\n  <mat-drawer-content>\n    <div class=\"row fixed-top\" style=\"margin-top: 91px; margin-left: 15px\">\n      <div class=\"d-flex\">\n        <button class=\"btn btn-dark-blue-grey text-white\" *ngIf=\"!sidebarOpened\" (click)=\"sidebarOpened=!sidebarOpened\"> >></button>\n      </div>\n    </div>\n\n    <ng-container [formGroup]=\"rootForm\">\n      <ng-container *ngFor=\"let stage of stages$ | async; let i=index;\">\n        <app-t-cell-prediction\n          formGroupName=\"mhci\"\n          [resultUrl]=\"stage.result_url\"\n          [index]=\"i\"\n          (emitIndex)=\"onRunAll(i)\"\n          (emitOnCancel)=\"onCancelRuns()\"\n          *ngIf=\"stage.tool_group==='mhci'\"\n          (openEmailModal)=onOpenEmailModal()\n          [emailForm]=\"emailForm\"\n          [events]=\"runTCellSubject.asObservable()\"\n          [runAllEvent]=\"runAllTCellSubject.asObservable()\"></app-t-cell-prediction>\n        <!--        [showEmailModal]=\"showEmailModal\"-->\n        <!--        (shoeEmailModalChange)=\"onShowEmailChange($event)\"-->\n        <app-cluster\n          formGroupName=\"cluster\"\n          [resultUrl]=\"stage.result_url\"\n          [index]=\"i\"\n          (emitIndex)=\"onRunAll(i)\"\n          (emitOnCancel)=\"onCancelRuns()\"\n          *ngIf=\"stage.tool_group==='cluster'\"\n          (openEmailModal)=onOpenEmailModal()\n          [emailForm]=\"emailForm\"\n          [events]=\"runClusterSubject.asObservable()\"\n          [runAllEvent]=\"runAllClusterSubject.asObservable()\"></app-cluster>\n        <!--        [showEmailModal]=\"showEmailModal\"-->\n        <!--        (shoeEmailModalChange)=\"onShowEmailChange($event)\"-->\n        <app-pepmatch\n          formGroupName=\"pepmatch\"\n          [resultUrl]=\"stage.result_url\"\n          [index]=\"i\"\n          (emitIndex)=\"onRunAll(i)\"\n          (emitOnCancel)=\"onCancelRuns()\"\n          *ngIf=\"stage.tool_group==='pepmatch'\"\n          (openEmailModal)=onOpenEmailModal()\n          [emailForm]=\"emailForm\"\n          [events]=\"runPepmatchSubject.asObservable()\"\n          [runAllEvent]=\"runAllPepmatchSubject.asObservable()\"></app-pepmatch>\n        <app-pepx\n          formGroupName=\"pepx\"\n          [resultUrl]=\"stage.result_url\"\n          [index]=\"i\"\n          (emitIndex)=\"onRunAll(i)\"\n          (emitOnCancel)=\"onCancelRuns()\"\n          *ngIf=\"stage.tool_group==='pepx'\"\n          (openEmailModal)=onOpenEmailModal()\n          [emailForm]=\"emailForm\"\n          [events]=\"runPepxSubject.asObservable()\"\n          [runAllEvent]=\"runAllPepxSubject.asObservable()\"></app-pepx>\n        <app-peptide-variant-comparison\n          formGroupName=\"pepcomp\"\n          [resultUrl]=\"stage.result_url\"\n          [index]=\"i\"\n          (emitIndex)=\"onRunAll(i)\"\n          (emitOnCancel)=\"onCancelRuns()\"\n          *ngIf=\"stage.tool_group==='peptide_variant_comparison'\"\n          (openEmailModal)=onOpenEmailModal()\n          [emailForm]=\"emailForm\"\n          [events]=\"runPepcompSubject.asObservable()\"\n          [runAllEvent]=\"runAllPepcompSubject.asObservable()\"></app-peptide-variant-comparison>\n        <app-mutated-peptide-generator\n          formGroupName=\"mutgen\"\n          [resultUrl]=\"stage.result_url\"\n          [index]=\"i\"\n          (emitIndex)=\"onRunAll(i)\"\n          (emitOnCancel)=\"onCancelRuns()\"\n          *ngIf=\"stage.tool_group==='mutgen'\"\n          (openEmailModal)=onOpenEmailModal()\n          [emailForm]=\"emailForm\"\n          [events]=\"runMutgenSubject.asObservable()\"\n          [runAllEvent]=\"runAllMutgenSubject.asObservable()\"></app-mutated-peptide-generator>\n\n      </ng-container>\n    </ng-container>\n\n    <!--  DEBUGGER -->\n    <!--    <pre style=\"margin-top:50px; border: 1px solid red; width: fit-content\">-->\n    <!--      {{rootForm.value | json}}-->\n    <!--    </pre>-->\n  </mat-drawer-content>\n</mat-drawer-container>\n\n<!--Alert Modal -->\n<ng-template #alertModal let-modal4>\n  <div class=\"modal-header\">\n    <h4 class=\"modal-title\" id=\"alert-modal-title\">Missing/Invalid Parameters</h4>\n    <button type=\"button\" class=\"btn-close\" aria-label=\"Close\" (click)=\"modal4.dismiss('Cross click')\">\n    </button>\n  </div>\n  <div class=\"modal-body\">\n    <p> Please address the following issues in order for the pipeline to run:</p>\n    <ngb-accordion #acc=\"ngbAccordion\">\n      <!--  Error -->\n      <ngb-panel *ngIf=\"errorMessages.length\" id=\"error-accordion\">\n        <!--    Header -->\n        <ng-template ngbPanelHeader let-opened=\"opened\">\n          <div class=\"d-flex align-items-center justify-content-center\">\n            <span class=\"text-danger\">Errors ({{ errorMessages.length }})</span>\n            <button ngbPanelToggle class=\"btn btn-link\" style=\"color: #dc3545;\">\n              <div *ngIf=\"!opened\">\n                <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n                     class=\"bi bi-arrow-left-circle-fill\" viewBox=\"0 0 16 16\">\n                  <path\n                    d=\"M8 0a8 8 0 1 0 0 16A8 8 0 0 0 8 0zm3.5 7.5a.5.5 0 0 1 0 1H5.707l2.147 2.146a.5.5 0 0 1-.708.708l-3-3a.5.5 0 0 1 0-.708l3-3a.5.5 0 1 1 .708.708L5.707 7.5H11.5z\"/>\n                </svg>\n              </div>\n              <svg *ngIf=\"opened\" xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n                   class=\"bi bi-arrow-down-circle-fill\" viewBox=\"0 0 16 16\">\n                <path\n                  d=\"M16 8A8 8 0 1 1 0 8a8 8 0 0 1 16 0zM8.5 4.5a.5.5 0 0 0-1 0v5.793L5.354 8.146a.5.5 0 1 0-.708.708l3 3a.5.5 0 0 0 .708 0l3-3a.5.5 0 0 0-.708-.708L8.5 10.293V4.5z\"/>\n              </svg>\n            </button>\n          </div>\n        </ng-template>\n        <!--    Content -->\n        <ng-template ngbPanelContent>\n          <ol>\n            <li *ngFor=\"let message of errorMessages; let i=index;\">{{ message }}</li>\n          </ol>\n        </ng-template>\n      </ngb-panel>\n      <!--  Warning -->\n      <ngb-panel *ngIf=\"warningMessages.length\" id=\"warning-accordion\">\n        <!--    Header -->\n        <ng-template ngbPanelHeader let-opened=\"opened\" [class.collapsed]=\"!opened\">\n          <div class=\"d-flex align-items-center justify-content-center\">\n            <span class=\"text-warning\">Warnings ({{ warningMessages.length }}) </span>\n            <button ngbPanelToggle class=\"btn btn-link\" style=\"color: #f0ad4d;\">\n              <div *ngIf=\"!opened\">\n                <svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n                     class=\"bi bi-arrow-left-circle-fill\" viewBox=\"0 0 16 16\">\n                  <path\n                    d=\"M8 0a8 8 0 1 0 0 16A8 8 0 0 0 8 0zm3.5 7.5a.5.5 0 0 1 0 1H5.707l2.147 2.146a.5.5 0 0 1-.708.708l-3-3a.5.5 0 0 1 0-.708l3-3a.5.5 0 1 1 .708.708L5.707 7.5H11.5z\"/>\n                </svg>\n              </div>\n              <svg *ngIf=\"opened\" xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" fill=\"currentColor\"\n                   class=\"bi bi-arrow-down-circle-fill\" viewBox=\"0 0 16 16\">\n                <path\n                  d=\"M16 8A8 8 0 1 1 0 8a8 8 0 0 1 16 0zM8.5 4.5a.5.5 0 0 0-1 0v5.793L5.354 8.146a.5.5 0 1 0-.708.708l3 3a.5.5 0 0 0 .708 0l3-3a.5.5 0 0 0-.708-.708L8.5 10.293V4.5z\"/>\n              </svg>\n            </button>\n          </div>\n        </ng-template>\n        <!--    Content -->\n        <ng-template ngbPanelContent>\n          <ol>\n            <li *ngFor=\"let message of warningMessages; let i=index;\">{{ message }}</li>\n          </ol>\n        </ng-template>\n      </ngb-panel>\n    </ngb-accordion>\n  </div>\n  <div class=\"modal-footer\">\n  </div>\n</ng-template>\n\n<!--Email Modal-->\n<ng-template #emailModal let-modal3>\n  <div class=\"modal-header\">\n    <h4 class=\"modal-title\" id=\"modal-email-title\">\n      Pipeline Name and Email\n    </h4>\n    <button type=\"button\" id=\"emailModalCloseButton\" class=\"btn-close\" aria-label=\"Close\"\n            (click)=\"modal3.dismiss('Cross click');\">\n    </button>\n  </div>\n  <form [formGroup]=\"emailForm\" (ngSubmit)=\"onSubmitEmailModal()\">\n    <div class=\"modal-body\">\n      <p>\n        Add or change the pipeline title and email address and we will send you an email when your job has finished.\n      </p>\n      <div class=\"clearfix\"></div>\n      <div class=\"form-group row\">\n        <label for=\"pipelineName\" class=\"col-sm-2 col-form-label font-weight-bold\">Pipeline Name</label>\n        <div class=\"col-sm-10\">\n          <input id=\"pipelineName\" type=\"text\" class=\"form-control\" formControlName=\"name\"/>\n        </div>\n      </div>\n      <div class=\"form-group row\">\n        <label for=\"email\" class=\"col-sm-2 col-form-label font-weight-bold\">Email</label>\n        <div class=\"col-sm-10\">\n          <input type=\"email\"\n                 id=\"email\"\n                 class=\"form-control\"\n                 formControlName=\"email\"\n                 placeholder=\"Ex: abc@lji.org\"/>\n        </div>\n      </div>\n    </div>\n    <div class=\"modal-footer\">\n      <button type=\"submit\" class=\"btn btn-dark-blue-grey text-white\">Submit</button>\n    </div>\n  </form>\n</ng-template>\n\n","import {Component, ElementRef, OnDestroy, OnInit, ViewChild} from '@angular/core';\nimport { Title } from '@angular/platform-browser';\n\nimport Stage from \"../_global/Stage\";\nimport {Observable, Subject} from \"rxjs\";\nimport {UntypedFormBuilder, UntypedFormControl, UntypedFormGroup, Validators} from \"@angular/forms\";\nimport {PipelineService} from \"../services/pipeline-service/pipeline.service\";\nimport {PipelineStateService} from \"../services/state-services/pipeline-state-service/pipeline-state.service\";\nimport {ActivatedRoute, Router, Params} from \"@angular/router\";\nimport {HttpClient} from \"@angular/common/http\";\nimport {takeUntil} from \"rxjs/operators\";\nimport Allele from \"../_global/Allele\";\nimport _ from 'lodash';\n\nimport * as pipelineData from \"../services/data/pipeline-example.json\";\nimport * as clusterData from \"../services/data/cluster-sample.json\";\nimport * as tCellData from \"../services/data/t-cell-sample.json\";\nimport * as pepmatchiData from \"../services/data/pepmatch-mismatch-sample.json\";\nimport * as pepxData from \"../services/data/pepx-sample.json\";\nimport * as peptideBindingComparisonData from \"../services/data/pepcomp-sample.json\";\n\n\nimport {environment} from \"../../environments/environment\";\nimport Tool from \"../_global/Tool\";\nimport PipelineParams from \"../_global/PipelineParams\";\nimport {Location} from \"@angular/common\";\nimport {GoogleAnalyticsService} from \"ngx-google-analytics\";\n\nimport {NgbModal} from \"@ng-bootstrap/ng-bootstrap\";\n// import * as sarsSampleData from \"../services/data/t-cell-sample.json\";\n\nimport {\n  initClusterState,\n  initParams,\n  initPepMatchState,\n  initTCellPredictionState,\n  initPepXState,\n  initPeptideBindingComparisonState,\n  initMutatedPeptideGeneratorState,\n} from \"../services/state-services/default-stage-states\";\n\n@Component({\n  selector: 'app-pipeline-new',\n  templateUrl: './pipeline-new.component.html',\n  styleUrls: ['./pipeline-new.component.scss']\n})\nexport class PipelineNewComponent implements OnInit, OnDestroy {\n\n  @ViewChild('alertModal') alertModal!: ElementRef;\n  @ViewChild('emailModal') emailModal!: ElementRef;\n\n  runTCellSubject: Subject<void> = new Subject<void>();\n  runClusterSubject: Subject<void> = new Subject<void>();\n  runPepmatchSubject: Subject<void> = new Subject<void>();\n  runPepxSubject: Subject<void> = new Subject<void>();\n  runPepcompSubject: Subject<void> = new Subject<void>();\n  runMutgenSubject: Subject<void> = new Subject<void>();\n\n  runAllTCellSubject: Subject<void> = new Subject<void>();\n  runAllClusterSubject: Subject<void> = new Subject<void>();\n  runAllPepmatchSubject: Subject<void> = new Subject<void>();\n  runAllPepxSubject: Subject<void> = new Subject<void>();\n  runAllPepcompSubject: Subject<void> = new Subject<void>();\n  runAllMutgenSubject: Subject<void> = new Subject<void>();\n\n  sidebarOpened = true;\n\n  // state\n  stages: Stage[] = []\n\n  tools: Tool[] = []\n  params!: PipelineParams\n  paramsString: string = ''\n  pipelineId: string = ''\n  pipelineUrl: string = ''\n  pipelineSpecUrl: string = ''\n  maxCharacters = 1000000\n  maxVcfLines = 5000\n\n  stages$: Observable<Stage[]> = this._stateService.stages$;\n  tools$: Observable<Tool[]> = this._stateService.tools$;\n  pipelineId$: Observable<string> = this._stateService.pipelineId$;\n  pipelineSpecId$: Observable<string> = this._stateService.pipelineSpecId$;\n  params$: Observable<PipelineParams> = this._stateService.params$;\n\n  /**\n   {\n  \"mhci\": [\n    {\n      \"valid_next_step\": \"cluster\",\n      \"columns_to_pipe\": [\n        \"peptide\"\n      ]\n    },\n    {\n      \"valid_next_step\": \"pepmatch\",\n      \"columns_to_pipe\": [\n        \"peptide\"\n      ]\n    }\n  ],\n  \"cluster\": [\n    {\n      \"valid_next_step\": \"mhci\",\n      \"columns_to_pipe\": [\n        \"peptide\",\n        \"cluster_consensus\"\n      ]\n    },\n    {\n      \"valid_next_step\": \"pepmatch\",\n      \"columns_to_pipe\": [\n        \"peptide\",\n        \"cluster_consensus\"\n      ]\n    }\n  ],\n  \"pepmatch\": [\n    {\n      \"valid_next_step\": \"mhci\",\n      \"columns_to_pipe\": [\n        \"peptide\"\n      ]\n    },\n    {\n      \"valid_next_step\": \"cluster\",\n      \"columns_to_pipe\": [\n        \"peptide\"\n      ]\n    }\n  ]\n}\n   * */\n  possibleInputsMHCI = [\n    {stage_type: 'prediction', tool_group: 'cluster', name: 'Cluster', enabled: true},\n  ]\n  possibleInputsCluster = [\n    {stage_type: 'prediction', tool_group: 'mhci', name: 'T-Cell Prediction', enabled: true},\n  ]\n\n  validSteps: object = {};\n\n  rootForm!: UntypedFormGroup;\n\n  emailForm!: UntypedFormGroup;\n  submittedEmailForm: { name: string, email: string } = {name: '', email: ''};\n\n  inputSequenceText = '';\n\n  unsubscribe$ = new Subject();\n\n  showEmailModal: boolean = false;\n\n  // get pipeline\n  loading: boolean = false\n  errorMessages: string[] = []\n  warningMessages: string[] = []\n\n  pipelineLoading = false;\n\n\n  constructor(\n    private _pipelineService: PipelineService,\n    private _stateService: PipelineStateService,\n    private fb: UntypedFormBuilder,\n    private modalService: NgbModal,\n    private router: Router, private activatedRoute: ActivatedRoute, private location: Location,\n    private http: HttpClient,\n    private titleService: Title,\n    protected $gaService: GoogleAnalyticsService\n  ) {\n    // console.log(this.router.getCurrentNavigation()!.extras.state);\n  }\n\n  ngOnInit(): void {\n    // this.$gaService.pageView('/pipeline-new', 'Teste de Title')\n\n\n    this.activatedRoute.params.subscribe((params: Params) => {\n      console.log(params)\n      const id = params['id'];\n      if (id) {\n        this.loading = true;\n        this._pipelineService.getPipeline(id).subscribe({\n          next: (resp) => {\n            /**\n             if pipeline doesn't exist, navigate back to /pipeline\n\n             {\n             \"errors\": [\n             \"pipeline: aaaa4968-744f-49e9-be96-95d49a does not exist\"\n             ]\n             }\n             */\n            if (resp.errors) {\n              this.router.navigate(['/error'])\n            }\n\n            console.log(JSON.stringify(resp, null, 2));\n\n            this._stateService.setPipelineId(id);\n            this._stateService.setPipelineIdToParams(id);\n            this._stateService.setPipelineSpecId(resp.pipeline_spec_id);\n\n            /** set emailForm and submittedEmailForm */\n            // const emailValue = {\n            //   email: resp.email,\n            //   name: resp.pipeline_title\n            // }\n            // this.emailForm.setValue(emailValue)\n            // this.submittedEmailForm = emailValue\n\n            /** stages */\n            const stages = resp.stages;\n            this.initPipeline(stages)\n            this.titleService.setTitle(`${stages[0].stage_display_name}`)\n          },\n          error: (err) => {\n            console.error(err)\n          }\n        })\n      }\n\n      const specId = params['pipelineSpecId']\n      if (specId) {\n        console.log(specId)\n        this.loading = true;\n        this._pipelineService.getPipelineSpec(specId).subscribe((resp) => {\n\n          console.log(JSON.stringify(resp, null, 2));\n\n          /** stages */\n          const stages = resp.pipeline_params.stages;\n          this.initPipeline(stages)\n\n          this.titleService.setTitle(`${stages[0].stage_display_name}`);\n        })\n\n        this.location.replaceState('pipeline');\n\n      }\n\n      this.fetchValidSteps();\n      this.stages$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n        console.log(value);\n        this.stages = value;\n      })\n      this.tools$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n        console.log(value);\n        this.tools = value;\n        !id && !specId && value.length === 1 && !value[0].submitted && !value[0].loading && this.setInitialForm(value[0]);\n\n        this.pipelineLoading = _.some(this.tools, {loading: true})\n      })\n      this.params$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n        console.log(value);\n        this.params = value;\n        this.paramsString = JSON.stringify(value, null, 2)\n      })\n\n      this.pipelineId$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n        console.log(`pipelineId=${value}`);\n        this.pipelineId = value;\n        this.pipelineUrl = `${window.location.origin}/pipeline/${value}`;\n      })\n\n      this.pipelineSpecId$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n        console.log(`pipelineSpecId=${value}`);\n        this.pipelineSpecUrl = `${window.location.origin}/pipeline_spec/${value}`;\n      })\n    })\n\n    this.activatedRoute.queryParamMap.subscribe(data => {\n      /**\n       * init pipeline setup\n       default) /pipeline\n       1) T-Cell Class I - http://localhost:4200/pipeline?tool=tc1\n       2) Cluster - http://localhost:4200/pipeline?tool=cluster\n       3) PEPMatch - http://localhost:4200/pipeline?tool=pepmatch\n       4) PepX - http://localhost:4200/pipeline?tool=pepx\n       5) Peptide Comparision - http://localhost:4200/pipeline?tool=pepvcomp\n       6) Mutated Peptide Generator - http://localhost:4200/pipeline?tool=mutpepgen\n       * */\n      const data1 = data\n      console.log(data1)\n      const initTool = data1.get('tool');\n      if(initTool) {\n        switch (data1.get('tool')) {\n          case 'cluster':\n            this.titleService.setTitle(`Epitope Cluster Analysis`);\n            const initClusterTool: Tool = {\n              name: 'Cluster',\n              toolGroup: 'cluster',\n              loading: false,\n              submitted: false,\n              appliedFilters: undefined,\n              disabled: false\n            }\n            this.setInitialStageAndToolGroup(initClusterState, initClusterTool);\n            break;\n          case 'tc1':\n            this.titleService.setTitle(`T Cell Prediction - Class I`);\n            const initTCellPredictionTool: Tool = {\n              name: 'T-Cell Prediction',\n              toolGroup: 'mhci',\n              loading: false,\n              submitted: false,\n              appliedFilters: undefined,\n              disabled: false\n            }\n            this.setInitialStageAndToolGroup(initTCellPredictionState, initTCellPredictionTool)\n            break\n          case 'pepmatch':\n            this.titleService.setTitle(`PEPMatch`);\n            const initPepmatchTool = {\n              name: 'Pepmatch',\n              toolGroup: 'pepmatch',\n              loading: false,\n              submitted: false,\n              appliedFilters: undefined,\n              disabled: false\n            }\n            this.setInitialStageAndToolGroup(initPepMatchState, initPepmatchTool)\n            break\n          case 'pepx': // http://localhost:4200/pipeline?tool=pepx\n            this.titleService.setTitle(`PepX`);\n            const initPepxTool = {\n              name: 'Pepx',\n              toolGroup: 'pepx',\n              loading: false,\n              submitted: false,\n              appliedFilters: undefined,\n              disabled: false\n            }\n            this.setInitialStageAndToolGroup(initPepXState, initPepxTool)\n            break\n          case 'pepvcomp': // http://localhost:4200/pipeline?tool=pepvcomp\n            this.titleService.setTitle(`Peptide Variant Comparison`);\n            const initPeptideVariantComparisonTool = {\n              name: 'Peptide Variant Comparison',\n              toolGroup: 'peptide_variant_comparison',\n              loading: false,\n              submitted: false,\n              appliedFilters: undefined,\n              disabled: false\n            }\n            this.setInitialStageAndToolGroup(initPeptideBindingComparisonState, initPeptideVariantComparisonTool)\n            break\n          case 'mutpepgen': // http://localhost:4200/pipeline?tool=mutpepgen\n            this.titleService.setTitle(`Mutated Peptide Generator`);\n            const initMPGTool = {\n              name: 'Mutated Peptide Generator',\n              toolGroup: 'mutgen',\n              loading: false,\n              submitted: false,\n              appliedFilters: undefined,\n              disabled: false\n            }\n            this.setInitialStageAndToolGroup(initMutatedPeptideGeneratorState, initMPGTool)\n            break\n          default:\n            this.location.replaceState('pipeline');\n            this.titleService.setTitle(`IEDB NG Tools Pipeline`);\n            break;\n        }\n      }\n    });\n\n\n    this.emailForm = this.fb.group({\n      email: '',\n      name: ''\n    });\n  }\n\n  emitEventToChild() {\n    // !tools[tools.length-1].submitted\n    if(this.tools[this.tools.length-1].toolGroup === 'mhci'){\n      this.runTCellSubject.next();\n    }\n    if(this.tools[this.tools.length-1].toolGroup === 'cluster'){\n      this.runClusterSubject.next();\n    }\n    if(this.tools[this.tools.length-1].toolGroup === 'pepmatch'){\n      this.runPepmatchSubject.next()\n    }\n    if(this.tools[this.tools.length-1].toolGroup === 'pepx'){\n      this.runPepxSubject.next()\n    }\n    if(this.tools[this.tools.length-1].toolGroup === 'peptide_variant_comparison'){\n      this.runPepcompSubject.next()\n    }\n    if(this.tools[this.tools.length-1].toolGroup === 'mutgen'){\n      this.runMutgenSubject.next()\n    }\n  }\n\n  emitRunAllToChild() {\n    if(this.tools[this.tools.length-1].toolGroup === 'mhci'){\n      this.runAllTCellSubject.next()\n    }\n    if(this.tools[this.tools.length-1].toolGroup === 'cluster'){\n      this.runAllClusterSubject.next();\n    }\n    if(this.tools[this.tools.length-1].toolGroup === 'pepmatch'){\n      this.runAllPepmatchSubject.next()\n    }\n    if(this.tools[this.tools.length-1].toolGroup === 'pepx'){\n      this.runAllPepxSubject.next()\n    }\n    if(this.tools[this.tools.length-1].toolGroup === 'peptide_variant_comparison'){\n      this.runAllPepcompSubject.next()\n    }\n    if(this.tools[this.tools.length-1].toolGroup === 'mutgen'){\n      this.runAllMutgenSubject.next()\n    }\n  }\n\n\n  generateStage(stage: any): Stage {\n    /**\n     * export default interface Stage {\n     *   stage_number: number // index\n     *   stage_type: string // prediction | filter\n     *   tool_group: string // mhci | cluster | ''\n     *   input_sequence_text?: string\n     *   input_stage_number?: number\n     *   data_to_pipe?: string\n     *   input_parameters: any\n     *   name: string\n     *   result_url?: string\n     * }\n     * */\n\n    return {\n      stage_display_name: stage.stage_display_name,\n      stage_number: stage.stage_number,\n      stage_type: stage.stage_type,\n      tool_group: stage.tool_group,\n      input_parameters: stage.input_parameters,\n      result_url: stage.stage_result_uri ? stage.stage_result_uri : undefined,\n      input_sequence_text: stage.input_sequence_text ? stage.input_sequence_text : undefined,\n      input_vcf_text: stage.input_vcf_text ? stage.input_vcf_text : undefined,\n      piped_data: stage.piped_data ? stage.piped_data : undefined,\n      // piped_input: stage.piped_input ? stage.piped_input : undefined,\n      table_state: stage.table_state ? stage.table_state : [\n        {\n          \"table\": \"\",\n          \"columns\": {}\n        }\n      ],\n      stage_messages: stage.stage_messages ? stage.stage_messages : {errors: [], warnings: []}\n    }\n  }\n\n  generateTool(stage: any, loading = true): Tool {\n    /**\n     *  toolGroup: 'mhci',\n     *   loading: false,\n     *   submitted: false,\n     *   appliedFilters: undefined,\n     *   disabled: false\n     * */\n    const appliedFilters = !_.isEmpty(stage.table_state[0]?.columns) || !_.isEmpty(stage.table_state[1]?.columns)\n    return {\n      name: stage.tool_group,\n      toolGroup: stage.tool_group,\n      loading,\n      appliedFilters,\n      disabled: false,\n      submitted: false,\n      input_data_uri: stage.input_data_uri ? stage.input_data_uri : undefined\n    }\n  }\n\n  initPipeline(stages: Stage[]) {\n    /**\n     * Used for GET Pipeline and PipelineSpec\n     * */\n    let finalStages: Stage[] = []\n    let paramStages: Stage[] = []\n    let finalTools: Tool[] = []\n    _.forEach(stages, (stage, i) => {\n\n      const newStage = this.generateStage(stage);\n\n      // this._stateService.setInitialStage(newStage);\n      finalStages.push(newStage)\n      paramStages.push({...newStage, result_url: undefined});\n\n      const newTool = this.generateTool(stage, !!this.pipelineId);\n      finalTools.push(newTool)\n\n      const data = stage.input_parameters;\n\n      // Sequence Input\n      const input_sequence_text = stage.input_sequence_text;\n\n      if (stage.tool_group === 'cluster') { // #1\n        if (stage.stage_number === 1) {\n          this.setClusterFormGroup(data, input_sequence_text);\n        } else {\n          this.setClusterFormGroup2(data)\n        }\n      } else if (stage.tool_group === 'mhci') { // #2\n        if (stage.stage_number === 1) {\n          this.setMhciFormGroup(data, input_sequence_text);\n        } else {\n          this.setMhciFormGroup2(data)\n        }\n      } else if (stage.tool_group === 'pepmatch') { // #3\n        if (stage.stage_number === 1) {\n          this.setPepmatchFormGroup(data, input_sequence_text);\n        } else {\n          this.setPepmatchFormGroup2(data)\n        }\n      } else if (stage.tool_group === 'pepx') { // # 4\n        if (stage.stage_number === 1) {\n          this.setPepXFormGroup(data, input_sequence_text);\n        } else {\n          this.setPepXFormGroup2(data)\n        }\n      } else if (stage.tool_group === 'peptide_variant_comparison') { // # 5\n        if (stage.stage_number === 1) {\n          this.setPepCompFormGroup(data, input_sequence_text);\n        } else {\n          this.setPepCompFormGroup2(data)\n        }\n      } else if (stage.tool_group === 'mutgen') { // # 6\n        const input_vcf_text = stage.input_vcf_text;\n        if (stage.stage_number === 1) {\n          this.setMutGenFormGroup(data, input_vcf_text);\n        } else {\n          // this.setPepXFormGroup2(data)\n        }\n      }\n    })\n\n    this._stateService.setTools(finalTools);\n    this._stateService.setStages(finalStages);\n    this._stateService.setStagesToParams(paramStages);\n\n    this.loading = false;\n  }\n\n  /** Pipeline Error Modal Functions */\n  open(content: any) {\n    this.modalService.open(content, {\n      ariaLabelledBy: 'modal-basic-title',\n      size: 'lg',\n      animation: true,\n      backdrop: \"static\"\n    }).result.then((result) => {\n      // this.closeResult = `Closed with: ${result}`;\n    }, (reason) => {\n      // this.alleleSearch.nativeElement.focus();\n      // this.closeResult = `Dismissed ${TCellPredictionComponent.getDismissReason(reason)}`;\n    });\n  }\n\n  /**\n   Set FormGroup\n   * */\n  setMhciFormGroup(data: any, inputSequenceText = '') {\n    console.log(data);\n    console.log(inputSequenceText);\n\n    const {alleles, predictors, peptide_length_range, break_peptides} = data;\n    // alleles\n    const allelesFormatted = _.map(alleles.split(','), (a: string) => {\n      return {label: a, synonym: null, score: null}\n    })\n\n    // predictors\n    const predictorsFormatted: UntypedFormGroup[] = _.map(predictors, (p) => {\n      if (p.type === 'binding') {\n        return this.mhcBindingFormGroup(p.method)\n      } else if (p.type === 'processing') {\n        return this.mhcIProcessingFormGroup(p)\n      } else if (p.type === 'immunogenicity') {\n        const {mask_choice, position_to_mask} = p;\n        return this.pmhcImmunogencityFormGroup(mask_choice, position_to_mask)\n      } else if (p.type === 'mhcnp') {\n        return this.mhcNpFormGroup()\n      }\n      return this.fb.group({})\n    });\n\n    const fg = this.addTCellPredictionFormGroup(\n      inputSequenceText,\n      peptide_length_range ? peptide_length_range[0] : 9,\n      peptide_length_range ? peptide_length_range[1] : 9,\n      allelesFormatted,\n      !peptide_length_range,\n      predictorsFormatted\n    )\n    let root_config = {mhci: fg}\n    this.rootForm = this.fb.group(root_config);\n  }\n\n  setMhciFormGroup2(data: any) {\n    console.log(data);\n\n    const {alleles, predictors, peptide_length_range, break_peptides} = data;\n\n    const allelesFormatted = _.map(alleles.split(','), (a: string) => {\n      return {label: a, synonym: null, score: null}\n    })\n\n    const predictorsFormatted: UntypedFormGroup[] = _.map(predictors, (p) => {\n      if (p.type === 'binding') {\n        return this.mhcBindingFormGroup(p.method)\n      } else if (p.type === 'processing') {\n        return this.mhcIProcessingFormGroup(p)\n      }\n      return this.fb.group({})\n    });\n\n    const initialControlConfig = {\n      peptideLength: new UntypedFormControl([\n        peptide_length_range ? peptide_length_range[0] : 9,\n        peptide_length_range ? peptide_length_range[1] : 9,\n      ]),\n      alleles: this.fb.array(allelesFormatted),\n      predictionModels: this.fb.array(predictorsFormatted),\n      breakPeptides: !peptide_length_range,\n    };\n\n    const fg = this.fb.group(initialControlConfig)\n    this.rootForm.addControl('mhci', fg);\n    // let root_config = {mhci: fg}\n    // this.rootForm = this.fb.group(root_config);\n  }\n\n  setClusterFormGroup(data: any, inputSequenceText = '') {\n    console.log(data);\n    const {cluster_pct_identity, predictors, peptide_length_range} = data;\n    const method = predictors[0].method;\n    // const allelesFormatted = _.map(alleles.split(','), (a: string) => {return {label: a, synonym: null, score: null}})\n\n\n    const fg = this.addClusterFormGroup(\n      inputSequenceText,\n      cluster_pct_identity,\n      peptide_length_range[0],\n      peptide_length_range[1],\n      method\n    )\n    let root_config = {cluster: fg}\n    this.rootForm = this.fb.group(root_config);\n  }\n\n  setClusterFormGroup2(data: any) {\n    console.log(data);\n    const {cluster_pct_identity, predictors, peptide_length_range} = data;\n    const method = predictors[0].method;\n    // const allelesFormatted = _.map(alleles.split(','), (a: string) => {return {label: a, synonym: null, score: null}})\n\n    let minPeptideLength = peptide_length_range[0];\n    let maxPeptideLength = peptide_length_range[1];\n\n    minPeptideLength = minPeptideLength === 0 ? 4 : minPeptideLength\n    maxPeptideLength = maxPeptideLength === 0 ? 26 : maxPeptideLength\n\n    /** state update*/\n    this._stateService.addStage({\n      stage_number: this.stages.length + 1,\n      stage_type: 'prediction',\n      tool_group: 'cluster',\n      stage_display_name: 'Epitope Cluster Analysis',\n      // data_to_pipe: 'peptide',\n      input_parameters: {}\n    })\n\n    this._stateService.insertTool({\n      name: 'Cluster',\n      toolGroup: 'cluster',\n      loading: false,\n      submitted: false,\n      disabled: false\n    }, this.tools.length)\n\n    this._stateService.setToolDisabled(true, this.tools.length - 1)\n\n    const initialControlConfig = {\n      threshold: cluster_pct_identity,\n      peptideLength: new UntypedFormControl([minPeptideLength, maxPeptideLength]),\n      method\n    };\n\n    const fg = this.fb.group(initialControlConfig)\n    // let root_config = {cluster: fg}\n    this.rootForm.addControl('cluster', fg);\n  }\n\n  setPepmatchFormGroup(data: any, inputSequenceText = '') {\n    console.log(data);\n    const {proteome, mismatch, best_match, include_unmatched_peptides} = data;\n    // const method = predictors[0].method;\n    const fg = this.addPepmatchFormGroup(\n      inputSequenceText,\n      proteome,\n      mismatch,\n      best_match,\n      include_unmatched_peptides\n    )\n    let root_config = {pepmatch: fg}\n    this.rootForm = this.fb.group(root_config);\n  }\n\n  setPepmatchFormGroup2(data: any) {\n    console.log(data);\n\n    /** state update*/\n    this._stateService.addStage({\n      stage_number: this.stages.length + 1,\n      stage_type: 'prediction',\n      tool_group: 'pepmatch',\n      stage_display_name: 'Pepmatch',\n      // data_to_pipe: 'peptide',\n      input_parameters: {}\n    })\n\n    this._stateService.insertTool({\n      name: 'Pepmatch',\n      toolGroup: 'pepmatch',\n      loading: false,\n      submitted: false,\n      disabled: false\n    }, this.tools.length)\n\n    const {proteome, mismatch, best_match, include_unmatched_peptides} = data;\n\n    const initialControlConfig = {\n      proteome,\n      mismatch,\n      bestMatch: best_match,\n      include_unmatched_peptides\n    };\n\n    const fg = this.fb.group(initialControlConfig)\n    this.rootForm.addControl('pepmatch', fg);\n  }\n\n  setPepXFormGroup(data: any, inputSequenceText = '') {\n    console.log(data);\n    const {qlevel, datasource, dataset_id } = data;\n    const fg = this.addPepXFormGroup(\n      inputSequenceText,\n      qlevel,\n      datasource,\n      dataset_id\n    )\n    let root_config = {pepx: fg}\n    this.rootForm = this.fb.group(root_config);\n  }\n\n  setPepXFormGroup2(data: any) {\n    console.log(data);\n\n    /** state update*/\n    this._stateService.addStage({\n      stage_number: this.stages.length + 1,\n      stage_type: 'prediction',\n      tool_group: 'pepx',\n      stage_display_name: 'PepX',\n      // data_to_pipe: 'peptide',\n      input_parameters: {}\n    })\n\n    this._stateService.insertTool({\n      name: 'PepX',\n      toolGroup: 'pepx',\n      loading: false,\n      submitted: false,\n      disabled: false\n    }, this.tools.length)\n\n    const {qlevel, datasource, dataset_id} = data;\n\n    const initialControlConfig = {\n      qlevel,\n      datasource,\n      dataset_id\n    };\n\n    const fg = this.fb.group(initialControlConfig)\n    this.rootForm.addControl('pepx', fg);\n  }\n\n  setPepCompFormGroup(data: any, inputSequenceText = '') {\n    console.log(data);\n    console.log(inputSequenceText);\n\n    const {alleles, predictors, break_peptides} = data;\n    // alleles\n    const allelesFormatted = _.map(alleles.split(','), (a: string) => {\n      return {label: a, synonym: null, score: null}\n    })\n\n    // predictors\n    const predictorsFormatted: UntypedFormGroup[] = _.map(predictors, (p) => {\n      if (p.type === 'binding') {\n        return this.mhcBindingFormGroup(p.method)\n      } else if (p.type === 'processing') {\n        return this.mhcIProcessingFormGroup(p)\n      } else if (p.type === 'immunogenicity') {\n        const {mask_choice, position_to_mask} = p;\n        return this.pmhcImmunogencityFormGroup(mask_choice, position_to_mask)\n      } else if (p.type === 'mhcnp') {\n        return this.mhcNpFormGroup()\n      }\n      return this.fb.group({})\n    });\n\n    const fg = this.initPepCompFormGroup(\n      inputSequenceText,\n      allelesFormatted,\n      predictorsFormatted\n    )\n    let root_config = {pepcomp: fg}\n    this.rootForm = this.fb.group(root_config);\n  }\n\n  setPepCompFormGroup2(data: any) {\n    console.log(data);\n\n    /** state update*/\n    this._stateService.addStage({\n      stage_number: this.stages.length + 1,\n      stage_type: 'prediction',\n      tool_group: 'peptide_variant_comparison',\n      stage_display_name: 'Peptide Variant Comparison',\n      input_parameters: {},\n      table_state: [{table: 'peptide_table', columns: {}}],\n      stage_messages: {errors: [], warnings: []}\n    })\n\n    this._stateService.insertTool({\n      name: 'Peptide Variant Comparison',\n      toolGroup: 'peptide_variant_comparison',\n      loading: false,\n      submitted: false,\n      appliedFilters: undefined,\n      disabled: false\n    }, this.tools.length)\n\n    const {alleles, predictors, break_peptides} = data;\n    // alleles\n    const allelesFormatted = _.map(alleles.split(','), (a: string) => {\n      return {label: a, synonym: null, score: null}\n    })\n\n    // predictors\n    const predictorsFormatted: UntypedFormGroup[] = _.map(predictors, (p) => {\n      if (p.type === 'binding') {\n        return this.mhcBindingFormGroup(p.method)\n      } else if (p.type === 'processing') {\n        return this.mhcIProcessingFormGroup(p)\n      } else if (p.type === 'immunogenicity') {\n        const {mask_choice, position_to_mask} = p;\n        return this.pmhcImmunogencityFormGroup(mask_choice, position_to_mask)\n      } else if (p.type === 'mhcnp') {\n        return this.mhcNpFormGroup()\n      }\n      return this.fb.group({})\n    });\n\n    const initialControlConfig = {\n      // inputSequenceText: [seq, Validators.maxLength(this.maxCharacters)],\n      // peptideLength: new UntypedFormControl([minPeptideLength, maxPeptideLength]),\n      alleles: this.fb.array(allelesFormatted),\n      predictionModels: this.fb.array(predictorsFormatted)\n    };\n\n\n    const fg = this.fb.group(initialControlConfig)\n    this.rootForm.addControl('pepcomp', fg);\n  }\n\n  setMutGenFormGroup(data: any, inputVcfText = '') {\n    // console.log(data);\n    // console.log(inputVcfText);\n    const {peptide_length, peptide_mutation_position1, peptide_mutation_position2,\n           frameshift_overlap, maximum_peptide_length} = data;\n\n    const fg = this.addMutGenFormGroup(\n      inputVcfText,\n      peptide_length,\n      peptide_mutation_position1,\n      peptide_mutation_position2,\n      frameshift_overlap,\n      maximum_peptide_length\n    )\n\n    let root_config = {mutgen: fg}\n    this.rootForm = this.fb.group(root_config);\n  }\n\n  ngOnDestroy() {\n    clearInterval(this._pipelineService.runSetInterval)\n    this.unsubscribe$.next();\n    this.unsubscribe$.complete();\n  }\n\n  get addedToolGroups() {\n    return _.map(this.stages, (o) => o.tool_group);\n  }\n\n  setInitialForm(stage: Tool) {\n    /**\n     Used to set rootForm with either 'mhci' or 'cluster'\n     * */\n    console.log(stage);\n    let root_config = {}\n    if (stage?.toolGroup === 'mhci') { // t-cell prediction\n      root_config = {mhci: this.addTCellPredictionFormGroup()}\n    } else if (stage?.toolGroup === 'cluster') { // cluster\n      root_config = {cluster: this.addClusterFormGroup()}\n    } else if (stage?.toolGroup === 'pepmatch') { // pepmatch\n      root_config = {pepmatch: this.addPepmatchFormGroup()}\n    } else if (stage?.toolGroup === 'pepx') { // pepx\n      root_config = {pepx: this.addPepXFormGroup()}\n    }\n    else if (stage?.toolGroup === 'peptide_variant_comparison') { // pepx\n      root_config = {pepcomp: this.addPepCompFormGroup()}\n    }\n    else if (stage?.toolGroup === 'mutgen') { // mutgen\n      root_config = {mutgen: this.addMutGenFormGroup()}\n    }\n    console.log(root_config);\n    this.rootForm = this.fb.group(root_config);\n  }\n\n  setInitialStageAndToolGroup(state: any, tool: any) {\n    /**\n     Mainly used in this.activatedRoute.queryParamMap.subscribe()\n     * */\n    const initState = _.cloneDeep(state)\n    // const initTool = _.cloneDeep(tool)\n\n    // const initState = JSON.parse(JSON.stringify(state))\n    // const initTool = JSON.parse(JSON.stringify(tool))\n\n    // const initState = Object.assign({}, state)\n    // const initTool = Object.assign({}, tool)\n\n    this._stateService.setInitialStage(initState)\n    this._stateService.setInitialTool(tool)\n    this._stateService.setParams(initParams)\n    this._stateService.setPipelineId('')\n    this._stateService.setPipelineSpecId('')\n  }\n\n  get tCellForm() {\n    return this.rootForm.get('mhci') as UntypedFormGroup;\n  }\n\n  get clusterForm() {\n    return this.rootForm.get('cluster') as UntypedFormGroup;\n  }\n\n  get pepmatchForm() {\n    return this.rootForm.get('pepmatch') as UntypedFormGroup;\n  }\n\n  get pepxForm() {\n    return this.rootForm.get('pepx') as UntypedFormGroup;\n  }\n\n  get pepcompForm() {\n    return this.rootForm.get('pepcomp') as UntypedFormGroup;\n  }\n\n  get mutgenForm() {\n    return this.rootForm.get('mutgen') as UntypedFormGroup;\n  }\n\n  get selectedAlleles() {\n    /**\n\n     * */\n    return this.tCellForm.controls['alleles'].value;\n  }\n\n  get selectedAlleles2() {\n    /**\n\n     * */\n    return this.pepcompForm.controls['alleles'].value;\n  }\n\n  get selectedAlleleLabels() {\n    /**\n     sidebar - Used to show min and max peptide length\n     * */\n    return this.tCellForm.controls['alleles'].value.map((o: Allele) => o.label).join(', ');\n  }\n\n  get predictionModels() {\n    /**\n     sidebar - Used to show min and max peptide length\n     * */\n    return this.tCellForm.controls['predictionModels'].value;\n  }\n\n  get predictionModels2() {\n    /**\n     sidebar - Used to show min and max peptide length\n     * */\n    return this.pepcompForm.controls['predictionModels'].value;\n  }\n\n  get clusterMinPeptideLength() {\n    return [4, 26].includes(this.clusterForm.controls['peptideLength'].value[0]) ?\n      0 : this.clusterForm.controls['peptideLength'].value[0]\n  }\n\n  get clusterMaxPeptideLength() {\n    return [4, 26].includes(this.clusterForm.controls['peptideLength'].value[1]) ?\n      0 : this.clusterForm.controls['peptideLength'].value[1]\n  }\n\n  debug() { // debugger\n    /** defaults - use Sars placeholders*/\n\n    console.log(this.inputSequenceText);\n    this.pipelineId$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n      console.log(`pipelineId=${value}`);\n    })\n    this.stages$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n      console.log('this.stages$');\n      console.log(value);\n    })\n    this.tools$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n      console.log('this.tools$');\n      console.log(value);\n    })\n    // this.inputSequenceText$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n    //   console.log(value);\n    // })\n    this.params$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n      console.log('this.params$');\n      console.log('params');\n      console.log(value);\n    })\n  }\n\n  onCancelRuns() {\n    /**\n     Sends a PUT request to change status to 'canceled'\n\n     Also stops\n     * */\n    const params = {\n      cancel_run: true\n    }\n\n    this._pipelineService.putPipeline(this.pipelineId, params).subscribe((resp) => {\n      console.log(resp)\n    })\n\n    _.forEach(this.tools, (tool, i) => {\n      console.log(tool)\n      const cancelTool = {\n        ...tool,\n        loading: false,\n      }\n      this._stateService.insertTool(cancelTool, i);\n    })\n  }\n\n  onShowEmailChange(e: boolean) {\n    console.log(e)\n    this.showEmailModal = e;\n  }\n\n  onOpenEmailModal() {\n    this.open(this.emailModal)\n  }\n\n  onRunAll(index: number) {\n    // debugger\n    // console.log(JSON.stringify(this.rootForm.value, null, 2));\n\n    $.fn.dataTable.ext.search = [];\n\n    const stage_number = index + 1;\n    /** run_stage_range */\n    const run_stage_range: [number, number] = [1, stage_number]\n\n    console.log(this.params);\n\n    const stages = this.stages.slice(0, stage_number)\n    console.log(stages);\n    this.params.run_stage_range = run_stage_range\n    let initTool: Tool;\n\n    _.forEach(this.stages, (stage, i) => {\n      console.log(stage)\n      const key = stage.tool_group\n\n      /** Input sequence text */\n\n      switch (key) {\n        case \"mhci\": {\n          if (i === 0) {\n            let seq: string = ''\n            let all: string = ''\n            if(environment.production || environment['name'] === 'DEV') { // prod or dev\n              const {input_sequence_text, alleles } = tCellData; // correct examples\n              seq = input_sequence_text\n              all = alleles\n            } else {\n              const {input_sequence_text, alleles } = pipelineData;\n              seq = input_sequence_text\n              all = alleles\n            }\n            // const {input_sequence_text} = tCellData;\n            let sequences = this.tCellForm.get('inputSequenceText')?.value;\n            if (!sequences) {\n              this._stateService.setInputSequenceText(seq); // TODO - delete (prob don't need)\n              this.tCellForm.controls.inputSequenceText.setValue(seq);\n              sequences = seq;\n            }\n            this.params.stages[i].input_sequence_text = sequences\n          }\n\n          if (i <= index) {\n            this.params.stages[i].input_parameters = this._pipelineService.convertTCellForm(this.tCellForm)\n            this._stateService.setToolLoading(true, false, i)\n          } else {\n            this.params.stages[i].input_parameters = {}\n            initTool = this.tools[i];\n            const unSubmittedTool = {\n              ...initTool,\n              loading: false,\n              submitted: false,\n            }\n            this._stateService.insertTool(unSubmittedTool, i);\n          }\n\n          break\n        }\n        case 'cluster': {\n          if (i === 0) {\n            const {input_sequence_text} = clusterData;\n            let sequences = this.clusterForm.get('inputSequenceText')?.value;\n            if (!sequences) {\n              this._stateService.setInputSequenceText(input_sequence_text); // TODO - delete (prob don't need)\n              this.clusterForm.controls.inputSequenceText.setValue(input_sequence_text);\n              sequences = input_sequence_text;\n            }\n            this.params.stages[i].input_sequence_text = sequences\n          }\n          if (i <= index) {\n            this.params.stages[i].input_parameters = this._pipelineService.convertClusterForm(this.clusterForm)\n            this._stateService.setToolLoading(true, false, i)\n          } else {\n            this.params.stages[i].input_parameters = {}\n            initTool = this.tools[i];\n            const unSubmittedTool = {\n              ...initTool,\n              loading: false,\n              submitted: false,\n            }\n            this._stateService.insertTool(unSubmittedTool, i);\n          }\n          break\n        }\n        case 'pepmatch': {\n\n          if (i === 0) {\n            const {input_sequence_text} = pepmatchiData;\n            let sequences = this.pepmatchForm.get('inputSequenceText')?.value;\n            if (!sequences) {\n              this._stateService.setInputSequenceText(input_sequence_text); // TODO - delete (prob don't need)\n              this.pepmatchForm.controls.inputSequenceText.setValue(input_sequence_text);\n              sequences = input_sequence_text;\n            }\n            this.params.stages[i].input_sequence_text = sequences\n          }\n          if (i <= index) {\n            this.params.stages[i].input_parameters = this._pipelineService.convertPepmatchForm(this.pepmatchForm)\n            this._stateService.setToolLoading(true, false, i)\n          } else {\n            this.params.stages[i].input_parameters = {}\n            initTool = this.tools[i];\n            const unSubmittedTool = {\n              ...initTool,\n              loading: false,\n              submitted: false,\n            }\n            this._stateService.insertTool(unSubmittedTool, i);\n          }\n          break\n        }\n        case 'pepx': {\n          if (i === 0) {\n            const {input_sequence_text} = pepxData;\n            let sequences = this.pepxForm.get('inputSequenceText')?.value;\n            if (!sequences) {\n              this._stateService.setInputSequenceText(input_sequence_text); // TODO - delete (prob don't need)\n              this.pepxForm.controls.inputSequenceText.setValue(input_sequence_text);\n              sequences = input_sequence_text;\n            }\n            this.params.stages[i].input_sequence_text = sequences\n          }\n          if (i <= index) {\n            this.params.stages[i].input_parameters = this._pipelineService.convertPepxForm(this.pepxForm)\n            this._stateService.setToolLoading(true, false, i)\n          } else {\n            this.params.stages[i].input_parameters = {}\n            initTool = this.tools[i];\n            const unSubmittedTool = {\n              ...initTool,\n              loading: false,\n              submitted: false,\n            }\n            this._stateService.insertTool(unSubmittedTool, i);\n          }\n          break\n        }\n        case 'peptide_variant_comparison': {\n          if (i === 0) {\n            const {input_sequence_text} = peptideBindingComparisonData;\n            let sequences = this.pepcompForm.get('inputSequenceText')?.value;\n            if (!sequences) {\n              this._stateService.setInputSequenceText(input_sequence_text); // TODO - delete (prob don't need)\n              this.pepcompForm.controls.inputSequenceText.setValue(input_sequence_text);\n              sequences = input_sequence_text;\n            }\n            this.params.stages[i].input_sequence_text = sequences\n          }\n          if (i <= index) {\n            this.params.stages[i].input_parameters = this._pipelineService.convertPepcompForm(this.pepcompForm)\n            this._stateService.setToolLoading(true, false, i)\n          } else {\n            this.params.stages[i].input_parameters = {}\n            initTool = this.tools[i];\n            const unSubmittedTool = {\n              ...initTool,\n              loading: false,\n              submitted: false,\n            }\n            this._stateService.insertTool(unSubmittedTool, i);\n          }\n          break\n        }\n        case 'mutgen': {\n          if (i === 0) {\n            let seq: string = ''\n            let all: string = ''\n            if(environment.production || environment['name'] === 'DEV') { // prod or dev\n              const {input_sequence_text, alleles } = tCellData; // correct examples\n              seq = input_sequence_text\n              all = alleles\n            } else {\n              const {input_sequence_text, alleles } = pipelineData;\n              seq = input_sequence_text\n              all = alleles\n            }\n            // const {input_sequence_text} = tCellData;\n            let sequences = this.mutgenForm.get('inputVcfText')?.value;\n            if (!sequences) {\n              this._stateService.setInputSequenceText(seq); // TODO - delete (prob don't need)\n              this.mutgenForm.controls.inputSequenceText.setValue(seq);\n              sequences = seq;\n            }\n            this.params.stages[i].input_sequence_text = sequences\n          }\n\n          if (i <= index) {\n            this.params.stages[i].input_parameters = this._pipelineService.convertMutgenForm(this.mutgenForm)\n            this._stateService.setToolLoading(true, false, i)\n          } else {\n            this.params.stages[i].input_parameters = {}\n            initTool = this.tools[i];\n            const unSubmittedTool = {\n              ...initTool,\n              loading: false,\n              submitted: false,\n            }\n            this._stateService.insertTool(unSubmittedTool, i);\n          }\n\n          break\n        }\n        default: {\n          break\n        }\n      }\n    })\n\n    this.params.pipeline_title = this.emailForm.controls['name'].value;\n    this.params.email = this.emailForm.controls['email'].value;\n\n\n    console.log(this.params);\n    this._stateService.setParams(this.params);\n\n    this.postPipelineAPI(this.params);\n  }\n\n  postPipelineAPI(params: PipelineParams, getResults: boolean = true) {\n    /**\n     * Run All Above Post Pipeline\n     * */\n    this._pipelineService.postPipeline(params).subscribe(\n      (resp) => {\n      console.log(resp);\n      if (resp.pipeline_id) {\n        this._stateService.setPipelineId(resp.pipeline_id);\n        this._stateService.setPipelineIdToParams(resp.pipeline_id);\n        this._stateService.setPipelineSpecId(resp.pipeline_spec_id);\n        this.location.replaceState(`pipeline/${resp.pipeline_id}`)\n        // this.titleService.setTitle(`IEDB NG Tools Pipeline`);\n\n        this._pipelineService.getPipeline(resp.pipeline_id).subscribe(value => {\n          console.log(value);\n          console.log(value.stages);\n          _.forEach(value.stages, (s, i: number) => {\n            console.log(i)\n            if (i===0) {\n              this.titleService.setTitle(`${s.stage_display_name}`)\n            }\n            this._stateService.changeResultUrl(s.stage_result_uri, i)\n          })\n        })\n      } else if (resp.errors || resp.warnings) {\n        this.errorMessages = resp.errors;\n        this.warningMessages = resp.warnings;\n        this.open(this.alertModal)\n        console.log(resp)\n      }\n    }, error => {\n        console.error(error)\n        this.errorMessages.push(error)\n        this.loading = false\n        // this.submitted = false\n        // this.tableStateSaving = false\n        // this.enableInputs()\n      });\n  }\n\n  fetchValidSteps() {\n    /**\n     /api/v1/pipeline/valid_steps\n     * */\n    const API_URL = `${environment['api_url']}/api/v1/pipeline/valid_steps`;\n    this.http.get(API_URL).subscribe(value => {\n      this.validSteps = value;\n      console.log(value);\n    })\n  }\n\n  addTCellPredictionFormGroup(\n    inputSequenceText = '',\n    minPeptideLength = 9,\n    maxPeptideLength = 9,\n    alleles: Allele[] = [],\n    breakPeptides: boolean = false,\n    predictions = [this.mhcBindingFormGroup()]\n  ) {\n    const seq = sessionStorage.getItem('sequences') ? sessionStorage.getItem('sequences') : inputSequenceText;\n    sessionStorage.removeItem('sequences');\n\n    const all = sessionStorage.getItem('selectedAlleles') ? JSON.parse(sessionStorage.getItem('selectedAlleles') as string) : alleles\n    sessionStorage.removeItem('selectedAlleles')\n\n    const initialControlConfig = {\n      inputSequenceText: [seq, Validators.maxLength(this.maxCharacters)],\n      peptideLength: new UntypedFormControl([minPeptideLength, maxPeptideLength]),\n      alleles: this.fb.array(all),\n      breakPeptides: breakPeptides,\n      predictionModels: this.fb.array(predictions)\n    };\n    return this.fb.group(initialControlConfig)\n  }\n\n  initPepCompFormGroup(\n    inputSequenceText = '',\n    // minPeptideLength = 9,\n    // maxPeptideLength = 9,\n    alleles: Allele[] = [],\n    // breakPeptides: boolean = false,\n    predictions = [this.mhcBindingFormGroup()]\n  ) {\n    const seq = sessionStorage.getItem('sequences') ? sessionStorage.getItem('sequences') : inputSequenceText;\n    sessionStorage.removeItem('sequences');\n\n    const all = sessionStorage.getItem('selectedAlleles') ? JSON.parse(sessionStorage.getItem('selectedAlleles') as string) : alleles\n    sessionStorage.removeItem('selectedAlleles')\n\n    const initialControlConfig = {\n      inputSequenceText: [seq, Validators.maxLength(this.maxCharacters)],\n      // peptideLength: new UntypedFormControl([minPeptideLength, maxPeptideLength]),\n      alleles: this.fb.array(all),\n      // breakPeptides: breakPeptides,\n      predictionModels: this.fb.array(predictions)\n    };\n    return this.fb.group(initialControlConfig)\n  }\n\n  removeToolFromPipeline(formControlName: string) {\n    /**\n     * pop - Remove an item from the end of an array (Tools)\n     2 situations:\n     When there is result\n     When there is no result.\n     * */\n    this._stateService.popStage()\n    this._stateService.popTool()\n    this._stateService.popStageFromParams()\n\n    this.rootForm.removeControl(formControlName)\n  }\n\n  addTCellPrediction(i: number, dataToPipe: string, tableName: string = 'peptide_table' ) {\n    const stage = {\n      stage_number: this.stages.length + 1,\n      stage_type: 'prediction',\n      tool_group: 'mhci',\n      piped_data: {piped_input: [\n        {\n          piped_fields: [`${tableName}.${dataToPipe}`],\n          piped_stage_number: i,\n        }\n      ]},\n      stage_display_name: 'T Cell Prediction - Class I',\n      input_parameters: {},\n      table_state: {columns: {}},\n      stage_messages: {errors: [], warnings: []},\n    }\n\n    this._stateService.addStage(stage)\n    this._stateService.addStageToParams(stage)\n\n    this._stateService.insertTool({\n      name: 'T-Cell Prediction',\n      toolGroup: 'mhci',\n      loading: false,\n      submitted: false,\n      disabled: false\n    }, i)\n    // this.stages.push({stage_number: 3, stage_type: 'prediction', tool_group: 'cluster', name: 'Cluster', input_parameters: {}});\n    const initialControlConfig = {\n      inputSequenceText: '',\n      // sequences: sessionStorage.getItem('sequences') ? sessionStorage.getItem('sequences') : '',\n      peptideLength: new UntypedFormControl([9, 10]),\n      alleles: this.fb.array([]),\n      // email: null,\n      // jobTitle: null,\n      breakPeptides: false,\n      predictionModels: this.fb.array([\n        this.mhcBindingFormGroup(),\n        // this.mhcBindingFormGroup('smmpmbec'),\n        // this.mhcBindingFormGroup('smm'),\n        // this.pmhcImmunogencityFormGroup(),\n        // this.mhcIProcessingFormGroup()\n      ])\n    };\n\n    this.rootForm.addControl('mhci', this.fb.group(initialControlConfig));\n  }\n\n  addClusterFormGroup(\n    inputSequenceText = '',\n    threshold = 0.7,\n    minPeptideLength = 4,\n    maxPeptideLength = 26,\n    method = 'cluster-break'\n  ) {\n\n    const seq = sessionStorage.getItem('sequences') ? sessionStorage.getItem('sequences') : inputSequenceText;\n    sessionStorage.removeItem('sequences');\n\n    minPeptideLength = minPeptideLength === 0 ? 4 : minPeptideLength\n    maxPeptideLength = maxPeptideLength === 0 ? 26 : maxPeptideLength\n\n    const initialControlConfig = {\n      inputSequenceText: [seq, Validators.maxLength(this.maxCharacters)],\n      threshold,\n      peptideLength: new UntypedFormControl([minPeptideLength, maxPeptideLength]),\n      method\n    };\n    return this.fb.group(initialControlConfig)\n  }\n\n  addCluster(i: number, dataToPipe: string = 'peptide', tableName: string = 'peptide_table') {\n    /**\n     i - tools.length\n     * */\n    console.log('add cluster');\n    const stage = {\n      stage_number: this.stages.length + 1,\n      stage_type: 'prediction',\n      tool_group: 'cluster',\n      stage_display_name: 'Epitope Cluster Analysis',\n      piped_data: {piped_input: [\n          {\n            piped_fields: [`${tableName}.${dataToPipe}`],\n            piped_stage_number: i,\n          }\n        ]},\n      input_parameters: {},\n      table_state: {columns: {}},\n      stage_messages: {errors: [], warnings: []},\n    }\n\n    /** state update*/\n    this._stateService.addStage(stage)\n    this._stateService.addStageToParams(stage)\n\n    this._stateService.insertTool({\n      name: 'Cluster',\n      toolGroup: 'cluster',\n      loading: false,\n      submitted: false,\n      appliedFilters: undefined,\n      disabled: false\n    }, i)\n\n    this._stateService.setToolDisabled(true, i - 1)\n    /** rootForm update */\n\n    const initialControlConfig = {\n      inputSequenceText: \"\",\n      threshold: 0.7,\n      peptideLength: new UntypedFormControl([4, 26]),\n      method: 'cluster-break'\n    };\n\n    this.rootForm.addControl('cluster', this.fb.group(initialControlConfig));\n  }\n\n  /**\n   Used in T-Cell Predictions\n   1) mhcBindingFormGroup\n   2) pmhcImmunogencityFormGroup\n   3) mhcIProcessingFormGroup\n   * */\n  mhcBindingFormGroup(method = 'netmhcpan_el') {\n    /**\n     * Creates mhcBindingFormGroup using formBuilder\n     *\n     * Currently defaulted to 'netmhcpan_el'\n     * */\n    return this.fb.group({\n      type: 'binding',\n      method: this.fb.control(method),\n    })\n  }\n\n  mhcNpFormGroup() {\n    /**\n     * Creates mhcNpFormGroup using formBuilder\n     * */\n    return this.fb.group({\n      type: 'mhcnp'\n    })\n  }\n\n  pmhcImmunogencityFormGroup(mask_choice = 'default', position_to_mask = '2,5,9') {\n    /**\n     * */\n    return this.fb.group({\n      type: 'immunogenicity',\n      mask_choice: mask_choice,\n      position_to_mask: this.fb.control(position_to_mask),\n    })\n  }\n\n  mhcIProcessingFormGroup(predictor: any) {\n    /**\n     * TODO: add the rest of methods in\n     * Creates mhcBindingFormGroup using formBuilder\n     *\n     * Currently defaulted to 'netmhcpan_el'\n     * */\n\n    const method = predictor.method\n\n    switch (method) {\n      case 'basic_processing': {\n        return this.fb.group({\n          type: \"processing\",\n          method: this.fb.control(method),\n          mhc_binding_method: \"netmhcpan_ba\",\n          proteasome: \"immuno\",\n          tap_precursor: 1,\n          tap_alpha: 0.2\n\n        })\n      }\n      case 'netchop': {\n        return this.fb.group({\n          type: 'processing',\n          method: this.fb.control(method),\n          network_method: predictor.network_method,\n          threshold: predictor.threshold\n        })\n      }\n      case 'netctl': {\n        return this.fb.group({\n          type: 'processing',\n          method: this.fb.control(method),\n          cleavage_weight: predictor.cleavage_weight,\n          tap_weight: predictor.tap_weight,\n          threshold: predictor.threshold\n        })\n      }\n      case 'netctlpan': {\n        return this.fb.group({\n          type: 'processing',\n          method: this.fb.control(method),\n          cleavage_weight: predictor.cleavage_weight,\n          tap_weight: predictor.tap_weight,\n          epitope_threshold: predictor.epitope_threshold\n        })\n      }\n      default:\n        return this.fb.group({\n          type: 'processing',\n          method: this.fb.control(method),\n        })\n    }\n\n\n  }\n\n  onGoToStage(toolGroup: string) {\n    /**\n     * used in pipeline sidebar to go to specific stage\n     * all Tools' labels' ids are set to ${toolGroup}-label\n     * */\n    const navbarHeight = 81 // same as $navbar-height: 81px;\n    window.scroll({\n      left: 0,\n      top: document.getElementById(`${toolGroup}-label`)!.offsetTop - navbarHeight,\n      behavior: 'smooth'\n    });\n  }\n\n  /* PepMatch Functions */\n  addPepmatchFormGroup(\n    inputSequenceText = '',\n    proteome = 'Human',\n    mismatch = 3,\n    bestMatch = true,\n    include_unmatched_peptides = false\n  ) {\n\n    const seq = sessionStorage.getItem('sequences') ? sessionStorage.getItem('sequences') : inputSequenceText;\n    sessionStorage.removeItem('sequences');\n\n    const initialControlConfig = {\n      inputSequenceText: [seq, Validators.maxLength(this.maxCharacters)],\n      proteome,\n      mismatch,\n      bestMatch,\n      include_unmatched_peptides\n    };\n    return this.fb.group(initialControlConfig)\n  }\n\n  addPepmatch(i: number, dataToPipe: string = 'peptide', tableName: string = 'peptide_table') {\n    console.log('add pepmatch');\n    const stage = {\n      stage_number: this.stages.length + 1,\n      stage_type: 'prediction',\n      tool_group: 'pepmatch',\n      stage_display_name: 'Pepmatch',\n      piped_data: {piped_input: [\n          {\n            piped_fields: [`${tableName}.${dataToPipe}`],\n            piped_stage_number: i,\n          }\n        ]},\n      input_parameters: {},\n      table_state: {columns: {}},\n      stage_messages: {errors: [], warnings: []},\n    }\n\n    /** state update*/\n    this._stateService.addStage(stage)\n    this._stateService.addStageToParams(stage)\n\n    this._stateService.insertTool({\n      name: 'Pepmatch',\n      toolGroup: 'pepmatch',\n      loading: false,\n      submitted: false,\n      disabled: false\n    }, i)\n\n    this._stateService.setToolDisabled(true, i - 1)\n    /** rootForm update */\n\n    const defaultFormGroup = this.addPepmatchFormGroup()\n\n    this.rootForm.addControl('pepmatch', defaultFormGroup);\n  }\n\n  /* PepX Functions */\n  addPepXFormGroup(\n    inputSequenceText = '',\n    qlevel = 'gene',\n    datasource = 'Abelin',\n    // dataset = 'v1'\n    dataset_id = 2\n  ) {\n\n    const seq = sessionStorage.getItem('sequences') ? sessionStorage.getItem('sequences') : inputSequenceText;\n    sessionStorage.removeItem('sequences');\n\n    const initialControlConfig = {\n      inputSequenceText: [seq, Validators.maxLength(this.maxCharacters)],\n      qlevel,\n      datasource,\n      // dataset\n      dataset_id\n    };\n    return this.fb.group(initialControlConfig)\n  }\n\n  addPepX(i: number, dataToPipe: string = 'peptide', tableName: string = 'peptide_table') {\n    console.log('add pepx');\n    const stage = {\n      stage_number: this.stages.length + 1,\n      stage_type: 'prediction',\n      tool_group: 'pepx',\n      stage_display_name: 'PepX',\n      piped_data: {piped_input: [\n          {\n            piped_fields: [`${tableName}.${dataToPipe}`],\n            piped_stage_number: i,\n          }\n        ]},\n      input_parameters: {},\n      table_state: {columns: {}},\n      stage_messages: {errors: [], warnings: []},\n    }\n\n    /** state update*/\n    this._stateService.addStage(stage)\n    this._stateService.addStageToParams(stage)\n\n    this._stateService.insertTool({\n      name: 'PepX',\n      toolGroup: 'pepx',\n      loading: false,\n      submitted: false,\n      disabled: false\n    }, i)\n\n    this._stateService.setToolDisabled(true, i - 1)\n    /** rootForm update */\n\n      // const defaultFormGroup = this.addPepmatchFormGroup()\n    const defaultFormGroup = this.addPepXFormGroup()\n\n    this.rootForm.addControl('pepx', defaultFormGroup);\n  }\n\n  /* PepComp Functions */\n  addPepCompFormGroup(\n    inputSequenceText = '',\n    alleles = this.fb.array([]),\n    predictionModels = this.fb.array([this.mhcBindingFormGroup()])\n  ) {\n\n    const seq = sessionStorage.getItem('sequences') ? sessionStorage.getItem('sequences') : inputSequenceText;\n    sessionStorage.removeItem('sequences');\n\n    const initialControlConfig = {\n      inputSequenceText: seq,\n      alleles: alleles,\n      predictionModels: predictionModels,\n    };\n\n    return this.fb.group(initialControlConfig)\n  }\n\n  addPepComp(i: number, tableName: string = 'unique_peptide', dataToPipe1: string = 'reference_peptide', dataToPipe2: string = 'mutant_peptide') {\n    console.log('addPepComp');\n    const stage = {\n      stage_number: this.stages.length + 1,\n      stage_type: 'prediction',\n      tool_group: 'peptide_variant_comparison',\n      stage_display_name: 'Peptide Variant Comparison',\n      piped_data: {piped_input: [\n          {\n            piped_fields: [`${tableName}.${dataToPipe1}`,`${tableName}.${dataToPipe2}`],\n            piped_stage_number: i,\n          }\n        ]},\n      input_parameters: {},\n      table_state: [{table: 'peptide_table', columns: {}}],\n      stage_messages: {errors: [], warnings: []}\n    }\n\n    this._stateService.addStage(stage)\n    this._stateService.addStageToParams(stage)\n\n    this._stateService.insertTool({\n      name: 'Peptide Variant Comparison',\n      toolGroup: 'peptide_variant_comparison',\n      loading: false,\n      submitted: false,\n      appliedFilters: undefined,\n      disabled: false\n    }, i)\n    this._stateService.setToolDisabled(true, i - 1)\n\n    const defaultFormGroup = this.addPepCompFormGroup()\n\n    this.rootForm.addControl('pepcomp', defaultFormGroup);\n  }\n\n  // isToolGroupSelected(toolGroup: string) {\n  //   /**\n  //    * Used to display different tools in root form\n  //    * filters and finds tool_group name (i.e 'mhci', 'cluster').\n  //    * */\n  //   const a = _.filter(this.stages, (o) => o.tool_group === toolGroup);\n  //   return a.length;\n  // }\n\n  /** MutGen Functions */\n  addMutGenFormGroup(\n    inputVcfText = '',\n    peptide_length: number = 21,\n    peptide_mutation_position1: number = 11,\n    peptide_mutation_position2: number | null = null,\n    frameshift_overlap: number = 9,\n    min_len_near_start_stop: number = 16,\n    maximum_peptide_length: number = 24\n  ) {\n\n    const seq = sessionStorage.getItem('sequences') ? sessionStorage.getItem('sequences') : inputVcfText;\n    sessionStorage.removeItem('sequences');\n\n    const initialControlConfig = {\n      inputVcfText: seq,\n      peptideLength: peptide_length,\n      peptideMutationPosition1: peptide_mutation_position1,\n      peptideMutationPosition2: peptide_mutation_position2,\n      frameshiftOverlap: frameshift_overlap,\n      minLengthNearStartStop: min_len_near_start_stop,\n      maximumPeptideLength: maximum_peptide_length\n    };\n\n    return this.fb.group(initialControlConfig)\n  }\n\n  /*** Email functions */\n  onSubmitEmailModal() {\n\n    this.submittedEmailForm = {...this.emailForm.value}\n\n    // console.log(this.submittedEmailForm)\n\n    if (this.pipelineId) {\n      const params = {\n        email: this.submittedEmailForm.email,\n        pipeline_title: this.submittedEmailForm.name\n      }\n\n      this._pipelineService.putPipeline(this.pipelineId, params).subscribe((resp) => {\n        // console.log(resp)\n      })\n    }\n\n    this.modalService.dismissAll()\n  }\n\n\n}\n","<div class=\"container\" id=\"version-component\">\n<!--  <h1>{{versionInfo}}</h1>-->\n\n  <div>\n    <h2 *ngFor=\"let e of versionArr\">\n      {{e}}\n    </h2>\n  </div>\n</div>\n","import { NgModule } from '@angular/core';\nimport { RouterModule, Routes } from '@angular/router';\n\nimport {BenchmarkComponent} from \"./benchmark/benchmark.component\";\nimport {CitationComponent} from './citation/citation.component';\nimport {ToolsListComponent} from './tools-list/tools-list.component';\nimport {ToolContributionComponent} from \"./tool-contribution/tool-contribution.component\";\nimport {HomeComponent} from \"./home/home.component\";\nimport {DownloadAllComponent} from \"./download-all/download-all.component\";\nimport {PipelineNewComponent} from \"./pipeline-new/pipeline-new.component\";\nimport {VersionComponent} from \"./version/version.component\";\nimport {PipelineErrorComponent} from \"./pipeline-error/pipeline-error.component\";\n\nconst routes: Routes = [\n  {\n    path: 'all-tools-list',\n    component: ToolsListComponent,\n    data: {title: 'IEDB NG Tools List'}\n  },\n  {\n    path: 'benchmark',\n    component: BenchmarkComponent,\n    data: {title: 'IEDB NG Tools Benchmarks'}\n  },\n  {\n    path: 'citation',\n    component: CitationComponent,\n    data: {title: 'IEDB NG Tools Citations'}\n  },\n  {\n    path: 'contributing-tools',\n    component: ToolContributionComponent,\n    data: {title: 'Contributing to IEDB NG Tools'}\n  },\n  {\n    path: 'download-all',\n    component: DownloadAllComponent,\n    data: {title: 'IEDB NG Tools Downloads'}\n  },\n  {\n    path: 'error',\n    component: PipelineErrorComponent,\n    data: {title: 'IEDB NG Tools Error'}\n  },\n  {\n    path: 'home',\n    component: HomeComponent,\n    data: {title: 'IEDB Next-Generation Tools'}\n  },\n  {\n    path: 'pipeline',\n    component: PipelineNewComponent\n  },\n  {\n    path: 'pipeline/:id',\n    component: PipelineNewComponent,\n  },\n  {\n    path: 'pipeline_spec/:pipelineSpecId',\n    component: PipelineNewComponent,\n  },\n  {\n    path: '_version',\n    component: VersionComponent,\n    data: {title: 'IEDB Version Info'},\n  },\n  {\n    path: '',\n    component: HomeComponent,\n    data: {title: 'IEDB Next-Generation Tools'},\n  },\n  { path: '**', redirectTo: ''}\n];\n\n@NgModule({\n  imports: [RouterModule.forRoot(routes)],\n  exports: [RouterModule]\n})\nexport class AppRoutingModule { }\n","import { Component } from '@angular/core';\nimport {PipelineStateService} from \"../services/state-services/pipeline-state-service/pipeline-state.service\";\nimport {Observable, Subject} from \"rxjs\";\nimport {takeUntil} from \"rxjs/operators\";\n\n@Component({\n  selector: 'app-pipeline-error',\n  templateUrl: './pipeline-error.component.html',\n  styleUrls: ['./pipeline-error.component.scss']\n})\nexport class PipelineErrorComponent {\n\n  pipelineId$: Observable<string> = this._stateService.pipelineId$;\n  pipelineId = '';\n\n  errorMessage = ''\n\n  unsubscribe$ = new Subject();\n\n  constructor(\n    private _stateService: PipelineStateService,\n  ) {\n  }\n\n  ngOnInit(): void {\n    this.pipelineId$.pipe(takeUntil(this.unsubscribe$)).subscribe(value => {\n      console.log(`pipelineId=${value}`);\n      this.pipelineId = value;\n      this.errorMessage = `Pipeline ${this.pipelineId} does not exist`\n    })\n\n  }\n\n}\n","\n<div class=\"container p-3\" id=\"error-component\">\n  <div class=\"alert alert-danger\" role=\"alert\">\n    <p>\n    {{errorMessage}}\n    </p>\n    <a routerLink=\"/home\">\n      Home\n    </a>\n  </div>\n</div>\n","import { Component, OnInit } from '@angular/core';\nimport {HttpClient} from \"@angular/common/http\";\nimport Citation from \"../_global/Citation\";\nimport {environment} from \"../../environments/environment\";\nimport * as _ from \"lodash\";\n\n@Component({\n  selector: 'app-version',\n  templateUrl: './version.component.html',\n  styleUrls: ['./version.component.scss']\n})\nexport class VersionComponent implements OnInit {\n\n  loading: boolean = false;\n  // citations: any[] = [];\n  // uniq: string[] = []\n  // groupedCitations: {\"T cell - class I\": Citation[]} = {\"T cell - class I\": []}\n\n  versionInfo: string = ''\n  versionArr: string[] = []\n\n\n  constructor(\n    private http: HttpClient\n  ) { }\n\n  ngOnInit(): void {\n    this.getVersionInfo()\n  }\n\n  getVersionInfo() {\n    this.loading = true;\n    const CITATIONS_API_URL = `${environment['api_url']}/api/v1/citations`;\n    const URL = 'assets/_version/versioninfo.yml'\n    this.http.get(URL, {responseType: 'text'}).subscribe(value => {\n      console.log(value)\n      this.versionInfo = value;\n      this.versionArr = value.split('\\n')\n      // this.citations = value.data;\n      // // this.citations =  _.orderBy(value.data, ['grouping_title', 'key']) /** uncomment later */\n      // this.uniq = []\n      // _.forEach(this.citations, (c) => {\n      //   if (!this.uniq.includes(c.grouping_title)) {\n      //     this.uniq.push(c.grouping_title)\n      //     console.log(c.grouping_title)\n      //     // @ts-ignore\n      //     this.groupedCitations[c.grouping_title] = [c]\n      //   } else {\n      //     // @ts-ignore\n      //     this.groupedCitations[c.grouping_title].push(c)\n      //   }\n      // })\n      // console.log(this.uniq)\n      // console.log(this.groupedCitations)\n      this.loading = false;\n    })\n  }\n\n}\n","<footer class=\"footer container-fluid p-2 mt-5\" style=\"height: 50px\">\n  <div class=\"d-sm-flex justify-content-center\">\n    <span class=\"text-muted text-center text-sm-left d-block d-sm-inline-block\">\n      © 2005-2024 | <a href=\"https://www.iedb.org/\" target=\"_blank\">IEDB Home</a> |\n      <a href=\"mailto: help@iedb.org\">Contact</a> |\n      <a [routerLink]=\"[]\" (click)=\"showCookieDialog()\">Privacy settings</a>\n<!--      <a [routerLink]=\"[]\" (click)=\"open(cookieModal)\">Cookie settings</a>-->\n\n<!--      <a href=\"https://www.lji.org/\" target=\"_blank\">La Jolla Institute for Immunology</a>. All rights reserved.-->\n    </span>\n  </div>\n</footer>\n\n<!--Cookie Modal-->\n<ng-template #cookieModal let-cookieModal>\n  <div class=\"modal-header\">\n    <h4 class=\"modal-title\" id=\"modal-email-title\">\n      Cookies\n    </h4>\n<!--    <button type=\"button\" id=\"CookieModalCloseButton\" class=\"btn-close\" aria-label=\"Close\"-->\n<!--            (click)=\"modal3.dismiss('Cross click');\">-->\n<!--    </button>-->\n  </div>\n\n  <div class=\"modal-body\">\n    <p class=\"smallerText text-start\">\n      We use cookies to provide you with an optimal website experience. By continuing to use the website, you agree to the use of cookies.\n      You can learn more about the cookies we use here: <a href=\"/datenschutz\">Privacy Policy</a>\n    </p>\n  </div>\n  <div class=\"modal-footer\">\n    <button type=\"submit\" class=\"btn btn-outline-primary\" (click)=\"cookieModal.dismiss()\">Accept</button>\n  </div>\n\n</ng-template>\n","import { Component, Input, OnInit } from '@angular/core';\n// import {NgbModal} from \"@ng-bootstrap/ng-bootstrap\";\nimport { CookieDialogComponent } from '../cookie-dialog/cookie-dialog.component';\n\n\n@Component({\n  selector: 'app-footer',\n  templateUrl: './footer.component.html',\n  styleUrls: ['./footer.component.scss']\n})\nexport class FooterComponent implements OnInit {\n\n  @Input()\n  public cookieComponent!: CookieDialogComponent;\n\n  // modalOpen = false;\n\n  constructor(\n    // private modalService: NgbModal,\n  ) { }\n\n  ngOnInit(): void {\n  }\n\n  showCookieDialog() {\n    this.cookieComponent.showCookieDialog();\n  }\n\n  // open(content: any) {\n  //   this.modalOpen = true;\n  //   this.modalService.open(content, {\n  //     ariaLabelledBy: 'modal-basic-title',\n  //     size: 'lg',\n  //     animation: true,\n  //     backdrop: 'static'\n  //   }).result.then((result) => {\n  //     // this.closeResult = `Closed with: ${result}`;\n  //     // this.saveState = false;\n  //     this.modalOpen = false;\n  //   }, (reason) => {\n  //     // this.saveState = false;\n  //     // this.alleleSearch.nativeElement.focus();\n  //     // this.closeResult = `Dismissed ${TCellPredictionComponent.getDismissReason(reason)}`;\n  //   });\n  // }\n\n}\n","import { Injectable } from '@angular/core';\n\ndeclare let gtag: Function;\n\n@Injectable({\n  providedIn: 'root',\n})\nexport class GoogleAnalyticsService {\n  constructor() {}\n  public eventEmitter(eventName: string, eventCategory: string, eventAction: string, eventLabel: string, eventValue: number) {\n    gtag('event', eventName, {\n      eventCategory,\n      eventLabel,\n      eventAction,\n      eventValue,\n    });\n  }\n}\n","import { Injectable } from '@angular/core';\n\n@Injectable({\n  providedIn: 'root',\n})\nexport class SharedService {\n  acceptedConsent: boolean = false;\n}\n","<div class=\"container\">\n  <div>\n    <ngb-toast class=\"fixed-bottom w-50 bg-dark text-white\" *ngIf=\"!this.closePopup\" [autohide]=\"false\"\n               (hidden)=\"deny()\">\n      <div class=\"text-start p-4 d-flex flex-column\">\n        <h4 class=\"veryLargeText\">Privacy settings</h4>\n        <p class=\"smallerText text-start\">\n          We use cookies to gather anonymized analytics data and use this information to monitor website performance and\n          make user interface improvements. You can learn more about our use of cookies and how your privacy is managed\n          in our <a routerLink=\"/docs/privacy/privacy-notice.html\"\n                    target=\"_blank\">Privacy Policy</a>\n<!--          href=\"https://nextgen-tools-dev.iedb.org/docs/privacy/privacy-notice.html\"-->\n        </p>\n        <div class=\"text-end\">\n          <button type=\"button\" (click)=\"deny(); setUserAnswered(true);\"\n                  class=\"btn btn-outline-light mr-3 mx-2 smallerText\" id=\"btnDeny\">\n            Reject non-essential cookies\n          </button>\n          <button type=\"button\" (click)=\"accept(); setUserAnswered(true);\" class=\"btn btn-light mx-2 smallerText\"\n                  id=\"btnAccept\">\n            Accept all cookies\n          </button>\n        </div>\n      </div>\n    </ngb-toast>\n  </div>\n</div>\n","import {Component, OnInit} from '@angular/core';\nimport {NavigationEnd, Router} from '@angular/router';\nimport {Title} from \"@angular/platform-browser\";\n\n// import {environment} from \"../../environments/environment\";\n\nimport {GoogleAnalyticsService} from '../services/google-analytics/google-analaytics.service';\nimport {SharedService} from '../services/google-analytics/shared.service';\n\ndeclare let gtag: Function;\n\n@Component({\n  selector: 'app-cookie-dialog',\n  templateUrl: './cookie-dialog.component.html',\n  styleUrls: ['./cookie-dialog.component.css'],\n  providers: [GoogleAnalyticsService]\n})\nexport class CookieDialogComponent implements OnInit {\n\n  constructor(private router: Router, private googleAnalyticsService: GoogleAnalyticsService, public sharedService: SharedService, private titleService:Title) { }\n  public closePopup = false;\n\n\n  ngOnInit() {\n    // if (this.getConsent()) {\n    if (this.getUserAnswered()) {\n\n      this.accept();\n    }\n    else {\n      //delete all cookies from this page\n      this.deny();\n      this.sharedService.acceptedConsent = false;\n      this.closePopup = false;\n    }\n  }\n\n  public showCookieDialog() {\n    this.closePopup = false;\n  }\n\n\n  public loadScript() {\n    let body = <HTMLDivElement>document.body;\n    let script = document.createElement('script');\n    script.innerHTML = '';\n    script.src = 'https://www.googletagmanager.com/gtag/js?id=G-MFNL7MJ8EV';\n    script.async = true;\n    script.defer = true;\n    body.appendChild(script);\n  }\n\n  public deny(): void {\n    this.sharedService.acceptedConsent = false;\n    this.deleteCookie(\"_ga\");\n    this.deleteCookie(\"_ga_MFNL7MJ8EV\");\n    this.setConsent(false);\n    this.closePopup = true;\n  }\n\n  public accept(): void {\n    this.router.events.subscribe(event => {\n      if (event instanceof NavigationEnd) {\n        if (typeof gtag !== 'undefined') {\n          gtag('config', 'G-MFNL7MJ8EV', {\n            page_title: event.urlAfterRedirects,\n            page_location: event.urlAfterRedirects,\n            page_path: event.urlAfterRedirects,\n          });\n        }\n      }\n    });\n    this.loadScript();\n    this.googleAnalyticsService.eventEmitter(this.titleService.getTitle(), window.location.href, \"Visit\", 'Visit', 1);\n    this.sharedService.acceptedConsent = true;\n    this.setConsent(true);\n    // this.setUserAnswered(true);\n    this.closePopup = true;\n  }\n\n  public contactFormUsed() {\n    if(this.getConsent()) {\n      this.googleAnalyticsService.eventEmitter('Contact', 'Contact', \"Contact\", 'Contact', 1);}\n  }\n\n  public getUserAnswered(): boolean {\n\n    return localStorage.getItem('user_answered') === 'true';\n\n  }\n\n  public setUserAnswered(value: boolean): void {\n    localStorage.setItem('user_answered', value ? 'true' : 'false');\n  }\n\n  public getConsent(): boolean {\n\n    return localStorage.getItem('cookies_consented') === 'true';\n\n  }\n\n  public setConsent(value: boolean): void {\n    localStorage.setItem('cookies_consented', value ? 'true' : 'false');\n  }\n\n  private deleteCookie(name: string) {\n    this.setCookie(name, '', -1);\n  }\n\n  private setCookie(name: string, value: string, expireDays: number, path: string = 'path=/;') {\n    let d: Date = new Date();\n    d.setTime(d.getTime() + expireDays * 24 * 60 * 60 * 1000);\n    let expires: string = `expires=${d.toUTCString()}`;\n    let domain : string = \"localhost\";\n\n    if(window.location.hostname != \"localhost\")\n        {\n          // if window.location.hostname is not equal to 'localhost' then check environment.production and set to prod/dev domain\n          domain = 'iedb.org'\n        }\n    let cpath: string = path ? `; path=${path}; domain=${domain}` : '';\n    document.cookie = `${name}=${value}; ${expires}${cpath}`;\n  }\n\n}\n","import {Component} from '@angular/core';\n\nexport const GLOBALS = {\n  logo: 'assets/logos/iedb/IEDB-logo-blue.svg',\n};\n\n@Component({\n  selector: 'app-navbar',\n  templateUrl: './navbar.component.html',\n  styleUrls: ['./navbar.component.scss']\n})\nexport class NavbarComponent {\n  logoImage = GLOBALS.logo;\n  status: boolean = false;\n\n  constructor() {}\n\n}\n","<div class=\"container-fluid fixed-top\">\n  <nav class=\"navbar navbar-expand-lg navbar-light bg-white\" style=\"height: 81px\">\n    <div class=\"container\">\n      <button class=\"navbar-toggler\" type=\"button\" data-bs-toggle=\"collapse\" data-bs-target=\"#navbarSupportedContent\"\n              aria-controls=\"navbarSupportedContent\" aria-expanded=\"false\" aria-label=\"Toggle navigation\">\n        <span class=\"navbar-toggler-icon\"></span>\n      </button>\n      <div class=\"collapse navbar-collapse\" id=\"navbarSupportedContent\">\n        <ul class=\"navbar-nav me-auto\" style=\"background-color:white\">\n          <li>\n            <a class=\"navbar-brand ms-3\" routerLink=\"/\">\n              <img [src]=\"logoImage\" width=\"274\" height=\"75\" alt=\"iedb-logo\" id=\"logo-image\"\n                   class=\"d-inline-block align-text-top px-2\">\n            </a>\n          </li>\n        </ul>\n\n        <ul class=\"navbar-nav\" style=\"background-color:white\">\n          <li class=\"nav-item dropdown\">\n            <a class=\"nav-link dropdown-toggle text-primary-new\" href=\"#\" id=\"toolsListNavbarDropdownMenuLink\"\n               data-bs-toggle=\"dropdown\"\n               data-toggle=\"dropdown\" aria-expanded=\"false\"\n               aria-haspopup=\"true\">\n              Tools\n            </a>\n            <div class=\"dropdown-menu dropdown-menu-right\" aria-labelledby=\"navbarDropdownMenuLink\">\n              <a class=\"dropdown-item\" [routerLink]=\"'/pipeline'\" [queryParams]=\"{tool: 'tc1'}\">T Cell Prediction -\n                Class I </a>\n              <a class=\"dropdown-item\" [routerLink]=\"'/pipeline'\" [queryParams]=\"{tool: 'cluster'}\">Cluster </a>\n              <a class=\"dropdown-item\" [routerLink]=\"'/pipeline'\" [queryParams]=\"{tool: 'pepmatch'}\">PEPMatch </a>\n              <a class=\"dropdown-item\" [routerLink]=\"'/pipeline'\" [queryParams]=\"{tool: 'pepx'}\">PepX\n                <img src=\"assets/symbols/cedar/symbol.svg\" width=\"16\" height=\"16\" alt=\"cedar-symbol.svg\">\n              </a>\n              <a class=\"dropdown-item\" [routerLink]=\"'/pipeline'\" [queryParams]=\"{tool: 'pepvcomp'}\">Peptide Variant\n                Comparison\n                <img src=\"assets/symbols/cedar/symbol.svg\" width=\"16\" height=\"16\" alt=\"cedar-symbol.svg\">\n              </a>\n              <a class=\"dropdown-item\" [routerLink]=\"'/pipeline'\" [queryParams]=\"{tool: 'mutpepgen'}\">Mutated Peptide\n                Generator\n                <img src=\"assets/symbols/cedar/symbol.svg\" width=\"16\" height=\"16\" alt=\"cedar-symbol.svg\">\n              </a>\n\n              <div class=\"dropdown-divider\"></div>\n              <a class=\"dropdown-item\" routerLink=\"/all-tools-list\">All Tools List</a>\n            </div>\n          </li>\n          <li class=\"nav-item dropdown\">\n            <a class=\"nav-link dropdown-toggle text-primary-new\" href=\"#\" id=\"navbarDropdownMenuLink\"\n               data-bs-toggle=\"dropdown\"\n               data-toggle=\"dropdown\"\n               aria-haspopup=\"true\" aria-expanded=\"false\">\n              Help & Info\n            </a>\n            <div class=\"dropdown-menu dropdown-menu-right\" aria-labelledby=\"navbarDropdownMenuLink\">\n              <!-- Link to readthedocs-style (e.g. sphinx)  documentation -->\n              <a class=\"dropdown-item\" routerLink=\"/docs\" target=\"_blank\">Tools Documentation</a>\n              <a class=\"dropdown-item\" href=\"https://iedb.zendesk.com \" target=\"_blank\">Support</a>\n              <!--              Links to Discourse where we have user forum and ticketing -->\n              <a class=\"dropdown-item\" routerLink=\"/citation\">Cite Us</a>\n              <a class=\"dropdown-item\" routerLink=\"/download-all\">Licensing</a>\n              <a class=\"dropdown-item\" routerLink=\"/contributing-tools\">Contribute a Tool</a>\n            </div>\n          </li>\n        </ul>\n\n      </div>\n    </div>\n  </nav>\n\n</div>\n","import { Component } from '@angular/core';\nimport { Title } from '@angular/platform-browser';\nimport { Router, NavigationEnd, ActivatedRoute } from '@angular/router';\nimport { filter, map } from 'rxjs/operators';\n\n@Component({\n  selector: 'app-root',\n  templateUrl: './app.component.html',\n  styleUrls: ['./app.component.scss']\n})\nexport class AppComponent {\n  constructor(\n    private router: Router,\n    private titleService: Title\n  ) {}\n\n  ngOnInit() {\n    this.router.events\n      .pipe(\n        filter((event) => event instanceof NavigationEnd),\n        map(() => {\n          let route: ActivatedRoute = this.router.routerState.root;\n          let routeTitle = '';\n          while (route!.firstChild) {\n            route = route.firstChild;\n          }\n          if (route.snapshot.data['title']) {\n            routeTitle = route!.snapshot.data['title'];\n          }\n          return routeTitle;\n        })\n      )\n      .subscribe((title: string) => {\n        if (title) {\n          this.titleService.setTitle(`${title}`);\n        }\n      });\n  }\n\n  // title = 'Nextgen IEDB Tools';\n}\n","<app-navbar></app-navbar>\n<router-outlet></router-outlet>\n<app-footer [cookieComponent]=\"cookieContext\"></app-footer>\n<app-cookie-dialog #cookieContext></app-cookie-dialog>\n","import { NgModule } from '@angular/core';\nimport { BrowserModule, Title } from '@angular/platform-browser';\n\nimport {HttpClientModule} from '@angular/common/http';\nimport {FormsModule, ReactiveFormsModule} from '@angular/forms';\nimport {DragDropModule} from '@angular/cdk/drag-drop';\n\nimport {DataTablesModule} from \"angular-datatables\";\nimport { NgxSliderModule } from 'ngx-slider-v2';\nimport {\n  NgbTypeaheadModule,\n  NgbAccordionModule,\n  NgbDropdownModule,\n  NgbTooltipModule,\n  NgbPopoverModule,\n  NgbNavModule,\n  NgbAlertModule,\n  NgbToastModule, NgbModule\n} from '@ng-bootstrap/ng-bootstrap';\n\n// import { NgxGoogleAnalyticsModule, NgxGoogleAnalyticsRouterModule } from 'ngx-google-analytics';\n\n// import {environment} from \"../environments/environment\";\n\nimport {AppRoutingModule} from './app-routing.module';\n\nimport {AppComponent} from './app.component';\nimport {AlertComponentComponent} from './alert-component/alert-component.component';\nimport {HomeComponent} from './home/home.component';\nimport {FooterComponent} from './footer/footer.component';\nimport { CookieDialogComponent } from './cookie-dialog/cookie-dialog.component';\nimport {NavbarComponent} from \"./navbar/navbar.component\";\nimport {DndDirectiveDirective} from './directives/dnd-directive.directive';\n// import {PlaygroundComponent} from './playground/playground.component';\nimport {TCellPredictionComponent} from './mhci/t-cell-prediction/t-cell-prediction.component';\n\nimport { BenchmarkComponent } from './benchmark/benchmark.component';\nimport { CitationComponent } from './citation/citation.component';\nimport { ToolContributionComponent } from './tool-contribution/tool-contribution.component';\nimport { DownloadAllComponent } from './download-all/download-all.component';\nimport { MhcBindingFormgroupComponent } from './mhci/prediction-model-formgroups/mhc-binding-formgroup/mhc-binding-formgroup.component';\nimport { PmhcImmunogenicityFormgroupComponent } from './mhci/prediction-model-formgroups/pmhc-immunogenicity-formgroup/pmhc-immunogenicity-formgroup.component';\nimport { MhcIProcessingFormgroupNewComponent } from './mhci/prediction-model-formgroups/mhc-i-processing-formgroup-new/mhc-i-processing-formgroup-new.component';\n\n// import { MhcNpFormgroupComponent } from './mhci/prediction-model-formgroups/mhc-np-formgroup/mhc-np-formgroup.component';\nimport { ResultTableComponent } from './result-table/result-table.component';\nimport { ClusterComponent } from './cluster/cluster.component';\nimport {ToolsListComponent} from './tools-list/tools-list.component';\nimport { SequenceInputComponent } from './sequence-input/sequence-input.component';\nimport { D3ForceComponent } from './d3-force/d3-force.component';\nimport { KeysPipe } from \"./_pipes/keys.pipe\";\nimport { tagPipe } from \"./_pipes/tag.pipe\";\nimport { DashToDecimalPipe } from \"./_pipes/dash-to-decimal.pipe\";\nimport { BrowserAnimationsModule } from '@angular/platform-browser/animations';\nimport {MatSidenavModule} from \"@angular/material/sidenav\";\nimport {ClipboardModule} from \"@angular/cdk/clipboard\";\nimport {MatMenuModule} from '@angular/material/menu';\nimport {MatChipsModule} from '@angular/material/chips';\nimport {MatIconModule} from \"@angular/material/icon\";\nimport {PipelineNewComponent} from \"./pipeline-new/pipeline-new.component\";\nimport { PepmatchComponent } from './pepmatch/pepmatch.component';\nimport { VersionComponent } from './version/version.component';\nimport { ResultTableAngularComponent } from './result-table-angular/result-table-angular.component';\nimport { PipelineErrorComponent } from './pipeline-error/pipeline-error.component';\nimport { PepxComponent } from './pepx/pepx.component';\nimport { PeptideVariantComparisonComponent } from './mhci/peptide-variant-comparison/peptide-variant-comparison.component';\nimport { D3PlotComponent } from './d3-plot/d3-plot.component';\nimport { MutatedPeptideGeneratorComponent } from './mutated-peptide-generator/mutated-peptide-generator.component';\n@NgModule({\n  declarations: [\n    AppComponent,\n    AlertComponentComponent,\n    FooterComponent,\n    CookieDialogComponent,\n    HomeComponent,\n    NavbarComponent,\n    DndDirectiveDirective,\n    TCellPredictionComponent,\n    BenchmarkComponent,\n    CitationComponent,\n    ToolContributionComponent,\n    ToolsListComponent,\n    DownloadAllComponent,\n    MhcBindingFormgroupComponent,\n    // MhcNpFormgroupComponent,\n    PmhcImmunogenicityFormgroupComponent,\n    ResultTableComponent,\n    ClusterComponent,\n    SequenceInputComponent,\n    D3ForceComponent,\n    KeysPipe,\n    tagPipe,\n    DashToDecimalPipe,\n    PipelineNewComponent,\n    MhcIProcessingFormgroupNewComponent,\n    PepmatchComponent,\n    VersionComponent,\n    ResultTableAngularComponent,\n    PipelineErrorComponent,\n    PepxComponent,\n    PeptideVariantComparisonComponent,\n    D3PlotComponent,\n    MutatedPeptideGeneratorComponent\n  ],\n  imports: [\n    BrowserModule,\n    HttpClientModule,\n    // ...environment.optionalModules,\n    AppRoutingModule,\n    DragDropModule,\n    FormsModule,\n    ReactiveFormsModule,\n    DataTablesModule,\n    NgbAlertModule,\n    NgbTypeaheadModule,\n    NgbAccordionModule,\n    NgbDropdownModule,\n    NgbTooltipModule,\n    NgbPopoverModule,\n    NgbNavModule,\n    NgbToastModule,\n    NgxSliderModule,\n    BrowserAnimationsModule,\n    MatSidenavModule,\n    MatMenuModule,\n    MatChipsModule,\n    MatIconModule,\n    ClipboardModule,\n    NgbModule\n  ],\n  providers: [Title],\n  bootstrap: [AppComponent]\n})\nexport class AppModule { }\n","/// <reference types=\"@angular/localize\" />\n\nimport { enableProdMode } from '@angular/core';\nimport { platformBrowserDynamic } from '@angular/platform-browser-dynamic';\n\nimport { AppModule } from './app/app.module';\nimport { environment } from './environments/environment';\n\nif (environment.production) {\n  enableProdMode();\n  window.console.log = () => { }\n}\n\nplatformBrowserDynamic().bootstrapModule(AppModule)\n  .catch(err => console.error(err));\n"],"x_google_ignoreList":[]}