\n
\n","import {Component, OnInit, OnDestroy, OnChanges, Input, Output, EventEmitter, ViewChild, ElementRef, SimpleChanges} from '@angular/core';\nimport {UntypedFormGroup, UntypedFormBuilder, FormGroupDirective, UntypedFormArray} 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\n
\n \n Loading...\n
\n \n
\n
\nCite Us
\nPublications 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.
\n\n
\n \n \n \n \n
\n\n {{citation.key}}
\n\n {{article.display_name}} ({{article.method_version}})\n
\n \n
\n\n\n
\n \n \n \n
\n\n
\n \n \n \n
\n - \n
- {{message}} \n
\n
\n\n \n
\n\n
\n \n \n \n
\n - \n
- {{message}} \n
\n \n
\n\n\n
\n\n\n\n Loading...\n
\n \n \n\n
\n\n\n- \n
- \n Peptide Table\n
\n \n\n \n - \n Visualization\n
\n \n\n \n - \n Sequence Table \n
\n \n\n \n
\n
\n Validation Error(s)
\n \n\n
\n \n\n
\n Are you sure?
\n \n\n \n \n \n
\n \n\n
\n Re-running this step of the pipeline will delete all downstream results, including:
\n- \n
- {{tool.name}} \n
To access the current results, you can use this link
\nApplying these filters for input to the next stage will delete results from all downstream steps in\n this session, including:
\n- \n
- {{tool.name}} \n
To access the current results, you can use this link
\n\n \n \n
\n \n
\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\n \n \n
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\n \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
\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\n
\nInteractive Cluster Visualization
\n \n Visualize a selected Sub-cluster\n \n \n \n\n peptide B: ${d.sequenceB}`)\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","
\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\n \n Metric\n \n \n \n Allele\n \n \n
\n \n \n
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\n","import {Component, OnInit} from '@angular/core';\nimport {HttpClient} from \"@angular/common/http\";\nimport {ActivatedRoute, Router} from \"@angular/router\";\nimport {Location} from \"@angular/common\";\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: string = '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 'mhc-class-ii-binding':\n window.open('https://downloads.iedb.org/nextgen-tools/retrieve_package.php?tool=tcell_mhcii', '_self')\n return\n case 'pepmatch':\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 });\n }\n\n}\n","\n\n\n\n
\nIEDB Tools: Website Usage
\n\n\n
\n\n \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
\nIEDB Tools: Download
\n\n
\n\n Complete Download: Entire IEDB Analysis Resource
\n\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 contact us for details on\n licensing options.\n
\n\n
\n\n Standalone Download
\n\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 here.\n
\n\n\n
\n\n IEDB Tools: License Agreement
\n \n\n
\n\n \n Agree and Download\n \n Description
\n\n This tool wraps up several methods to support the prediction of class I peptide: MHC binding, elution, immunogenicity, and antigen processing.\n
\n\n This tool wraps up several methods to support the prediction of class II peptide: MHC binding, elution, and immunogenicity.\n
\n\n This tool groups epitopes into clusters based on sequence identity using one of 3 different algorithms.\n
\n\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
\n\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
\n\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
\n\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
\n\nLicense Agreements
\n\n All standalone tools are distributed under the Non-Profit Open Software License (Non-Profit OSL) version 3.0.\n Some tools, developed in coordination with the Technical University of Denmark, are distributed with additional\n terms and conditions. By downloading the tools, you are implicitly agreeing to the terms of all applicable\n licenses.\n
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\n \n\n\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: Privacy Policy\n
\n\n
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\n\n Announcements
\n- \n
- \n \n \n {{i.title}}\n \n \n
\n \n \n
\n\n
\n\n Appearances & Events
\n\n| \n \n Virtual User Workshop\n \n | \nNov 5-7, 2024 | \n
| \n * recordings here\n | \n|
| Festival of Biologics | \nApril 23-25, 2025 | \n
| AACR 2025 | \nApril 25-30, 2025 | \n
| Immunology 2025 | \nMay 3-7, 2025 | \n
\n
\n Additional Resources
\n\n \n API\n \n \n Downloads\n \n
\n \n
\nWelcome to the Next-Generation IEDB Tools site!
\nAs 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.
\n\n New User? Learn to\n use the website here!\n \n\n \n\n
\n\n \n \n \n T Cell Prediction - Class I\n
\n\n
\n \n\n \n \n\n
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10\">\n ...\n
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\n \n Loading...\n
\n \n \n \n Click to run tool\n \n \n \n \n
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\n\n \n Additional Tools\n \n \n \n \n T Cell Prediction - Class II\n
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\n \n \n \n Click to run tool\n \n \n \n \n
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\n \n \n Cluster\n
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\n \n \n Peptide Variant Comparison\n
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\n\n \n\n \n \n - \n Sequence Table \n
\n \n\n \n\n - \n Scatter Plots\n
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\n \n\n
\n \n\n
\n Are you sure?
\n \n\n \n \n \n
\n \n\n
\n Re-running this step of the pipeline will delete all downstream results, including:
\n- \n
- {{tool.name}} \n
To access the current results, you can use this link
\nApplying these filters for input to the next stage will delete results from all downstream steps in\n this session, including:
\n- \n
- {{tool.name}} \n
To access the current results, you can use this link
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- \n Peptide Table\n
\n\n\n\n\n\n \n\n \n - \n Residue Table\n
\n \n\n \n - \n NetMHCpan Allele Distance\n
\n \n\n \n - \n Processing Plots\n
\n \n\n\n\n\n\n\n Seq #\n \n\n\n\n\n Allele\n \n\n\n\n\n Length\n \n\n\n\n\n\n Loading...\n\n\n \n\n\n\n\n\n{{plot.method}}
\n\n\n\n Percentile Threshold\n\n\n Score Threshold\n \n \n \n\n
\n\nNO DATA AVAILABLE\n \n - \n Sequence Table \n
\n \n\n \n
\n
\n\n \n Number of Selected Alleles: {{modalAlleles.length}}\n
\n \n\n
\n\n
\n\n \n \n
\n \n \n \n
\n \n
\n \n
\n \n Loading...\n
\n 0\" class=\"p-2 d-flex flex-column justify-content-start\">\n\n
\n \n\n\n - \n \n
- {{i['label']}}\n \n \n
\n
\n Validation Error(s)
\n \n\n
\n \n\n
\n Are you sure?
\n \n\n \n \n \n
\n \n\n
\n Re-running this step of the pipeline will delete all downstream results, including:
\n- \n
- {{tool.name}} \n
To access the current results, you can use this link
\nApplying these filters for input to the next stage will delete results from all downstream steps in\n this session, including:
\n- \n
- {{tool.name}} \n
To access the current results, you can use this link
\n\n \n \n
\n \n
\n\n \n \n
\n \n \n \n
\n \n
\n \n Loading...\n
\n \n \n
\n \n \n
\n\n\n
\n \n \n \n
\n\n
\n \n \n \n
\n - \n
- {{message}} \n
\n
\n\n \n
\n\n
\n \n \n \n
\n - \n
- {{message}} \n
\n \n
\n\n\n
\n\n\n Loading...\n
\n \n \n\n
\n\n\n- \n
- \n Peptide Table\n
\n\n \n\n \n - \n Consolidated Peptide Table \n
\n \n\n \n - \n Sequence Table \n
\n \n\n \n
\n
\n\n \n Number of Selected Alleles: {{modalAlleles.length}}\n
\n \n\n
\n\n
\n\n \n \n
\n \n \n \n
\n \n
\n \n
\n \n Loading...\n
\n 0\" class=\"p-2 d-flex flex-column justify-content-start\">\n\n
\n \n\n\n - \n \n
- {{i['label']}}\n \n \n
\n
\n Validation Error(s)
\n \n\n
\n \n\n
\n Are you sure?
\n \n\n \n \n \n
\n \n\n
\n Re-running this step of the pipeline will delete all downstream results, including:
\n- \n
- {{tool.name}} \n
To access the current results, you can use this link
\nApplying these filters for input to the next stage will delete results from all downstream steps in\n this session, including:
\n- \n
- {{tool.name}} \n
To access the current results, you can use this link
\n\n \n \n
\n \n \n
\n\n\n
\n \n \n \n
\n\n
\n \n \n \n
\n - \n
- {{message}} \n
\n
\n\n \n
\n\n
\n \n \n \n
\n - \n
- {{message}} \n
\n \n
\n\n\n
\n\n\n Loading...\n
\n \n \n\n
\n\n\n- \n \n
- \n Unique Peptides \n
\n \n\n \n \n - \n All Peptides \n
\n \n\n \n \n - \n All SNPs\n
\n \n \n\n\n\n\n\n\n \n
\n
\n Validation Error(s)
\n \n\n
\n \n\n
\n Are you sure?
\n \n\n \n \n \n
\n \n\n
\n Re-running this step of the pipeline will delete all downstream results, including:
\n- \n
- {{tool.name}} \n
To access the current results, you can use this link
\nApplying these filters for input to the next stage will delete results from all downstream steps in\n this session, including:
\n- \n
- {{tool.name}} \n
To access the current results, you can use this link
\n\n \n \n
\n \n \n\n
\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\n \n
\n\n\n
\n \n \n \n
\n\n
\n \n \n \n
\n - \n
- {{message}} \n
\n
\n\n \n
\n\n
\n \n \n \n
\n - \n
- {{message}} \n
\n \n
\n\n\n
\n\n\n Loading...\n
\n \n\n
\n\n\n- \n \n
- \n Peptide Table\n
\n \n\n \n\n\n\n No matches found with the given input peptides and selected parameters.\n \n \n \n - \n Sequence Table \n
\n \n\n \n
\n
\n Are you sure?
\n \n\n \n \n \n
\n \n\n
\n Re-running this step of the pipeline will delete all downstream results, including:
\n- \n
- {{stage.stage_display_name}} \n
To access the current results, you can use this link
\nApplying these filters for input to the next stage will delete results from all downstream steps in\n this session, including:
\n- \n
- {{stage.stage_display_name}} \n
To access the current results, you can use this link
\n\n \n \n
\n \n
\n Validation Error(s)
\n \n\n
\n \n\n \n
\n\n\n
\n \n \n \n
\n\n
\n \n \n \n
\n - \n
- {{message}} \n
\n
\n\n \n
\n\n
\n \n \n \n
\n - \n
- {{message}} \n
\n \n
\n\n\n
\n\n\n Loading...\n
\n \n\n
\n\n\n- \n \n
- \n Peptide Table\n
\n \n\n \n\n\n\n No matches found with the given input peptides and selected parameters.\n \n \n \n - \n Peptide Gene Summary Table\n
\n \n\n \n\n\n\n No matches found with the given input peptides and selected parameters.\n \n \n \n - \n Sequence Table \n
\n \n\n \n
\n
\n Are you sure?
\n \n\n \n \n \n
\n \n\n
\n Re-running this step of the pipeline will delete all downstream results, including:
\n- \n
- {{stage.stage_display_name}} \n
To access the current results, you can use this link
\nApplying these filters for input to the next stage will delete results from all downstream steps in\n this session, including:
\n- \n
- {{stage.stage_display_name}} \n
To access the current results, you can use this link
\n\n \n \n
\n \n
\n Validation Error(s)
\n \n\n
\n \n\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, initTCellPrediction2State,\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\n
\n\n {{errorMessage}}\n
\n \n Home\n \n\n
\n\n\n Loading...\n
\n\n \n
\n\n \n Pipeline Map
\n \n\n \n \n \n \n \n
\n \n \n
\n
\n \n \n \n
\n\n
\n \n \n \n
\n \n
\n | Pipeline Name | \n\n {{ submittedEmailForm['name'] }}\n | \n
| \n {{ submittedEmailForm['email'] }}\n | \n
\n\n
\n \n
\n\n
\n \n \n
\n \n
\n\n