@sjcrh/proteinpaint-client 2.181.0 → 2.182.1

package/dist/Disco-IMLXEBPG.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/disco/arc/FullArcRenderer.ts", "../plots/disco/menu/MenuProvider.ts", "../plots/disco/fusion/FusionColorProvider.ts", "../plots/disco/fusion/FusionRenderer.ts", "../plots/disco/DiscoRenderer.ts", "../plots/disco/interactions/DiscoInteractions.ts", "../plots/disco/chromosome/Reference.ts", "../plots/disco/data/DataObjectMapper.ts", "../plots/disco/data/PercentileMapper.ts", "../plots/disco/data/DataMapper.ts", "../plots/disco/legend/Legend.ts", "../plots/disco/fusion/Fusion.ts", "../plots/disco/fusion/FusionSubgroup.ts", "../plots/disco/fusion/FusionMapper.ts", "../plots/disco/loh/GradientColorProvider.ts", "../plots/disco/loh/LohLegend.ts", "../plots/disco/viewmodel/ViewModel.ts", "../plots/disco/ring/Ring.ts", "../plots/disco/label/MLabel.ts", "../plots/disco/snv/SnvLegendElement.ts", "../plots/disco/snv/SnvArcsMapper.ts", "../plots/disco/cnv/CnvLegend.ts", "../plots/disco/cnv/CnvColorProvider.ts", "../plots/disco/cnv/CnvArcsMapper.ts", "../plots/disco/label/Line.ts", "../plots/disco/label/LabelFactory.ts", "../plots/disco/label/LabelsMapper.ts", "../plots/disco/label/Labels.ts", "../plots/disco/snv/NonExonicSnvArcsMapper.ts", "../plots/disco/loh/LohArcMapper.ts", "../plots/disco/ring/Rings.ts", "../plots/disco/waterfall/MutationWaterfallMapper.ts", "../plots/disco/viewmodel/ViewModelProvider.ts", "../plots/disco/viewmodel/ViewModelMapper.ts", "../plots/disco/legend/LegendJSONMapper.ts", "../plots/disco/cnv/renderCnvSourceLegend.ts", "../plots/disco/legend/LegendRenderer.ts", "../plots/disco/chromosome/ChromosomesRenderer.ts", "../plots/disco/snv/vafTooltip.ts", "../plots/disco/label/LabelsRenderer.ts", "../plots/disco/defaults.ts", "../plots/disco/snv/NonExonicSnvRenderer.ts", "../plots/disco/snv/SnvRenderer.ts", "../plots/disco/loh/LohRenderer.ts", "../plots/disco/cnv/CnvBarRenderer.ts", "../plots/disco/cnv/CnvHeatmapRenderer.ts", "../plots/disco/waterfall/MutationWaterfallRenderer.ts", "../plots/disco/Disco.ts"],
+  "sourcesContent": ["import * as d3 from 'd3'\nimport type Arc from './Arc.ts'\n\nexport default class FullArcRenderer {\n\tprivate radius: number\n\tprivate width: number\n\tprivate color: string\n\tconstructor(radius: number, width: number, color: string) {\n\t\tthis.radius = radius\n\t\tthis.width = width\n\t\tthis.color = color\n\t}\n\trender(holder: any) {\n\t\tconst donutGenerator = d3.arc<Arc>()\n\t\tconst arc: Arc = {\n\t\t\tstartAngle: 0,\n\t\t\tendAngle: Math.PI * 2,\n\t\t\tinnerRadius: this.radius,\n\t\t\touterRadius: this.radius + this.width,\n\t\t\tcolor: this.color,\n\t\t\ttext: 'No label'\n\t\t}\n\n\t\tconst array: Array<Arc> = []\n\t\tarray.push(arc)\n\t\tconst donutArc = holder.append('g')\n\t\tdonutArc\n\t\t\t.selectAll('path')\n\t\t\t.data(array)\n\t\t\t.enter()\n\t\t\t.append('path')\n\t\t\t.attr('d', (d: Arc) => donutGenerator(d))\n\t\t\t.attr('fill', (d: Arc) => d.color)\n\t}\n}\n", "import { Menu } from '#dom/menu'\n\nexport default class MenuProvider {\n\tstatic create(): Menu {\n\t\tconst menu = new Menu({ padding: 5 })\n\t\tmenu.d.style('border', '1px solid #FFF').style('position', 'absolute').style('z-index', 1001)\n\n\t\treturn menu\n\t}\n}\n", "import { FusionLegend } from '#plots/disco/fusion/FusionLegend.ts'\n\nexport default class FusionColorProvider {\n\tstatic getColor(chrA: string, chrB: string) {\n\t\tif (chrA != chrB) {\n\t\t\treturn FusionLegend.Interchromosomal.valueOf()\n\t\t} else {\n\t\t\treturn FusionLegend.Intrachromosomal.valueOf()\n\t\t}\n\t}\n}\n", "import * as d3 from 'd3'\nimport FullArcRenderer from '#plots/disco/arc/FullArcRenderer.ts'\nimport type Fusion from './Fusion.ts'\nimport MenuProvider from '#plots/disco/menu/MenuProvider.ts'\nimport FusionColorProvider from '#plots/disco/fusion/FusionColorProvider.ts'\nimport { table2col } from '#dom/table2col'\nimport { dofetch3 } from '#common/dofetch'\nimport type { ClientGenome } from '../../../types/clientGenome.ts'\n\n// dynamically load svgraph when user clicks on a fusion arc\n\nexport default class FusionRenderer {\n\tprivate genome: ClientGenome\n\n\tconstructor(genome: ClientGenome) {\n\t\tthis.genome = genome\n\t}\n\n\trender(holder: any, fusions: Array<Fusion>, opacity = 1) {\n\t\tlet radius = 0\n\t\tconst fusionsWithTarget = fusions.filter(f => f.target)\n\t\tif (fusionsWithTarget.length > 0) {\n\t\t\tradius = fusionsWithTarget[0].target.radius\n\t\t\tconst fullArcRenderer = new FullArcRenderer(radius, 2, '#6464641A')\n\t\t\tfullArcRenderer.render(holder)\n\t\t} else return\n\n\t\tconst ribbon = d3.ribbon().radius(radius)\n\t\tconst ribbons = holder.selectAll('.chord').data(fusions)\n\n\t\t//Used in the fusion elems (i.e. ribbons) mouse and click events\n\t\tconst menu = MenuProvider.create()\n\t\tconst createTooltip = this.createTooltip.bind(this)\n\t\tconst genome = this.genome\n\n\t\tribbons\n\t\t\t.enter()\n\t\t\t.append('path')\n\t\t\t.attr('class', 'chord')\n\t\t\t.attr('d', ribbon)\n\t\t\t.attr('fill', (fusion: Fusion) => {\n\t\t\t\treturn FusionColorProvider.getColor(\n\t\t\t\t\tfusion.source.positionInChromosome.chromosome,\n\t\t\t\t\tfusion.target.positionInChromosome.chromosome\n\t\t\t\t)\n\t\t\t})\n\t\t\t.style('opacity', opacity)\n\t\t\t.each(function (this: any, d: Fusion) {\n\t\t\t\tconst path = d3.select(this)\n\t\t\t\t//Create a new tooltip for each fusion arc\n\t\t\t\t//Allows the graph to presist whilst allowing\n\t\t\t\t//the user to see tooltips on other elemenets\n\t\t\t\tconst tip = MenuProvider.create()\n\n\t\t\t\tpath.on('click', async function (event: MouseEvent) {\n\t\t\t\t\ttip.clear().show(event.x, event.y)\n\t\t\t\t\tconst div = tip.d.append('div')\n\t\t\t\t\tawait makeSvgraph(d, div, genome)\n\t\t\t\t})\n\t\t\t})\n\t\t\t.on('mouseover', async function (mouseEvent: MouseEvent, fusion: Fusion) {\n\t\t\t\t//TODO: Add note to user \"click to see fusion graph\"?\n\t\t\t\tconst table = table2col({ holder: menu.d })\n\t\t\t\tcreateTooltip(table, fusion)\n\t\t\t\tmenu.show(mouseEvent.x, mouseEvent.y)\n\t\t\t})\n\t\t\t.on('mouseout', () => {\n\t\t\t\tmenu.clear()\n\t\t\t\tmenu.hide()\n\t\t\t})\n\t}\n\n\tcreateTooltip(table: any, fusion: Fusion) {\n\t\t{\n\t\t\tconst [td1, td2] = table.addRow()\n\t\t\ttd1.text('Data type')\n\t\t\ttd2.append('span').style('margin-left', '5px').text('Fusion transcript')\n\t\t}\n\t\t{\n\t\t\tconst positionInChromosomeSource = fusion.source.positionInChromosome\n\t\t\tconst positionInChromosomeTarget = fusion.target.positionInChromosome\n\n\t\t\tconst [td1, td2] = table.addRow()\n\t\t\ttd1.text('Position')\n\t\t\ttd2\n\t\t\t\t.append('span')\n\t\t\t\t.style('margin-left', '5px')\n\t\t\t\t.text(\n\t\t\t\t\t` ${fusion.source.gene || ''} ${positionInChromosomeSource.chromosome}:${\n\t\t\t\t\t\tpositionInChromosomeSource.position\n\t\t\t\t\t} ${fusion.source.strand === '+' ? 'forward' : 'reverse'} > ` +\n\t\t\t\t\t\t` ${fusion.target.gene || ''} ${positionInChromosomeTarget.chromosome}:${\n\t\t\t\t\t\t\tpositionInChromosomeTarget.position\n\t\t\t\t\t\t} ${fusion.target.strand === '+' ? 'forward' : 'reverse'} `\n\t\t\t\t)\n\t\t}\n\t}\n}\n\nasync function makeSvgraph(fusion: Fusion, div: any, genome: ClientGenome) {\n\tconst wait = div.append('div').text('Loading...')\n\tconst svpair = {\n\t\ta: {\n\t\t\tchr: fusion.source.positionInChromosome.chromosome,\n\t\t\tposition: fusion.source.positionInChromosome.position,\n\t\t\tstrand: fusion.source.strand\n\t\t},\n\t\tb: {\n\t\t\tchr: fusion.target.positionInChromosome.chromosome,\n\t\t\tposition: fusion.target.positionInChromosome.position,\n\t\t\tstrand: fusion.target.strand\n\t\t}\n\t}\n\n\tawait getGm(svpair.a, genome.name, fusion.source.gene)\n\tawait getGm(svpair.b, genome.name, fusion.target.gene)\n\n\twait.remove()\n\n\tconst _ = await import('#src/svgraph')\n\t_.default({\n\t\tpairlst: [svpair],\n\t\tgenome,\n\t\tholder: div\n\t})\n}\n\nasync function getGm(p: any, genome: string, name: string) {\n\tconst d = await dofetch3('isoformbycoord', {\n\t\tbody: { genome, chr: p.chr, pos: p.position }\n\t})\n\tif (d.error) throw d.error\n\tconst u = d.lst.find((i: any) => i.isdefault && name === i.name) || d.lst[0]\n\tif (u) {\n\t\tp.name = u.name\n\t\tp.gm = { isoform: u.isoform }\n\t}\n}\n", "import type IRenderer from './IRenderer.ts'\nimport type ViewModel from './viewmodel/ViewModel.ts'\nimport type LegendRenderer from './legend/LegendRenderer.ts'\nimport type { RingType } from './ring/RingType.ts'\nimport FusionRenderer from './fusion/FusionRenderer.ts'\n\nexport class DiscoRenderer {\n\tprivate renders: Map<RingType, IRenderer>\n\tprivate legendRenderer: LegendRenderer\n\tprivate fusionRenderer: FusionRenderer\n\n\tconstructor(renders: Map<RingType, IRenderer>, legendRenderer: LegendRenderer, genome: any) {\n\t\tthis.renders = renders\n\t\tthis.legendRenderer = legendRenderer\n\t\tthis.fusionRenderer = new FusionRenderer(genome)\n\t}\n\n\trender(holder: any, viewModel: ViewModel, onCnvSourceSelect: (index: number) => void) {\n\t\tconst svgDiv = holder.append('div').style('display', 'inline-block').style('font-family', 'Arial')\n\n\t\tconst svg = svgDiv\n\t\t\t.append('svg')\n\t\t\t.attr('id', 'sjpp_disco_plot')\n\t\t\t.attr('data-testid', 'sjpp_disco_plot')\n\t\t\t.attr('width', viewModel.width)\n\t\t\t.attr('height', viewModel.height + viewModel.legendHeight)\n\n\t\tconst mainG = svg\n\t\t\t.append('g')\n\t\t\t.attr('class', 'mainG')\n\t\t\t.attr(\n\t\t\t\t'transform',\n\t\t\t\t`translate(${\n\t\t\t\t\tviewModel.settings.rings.labelLinesInnerRadius + viewModel.settings.rings.labelsToLinesDistance + 100\n\t\t\t\t},${viewModel.height / 2})`\n\t\t\t)\n\n\t\tfor (const [ringType, renderer] of this.renders) {\n\t\t\tconst elements = viewModel.getElements(ringType)\n\t\t\tconst collisions = viewModel.getCollisions(ringType)\n\n\t\t\trenderer.render(mainG, elements, collisions)\n\t\t}\n\n\t\tthis.fusionRenderer.render(mainG, viewModel.fusions, viewModel.settings.Disco.fusionOpacity)\n\n\t\tif (viewModel.settings.Disco.centerText) {\n\t\t\tconst chrRingBbox = mainG.select('[data-testid=\"sjpp_chromosomes_arc_group\"]').node().getBBox()\n\t\t\t/** Truncate longer texts to stay within the center */\n\t\t\tconst text =\n\t\t\t\tviewModel.settings.Disco.centerText.length > 20\n\t\t\t\t\t? viewModel.settings.Disco.centerText.slice(0, 20) + '...'\n\t\t\t\t\t: viewModel.settings.Disco.centerText\n\t\t\tconst textElem = mainG.append('text').attr('class', 'sjpp-disco-center-text').text(text)\n\t\t\tconst textBbox = textElem.node().getBBox()\n\t\t\ttextElem.attr('transform', `translate(${chrRingBbox.x + chrRingBbox.width / 2 - textBbox.width / 2},0)`)\n\t\t}\n\n\t\tthis.legendRenderer.render(\n\t\t\tmainG,\n\t\t\tviewModel.legend,\n\t\t\t-1 * (viewModel.settings.rings.labelLinesInnerRadius + viewModel.settings.rings.labelsToLinesDistance + 75),\n\t\t\tviewModel.width,\n\t\t\tviewModel.height / 2,\n\t\t\tviewModel,\n\t\t\tonCnvSourceSelect\n\t\t)\n\t}\n}\n", "import { getNormalRoot } from '#filter'\n\nexport class DiscoInteractions {\n\tdiscoApp: any\n\n\tdownloadClickListener: (d: any) => void\n\tgeneClickListener: (gene: string, mnames: Array<string>) => void\n\tcolorScaleNumericInputsCallback: (obj: {\n\t\tcutoffMode: string\n\t\tmin?: number\n\t\tmax?: number\n\t\tpercentile?: number\n\t}) => void\n\tonMutationWaterfallColorChange: (color: string) => void\n\n\tconstructor(discoApp: any) {\n\t\t// note: discoApp will be set when discoApp.state{} is created\n\t\tthis.discoApp = discoApp\n\n\t\tthis.downloadClickListener = (svg: any) => {\n\t\t\tconst downloadImgName = this.discoApp.state.settings.downloadImgName || 'disco.plot'\n\t\t\tconst a = document.createElement('a')\n\t\t\tdocument.body.appendChild(a)\n\n\t\t\ta.addEventListener(\n\t\t\t\t'click',\n\t\t\t\t() => {\n\t\t\t\t\t// must use arrow function but not \"function()\", so this.downloadImgName is accessible\n\t\t\t\t\tconst serializer = new XMLSerializer()\n\t\t\t\t\tconst svg_blob = new Blob([serializer.serializeToString(svg)], {\n\t\t\t\t\t\ttype: 'image/svg+xml'\n\t\t\t\t\t})\n\t\t\t\t\ta.download = downloadImgName + '.svg'\n\t\t\t\t\ta.href = URL.createObjectURL(svg_blob)\n\t\t\t\t\tdocument.body.removeChild(a)\n\t\t\t\t},\n\t\t\t\tfalse\n\t\t\t)\n\t\t\ta.click()\n\t\t}\n\n\t\tthis.geneClickListener = async (gene: string, mnames: Array<string>) => {\n\t\t\tconst { filter, filter0 } = this.discoApp.app.getState().termfilter\n\t\t\tconst arg = {\n\t\t\t\tholder: this.discoApp.app.opts.holder,\n\t\t\t\tgenome: this.discoApp.app.opts.state.args.genome,\n\t\t\t\tnobox: true,\n\t\t\t\tquery: gene,\n\t\t\t\ttklst: [\n\t\t\t\t\t{\n\t\t\t\t\t\ttype: 'mds3',\n\t\t\t\t\t\tdslabel: this.discoApp.app.opts.state.vocab.dslabel,\n\t\t\t\t\t\thlaachange: mnames.join(','),\n\t\t\t\t\t\tfilter0,\n\t\t\t\t\t\tfilterObj: getNormalRoot(filter) // must not pass filter as frozen. pass unfrozen, normalized copy so mds3 code will work\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t}\n\t\t\tconst _ = await import('#src/block.init')\n\t\t\tawait _.default(arg)\n\t\t}\n\n\t\t/** Corresponds to the numericInputs callback in dom/ColorScale.ts\n\t\t * Used for CNV legend items only. */\n\t\tthis.colorScaleNumericInputsCallback = async (obj: {\n\t\t\tcutoffMode: string\n\t\t\tmin?: number\n\t\t\tmax?: number\n\t\t\tpercentile?: number\n\t\t}) => {\n\t\t\tconst callAppDispatch = (settings: Record<string, any>) => {\n\t\t\t\tthis.discoApp.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: this.discoApp.id,\n\t\t\t\t\tconfig: { settings: { Disco: Object.assign({ cnvCutoffMode: obj.cutoffMode }, settings) } }\n\t\t\t\t})\n\t\t\t}\n\t\t\tif (obj.cutoffMode == 'auto') {\n\t\t\t\tif (obj.min == null || obj.max == null)\n\t\t\t\t\tthrow new Error('Color scale must return min and max if cutoffMode \"auto\"')\n\t\t\t\tcallAppDispatch({\n\t\t\t\t\tcnvCapping: this.discoApp.state.settings.cnv.capping,\n\t\t\t\t\tcnvPercentile: this.discoApp.state.settings.cnv.percentile\n\t\t\t\t})\n\t\t\t} else if (obj.cutoffMode == 'fixed') {\n\t\t\t\tif (obj.min == null || obj.max == null)\n\t\t\t\t\tthrow new Error('Color scale must return min and max if cutoffMode \"fixed\"')\n\t\t\t\tconst diffValue = obj.max !== this.discoApp.state.settings.cnv.capping ? obj.max : Math.abs(obj.min)\n\t\t\t\tcallAppDispatch({\n\t\t\t\t\tcnvCapping: diffValue\n\t\t\t\t})\n\t\t\t} else if (obj.cutoffMode == 'percentile') callAppDispatch({ cnvPercentile: obj.percentile })\n\t\t\telse throw new Error('Unknown cutoff mode returned from dom/ColorScale')\n\t\t}\n\n\t\tthis.onMutationWaterfallColorChange = (color: string) => {\n\t\t\tthis.discoApp.app.dispatch({\n\t\t\t\ttype: 'plot_edit',\n\t\t\t\tid: this.discoApp.id,\n\t\t\t\tconfig: { settings: { Disco: { mutationWaterfallColor: color } } }\n\t\t\t})\n\t\t}\n\t}\n}\n", "import type Chromosome from './Chromosome.ts'\nimport type Settings from '../Settings.ts'\n\nexport default class Reference {\n\tchromosomes: Array<Chromosome> = []\n\tchromosomesOrder: Array<string> = []\n\ttotalSize: number\n\n\ttotalPadAngle: number\n\ttotalChromosomesAngle: number\n\n\tprivate keysArray: Array<string> = []\n\tprivate totalSizeArray: Array<number> = []\n\tprivate chrSizesArray: Array<number> = []\n\n\tprivate settings: Settings\n\n\t/**\n\t * Creates a Reference object that contains information about chromosomes.\n\t * @param settings State settings\n\t * @param chromosomes Chromosome order. This function formats into an obj with `chr` removed.\n\t * @param chromosomeOverride Obj of chromsome keys and sizes. Filtered to remove hidden chromosomes in settings.\n\t */\n\tconstructor(\n\t\tsettings: Settings,\n\t\tchromosomes: string[] | { [chromosome: string]: number },\n\t\tchromosomeOverride?: { [chromosome: string]: number }\n\t) {\n\t\tconst chrSizes = chromosomeOverride || chromosomes\n\n\t\tthis.settings = settings\n\n\t\tthis.chromosomesOrder = []\n\t\tlet totalSize = 0\n\t\tthis.totalPadAngle = Object.keys(chrSizes).length * this.settings.padAngle\n\t\tthis.totalChromosomesAngle = 2 * Math.PI - this.totalPadAngle\n\n\t\tfor (const chr in chrSizes) {\n\t\t\tconst key = chr.slice(0, 3) === 'chr' ? chr.slice(3) : chr\n\t\t\tthis.chromosomesOrder.push(chr)\n\t\t\tthis.keysArray.push(key)\n\t\t\tthis.totalSizeArray.push(totalSize)\n\t\t\tthis.chrSizesArray.push(chrSizes[chr])\n\n\t\t\ttotalSize += chrSizes[chr]\n\t\t}\n\n\t\tthis.totalSize = totalSize\n\n\t\tlet lastAngle = 0\n\n\t\tfor (let i = 0; i < this.keysArray.length; i++) {\n\t\t\tconst chromosomeAngle = this.totalChromosomesAngle * (this.chrSizesArray[i] / totalSize)\n\n\t\t\tconst startAngle = i == 0 ? this.settings.padAngle / 2 : lastAngle + this.settings.padAngle\n\t\t\tconst endAngle =\n\t\t\t\ti == 0 ? this.settings.padAngle / 2 + chromosomeAngle : lastAngle + this.settings.padAngle + chromosomeAngle\n\t\t\tconst chromosome: Chromosome = {\n\t\t\t\tstart: this.totalSizeArray[i],\n\t\t\t\tsize: this.chrSizesArray[i],\n\t\t\t\tfactor: 1,\n\t\t\t\tstartAngle: startAngle,\n\t\t\t\tendAngle: endAngle,\n\t\t\t\tangle: (startAngle + endAngle) / 2,\n\t\t\t\tinnerRadius: this.settings.rings.chromosomeInnerRadius,\n\t\t\t\touterRadius: this.settings.rings.chromosomeInnerRadius + this.settings.rings.chromosomeWidth,\n\t\t\t\tcolor: '#AAA',\n\t\t\t\ttext: this.keysArray[i]\n\t\t\t}\n\n\t\t\tthis.chromosomes.push(chromosome)\n\n\t\t\tif (chromosome.endAngle != null) {\n\t\t\t\tlastAngle = chromosome.endAngle\n\t\t\t}\n\t\t}\n\t}\n}\n", "import type Data from './Data.ts'\n\nexport default class DataObjectMapper {\n\tprivate sampleName: string\n\tprivate prioritizedGenes: Array<string>\n\n\tconstructor(sampleName: string, prioritizedGenes: Array<string>) {\n\t\tthis.sampleName = sampleName\n\t\tthis.prioritizedGenes = prioritizedGenes\n\t}\n\n\tmap(dObject: any): Data {\n\t\treturn {\n\t\t\tdt: dObject.dt,\n\t\t\tmname: dObject.mname,\n\t\t\tmClass: dObject.class,\n\t\t\tgene: dObject.gene,\n\t\t\tchr: dObject.chr,\n\t\t\tref: dObject.ref,\n\t\t\talt: dObject.alt,\n\t\t\tvafs: dObject.vafs,\n\t\t\tposition: dObject.pos ? dObject.pos : dObject.position,\n\t\t\tposchr: dObject.poschr,\n\t\t\tposbins: dObject.posbins,\n\t\t\tposlabel: dObject.poslabel,\n\t\t\tsampleName: this.sampleName,\n\t\t\tssm_id: dObject.ssm_id,\n\t\t\tstart: dObject.start,\n\t\t\tstop: dObject.stop,\n\t\t\tvalue: dObject.value,\n\t\t\tsegmean: dObject.segmean,\n\t\t\tisPrioritized: this.prioritizedGenes.some(cancerGene => cancerGene == dObject.gene),\n\t\t\tchrA: dObject.chrA,\n\t\t\tchrB: dObject.chrB,\n\t\t\tgeneA: dObject.geneA,\n\t\t\tgeneB: dObject.geneB,\n\t\t\tposA: dObject.posA,\n\t\t\tposB: dObject.posB,\n\t\t\tstrandA: dObject.strandA,\n\t\t\tstrandB: dObject.strandB\n\t\t}\n\t}\n}\n", "// import Data from '#plots/disco/data/Data.ts'\n\nexport class PercentileMapper {\n\tmap(data: Array<number>, percentile: number) {\n\t\treturn this.calculatePercentileForPositivesAndNegatives(data, percentile)\n\t}\n\n\tprivate calculatePercentileForPositivesAndNegatives(\n\t\tdata: Array<number>,\n\t\tpercentile: number\n\t): {\n\t\tpositive: number\n\t\tnegative: number\n\t} {\n\t\t// Filter positive and negative numbers\n\t\tconst positives = data.filter(x => x > 0)\n\t\tconst negatives = data.filter(x => x < 0).map(x => -1 * x)\n\n\t\tlet positive = NaN\n\t\tlet negative = NaN\n\n\t\tif (positives.length > 0) {\n\t\t\tpositive = this.calculatePercentile(positives, percentile)\n\t\t}\n\n\t\tif (negatives.length > 0) {\n\t\t\tnegative = -1 * this.calculatePercentile(negatives, percentile)\n\t\t}\n\n\t\treturn { positive: positive, negative: negative }\n\t}\n\n\tprivate calculatePercentile(data: Array<number>, percentile: number): number {\n\t\tif (data.length === 0) {\n\t\t\tthrow new Error('Array must contain at least one element.')\n\t\t}\n\n\t\tconst sortedValues = data.sort((a, b) => a - b)\n\t\tconst index = (percentile / 100) * (sortedValues.length - 1)\n\n\t\tconst lowerIndex = Math.floor(index)\n\t\tconst upperIndex = Math.ceil(index)\n\t\tconst fraction = index - lowerIndex\n\n\t\tif (lowerIndex === upperIndex) {\n\t\t\treturn sortedValues[lowerIndex]\n\t\t}\n\n\t\treturn sortedValues[lowerIndex] + fraction * (sortedValues[upperIndex] - sortedValues[lowerIndex])\n\t}\n}\n", "import type Data from './Data.ts'\nimport type Reference from '#plots/disco/chromosome/Reference.ts'\nimport DataObjectMapper from './DataObjectMapper.ts'\nimport type Settings from '#plots/disco/Settings.ts'\nimport { ViewModelMapper } from '#plots/disco/viewmodel/ViewModelMapper.ts'\nimport type { DataHolder } from '#plots/disco/data/DataHolder.ts'\nimport { dtsnvindel, dtfusionrna, dtsv, dtcnv, dtloh } from '#shared/common.js'\nimport { PercentileMapper } from '#plots/disco/data/PercentileMapper.ts'\nimport type { MutationWaterfallDatum } from '#plots/disco/waterfall/MutationWaterfallDatum.ts'\n\nexport default class DataMapper {\n\t// remove fields and extract filters to seperate classes\n\n\tprivate labelData: Array<Data> = []\n\n\tprivate nonExonicSnvData: Array<Data> = []\n\tprivate nonExonicInnerRadius = 0\n\n\tprivate snvRingDataMap: Map<number, Array<Data>> = new Map()\n\tprivate snvInnerRadius = 0\n\n\tprivate snvData: Array<Data> = []\n\tprivate bpx = 0\n\tprivate onePxArcAngle = 0\n\tprivate filteredSnvData: Array<Data> = []\n\tprivate filteredSnvCountByChr: Map<string, number> = new Map()\n\n\tprivate lohData: Array<Data> = []\n\tprivate lohInnerRadius = 0\n\n\tprivate cnvData: Array<Data> = []\n\tprivate cnvInnerRadius = 0\n\n\tprivate fusionData: Array<Data> = []\n\tprivate fusionRadius = 0\n\n\tprivate hasPrioritizedGenes = false\n\tprivate hasWaterfallEligibleChromosome = false\n\n\tprivate invalidEntries: { dataType: string; reason: string }[] = []\n\n\tprivate cnvLossMaxValue = 0\n\tprivate cnvGainMaxValue = 0\n\tprivate gainCapped: number\n\tprivate lossCapped: number\n\tprivate cappedCnvMaxAbsValue?: number\n\tprivate percentilePositive = 0\n\tprivate percentileNegative = 0\n\tprivate cnvMaxPercentileAbs = 0\n\n\tprivate mutationWaterfallData: Array<MutationWaterfallDatum> = []\n\tprivate mutationWaterfallInnerRadius = 0\n\tprivate mutationWaterfallRangeMin = Infinity\n\tprivate mutationWaterfallRangeMax = -Infinity\n\n\tprivate lohMaxValue?: number = undefined\n\tprivate lohMinValue?: number = undefined\n\n\tprivate settings: Settings\n\tprivate reference: Reference\n\tprivate sample: string\n\n\tprivate nonExonicFilter: (data: Data) => boolean\n\tprivate snvRingFilter: (data: Data) => boolean\n\tprivate dataObjectMapper: DataObjectMapper\n\tprivate lastInnerRadious: number\n\tprivate excludedChromosomes: string[]\n\n\tprivate snvFilter = (data: Data) => data.dt == dtsnvindel\n\tprivate fusionFilter = (data: Data) => data.dt == dtfusionrna || data.dt == dtsv\n\n\tprivate cnvFilter = (data: Data) => data.dt == dtcnv\n\tprivate lohFilter = (data: Data) => data.dt == dtloh\n\n\tprivate compareData = (a, b) => {\n\t\tconst chrDiff = this.reference.chromosomesOrder.indexOf(a.chr) - this.reference.chromosomesOrder.indexOf(b.chr)\n\t\tif (chrDiff != 0) {\n\t\t\treturn chrDiff\n\t\t}\n\n\t\tconst aPos = a.pos ? a.pos : a.start\n\n\t\tconst bPos = b.pos ? b.pos : b.start\n\n\t\treturn aPos - bPos\n\t}\n\n\tconstructor(settings: Settings, reference: Reference, sample: string, prioritizedGenes: Array<string> = []) {\n\t\tthis.settings = settings\n\t\tthis.reference = reference\n\t\tthis.sample = sample\n\t\tthis.excludedChromosomes = this.settings.Disco.hiddenChromosomes\n\t\tthis.lastInnerRadious = this.settings.rings.chromosomeInnerRadius\n\n\t\tthis.gainCapped = this.settings.Disco.cnvCapping\n\t\tthis.lossCapped = -1 * this.settings.Disco.cnvCapping\n\n\t\tthis.nonExonicFilter = (data: Data) => {\n\t\t\tif (prioritizedGenes.length > 0 && this.settings.Disco.prioritizeGeneLabelsByGeneSets) {\n\t\t\t\treturn (\n\t\t\t\t\tprioritizedGenes.includes(data.gene) &&\n\t\t\t\t\tsettings.rings.nonExonicFilterValues.includes(ViewModelMapper.snvClassLayer[data.mClass])\n\t\t\t\t)\n\t\t\t} else {\n\t\t\t\treturn settings.rings.nonExonicFilterValues.includes(ViewModelMapper.snvClassLayer[data.mClass])\n\t\t\t}\n\t\t}\n\n\t\tthis.snvRingFilter = (data: Data) => {\n\t\t\tif (prioritizedGenes.length > 0 && this.settings.Disco.prioritizeGeneLabelsByGeneSets) {\n\t\t\t\treturn (\n\t\t\t\t\tprioritizedGenes.includes(data.gene) &&\n\t\t\t\t\tsettings.rings.snvRingFilters.includes(ViewModelMapper.snvClassLayer[data.mClass])\n\t\t\t\t)\n\t\t\t} else {\n\t\t\t\treturn settings.rings.snvRingFilters.includes(ViewModelMapper.snvClassLayer[data.mClass])\n\t\t\t}\n\t\t}\n\n\t\tthis.dataObjectMapper = new DataObjectMapper(sample, prioritizedGenes)\n\t}\n\n\tmap(data: any) {\n\t\tconst dataArray: Array<Data> = []\n\n\t\tthis.filteredSnvCountByChr.clear()\n\t\tthis.hasWaterfallEligibleChromosome = false\n\t\tthis.mutationWaterfallData = []\n\t\tthis.mutationWaterfallInnerRadius = 0\n\t\tthis.mutationWaterfallRangeMin = Infinity\n\t\tthis.mutationWaterfallRangeMax = -Infinity\n\n\t\tdata.forEach(dObject => {\n\t\t\tconst index = this.reference.chromosomesOrder.indexOf(dObject.chr)\n\t\t\tconst indexA = this.reference.chromosomesOrder.indexOf(dObject.chrA)\n\t\t\tconst indexB = this.reference.chromosomesOrder.indexOf(dObject.chrB)\n\n\t\t\tif (dObject.dt == dtsnvindel) {\n\t\t\t\tif (index != -1 && this.snvData.length < this.settings.snv.maxMutationCount) {\n\t\t\t\t\tconst pos = dObject.pos ?? dObject.position\n\t\t\t\t\tconst chrSize = this.reference.chromosomes[index].size\n\t\t\t\t\t// ensure position is numeric and within chromosome range\n\t\t\t\t\tif (Number.isFinite(pos) && pos >= 0 && pos <= chrSize) {\n\t\t\t\t\t\tthis.addData(dObject, dataArray)\n\t\t\t\t\t} else {\n\t\t\t\t\t\tthis.invalidEntries.push({ dataType: 'SNV', reason: `Position ${pos} outside of ${dObject.chr}` })\n\t\t\t\t\t}\n\t\t\t\t} else if (index == -1) {\n\t\t\t\t\tif (!this.excludedChromosomes.includes(dObject.chr)) {\n\t\t\t\t\t\tthis.invalidEntries.push({ dataType: 'SNV', reason: `Unknown chr ${dObject.chr}` })\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} else if (dObject.dt == dtfusionrna || dObject.dt == dtsv) {\n\t\t\t\tif (indexA != -1 && indexB != -1) {\n\t\t\t\t\t// show sv/fusion event with valid A/B breakpoints.\n\t\t\t\t\tconst posA = dObject.posA\n\t\t\t\t\tconst posB = dObject.posB\n\t\t\t\t\tconst chrSizeA = this.reference.chromosomes[indexA].size\n\t\t\t\t\tconst chrSizeB = this.reference.chromosomes[indexB].size\n\t\t\t\t\t// verify that both breakpoints are numeric and within chromosome ranges\n\t\t\t\t\tif (\n\t\t\t\t\t\tNumber.isFinite(posA) &&\n\t\t\t\t\t\tNumber.isFinite(posB) &&\n\t\t\t\t\t\tposA >= 0 &&\n\t\t\t\t\t\tposA <= chrSizeA &&\n\t\t\t\t\t\tposB >= 0 &&\n\t\t\t\t\t\tposB <= chrSizeB\n\t\t\t\t\t) {\n\t\t\t\t\t\tthis.addData(dObject, dataArray)\n\t\t\t\t\t} else {\n\t\t\t\t\t\tconst reasonParts: string[] = []\n\t\t\t\t\t\tif (!(Number.isFinite(posA) && posA >= 0 && posA <= chrSizeA))\n\t\t\t\t\t\t\treasonParts.push(`Position ${posA} outside of ${dObject.chrA}`)\n\t\t\t\t\t\tif (!(Number.isFinite(posB) && posB >= 0 && posB <= chrSizeB))\n\t\t\t\t\t\t\treasonParts.push(`Position ${posB} outside of ${dObject.chrB}`)\n\t\t\t\t\t\tthis.invalidEntries.push({ dataType: 'Fusion', reason: reasonParts.join('; ') })\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\tconst missing: string[] = []\n\t\t\t\t\tif (indexA == -1 && !this.excludedChromosomes.includes(dObject.chrA)) missing.push(dObject.chrA)\n\t\t\t\t\tif (indexB == -1 && !this.excludedChromosomes.includes(dObject.chrB)) missing.push(dObject.chrB)\n\t\t\t\t\tif (missing.length) this.invalidEntries.push({ dataType: 'Fusion', reason: 'Unknown chr in fusion' })\n\t\t\t\t}\n\t\t\t} else if ([dtcnv, dtloh].includes(Number(dObject.dt))) {\n\t\t\t\tconst idx = this.reference.chromosomesOrder.indexOf(dObject.chr)\n\t\t\t\tif (dObject.chr && idx != -1) {\n\t\t\t\t\tconst chrSize = this.reference.chromosomes[idx].size\n\t\t\t\t\tconst start = dObject.start\n\t\t\t\t\tconst stop = dObject.stop\n\t\t\t\t\t// validate CNV/LOH segment boundaries are numeric and fall within chromosome range\n\t\t\t\t\tif (Number.isFinite(start) && Number.isFinite(stop) && start >= 0 && stop <= chrSize && start <= stop) {\n\t\t\t\t\t\tthis.addData(dObject, dataArray)\n\t\t\t\t\t} else {\n\t\t\t\t\t\tthis.invalidEntries.push({\n\t\t\t\t\t\t\tdataType: dObject.dt == dtcnv ? 'CNV' : 'LOH',\n\t\t\t\t\t\t\treason: `Position ${start}-${stop} outside of ${dObject.chr}`\n\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\tif (!this.excludedChromosomes.includes(dObject.chr)) {\n\t\t\t\t\t\tthis.invalidEntries.push({\n\t\t\t\t\t\t\tdataType: dObject.dt == dtcnv ? 'CNV' : 'LOH',\n\t\t\t\t\t\t\treason: `Unknown chr ${dObject.chr}`\n\t\t\t\t\t\t})\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tthrow Error('Unknown mutation type!')\n\t\t\t}\n\t\t})\n\n\t\tconst sortedData = dataArray.sort(this.compareData)\n\n\t\tif (this.settings.rings.nonExonicRingEnabled) {\n\t\t\tsortedData.forEach(data => {\n\t\t\t\tthis.filterNonExonicSnvData(data)\n\t\t\t})\n\t\t}\n\n\t\tif (this.nonExonicSnvData.length > 0) {\n\t\t\tthis.nonExonicInnerRadius = this.lastInnerRadious - this.settings.rings.nonExonicRingWidth\n\t\t\tthis.lastInnerRadious = this.nonExonicInnerRadius\n\t\t}\n\n\t\tsortedData.forEach(data => {\n\t\t\tthis.filterSnvs(data)\n\t\t})\n\n\t\tthis.hasWaterfallEligibleChromosome = Array.from(this.filteredSnvCountByChr.values()).some(count => count >= 2)\n\n\t\tif (this.settings.Disco.mutationWaterfallPlot && this.hasWaterfallEligibleChromosome) {\n\t\t\tthis.prepareMutationWaterfallData()\n\t\t}\n\n\t\tsortedData.forEach(data => {\n\t\t\tthis.filterLohs(data)\n\t\t})\n\n\t\tif (this.lohData.length > 0) {\n\t\t\tthis.lohInnerRadius = this.lastInnerRadious - this.settings.rings.lohRingWidth\n\t\t\tthis.lastInnerRadious = this.lohInnerRadius\n\t\t}\n\n\t\tsortedData.forEach(data => {\n\t\t\tthis.filterCnvs(data)\n\t\t})\n\n\t\tif (this.cnvData.length > 0) {\n\t\t\tthis.cnvInnerRadius = this.lastInnerRadious - this.settings.rings.cnvRingWidth\n\t\t\tthis.lastInnerRadious = this.cnvInnerRadius\n\n\t\t\tthis.cappedCnvMaxAbsValue = Math.min(\n\t\t\t\tthis.settings.Disco.cnvCapping,\n\t\t\t\tMath.max(\n\t\t\t\t\tMath.abs(DataMapper.capMaxValue(this.cnvLossMaxValue, this.gainCapped, this.lossCapped)),\n\t\t\t\t\tMath.abs(DataMapper.capMaxValue(this.cnvGainMaxValue, this.gainCapped, this.lossCapped))\n\t\t\t\t)\n\t\t\t)\n\n\t\t\tconst percentilePair = new PercentileMapper().map(\n\t\t\t\tthis.cnvData.map(data => data.value),\n\t\t\t\tthis.settings.Disco.cnvPercentile\n\t\t\t)\n\t\t\tthis.percentilePositive = DataMapper.capMaxValue(percentilePair.positive, this.gainCapped, this.lossCapped)\n\t\t\tthis.percentileNegative = DataMapper.capMaxValue(percentilePair.negative, this.gainCapped, this.lossCapped)\n\n\t\t\tthis.cnvMaxPercentileAbs = Math.min(\n\t\t\t\tthis.settings.Disco.cnvCapping,\n\t\t\t\tMath.max(this.percentilePositive, Math.abs(this.percentileNegative))\n\t\t\t)\n\t\t}\n\n\t\tsortedData.forEach(data => {\n\t\t\tthis.filterFusion(data)\n\t\t})\n\n\t\tif (this.fusionData.length > 0) {\n\t\t\tthis.fusionRadius = this.lastInnerRadious\n\t\t}\n\n\t\tconst dataHolder: DataHolder = {\n\t\t\tlabelData: this.labelData,\n\t\t\tnonExonicSnvData: this.nonExonicSnvData,\n\t\t\tnonExonicInnerRadius: this.nonExonicInnerRadius,\n\t\t\tsnvRingDataMap: this.snvRingDataMap,\n\t\t\tsnvInnerRadius: this.snvInnerRadius,\n\n\t\t\tsnvData: this.snvData,\n\t\t\tbpx: this.bpx,\n\t\t\tonePxArcAngle: this.onePxArcAngle,\n\t\t\tfilteredSnvData: this.filteredSnvData,\n\n\t\t\tlohData: this.lohData,\n\t\t\tlohInnerRadius: this.lohInnerRadius,\n\n\t\t\tcnvData: this.cnvData,\n\t\t\tcnvInnerRadius: this.cnvInnerRadius,\n\n\t\t\tfusionData: this.fusionData,\n\t\t\tfusionRadius: this.fusionRadius,\n\n\t\t\thasPrioritizedGenes: this.hasPrioritizedGenes,\n\t\t\thasWaterfallEligibleChromosome: this.hasWaterfallEligibleChromosome,\n\n\t\t\tcnvGainMaxValue: this.cnvGainMaxValue,\n\t\t\tcnvLossMaxValue: this.cnvLossMaxValue,\n\t\t\tcappedCnvMaxAbsValue: this.cappedCnvMaxAbsValue,\n\t\t\tpercentilePositive: this.percentilePositive,\n\t\t\tpercentileNegative: this.percentileNegative,\n\t\t\tcnvMaxPercentileAbs: this.cnvMaxPercentileAbs,\n\n\t\t\tlohMaxValue: this.lohMaxValue,\n\t\t\tlohMinValue: this.lohMinValue,\n\n\t\t\tmutationWaterfallData: this.mutationWaterfallData,\n\t\t\tmutationWaterfallInnerRadius: this.mutationWaterfallInnerRadius,\n\t\t\tmutationWaterfallLogRange: this.mutationWaterfallData.length\n\t\t\t\t? { min: this.mutationWaterfallRangeMin, max: this.mutationWaterfallRangeMax }\n\t\t\t\t: undefined,\n\n\t\t\tinvalidDataInfo: {\n\t\t\t\tentries: this.invalidEntries,\n\t\t\t\terrorMsg: `Entries listed above were skipped due to invalid or unsupported chromosome information.`\n\t\t\t}\n\t\t}\n\n\t\treturn dataHolder\n\t}\n\n\tprivate addData(dObject, dataArray: Array<Data>) {\n\t\tconst instance = this.dataObjectMapper.map(dObject)\n\n\t\tif (instance.isPrioritized) {\n\t\t\tthis.hasPrioritizedGenes = true\n\t\t}\n\n\t\tdataArray.push(instance)\n\t}\n\n\tprivate filterNonExonicSnvData(data: Data) {\n\t\tif (this.snvFilter(data)) {\n\t\t\tif (this.settings.rings.nonExonicRingEnabled && this.nonExonicFilter(data)) {\n\t\t\t\tthis.nonExonicSnvData.push(data)\n\t\t\t}\n\t\t}\n\t}\n\n\tprivate filterSnvs(data: Data) {\n\t\tif (this.snvFilter(data)) {\n\t\t\tthis.snvData.push(data)\n\n\t\t\tif (this.snvRingFilter(data)) {\n\t\t\t\tif (this.snvInnerRadius == 0) {\n\t\t\t\t\tthis.snvInnerRadius = this.lastInnerRadious - this.settings.rings.snvRingWidth\n\t\t\t\t\tthis.lastInnerRadious = this.snvInnerRadius\n\n\t\t\t\t\t// number of base pairs per pixel\n\t\t\t\t\t// TODO verify place of bpx calculation\n\t\t\t\t\tthis.bpx = Math.floor(this.reference.totalSize / (this.reference.totalChromosomesAngle * this.snvInnerRadius))\n\t\t\t\t\tthis.onePxArcAngle = 1 / this.snvInnerRadius\n\t\t\t\t}\n\n\t\t\t\tthis.filteredSnvData.push(data)\n\t\t\t\tthis.labelData.push(data)\n\n\t\t\t\tconst currentCount = this.filteredSnvCountByChr.get(data.chr) || 0\n\t\t\t\tthis.filteredSnvCountByChr.set(data.chr, currentCount + 1)\n\n\t\t\t\tconst arcAngle = this.calculateArcAngle(data)\n\t\t\t\tlet dataArray = this.snvRingDataMap.get(arcAngle)\n\t\t\t\tif (!dataArray) {\n\t\t\t\t\tdataArray = new Array<Data>()\n\t\t\t\t}\n\t\t\t\tdataArray.push(data)\n\t\t\t\tthis.snvRingDataMap.set(arcAngle, dataArray)\n\t\t\t}\n\t\t}\n\t}\n\n\tprivate filterFusion(data: Data) {\n\t\tif (this.fusionFilter(data)) {\n\t\t\tdata.isPrioritized = true\n\t\t\tthis.fusionData.push(data)\n\t\t\tthis.labelData.push(data)\n\t\t}\n\t}\n\n\tprivate filterLohs(data: Data) {\n\t\tif (this.lohFilter(data)) {\n\t\t\tif (this.lohMaxValue == undefined || this.lohMaxValue < data.value) {\n\t\t\t\tthis.lohMaxValue = data.segmean\n\t\t\t}\n\n\t\t\tif (this.lohMinValue == undefined || this.lohMinValue > data.value) {\n\t\t\t\tthis.lohMinValue = data.segmean\n\t\t\t}\n\n\t\t\tthis.lohData.push(data)\n\t\t}\n\t}\n\n\tprivate filterCnvs(data: Data) {\n\t\tif (this.cnvFilter(data)) {\n\t\t\tif (!data.chr || this.reference.chromosomesOrder.indexOf(data.chr) == -1) {\n\t\t\t\t// when chr is unknown or not in reference chromosomes (chr1-22, X, Y), do not render arc\n\t\t\t\treturn\n\t\t\t}\n\n\t\t\tif (this.cnvGainMaxValue == undefined || this.cnvGainMaxValue < data.value) {\n\t\t\t\tthis.cnvGainMaxValue = data.value\n\t\t\t}\n\n\t\t\tif (this.cnvLossMaxValue == undefined || this.cnvLossMaxValue > data.value) {\n\t\t\t\tthis.cnvLossMaxValue = data.value\n\t\t\t}\n\t\t\tthis.cnvData.push(data)\n\t\t}\n\t}\n\n\tprivate prepareMutationWaterfallData() {\n\t\tthis.mutationWaterfallInnerRadius = this.lastInnerRadious - this.settings.rings.mutationWaterfallRingWidth\n\t\tthis.lastInnerRadious = this.mutationWaterfallInnerRadius\n\n\t\tconst groupedSnvs: Map<string, Array<Data>> = new Map()\n\t\tconst firstMutationByChr: MutationWaterfallDatum[] = []\n\t\tfor (const snv of this.filteredSnvData) {\n\t\t\tconst list = groupedSnvs.get(snv.chr) || []\n\t\t\tlist.push(snv)\n\t\t\tgroupedSnvs.set(snv.chr, list)\n\t\t}\n\n\t\tfor (const [, snvs] of groupedSnvs) {\n\t\t\tif (snvs.length < 2) continue\n\t\t\tsnvs.sort((a, b) => a.position - b.position)\n\t\t\tfirstMutationByChr.push({\n\t\t\t\tchr: snvs[0].chr,\n\t\t\t\tposition: snvs[0].position,\n\t\t\t\tlogDistance: 0 // placeholder updated after range computed\n\t\t\t})\n\t\t\tfor (let i = 1; i < snvs.length; i++) {\n\t\t\t\tconst prev = snvs[i - 1]\n\t\t\t\tconst curr = snvs[i]\n\t\t\t\tconst distance = Math.max(1, Math.abs(curr.position - prev.position))\n\t\t\t\tconst logDistance = Math.log10(distance)\n\t\t\t\tthis.mutationWaterfallData.push({\n\t\t\t\t\tchr: curr.chr,\n\t\t\t\t\tposition: curr.position,\n\t\t\t\t\tlogDistance\n\t\t\t\t})\n\t\t\t\tif (logDistance < this.mutationWaterfallRangeMin) {\n\t\t\t\t\tthis.mutationWaterfallRangeMin = logDistance\n\t\t\t\t}\n\t\t\t\tif (logDistance > this.mutationWaterfallRangeMax) {\n\t\t\t\t\tthis.mutationWaterfallRangeMax = logDistance\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tif (!this.mutationWaterfallData.length) {\n\t\t\tthis.mutationWaterfallRangeMin = 0\n\t\t\tthis.mutationWaterfallRangeMax = 0\n\t\t}\n\n\t\tconst topLogDistance = this.mutationWaterfallRangeMax\n\t\tfor (const first of firstMutationByChr) {\n\t\t\tthis.mutationWaterfallData.push({\n\t\t\t\t...first,\n\t\t\t\tlogDistance: topLogDistance\n\t\t\t})\n\t\t}\n\t}\n\n\tprivate calculateArcAngle(data: Data) {\n\t\tconst currentChromosome =\n\t\t\tthis.reference.chromosomes[\n\t\t\t\tthis.reference.chromosomesOrder.findIndex(chromosomeOrder => data.chr == chromosomeOrder)\n\t\t\t]\n\n\t\tconst dataAnglePos = Math.floor(data.position / this.bpx)\n\n\t\treturn currentChromosome.startAngle + dataAnglePos * this.onePxArcAngle\n\t}\n\n\tstatic capMaxValue(value: number, gainCapped: number, lossCapped: number) {\n\t\tif (value && Math.sign(value) == 1) {\n\t\t\treturn value > gainCapped ? gainCapped : value\n\t\t}\n\n\t\tif (Math.sign(value) == -1) {\n\t\t\treturn value < lossCapped ? lossCapped : value\n\t\t}\n\n\t\treturn 0\n\t}\n\n\tstatic capMinValue(value: number, capMinValue = 1) {\n\t\tif (Math.sign(value) == 1) {\n\t\t\treturn value > capMinValue ? value : capMinValue\n\t\t}\n\n\t\tif (Math.sign(value) == -1) {\n\t\t\treturn value < -1 * capMinValue ? value : -1 * capMinValue\n\t\t}\n\n\t\treturn 1\n\t}\n}\n", "import type SnvLegendElement from '#plots/disco/snv/SnvLegendElement.ts'\nimport type CnvLegend from '#plots/disco/cnv/CnvLegend.ts'\nimport type LohLegend from '#plots/disco/loh/LohLegend.ts'\nimport type { CnvType } from '#plots/disco/cnv/CnvType.ts'\nimport type { DiscoInteractions } from '../interactions/DiscoInteractions'\n\nexport type MutationWaterfallLegend = {\n\tcolor: string\n\tonColorChange: (color: string) => void\n}\n\nexport default class Legend {\n\tsnvTitle: string\n\tsnvClassMap: Map<string, SnvLegendElement>\n\n\tcnvTitle: string\n\tcnvClassMap: Map<CnvType, CnvLegend>\n\tcnvPercentile: number\n\tcnvCutoffMode: string\n\n\tlohTitle: string\n\tlohLegend?: LohLegend\n\n\tfusionTitle: string\n\tfusionLegend: boolean\n\tcnvRenderingType: string\n\n\tdiscoInteractions: DiscoInteractions\n\n\tmutationWaterfallLegend?: MutationWaterfallLegend\n\n\tconstructor(\n\t\tsnvTitle: string,\n\t\tcnvTitle: string,\n\t\tlohTitle: string,\n\t\tfusionTitle: string,\n\t\tcnvPercentile: number,\n\t\tcnvCutoffmode: string,\n\t\tsnvClassMap: Map<string, SnvLegendElement>,\n\t\tcnvClassMap: Map<CnvType, CnvLegend>,\n\t\tcnvRenderingType: string,\n\t\tfusionLegend: boolean,\n\t\tdiscoInteractions: DiscoInteractions,\n\t\tlohLegend?: LohLegend,\n\t\tmutationWaterfallLegend?: MutationWaterfallLegend\n\t) {\n\t\tthis.snvTitle = snvTitle\n\t\tthis.cnvTitle = cnvTitle\n\t\tthis.lohTitle = lohTitle\n\t\tthis.fusionTitle = fusionTitle\n\t\tthis.cnvPercentile = cnvPercentile\n\t\tthis.cnvCutoffMode = cnvCutoffmode\n\t\tthis.snvClassMap = snvClassMap\n\t\tthis.cnvClassMap = cnvClassMap\n\t\tthis.cnvRenderingType = cnvRenderingType\n\t\tthis.lohLegend = lohLegend\n\t\tthis.fusionLegend = fusionLegend\n\t\tthis.discoInteractions = discoInteractions\n\t\tthis.mutationWaterfallLegend = mutationWaterfallLegend\n\t}\n\n\tlegendCount(): number {\n\t\treturn (\n\t\t\t(this.snvClassMap.size > 0 ? 1 : 0) +\n\t\t\t(this.cnvClassMap.size > 0 ? 1 : 0) +\n\t\t\t(this.lohLegend ? 1 : 0) +\n\t\t\t(this.fusionLegend ? 1 : 0) +\n\t\t\t(this.mutationWaterfallLegend ? 1 : 0)\n\t\t)\n\t}\n}\n", "import type { Ribbon } from 'd3'\nimport type FusionSubgroup from './FusionSubgroup.ts'\n\nexport default class Fusion implements Ribbon {\n\tsource: FusionSubgroup\n\ttarget: FusionSubgroup\n\tgenes: string\n\tcount: number\n\tendpts: string\n\n\tconstructor(source: FusionSubgroup, target: FusionSubgroup, genes: string, count: number, endpts: string) {\n\t\tthis.source = source\n\t\tthis.target = target\n\t\tthis.genes = genes\n\t\tthis.count = count\n\t\tthis.endpts = endpts\n\t}\n}\n", "import type { RibbonSubgroup } from 'd3'\nimport type PositionInChromosome from './PositionInChromosome.ts'\n\nexport default class FusionSubgroup implements RibbonSubgroup {\n\tstartAngle: number\n\tendAngle: number\n\tradius: number\n\n\tgene: string\n\tvalue: number\n\tgenes: Set<string>\n\tpositionInChromosome: PositionInChromosome\n\tstrand: string\n\n\tconstructor(\n\t\tstartAngle: number,\n\t\tendAngle: number,\n\t\tradius: number,\n\t\tgene: string,\n\t\tvalue: number,\n\t\tgenes: Set<string>,\n\t\tpositionInChromosome: PositionInChromosome,\n\t\tstrand: string\n\t) {\n\t\tthis.startAngle = startAngle\n\t\tthis.endAngle = endAngle\n\t\tthis.radius = radius\n\t\tthis.gene = gene\n\t\tthis.value = value\n\t\tthis.genes = genes\n\t\tthis.positionInChromosome = positionInChromosome\n\t\tthis.strand = strand\n\t}\n}\n", "import type Reference from '#plots/disco/chromosome/Reference.ts'\nimport type Data from '#plots/disco/data/Data.ts'\nimport Fusion from './Fusion.ts'\nimport FusionSubgroup from './FusionSubgroup.ts'\n\nexport default class FusionMapper {\n\tprivate radius: number\n\tprivate sampleName: string\n\tprivate reference: Reference\n\n\tconstructor(radius: number, sampleName: string, reference: Reference) {\n\t\tthis.radius = radius\n\t\tthis.sampleName = sampleName\n\t\tthis.reference = reference\n\t}\n\n\tmap(fusionData: Array<Data>): Array<Fusion> {\n\t\tconst fusions: Array<Fusion> = []\n\n\t\tfusionData.forEach(data => {\n\t\t\tconst genes = new Set<string>()\n\t\t\tgenes.add(data.geneA)\n\t\t\tgenes.add(data.geneB)\n\n\t\t\t/** skip any null (i.e. from isoforms or minor chrs) fusions */\n\t\t\tconst startAngle = this.calculateStartAngle(data.chrA, data.posA)\n\t\t\tconst endAngle = this.calculateEndAngle(data.chrA, data.posA)\n\t\t\tif (startAngle === null || endAngle === null) return\n\n\t\t\tconst source = new FusionSubgroup(\n\t\t\t\tstartAngle,\n\t\t\t\tendAngle,\n\t\t\t\tthis.radius,\n\t\t\t\tdata.geneA,\n\t\t\t\tdata.value,\n\t\t\t\tgenes,\n\t\t\t\t{\n\t\t\t\t\tchromosome: data.chrA,\n\t\t\t\t\tposition: data.posA\n\t\t\t\t},\n\t\t\t\tdata.strandA\n\t\t\t)\n\n\t\t\tlet target\n\t\t\tif (data.chrB && data.posB) {\n\t\t\t\t/** skip any null (i.e. from isoforms or minor chrs) fusions */\n\t\t\t\tconst startAngle = this.calculateStartAngle(data.chrB, data.posB)\n\t\t\t\tconst endAngle = this.calculateEndAngle(data.chrB, data.posB)\n\t\t\t\tif (startAngle === null || endAngle === null) return\n\t\t\t\ttarget = new FusionSubgroup(\n\t\t\t\t\tstartAngle,\n\t\t\t\t\tendAngle,\n\t\t\t\t\tthis.radius,\n\t\t\t\t\tdata.geneB,\n\t\t\t\t\tdata.value,\n\t\t\t\t\tgenes,\n\t\t\t\t\t{\n\t\t\t\t\t\tchromosome: data.chrB,\n\t\t\t\t\t\tposition: data.posB\n\t\t\t\t\t},\n\t\t\t\t\tdata.strandB\n\t\t\t\t)\n\t\t\t}\n\t\t\tconst fusion = new Fusion(source, target, 'genes', -1, 'Endpoints')\n\n\t\t\tfusions.push(fusion)\n\t\t})\n\n\t\treturn fusions\n\t}\n\n\tcalculateStartAngle(chr: string, pos: number) {\n\t\tconst index = this.reference.chromosomesOrder.indexOf(chr)\n\t\t/** Return null for isforms or minor chr */\n\t\tif (index === -1) return null\n\t\tconst chromosome = this.reference.chromosomes[index]\n\t\t// TODO calculate 0.01 base on BPs\n\t\treturn (\n\t\t\tchromosome.startAngle + (chromosome.endAngle - chromosome.startAngle) * (Number(pos) / chromosome.size) - 0.01\n\t\t)\n\t}\n\n\tprivate calculateEndAngle(chr: string, pos: number) {\n\t\tconst index = this.reference.chromosomesOrder.indexOf(chr)\n\t\t/** Return null for isforms or minor chr*/\n\t\tif (index === -1) return null\n\t\tconst chromosome = this.reference.chromosomes[index]\n\t\t// TODO calculate 0.01 base on BPs\n\t\treturn (\n\t\t\t0.01 + chromosome.startAngle + (chromosome.endAngle - chromosome.startAngle) * (Number(pos) / chromosome.size)\n\t\t)\n\t}\n}\n", "export default class GradientColorProvider {\n    static provide(value: number): string {\n        const clampedValue = Math.min(Math.max(value, 0), 1);\n\n        const colorValue = Math.round(clampedValue * 255);\n\n        return `rgb(${colorValue}, ${colorValue}, ${colorValue})`;\n    }\n}", "import GradientColorProvider from './GradientColorProvider.ts'\n\nexport default class LohLegend {\n\tminValue: number\n\tmaxValue: number\n\tcolorStartValue: string\n\tcolorEndValue: string\n\tconstructor(minValue: number, maxValue: number) {\n\t\tthis.minValue = minValue\n\t\tthis.maxValue = maxValue\n\t\tthis.colorStartValue = GradientColorProvider.provide(minValue)\n\t\tthis.colorEndValue = GradientColorProvider.provide(maxValue)\n\t}\n}\n", "import type Rings from '#plots/disco/ring/Rings.ts'\nimport type Legend from '#plots/disco/legend/Legend.ts'\nimport { RingType } from '#plots/disco/ring/RingType.ts'\nimport type Arc from '#plots/disco/arc/Arc.ts'\nimport type Settings from '#plots/disco/Settings.ts'\nimport { select } from 'd3-selection'\nimport { getMaxLabelWidth } from '#dom/maxLabelWidth'\nimport type Fusion from '#plots/disco/fusion/Fusion.ts'\nimport type { DataHolder } from '#plots/disco/data/DataHolder.ts'\nimport type { InvalidDataInfo } from '#dom'\n\nexport default class ViewModel {\n\tpublic appState: any\n\tpublic svgDiv: any\n\n\twidth: number\n\theight: number\n\tlegendHeight: number\n\n\trings: Rings\n\tlegend: Legend\n\n\tfusions: Array<Fusion>\n\n\tsettings: Settings\n\tsnvDataLength: number\n\tfilteredSnvDataLength: number\n\tsnvDataLengthAll: number\n\tgenesetName: string\n\tcnvMaxValue?: number\n\tcnvMinValue?: number\n\tcappedCnvMaxAbsValue?: number\n\tnegativePercentile?: number\n\tpositivePercentile?: number\n\tinvalidDataInfo?: InvalidDataInfo\n\tcanShowMutationWaterfallPlot: boolean\n\n\tconstructor(\n\t\tsettings: Settings,\n\t\trings: Rings,\n\t\tlegend: Legend,\n\t\tfusions: Array<Fusion>,\n\t\tdataHolder: DataHolder,\n\t\tgenesetName: string,\n\t\t// TODO do we need this?\n\t\tsnvDataLengthAll: number\n\t) {\n\t\tthis.settings = settings\n\t\tthis.rings = rings\n\t\tthis.legend = legend\n\t\tthis.fusions = fusions\n\t\tthis.genesetName = genesetName\n\n\t\tconst tempHolder = select('body').append('div').style('position', 'absolute').style('visibility', 'hidden')\n\t\tconst tempSvg = tempHolder.append('svg')\n\t\tconst labels = rings.labelsRing?.elementsToDisplay?.map(l => l.text) || []\n\t\tconst maxLabelSpace = getMaxLabelWidth(tempSvg as any, labels)\n\t\ttempHolder.remove()\n\n\t\t//Diameter of the disco and labels usedd to calculate height and with of canvas\n\t\tthis.width =\n\t\t\t2 *\n\t\t\t(this.settings.horizontalPadding +\n\t\t\t\tthis.settings.rings.labelLinesInnerRadius +\n\t\t\t\tthis.settings.rings.labelsToLinesDistance +\n\t\t\t\tmaxLabelSpace)\n\t\tthis.height =\n\t\t\t2 *\n\t\t\t(this.settings.rings.labelLinesInnerRadius +\n\t\t\t\tthis.settings.rings.labelsToLinesDistance +\n\t\t\t\tthis.settings.verticalPadding +\n\t\t\t\tthis.settings.label.fontSize * 2 +\n\t\t\t\tmaxLabelSpace)\n\n\t\tthis.legendHeight = this.calculateLegendHeight(legend)\n\t\tthis.snvDataLength = dataHolder.snvData.length\n\t\tthis.filteredSnvDataLength = dataHolder.filteredSnvData.length\n\t\tthis.snvDataLengthAll = snvDataLengthAll\n\n\t\tthis.cnvMaxValue = dataHolder.cnvGainMaxValue\n\t\tthis.cnvMinValue = dataHolder.cnvLossMaxValue\n\t\tthis.cappedCnvMaxAbsValue = dataHolder.cappedCnvMaxAbsValue\n\t\tthis.negativePercentile = dataHolder.percentileNegative\n\t\tthis.positivePercentile = dataHolder.percentilePositive\n\t\tthis.invalidDataInfo = dataHolder.invalidDataInfo\n\t\tthis.canShowMutationWaterfallPlot = dataHolder.hasWaterfallEligibleChromosome\n\t}\n\n\tgetElements(ringType: RingType): Array<Arc> {\n\t\tswitch (ringType) {\n\t\t\tcase RingType.CHROMOSOME:\n\t\t\t\treturn this.rings.chromosomesRing ? this.rings.chromosomesRing.elements : []\n\t\t\tcase RingType.LABEL:\n\t\t\t\treturn this.rings.labelsRing.elementsToDisplay\n\t\t\tcase RingType.NONEXONICSNV:\n\t\t\t\treturn this.rings.nonExonicArcRing ? this.rings.nonExonicArcRing.elements : []\n\t\t\tcase RingType.SNV:\n\t\t\t\treturn this.rings.snvArcRing ? this.rings.snvArcRing.elements : []\n\t\t\tcase RingType.CNV:\n\t\t\t\treturn this.rings.cnvArcRing ? this.rings.cnvArcRing.elements : []\n\t\t\tcase RingType.LOH:\n\t\t\t\treturn this.rings.lohArcRing ? this.rings.lohArcRing.elements : []\n\t\t\tcase RingType.MUTATION_WATERFALL:\n\t\t\t\treturn this.rings.mutationWaterfallRing ? this.rings.mutationWaterfallRing.elements : []\n\t\t\tdefault:\n\t\t\t\tthrow new Error(`ringType ${ringType} not defined`)\n\t\t}\n\t}\n\n\tgetCollisions(ringType: RingType): Array<Arc> | undefined {\n\t\tif (ringType == RingType.LABEL) {\n\t\t\treturn this.rings.labelsRing.collisions\n\t\t} else {\n\t\t\treturn undefined\n\t\t}\n\t}\n\n\tprivate calculateLegendHeight(legend: Legend): number {\n\t\tconst rawHeight = this.settings.legend.rowHeight\n\t\treturn rawHeight * legend.legendCount()\n\t}\n}\n", "import type Arc from '#plots/disco/arc/Arc.ts'\n\nexport default class Ring<T extends Arc> {\n\twidth: number\n\n\tinnerRadius: number\n\touterRadius: number\n\n\telements: Array<T>\n\n\tconstructor(innerRadius: number, width: number, elements: Array<T>) {\n\t\tthis.innerRadius = innerRadius\n\t\tthis.outerRadius = innerRadius + width\n\t\tthis.width = width\n\t\tthis.elements = elements\n\t}\n}\n", "import { mclass } from '#shared/common.js'\nexport default class MLabel {\n\tprivate static instance: MLabel\n\treadonly mlabel\n\n\t/**\n\t * The Singleton's constructor should always be private to prevent direct\n\t * construction calls with the `new` operator.\n\t */\n\tprivate constructor() {\n\t\tconst mlabel = {}\n\t\tfor (const key in mclass) {\n\t\t\tmlabel[mclass[key].label] = mclass[key]\n\t\t\tmlabel[key] = mclass[key]\n\t\t}\n\n\t\tthis.mlabel = mlabel\n\t}\n\n\t/**\n\t * The static method that controls the access to the singleton instance.\n\t *\n\t * This implementation let you subclass the Singleton class while keeping\n\t * just one instance of each subclass around.\n\t */\n\tpublic static getInstance(): MLabel {\n\t\tif (!MLabel.instance) {\n\t\t\tMLabel.instance = new MLabel()\n\t\t}\n\n\t\treturn MLabel.instance\n\t}\n}\n", "export default class SnvLegendElement {\n    snvType: string\n    color: string\n    count: number;\n\n    constructor(snvType: string, color: string, count: number) {\n        this.snvType = snvType;\n        this.color = color;\n        this.count = count\n    }\n}", "import type Reference from '#plots/disco/chromosome/Reference.ts'\nimport type Data from '#plots/disco/data/Data.ts'\nimport type SnvArc from './SnvArc.ts'\nimport MLabel from '#plots/disco/label/MLabel.ts'\nimport SnvLegendElement from './SnvLegendElement.ts'\n\nexport default class SnvArcsMapper {\n\tsnvClassMap: Map<string, SnvLegendElement> = new Map()\n\n\tprivate sampleName: string\n\tprivate reference: Reference\n\n\tprivate onePxArcAngle: number\n\tprivate bpx: number\n\tprivate svnInnerRadius: number\n\tprivate svnWidth: number\n\n\tconstructor(svnInnerRadius: number, svnWidth: number, sampleName: string, reference: Reference) {\n\t\tthis.svnInnerRadius = svnInnerRadius\n\t\tthis.svnWidth = svnWidth\n\t\tthis.sampleName = sampleName\n\t\tthis.reference = reference\n\n\t\t// number of base pairs per pixel\n\t\tthis.bpx = Math.floor(this.reference.totalSize / (this.reference.totalChromosomesAngle * svnInnerRadius))\n\t\tthis.onePxArcAngle = 1 / svnInnerRadius\n\t}\n\n\tmap(exonicSnvDataMap: Map<number, Array<Data>>): Array<SnvArc> {\n\t\tconst snvArray: Array<SnvArc> = []\n\t\tfor (const angle of exonicSnvDataMap.keys()) {\n\t\t\tconst array = exonicSnvDataMap.get(angle)\n\t\t\tif (array) {\n\t\t\t\tconst arraySize = array.length\n\n\t\t\t\tfor (let i = 0; i < array.length; i++) {\n\t\t\t\t\tconst data = array[i]\n\t\t\t\t\tconst snvLegendElement = this.snvClassMap.get(data.mClass)\n\t\t\t\t\tif (snvLegendElement) {\n\t\t\t\t\t\tthis.snvClassMap.set(data.mClass, this.createSnvLegend(data.mClass, ++snvLegendElement.count))\n\t\t\t\t\t} else {\n\t\t\t\t\t\tthis.snvClassMap.set(data.mClass, this.createSnvLegend(data.mClass, 1))\n\t\t\t\t\t}\n\n\t\t\t\t\tconst startAngle = angle\n\t\t\t\t\tconst endAngle = angle + this.onePxArcAngle\n\n\t\t\t\t\tconst mLabel = MLabel.getInstance().mlabel ? MLabel.getInstance().mlabel[data.mClass] : undefined\n\n\t\t\t\t\tconst arc: SnvArc = {\n\t\t\t\t\t\tstartAngle: startAngle,\n\t\t\t\t\t\tendAngle: endAngle,\n\t\t\t\t\t\tinnerRadius: this.svnInnerRadius + (i * this.svnWidth) / arraySize,\n\t\t\t\t\t\touterRadius: this.svnInnerRadius + ((i + 1) * this.svnWidth) / arraySize,\n\t\t\t\t\t\tcolor: mLabel.color,\n\t\t\t\t\t\ttext: data.gene,\n\t\t\t\t\t\tdataClass: mLabel.label,\n\t\t\t\t\t\tmname: data.mname,\n\t\t\t\t\t\tchr: data.chr,\n\t\t\t\t\t\tpos: data.position,\n\t\t\t\t\t\tvafs: data.vafs,\n\t\t\t\t\t\tsampleName: [data.sampleName]\n\t\t\t\t\t}\n\t\t\t\t\tsnvArray.push(arc)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\treturn snvArray\n\t}\n\n\tprivate createSnvLegend(dataClass: string, count: number) {\n\t\tconst mClass = MLabel.getInstance().mlabel[dataClass]\n\t\treturn new SnvLegendElement(mClass.label, mClass.color, count)\n\t}\n}\n", "import type { CnvType } from './CnvType.ts'\n\nexport default class CnvLegend {\n\ttext: string\n\tcnvType: CnvType\n\tcolor: string\n\tvalue: number\n\n\tconstructor(text: string, cnvType: CnvType, color: string, value: number) {\n\t\tthis.text = text\n\t\tthis.cnvType = cnvType\n\t\tthis.color = color\n\t\tthis.value = value\n\t}\n}\n", "import type Settings from '#plots/disco/Settings.ts'\nimport { CnvRenderingType } from '#plots/disco/cnv/CnvRenderingType.ts'\n\nexport default class CnvColorProvider {\n\tstatic getColor(value: number, settings: Settings, cnvMaxPercentileAbs = 0) {\n\t\tconst cnv = settings.cnv\n\t\tconst gainCapped =\n\t\t\tsettings.Disco.cnvRenderingType == CnvRenderingType.heatmap ? settings.Disco.cnvCapping : cnvMaxPercentileAbs\n\t\tconst lossCapped =\n\t\t\tsettings.Disco.cnvRenderingType == CnvRenderingType.heatmap\n\t\t\t\t? -1 * settings.Disco.cnvCapping\n\t\t\t\t: -1 * cnvMaxPercentileAbs\n\t\tif (value < lossCapped) {\n\t\t\treturn cnv.cappedLossColor\n\t\t} else if (value >= lossCapped && value <= 0) {\n\t\t\treturn cnv.lossColor\n\t\t} else if (value > 0 && value <= gainCapped) {\n\t\t\treturn cnv.ampColor\n\t\t} else {\n\t\t\treturn cnv.cappedAmpColor\n\t\t}\n\t}\n}\n", "import type Data from '#plots/disco/data/Data.ts'\nimport type Reference from '#plots/disco/chromosome/Reference.ts'\nimport type CnvArc from './CnvArc.ts'\nimport CnvLegend from './CnvLegend.ts'\nimport { CnvType } from './CnvType.ts'\nimport type Settings from '#plots/disco/Settings.ts'\nimport CnvColorProvider from '#plots/disco/cnv/CnvColorProvider.ts'\nimport { CnvRenderingType } from '#plots/disco/cnv/CnvRenderingType.ts'\nimport DataMapper from '#plots/disco/data/DataMapper.ts'\n\nexport default class CnvArcsMapper {\n\tcnvClassMap: Map<CnvType, CnvLegend> = new Map()\n\n\tprivate settings: Settings\n\tprivate sampleName: string\n\tprivate reference: Reference\n\tprivate cnvMaxValue: number\n\tprivate cnvMinValue: number\n\tprivate cnvUnit: string\n\n\tprivate onePxArcAngle: number\n\tprivate lossOnly: boolean\n\tprivate gainOnly: boolean\n\tprivate gainCapped: number\n\tprivate lossCapped: number\n\tprivate cnvMaxAbsValue: number\n\tprivate cnvInnerRadius: number\n\tprivate cnvWidth: number\n\tprivate cnvRenderingType: string\n\tprivate cnvAbsPercentile: number\n\n\tconstructor(\n\t\tcnvInnerRadius: number,\n\t\tcnvWidth: number,\n\t\tsettings: Settings,\n\t\tsampleName: string,\n\t\treference: Reference,\n\t\tcnvMaxValue = 0,\n\t\tcnvMinValue = 0,\n\t\tcnvMaxAbsValue = 0,\n\t\tcnvAbsPercentile = 0,\n\t\tcnvUnit = '',\n\t\tcnvRenderingType: string\n\t) {\n\t\tthis.cnvInnerRadius = cnvInnerRadius\n\t\tthis.cnvWidth = cnvWidth\n\t\tthis.settings = settings\n\t\tthis.sampleName = sampleName\n\t\tthis.reference = reference\n\t\tthis.cnvMaxValue = cnvMaxValue\n\t\tthis.cnvMinValue = cnvMinValue\n\t\tthis.cnvMaxAbsValue = cnvMaxAbsValue\n\t\tthis.cnvAbsPercentile = cnvAbsPercentile\n\t\tthis.cnvUnit = cnvUnit\n\t\tthis.cnvRenderingType = cnvRenderingType\n\n\t\tthis.gainCapped = Math.min(cnvAbsPercentile, this.settings.Disco.cnvCapping)\n\t\tthis.lossCapped = -1 * Math.min(cnvAbsPercentile, this.settings.Disco.cnvCapping)\n\n\t\tthis.lossOnly = cnvMaxValue <= 0\n\t\tthis.gainOnly = cnvMinValue >= 0\n\n\t\tthis.onePxArcAngle = 1 / this.cnvInnerRadius\n\n\t\tconst gain = new CnvLegend(\n\t\t\t'Max',\n\t\t\tcnvMaxValue > 0 ? CnvType.Gain : CnvType.Loss,\n\t\t\tthis.getColor(cnvMaxValue),\n\t\t\tcnvMaxValue\n\t\t)\n\t\tconst loss = new CnvLegend(\n\t\t\t'Min',\n\t\t\tcnvMinValue > 0 ? CnvType.Gain : CnvType.Loss,\n\t\t\tthis.getColor(cnvMinValue),\n\t\t\tcnvMinValue\n\t\t)\n\t\tconst cap = new CnvLegend(\n\t\t\t'Capping',\n\t\t\tCnvType.Loss,\n\t\t\tthis.getColor(cnvMinValue > 0 ? cnvMinValue : cnvMaxValue),\n\t\t\tthis.settings.Disco.cnvCapping\n\t\t)\n\n\t\tthis.cnvClassMap.set(CnvType.Gain, gain)\n\t\tthis.cnvClassMap.set(CnvType.Loss, loss)\n\t\tthis.cnvClassMap.set(CnvType.Cap, cap)\n\t}\n\n\tmap(arcData: Array<Data>): Array<CnvArc> {\n\t\tconst arcs: Array<CnvArc> = []\n\n\t\tarcData.forEach(data => {\n\t\t\tlet startAngle = this.calculateStartAngle(data)\n\t\t\tlet endAngle = this.calculateEndAngle(data)\n\n\t\t\tif (startAngle === null || endAngle === null) return\n\n\t\t\tif (endAngle - startAngle < this.onePxArcAngle) {\n\t\t\t\tconst restAngle = this.onePxArcAngle - (endAngle - startAngle)\n\t\t\t\tstartAngle = startAngle - restAngle / 2\n\t\t\t\tendAngle = startAngle + restAngle / 2\n\t\t\t}\n\n\t\t\tconst innerRadius = this.calculateInnerRadius(data)\n\n\t\t\tconst outerRadius = this.calculateOuterRadius(data)\n\n\t\t\tconst color = this.getColor(data.value)\n\n\t\t\tconst arc: CnvArc = {\n\t\t\t\tstartAngle: startAngle,\n\t\t\t\tendAngle: endAngle,\n\t\t\t\tinnerRadius: innerRadius,\n\t\t\t\touterRadius: outerRadius,\n\t\t\t\tcolor: color,\n\t\t\t\ttext: data.gene,\n\t\t\t\tchr: data.chr,\n\t\t\t\tstart: data.start,\n\t\t\t\tstop: data.stop,\n\t\t\t\tvalue: data.value,\n\t\t\t\tunit: this.cnvUnit,\n\t\t\t\tsampleName: [this.sampleName]\n\t\t\t}\n\t\t\t\n\n\t\t\tarcs.push(arc)\n\t\t})\n\n\t\treturn arcs\n\t}\n\n\tcalculateStartAngle(data: Data) {\n\t\tconst index = this.reference.chromosomesOrder.indexOf(data.chr)\n\t\tif (index == -1) return null\n\t\tconst chromosome = this.reference.chromosomes[index]\n\t\treturn (\n\t\t\tchromosome.startAngle + (chromosome.endAngle - chromosome.startAngle) * (Number(data.start) / chromosome.size)\n\t\t)\n\t}\n\n\tprivate calculateEndAngle(data: Data) {\n\t\tconst index = this.reference.chromosomesOrder.indexOf(data.chr)\n\t\tconst chromosome = this.reference.chromosomes[index]\n\t\treturn chromosome.startAngle + (chromosome.endAngle - chromosome.startAngle) * (Number(data.stop) / chromosome.size)\n\t}\n\n\tgetColor(value: number) {\n\t\treturn CnvColorProvider.getColor(value, this.settings, this.cnvAbsPercentile)\n\t}\n\n\tprivate calculateInnerRadius(data: Data) {\n\t\tif (this.cnvRenderingType == CnvRenderingType.heatmap) {\n\t\t\treturn this.cnvInnerRadius\n\t\t}\n\n\t\tif (this.gainOnly) {\n\t\t\treturn this.cnvInnerRadius\n\t\t}\n\n\t\tif (this.lossOnly) {\n\t\t\tconst outerRadius = this.cnvInnerRadius + this.cnvWidth\n\n\t\t\treturn (\n\t\t\t\touterRadius +\n\t\t\t\tDataMapper.capMinValue(\n\t\t\t\t\t(this.cnvWidth * DataMapper.capMaxValue(data.value, this.gainCapped, this.lossCapped)) / this.cnvAbsPercentile\n\t\t\t\t)\n\t\t\t)\n\t\t}\n\n\t\tconst centerRadius = this.cnvInnerRadius + this.cnvWidth / 2\n\n\t\tif (Math.sign(data.value) == 1) {\n\t\t\treturn centerRadius\n\t\t}\n\n\t\tif (Math.sign(data.value) == -1) {\n\t\t\treturn (\n\t\t\t\tcenterRadius +\n\t\t\t\tDataMapper.capMinValue(\n\t\t\t\t\t(DataMapper.capMaxValue(data.value, this.gainCapped, this.lossCapped) / this.cnvAbsPercentile) *\n\t\t\t\t\t\t(this.cnvWidth / 2)\n\t\t\t\t)\n\t\t\t)\n\t\t}\n\n\t\treturn 1\n\t}\n\n\tprivate calculateOuterRadius(data: Data) {\n\t\tconst maxOuterRadius = this.cnvInnerRadius + this.cnvWidth\n\n\t\tif (this.cnvRenderingType == CnvRenderingType.heatmap) {\n\t\t\treturn maxOuterRadius\n\t\t}\n\n\t\tif (this.gainOnly) {\n\t\t\treturn (\n\t\t\t\tthis.cnvInnerRadius +\n\t\t\t\tDataMapper.capMinValue(\n\t\t\t\t\t(this.cnvWidth * DataMapper.capMaxValue(data.value, this.gainCapped, this.lossCapped)) / this.cnvAbsPercentile\n\t\t\t\t)\n\t\t\t)\n\t\t}\n\n\t\tif (this.lossOnly) {\n\t\t\treturn maxOuterRadius\n\t\t}\n\n\t\tconst centerRadius = this.cnvInnerRadius + this.cnvWidth / 2\n\n\t\tif (Math.sign(data.value) == 1) {\n\t\t\treturn (\n\t\t\t\tcenterRadius +\n\t\t\t\tDataMapper.capMinValue(\n\t\t\t\t\t(DataMapper.capMaxValue(data.value, this.gainCapped, this.lossCapped) / this.cnvMaxAbsValue) *\n\t\t\t\t\t\t(this.cnvWidth / 2)\n\t\t\t\t)\n\t\t\t)\n\t\t}\n\n\t\tif (Math.sign(data.value) == -1) {\n\t\t\treturn centerRadius\n\t\t}\n\t\treturn 1\n\t}\n}\n", "import type Point from './Point.ts'\n\nexport default class Line {\n\tcolor: string\n\tpoints = new Array<Point>()\n\n\tconstructor(points: Array<Point>, color: string) {\n\t\tthis.points = points\n\t\tthis.color = color\n\t}\n}\n", "import type Label from './Label.ts'\nimport type Point from './Point.ts'\nimport Line from './Line.ts'\nimport type MutationTooltip from '#plots/disco/label/MutationTooltip.ts'\nimport type FusionTooltip from '#plots/disco/fusion/FusionTooltip.ts'\n\nexport default class LabelFactory {\n\tstatic createLabel(\n\t\tstartAngle: number,\n\t\tendAngle: number,\n\t\tinnerRadius: number,\n\t\touterRadius: number,\n\t\tvalue: number,\n\t\tgene: string,\n\t\tcolor: string,\n\t\tdataClass: string,\n\t\tchr: string,\n\t\tposition: number,\n\t\tisPrioritized = false,\n\t\tlabelsToLinesGap: number,\n\t\tmutationTooltip?: MutationTooltip,\n\t\tfusionTooltip?: FusionTooltip\n\t) {\n\t\tconst angle = (startAngle + endAngle) / 2\n\t\tconst ccAngle = angle - Math.PI / 2\n\t\tconst transform = `rotate(${(angle * 180) / Math.PI - 90}) translate(${outerRadius})${\n\t\t\tangle > Math.PI ? 'rotate(180)' : ''\n\t\t}`\n\t\tconst textAnchor = angle > Math.PI ? 'end' : ''\n\t\tconst r0 = innerRadius\n\t\tconst r1 = outerRadius - labelsToLinesGap\n\n\t\tconst points: Array<Point> = []\n\t\tconst point0: Point = {\n\t\t\tx: r0 * Math.cos(ccAngle),\n\t\t\ty: r0 * Math.sin(ccAngle)\n\t\t}\n\t\tconst point1: Point = {\n\t\t\tx: r1 * Math.cos(ccAngle),\n\t\t\ty: r1 * Math.sin(ccAngle)\n\t\t}\n\n\t\tpoints.push(point0)\n\t\tpoints.push(point1)\n\n\t\tconst line = new Line(points, color)\n\n\t\tconst label: Label = {\n\t\t\tstartAngle,\n\t\t\tendAngle,\n\t\t\tinnerRadius,\n\t\t\touterRadius,\n\t\t\tangle,\n\t\t\tvalue,\n\t\t\ttext: gene,\n\t\t\tcolor,\n\t\t\ttransform,\n\t\t\ttextAnchor,\n\t\t\tccAngle,\n\t\t\tline,\n\t\t\tisPrioritized,\n\t\t\tstart: position,\n\t\t\tstop: position,\n\t\t\tchr: chr,\n\t\t\tmutationsTooltip: mutationTooltip ? [mutationTooltip] : undefined,\n\t\t\tfusionTooltip: fusionTooltip ? [fusionTooltip] : undefined\n\t\t}\n\n\t\treturn label\n\t}\n\n\tstatic createMovedLabel(element: Label, overlap: number): Label {\n\t\tconst startAngle = element.startAngle + overlap\n\t\tconst endAngle = element.endAngle + overlap\n\n\t\tconst angle = (startAngle + endAngle) / 2\n\t\tconst ccAngle = angle - Math.PI / 2\n\n\t\tconst r0 = element.innerRadius\n\t\tconst r1 = element.outerRadius - 2\n\t\tconst dr = (r1 - r0) / 3\n\t\tconst cos0 = Math.cos(element.ccAngle)\n\t\tconst sin0 = Math.sin(element.ccAngle)\n\t\tconst cos1 = Math.cos(element.ccAngle + overlap)\n\t\tconst sin1 = Math.sin(element.ccAngle + overlap)\n\n\t\tconst points: Array<Point> = []\n\n\t\tconst point0: Point = {\n\t\t\tx: r0 * cos0,\n\t\t\ty: r0 * sin0\n\t\t}\n\t\tconst point1: Point = {\n\t\t\tx: (r0 + dr) * cos0,\n\t\t\ty: (r0 + dr) * sin0\n\t\t}\n\t\tconst point2: Point = {\n\t\t\tx: (r0 + 2 * dr) * cos1,\n\t\t\ty: (r0 + 2 * dr) * sin1\n\t\t}\n\n\t\tconst point3: Point = {\n\t\t\tx: (r0 + 3 * dr) * cos1,\n\t\t\ty: (r0 + 3 * dr) * sin1\n\t\t}\n\n\t\tpoints.push(point0)\n\t\tpoints.push(point1)\n\t\tpoints.push(point2)\n\t\tpoints.push(point3)\n\n\t\tconst line = new Line(points, element.color)\n\n\t\tconst transform: string =\n\t\t\t'rotate(' +\n\t\t\t((angle * 180) / Math.PI - 90) +\n\t\t\t')' +\n\t\t\t'translate(' +\n\t\t\telement.outerRadius +\n\t\t\t')' +\n\t\t\t(angle > Math.PI ? 'rotate(180)' : '')\n\n\t\tconst textAnchor = angle > Math.PI ? 'end' : ''\n\n\t\tconst color = element.mutationsTooltip\n\t\t\t? element.mutationsTooltip[0].color\n\t\t\t: element.fusionTooltip\n\t\t\t? element.fusionTooltip[0].color\n\t\t\t: undefined\n\n\t\tconst label: Label = {\n\t\t\tstartAngle: startAngle,\n\t\t\tendAngle: endAngle,\n\t\t\tinnerRadius: element.innerRadius,\n\t\t\touterRadius: element.outerRadius,\n\t\t\tangle: angle,\n\t\t\tvalue: element.value,\n\t\t\ttext: element.text,\n\t\t\ttransform: transform,\n\t\t\ttextAnchor: textAnchor,\n\t\t\tccAngle: ccAngle,\n\t\t\tcolor: color,\n\t\t\tline: line,\n\t\t\tisPrioritized: element.isPrioritized,\n\t\t\tstart: element.start,\n\t\t\tstop: element.stop,\n\t\t\tchr: element.chr,\n\t\t\tmutationsTooltip: element.mutationsTooltip,\n\t\t\tfusionTooltip: element.fusionTooltip\n\t\t}\n\n\t\treturn label\n\t}\n}\n", "import type Data from '#plots/disco/data/Data.ts'\nimport type Reference from '#plots/disco/chromosome/Reference.ts'\nimport type Label from './Label.ts'\nimport LabelFactory from './LabelFactory.ts'\nimport MLabel from './MLabel.ts'\nimport type MutationTooltip from '#plots/disco/label/MutationTooltip.ts'\nimport type Settings from '#plots/disco/Settings.ts'\nimport FusionColorProvider from '#plots/disco/fusion/FusionColorProvider.ts'\nimport type FusionTooltip from '#plots/disco/fusion/FusionTooltip.ts'\nimport type CnvTooltip from '#plots/disco/cnv/CnvTooltip.ts'\nimport CnvColorProvider from '#plots/disco/cnv/CnvColorProvider.ts'\nimport { dtsnvindel, dtfusionrna } from '#shared/common.js'\n\nexport default class LabelsMapper {\n\tprivate settings: Settings\n\tprivate sampleName: string\n\tprivate reference: Reference\n\n\tprivate labelMap: Map<string, Label> = new Map()\n\tprivate cnvMaxPercentileAbs: number\n\n\tconstructor(settings: Settings, sampleName: string, reference: Reference, cnvMaxPercentileAbs = 0) {\n\t\tthis.settings = settings\n\t\tthis.sampleName = sampleName\n\t\tthis.reference = reference\n\t\tthis.cnvMaxPercentileAbs = cnvMaxPercentileAbs\n\t}\n\n\tmap(data: Array<Data>, cnvData: Array<Data> = []): Array<Label> {\n\t\tconst innerRadius = this.settings.rings.labelLinesInnerRadius\n\t\tconst outerRadius = innerRadius + this.settings.rings.labelsToLinesDistance\n\n\t\tdata.forEach(data => {\n\t\t\tif (data.dt == dtsnvindel) {\n\t\t\t\tconst startAngle = this.calculateStartAngle(data.chr, data.position)\n\t\t\t\tconst endAngle = this.calculateEndAngle(data.chr, data.position)\n\t\t\t\tif (startAngle === null || endAngle === null) return\n\n\t\t\t\tconst mLabel = MLabel.getInstance().mlabel ? MLabel.getInstance().mlabel[data.mClass] : undefined\n\n\t\t\t\tthis.addLabelOrMutation(\n\t\t\t\t\tdata,\n\t\t\t\t\tdata.gene,\n\t\t\t\t\tdata.mname,\n\t\t\t\t\tstartAngle,\n\t\t\t\t\tendAngle,\n\t\t\t\t\tinnerRadius,\n\t\t\t\t\touterRadius,\n\t\t\t\t\tmLabel.color,\n\t\t\t\t\tmLabel.label\n\t\t\t\t)\n\t\t\t}\n\n\t\t\tif (data.dt == dtfusionrna) {\n\t\t\t\tconst color = FusionColorProvider.getColor(data.chrA, data.chrB)\n\t\t\t\tif (data.geneA) {\n\t\t\t\t\tconst startAngleSource = this.calculateStartAngle(data.chrA, data.posA)\n\t\t\t\t\tconst endAngleSource = this.calculateEndAngle(data.chrA, data.posA)\n\t\t\t\t\tif (startAngleSource === null || endAngleSource === null) return\n\n\t\t\t\t\tthis.addLabelOrFusion(\n\t\t\t\t\t\tdata,\n\t\t\t\t\t\tdata.geneA,\n\t\t\t\t\t\tdata.posA,\n\t\t\t\t\t\tstartAngleSource,\n\t\t\t\t\t\tendAngleSource,\n\t\t\t\t\t\tinnerRadius,\n\t\t\t\t\t\touterRadius,\n\t\t\t\t\t\tcolor\n\t\t\t\t\t)\n\t\t\t\t}\n\n\t\t\t\tif (data.geneB && data.geneA != data.geneB) {\n\t\t\t\t\tconst startAngleTarget = this.calculateStartAngle(data.chrB, data.posB)\n\t\t\t\t\tconst endAngleTarget = this.calculateEndAngle(data.chrB, data.posB)\n\n\t\t\t\t\tif (startAngleTarget == null || endAngleTarget == null) return\n\n\t\t\t\t\tthis.addLabelOrFusion(\n\t\t\t\t\t\tdata,\n\t\t\t\t\t\tdata.geneB,\n\t\t\t\t\t\tdata.posB,\n\t\t\t\t\t\tstartAngleTarget,\n\t\t\t\t\t\tendAngleTarget,\n\t\t\t\t\t\tinnerRadius,\n\t\t\t\t\t\touterRadius,\n\t\t\t\t\t\tcolor\n\t\t\t\t\t)\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\n\t\tconst labelsArray = Array.from(this.labelMap.values())\n\t\tlabelsArray.forEach((label: Label) => {\n\t\t\tcnvData.forEach((cnv: Data) => {\n\t\t\t\tif (label.stop >= cnv.start && cnv.stop >= label.start && label.chr == cnv.chr) {\n\t\t\t\t\tconst mutation: CnvTooltip = {\n\t\t\t\t\t\tvalue: cnv.value,\n\t\t\t\t\t\tcolor: CnvColorProvider.getColor(cnv.value, this.settings, this.cnvMaxPercentileAbs),\n\t\t\t\t\t\tchr: cnv.chr,\n\t\t\t\t\t\tstart: cnv.start,\n\t\t\t\t\t\tstop: cnv.stop\n\t\t\t\t\t}\n\t\t\t\t\tif (label.cnvTooltip) {\n\t\t\t\t\t\tlabel.cnvTooltip.push(mutation)\n\t\t\t\t\t} else {\n\t\t\t\t\t\tlabel.cnvTooltip = []\n\t\t\t\t\t\tlabel.cnvTooltip.push(mutation)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t})\n\t\t})\n\n\t\treturn Array.from(this.labelMap.values())\n\t}\n\n\tprivate addLabelOrMutation(\n\t\tdata: Data,\n\t\tgene: string,\n\t\tmname: string,\n\t\tstartAngle: number,\n\t\tendAngle: number,\n\t\tinnerRadius,\n\t\touterRadius,\n\t\tcolor,\n\t\tdataClass\n\t) {\n\t\tconst label = this.labelMap.get(gene)\n\t\tconst mutation: MutationTooltip = {\n\t\t\tmname: mname,\n\t\t\tcolor: color,\n\t\t\tdataClass: dataClass,\n\t\t\tchr: data.chr,\n\t\t\tposition: data.position,\n\t\t\tvafs: data.vafs\n\t\t}\n\t\tif (!label) {\n\t\t\tthis.labelMap.set(\n\t\t\t\tgene,\n\t\t\t\tLabelFactory.createLabel(\n\t\t\t\t\tstartAngle,\n\t\t\t\t\tendAngle,\n\t\t\t\t\tinnerRadius,\n\t\t\t\t\touterRadius,\n\t\t\t\t\tdata.value,\n\t\t\t\t\tgene,\n\t\t\t\t\tcolor,\n\t\t\t\t\tdataClass,\n\t\t\t\t\tdata.chr,\n\t\t\t\t\tdata.position,\n\t\t\t\t\tdata.isPrioritized,\n\t\t\t\t\tthis.settings.rings.labelsToLinesGap,\n\t\t\t\t\tmutation\n\t\t\t\t)\n\t\t\t)\n\t\t} else {\n\t\t\tif (label.mutationsTooltip) {\n\t\t\t\tlabel.start = Math.min(label.start, data.position)\n\t\t\t\tlabel.stop = Math.max(label.stop, data.position)\n\t\t\t\tlabel.mutationsTooltip.push(mutation)\n\t\t\t} else {\n\t\t\t\tlabel.mutationsTooltip = []\n\t\t\t\tlabel.start = Math.min(label.start, data.position)\n\t\t\t\tlabel.stop = Math.max(label.stop, data.position)\n\t\t\t\tlabel.mutationsTooltip.push(mutation)\n\t\t\t}\n\t\t}\n\t}\n\n\tprivate addLabelOrFusion(\n\t\tdata: Data,\n\t\tgene: string,\n\t\tposition: number,\n\t\tstartAngle: number,\n\t\tendAngle: number,\n\t\tinnerRadius,\n\t\touterRadius,\n\t\tcolor\n\t) {\n\t\tconst label = this.labelMap.get(gene)\n\t\tconst fusionTooltip: FusionTooltip = {\n\t\t\tcolor: color,\n\t\t\tchrA: data.chrA,\n\t\t\tchrB: data.chrB,\n\t\t\tposA: data.posA,\n\t\t\tposB: data.posB,\n\t\t\tgeneA: data.geneA,\n\t\t\tgeneB: data.geneB,\n\t\t\tstrandA: data.strandA,\n\t\t\tstrandB: data.strandB\n\t\t}\n\t\tif (!label) {\n\t\t\tthis.labelMap.set(\n\t\t\t\tgene,\n\t\t\t\tLabelFactory.createLabel(\n\t\t\t\t\tstartAngle,\n\t\t\t\t\tendAngle,\n\t\t\t\t\tinnerRadius,\n\t\t\t\t\touterRadius,\n\t\t\t\t\tdata.value,\n\t\t\t\t\tgene,\n\t\t\t\t\tcolor,\n\t\t\t\t\t'Fusion transcript',\n\t\t\t\t\tdata.chr,\n\t\t\t\t\tdata.position,\n\t\t\t\t\tdata.isPrioritized,\n\t\t\t\t\tthis.settings.rings.labelsToLinesGap,\n\t\t\t\t\tundefined,\n\t\t\t\t\tfusionTooltip\n\t\t\t\t)\n\t\t\t)\n\t\t} else {\n\t\t\tif (label.fusionTooltip) {\n\t\t\t\tlabel.start = Math.min(label.start, position)\n\t\t\t\tlabel.stop = Math.max(label.stop, position)\n\t\t\t\tlabel.fusionTooltip.push(fusionTooltip)\n\t\t\t} else {\n\t\t\t\tlabel.fusionTooltip = []\n\t\t\t\tlabel.start = Math.min(label.start, position)\n\t\t\t\tlabel.stop = Math.max(label.stop, position)\n\t\t\t\tlabel.fusionTooltip.push(fusionTooltip)\n\t\t\t}\n\t\t}\n\t}\n\n\tprivate calculateStartAngle(chr: string, position: number) {\n\t\tconst index = this.reference.chromosomesOrder.findIndex(element => element == chr)\n\t\tif (index === -1) return null\n\t\tconst chromosome = this.reference.chromosomes[index]\n\n\t\treturn chromosome.startAngle + (chromosome.endAngle - chromosome.startAngle) * (Number(position) / chromosome.size)\n\t}\n\n\tprivate calculateEndAngle(chr: string, position: number) {\n\t\tconst index = this.reference.chromosomesOrder.findIndex(element => element == chr)\n\t\tif (index === -1) return null\n\t\tconst chromosome = this.reference.chromosomes[index]\n\n\t\treturn chromosome.startAngle + (chromosome.endAngle - chromosome.startAngle) * (Number(position) / chromosome.size)\n\t}\n}\n", "import Ring from '#plots/disco/ring/Ring.ts'\nimport type Label from './Label.ts'\nimport LabelFactory from './LabelFactory.ts'\nimport type Settings from '#plots/disco/Settings.ts'\n\nexport default class Labels extends Ring<Label> {\n\tcollisions?: Array<Label>\n\tsettings: any\n\telementsToDisplay: Array<Label> = []\n\n\tprivate hasPrioritizedGenes: boolean\n\tprivate overlapAngle: number\n\n\tconstructor(settings: Settings, elements: Array<Label>, hasPrioritizedGenes: boolean) {\n\t\tsuper(\n\t\t\tsettings.rings.labelLinesInnerRadius,\n\t\t\tsettings.rings.labelsToLinesDistance,\n\t\t\telements.sort((a, b) => {\n\t\t\t\treturn a.startAngle < b.startAngle ? -1 : a.startAngle > b.startAngle ? 1 : 0\n\t\t\t})\n\t\t)\n\n\t\tthis.settings = settings\n\t\tthis.hasPrioritizedGenes = hasPrioritizedGenes\n\n\t\tconst circumference = 2 * Math.PI * (settings.rings.labelLinesInnerRadius + settings.rings.labelsToLinesDistance)\n\t\tthis.overlapAngle = (this.settings.label.overlapAngleFactor * this.settings.label.fontSize) / circumference\n\n\t\tthis.calculateCollisions()\n\t}\n\n\tprivate calculateCollisions() {\n\t\tthis.collisions = []\n\n\t\tlet hasPrioritizedGenesList: Array<Label> = []\n\t\thasPrioritizedGenesList = this.elements.filter(label => label.isPrioritized)\n\n\t\tif (this.settings.label.prioritizeGeneLabelsByGeneSets) {\n\t\t\tthis.elementsToDisplay = this.getLabelsWithPrioritizedGenes(hasPrioritizedGenesList)\n\t\t} else if (this.hasPrioritizedGenes) {\n\t\t\tconst prioritizedGenesList = this.elements.filter(label => label.isPrioritized)\n\t\t\tconst filteredPrioritizedGenesList = this.getLabelsWithPrioritizedGenes(prioritizedGenesList)\n\n\t\t\tconst withoutPrioritizedGenesList = this.elements.filter(label => !label.isPrioritized)\n\n\t\t\tconst combinedAndSortedList = [...withoutPrioritizedGenesList, ...filteredPrioritizedGenesList].sort(\n\t\t\t\t(a, b) => a.startAngle - b.startAngle\n\t\t\t)\n\n\t\t\tthis.elementsToDisplay = this.getAllLabels(combinedAndSortedList)\n\t\t} else {\n\t\t\tthis.elementsToDisplay = this.getLabelsWithPrioritizedGenes(this.elements)\n\t\t}\n\t}\n\n\tprivate getLabelsWithPrioritizedGenes(elemenets: Array<Label>) {\n\t\tconst filteredList: Array<Label> = []\n\n\t\tlet prev = { endAngle: 0 }\n\t\telemenets.forEach((element, index) => {\n\t\t\tif (index == 0) {\n\t\t\t\tfilteredList.push(element)\n\t\t\t\tprev = element\n\t\t\t} else {\n\t\t\t\tconst overlap = prev.endAngle - element.startAngle + this.overlapAngle\n\n\t\t\t\tif (overlap > 0 && overlap < this.settings.label.maxDeltaAngle) {\n\t\t\t\t\tconst labelCopy = LabelFactory.createMovedLabel(element, overlap)\n\t\t\t\t\tfilteredList?.push(labelCopy)\n\t\t\t\t\tprev = labelCopy\n\t\t\t\t}\n\n\t\t\t\tif (overlap <= 0) {\n\t\t\t\t\tfilteredList.push(element)\n\t\t\t\t\tprev = element\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\n\t\treturn filteredList\n\t}\n\n\tprivate getAllLabels(elemenets: Array<Label>) {\n\t\tconst filteredList: Array<Label> = []\n\t\tlet prev = { endAngle: 0 }\n\t\tconst elemenetsLength = elemenets.length\n\t\tlet lastCancerGeneLabelIndex = -1\n\n\t\tfor (let index = 0; index < elemenets.length; index++) {\n\t\t\tconst element = elemenets[index]\n\t\t\tif (element.isPrioritized) {\n\t\t\t\tfilteredList.push(element)\n\t\t\t\tlastCancerGeneLabelIndex = index\n\t\t\t\tprev = element\n\t\t\t\tcontinue\n\t\t\t}\n\n\t\t\tif (index == 0) {\n\t\t\t\tif (elemenetsLength > 1) {\n\t\t\t\t\tif (this.isElementOverlappingNextCancerGene(elemenets, lastCancerGeneLabelIndex, element, 0)) {\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t\tfilteredList.push(element)\n\t\t\t\t\tprev = element\n\t\t\t\t}\n\t\t\t\tcontinue\n\t\t\t}\n\n\t\t\tconst prevOverlap = prev.endAngle - element.startAngle + this.overlapAngle\n\n\t\t\tif (prevOverlap > 0 && prevOverlap < this.settings.label.maxDeltaAngle) {\n\t\t\t\tif (index == length - 1) {\n\t\t\t\t\t// last element\n\t\t\t\t\tfilteredList.push(element)\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\n\t\t\t\tif (this.isElementOverlappingNextCancerGene(elemenets, lastCancerGeneLabelIndex, element, prevOverlap)) {\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\n\t\t\t\tconst labelCopy = LabelFactory.createMovedLabel(element, prevOverlap)\n\t\t\t\tthis.collisions?.push(labelCopy)\n\t\t\t\tfilteredList.push(element)\n\t\t\t\tprev = labelCopy\n\t\t\t}\n\n\t\t\tif (prevOverlap <= 0) {\n\t\t\t\tif (this.isElementOverlappingNextCancerGene(elemenets, lastCancerGeneLabelIndex, element, 0)) {\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\n\t\t\t\tfilteredList.push(element)\n\t\t\t\tprev = element\n\t\t\t}\n\t\t}\n\t\treturn filteredList\n\t}\n\n\tprivate isElementOverlappingNextCancerGene(\n\t\telemenets: Array<Label>,\n\t\tlastCancerGeneLabelIndex: number,\n\t\telement: Label,\n\t\tprevOverlap: number\n\t) {\n\t\tconst nextLabelWithCancerGene = this.getNextLabelWithCancerGene(elemenets, lastCancerGeneLabelIndex)\n\t\tif (nextLabelWithCancerGene) {\n\t\t\tconst nextOverlap = element.endAngle + prevOverlap - nextLabelWithCancerGene.startAngle + this.overlapAngle\n\t\t\tif (nextOverlap > 0) {\n\t\t\t\t// skip element\n\t\t\t\treturn true\n\t\t\t}\n\t\t}\n\n\t\treturn false\n\t}\n\n\tprivate getNextLabelWithCancerGene(elemenets: Array<Label>, lastCancerGeneLabelIndex: number) {\n\t\treturn elemenets.find((label, index) => label.isPrioritized && index > lastCancerGeneLabelIndex)\n\t}\n}\n", "import type Reference from '#plots/disco/chromosome/Reference.ts'\nimport type Data from '#plots/disco/data/Data.ts'\nimport MLabel from '#plots/disco/label/MLabel.ts'\nimport type SnvArc from './SnvArc.ts'\n\nexport default class NonExonicSnvArcsMapper {\n\tprivate sampleName: string\n\tprivate reference: Reference\n\tprivate onePxArcAngle: number\n\tprivate nonExonicInnerRadius: number\n\tprivate nonExonicWidht: number\n\n\tconstructor(nonExonicInnerRadius: number, nonExonicWidht: number, sampleName: string, reference: Reference) {\n\t\tthis.nonExonicInnerRadius = nonExonicInnerRadius\n\t\tthis.nonExonicWidht = nonExonicWidht\n\t\tthis.sampleName = sampleName\n\t\tthis.reference = reference\n\n\t\tthis.onePxArcAngle = 1 / nonExonicInnerRadius\n\t}\n\n\tmap(arcData: Array<Data>): Array<SnvArc> {\n\t\tconst innerRadius = this.nonExonicInnerRadius\n\t\tconst outerRadius = innerRadius + this.nonExonicWidht\n\n\t\tconst arcs: Array<SnvArc> = []\n\n\t\tarcData.forEach(data => {\n\t\t\tconst mLabel = MLabel.getInstance().mlabel ? MLabel.getInstance().mlabel[data.mClass] : undefined\n\n\t\t\tconst startAngle = this.calculateStartAngle(data)\n\t\t\tconst endAngle = this.calculateEndAngle(data)\n\t\t\tif (startAngle === null || endAngle === null) return\n\n\t\t\tconst arc: SnvArc = {\n\t\t\t\tstartAngle: startAngle,\n\t\t\t\tendAngle: endAngle,\n\t\t\t\tinnerRadius: innerRadius,\n\t\t\t\touterRadius: outerRadius,\n\t\t\t\tcolor: mLabel.color,\n\t\t\t\ttext: data.gene,\n\t\t\t\tdataClass: mLabel.label,\n\t\t\t\tmname: data.mname,\n\t\t\t\tchr: data.chr,\n\t\t\t\tpos: data.position,\n\t\t\t\tvafs: data.vafs,\n\t\t\t\tsampleName: [data.sampleName]\n\t\t\t}\n\n\t\t\tarcs.push(arc)\n\t\t})\n\n\t\treturn arcs\n\t}\n\n\tcalculateStartAngle(data: Data) {\n\t\tconst index = this.reference.chromosomesOrder.indexOf(data.chr)\n\t\tif (index === -1) return null\n\t\tconst chromosome = this.reference.chromosomes[index]\n\t\treturn (\n\t\t\tchromosome.startAngle +\n\t\t\t(chromosome.endAngle - chromosome.startAngle) * (Number(data.position) / chromosome.size) -\n\t\t\tthis.onePxArcAngle\n\t\t)\n\t}\n\n\tprivate calculateEndAngle(data: Data) {\n\t\tconst index = this.reference.chromosomesOrder.indexOf(data.chr)\n\t\tconst chromosome = this.reference.chromosomes[index]\n\t\treturn (\n\t\t\tthis.onePxArcAngle +\n\t\t\tchromosome.startAngle +\n\t\t\t(chromosome.endAngle - chromosome.startAngle) * (Number(data.position) / chromosome.size)\n\t\t)\n\t}\n}\n", "import type Reference from '#plots/disco/chromosome/Reference.ts'\nimport type Data from '#plots/disco/data/Data.ts'\nimport type LohArc from './LohArc.ts'\nimport GradientColorProvider from './GradientColorProvider.ts'\n\nexport default class LohArcMapper {\n\tprivate sampleName: string\n\tprivate reference: Reference\n\tprivate lohInnerRadius: number\n\tprivate lohWidth: number\n\n\tconstructor(lohInnerRadius: number, lohWidth: number, sampleName: string, reference: Reference) {\n\t\tthis.lohInnerRadius = lohInnerRadius\n\t\tthis.lohWidth = lohWidth\n\t\tthis.sampleName = sampleName\n\t\tthis.reference = reference\n\t}\n\n\tmap(arcData: Array<Data>): Array<LohArc> {\n\t\tconst arcs: Array<LohArc> = []\n\n\t\tarcData.forEach(data => {\n\t\t\tconst startAngle = this.calculateStartAngle(data)\n\t\t\tconst endAngle = this.calculateEndAngle(data)\n\n\t\t\tif (startAngle === null || endAngle === null) return\n\n\t\t\tconst innerRadius = this.lohInnerRadius\n\t\t\tconst outerRadius = innerRadius + this.lohWidth\n\t\t\tconst color = GradientColorProvider.provide(data.segmean)\n\n\t\t\tconst arc: LohArc = {\n\t\t\t\tstartAngle: startAngle,\n\t\t\t\tendAngle: endAngle,\n\t\t\t\tinnerRadius: innerRadius,\n\t\t\t\touterRadius: outerRadius,\n\t\t\t\tcolor: color,\n\t\t\t\ttext: data.gene,\n\t\t\t\tchr: data.chr,\n\t\t\t\tstart: data.start,\n\t\t\t\tstop: data.stop,\n\t\t\t\tvalue: data.segmean\n\t\t\t}\n\n\t\t\tarcs.push(arc)\n\t\t})\n\n\t\treturn arcs\n\t}\n\n\tprivate calculateStartAngle(data: Data) {\n\t\tconst index = this.reference.chromosomesOrder.indexOf(data.chr)\n\t\tif (index === -1) return null\n\t\tconst chromosome = this.reference.chromosomes[index]\n\t\treturn (\n\t\t\tchromosome.startAngle + (chromosome.endAngle - chromosome.startAngle) * (Number(data.start) / chromosome.size)\n\t\t)\n\t}\n\n\tprivate calculateEndAngle(data: Data) {\n\t\tconst index = this.reference.chromosomesOrder.indexOf(data.chr)\n\t\tconst chromosome = this.reference.chromosomes[index]\n\t\treturn chromosome.startAngle + (chromosome.endAngle - chromosome.startAngle) * (Number(data.stop) / chromosome.size)\n\t}\n}\n", "import type Ring from './Ring.ts'\nimport type Chromosome from '#plots/disco/chromosome/Chromosome.ts'\nimport type Labels from '#plots/disco/label/Labels.ts'\nimport type SnvArc from '#plots/disco/snv/SnvArc.ts'\nimport type CnvArc from '#plots/disco/cnv/CnvArc.ts'\nimport type LohArc from '#plots/disco/loh/LohArc.ts'\nimport type MutationWaterfallPoint from '#plots/disco/waterfall/MutationWaterfallPoint.ts'\n\nexport default class Rings {\n\tlabelsRing: Labels\n\tchromosomesRing: Ring<Chromosome>\n\tnonExonicArcRing?: Ring<SnvArc>\n\tsnvArcRing?: Ring<SnvArc>\n\tcnvArcRing?: Ring<CnvArc>\n\tlohArcRing?: Ring<LohArc>\n\tmutationWaterfallRing?: Ring<MutationWaterfallPoint>\n\n\tconstructor(\n\t\tlabelsRing: Labels,\n\t\tchromosomesRing: Ring<Chromosome>,\n\t\tnonExonicArcRing?: Ring<SnvArc>,\n\t\tsnvArcRing?: Ring<SnvArc>,\n\t\tcnvArcRing?: Ring<CnvArc>,\n\t\tlohArcRing?: Ring<LohArc>,\n\t\tmutationWaterfallRing?: Ring<MutationWaterfallPoint>\n\t) {\n\t\tthis.labelsRing = labelsRing\n\t\tthis.chromosomesRing = chromosomesRing\n\t\tthis.nonExonicArcRing = nonExonicArcRing\n\t\tthis.snvArcRing = snvArcRing\n\t\tthis.cnvArcRing = cnvArcRing\n\t\tthis.lohArcRing = lohArcRing\n\t\tthis.mutationWaterfallRing = mutationWaterfallRing\n\t}\n}\n", "import type Reference from '#plots/disco/chromosome/Reference.ts'\nimport type MutationWaterfallPoint from './MutationWaterfallPoint.ts'\nimport type { MutationWaterfallDatum, MutationWaterfallLogRange } from './MutationWaterfallDatum.ts'\n\nexport default class MutationWaterfallMapper {\n\tprivate innerRadius: number\n\tprivate ringWidth: number\n\tprivate reference: Reference\n\tprivate logRange?: MutationWaterfallLogRange\n\tprivate color: string\n\n\tconstructor(\n\t\tinnerRadius: number,\n\t\tringWidth: number,\n\t\treference: Reference,\n\t\tlogRange?: MutationWaterfallLogRange,\n\t\tcolor = '#4d4d4d'\n\t) {\n\t\tthis.innerRadius = innerRadius\n\t\tthis.ringWidth = ringWidth\n\t\tthis.reference = reference\n\t\tthis.logRange = logRange\n\t\tthis.color = color\n\t}\n\n\tmap(data: Array<MutationWaterfallDatum> = []): Array<MutationWaterfallPoint> {\n\t\tif (!data.length) return []\n\n\t\tconst min = this.logRange?.min ?? 0\n\t\tconst max = this.logRange?.max ?? min + 1\n\t\tconst span = max - min || 1\n\n\t\tconst points: MutationWaterfallPoint[] = []\n\t\tfor (const datum of data) {\n\t\t\tconst chrIndex = this.reference.chromosomesOrder.indexOf(datum.chr)\n\t\t\tif (chrIndex === -1) continue\n\n\t\t\tconst chromosome = this.reference.chromosomes[chrIndex]\n\t\t\tconst chrAngleSpan = chromosome.endAngle - chromosome.startAngle\n\t\t\tconst relPos = chromosome.size > 0 ? datum.position / chromosome.size : 0\n\t\t\tconst angle = chromosome.startAngle + chrAngleSpan * relPos\n\n\t\t\tconst normalized = Math.max(0, Math.min(1, (datum.logDistance - min) / span))\n\t\t\tconst radius = this.innerRadius + this.ringWidth * normalized\n\n\t\t\tpoints.push({\n\t\t\t\tstartAngle: angle,\n\t\t\t\tendAngle: angle,\n\t\t\t\tinnerRadius: radius,\n\t\t\t\touterRadius: radius,\n\t\t\t\ttext: chromosome.text,\n\t\t\t\tcolor: this.color,\n\t\t\t\tchr: datum.chr,\n\t\t\t\tposition: datum.position,\n\t\t\t\tlogDistance: datum.logDistance,\n\t\t\t\tringInnerRadius: this.innerRadius,\n\t\t\t\tringWidth: this.ringWidth,\n\t\t\t\trangeMin: min,\n\t\t\t\trangeMax: max\n\t\t\t})\n\t\t}\n\n\t\treturn points\n\t}\n}\n", "import type Settings from '#plots/disco/Settings.ts'\nimport type Reference from '#plots/disco/chromosome/Reference.ts'\nimport Legend from '#plots/disco/legend/Legend.ts'\nimport FusionMapper from '#plots/disco/fusion/FusionMapper.ts'\nimport LohLegend from '#plots/disco/loh/LohLegend.ts'\nimport ViewModel from './ViewModel.ts'\nimport type DataMapper from '#plots/disco/data/DataMapper.ts'\nimport Ring from '#plots/disco/ring/Ring.ts'\nimport SnvArcsMapper from '#plots/disco/snv/SnvArcsMapper.ts'\nimport type SnvArc from '#plots/disco/snv/SnvArc.ts'\nimport type LohArc from '#plots/disco/loh/LohArc.ts'\nimport CnvArcsMapper from '#plots/disco/cnv/CnvArcsMapper.ts'\nimport type CnvArc from '#plots/disco/cnv/CnvArc.ts'\nimport LabelsMapper from '#plots/disco/label/LabelsMapper.ts'\nimport Labels from '#plots/disco/label/Labels.ts'\nimport NonExonicSnvArcsMapper from '#plots/disco/snv/NonExonicSnvArcsMapper.ts'\nimport LohArcMapper from '#plots/disco/loh/LohArcMapper.ts'\nimport Rings from '#plots/disco/ring/Rings.ts'\nimport { dtsnvindel } from '#shared/common.js'\nimport type { DiscoInteractions } from '../interactions/DiscoInteractions.ts'\nimport MutationWaterfallMapper from '#plots/disco/waterfall/MutationWaterfallMapper.ts'\nimport type MutationWaterfallPoint from '#plots/disco/waterfall/MutationWaterfallPoint.ts'\n\nexport default class ViewModelProvider {\n\tprivate settings: Settings\n\tprivate reference: Reference\n\tprivate sampleName: string\n\tprivate genesetName: string\n\tprivate dataMapper: DataMapper\n\tprivate discoInteractions: DiscoInteractions\n\n\tprivate nonExonicArcRing?: Ring<SnvArc> = undefined\n\tprivate snvArcsMapper?: SnvArcsMapper\n\tprivate snvArcRing?: Ring<SnvArc>\n\tprivate lohArcRing?: Ring<LohArc>\n\tprivate cnvArcsMapper?: CnvArcsMapper\n\tprivate cnvArcRing?: Ring<CnvArc>\n\tprivate mutationWaterfallRing?: Ring<MutationWaterfallPoint>\n\n\tconstructor(\n\t\tsettings: Settings,\n\t\tdataMapper: DataMapper,\n\t\treference: Reference,\n\t\tsampleName: string,\n\t\tgenesetName: string,\n\t\tdiscoInteractions: DiscoInteractions\n\t) {\n\t\tthis.settings = settings\n\t\tthis.dataMapper = dataMapper\n\t\tthis.reference = reference\n\t\tthis.sampleName = sampleName\n\t\tthis.genesetName = genesetName\n\t\tthis.discoInteractions = discoInteractions\n\t}\n\n\tmap(data: Array<any>) {\n\t\tconst dataHolder = this.dataMapper.map(data)\n\n\t\tlet labelsRing: Labels\n\t\tif (this.settings.Disco.showGeneNames) {\n\t\t\tconst labelsMapper = new LabelsMapper(\n\t\t\t\tthis.settings,\n\t\t\t\tthis.sampleName,\n\t\t\t\tthis.reference,\n\t\t\t\tdataHolder.cnvMaxPercentileAbs\n\t\t\t)\n\n\t\t\tconst labelsData = labelsMapper.map(dataHolder.labelData, dataHolder.cnvData)\n\t\t\tlabelsRing = new Labels(this.settings, labelsData, dataHolder.hasPrioritizedGenes)\n\t\t} else {\n\t\t\tlabelsRing = new Labels(this.settings, [], false)\n\t\t}\n\n\t\tconst chromosomesRing = new Ring(\n\t\t\tthis.settings.rings.chromosomeInnerRadius,\n\t\t\tthis.settings.rings.chromosomeWidth,\n\t\t\tthis.reference.chromosomes\n\t\t)\n\n\t\tconst nonExonicSnvArcsMapper = new NonExonicSnvArcsMapper(\n\t\t\tdataHolder.nonExonicInnerRadius,\n\t\t\tthis.settings.rings.nonExonicRingWidth,\n\t\t\tthis.sampleName,\n\t\t\tthis.reference\n\t\t)\n\n\t\tconst nonExonicData = nonExonicSnvArcsMapper.map(dataHolder.nonExonicSnvData)\n\n\t\tif (nonExonicData.length > 0) {\n\t\t\tthis.nonExonicArcRing = new Ring(\n\t\t\t\tdataHolder.nonExonicInnerRadius,\n\t\t\t\tthis.settings.rings.nonExonicRingWidth,\n\t\t\t\tnonExonicData\n\t\t\t)\n\t\t}\n\n\t\tthis.snvArcsMapper = new SnvArcsMapper(\n\t\t\tdataHolder.snvInnerRadius,\n\t\t\tthis.settings.rings.snvRingWidth,\n\t\t\tthis.sampleName,\n\t\t\tthis.reference\n\t\t)\n\t\tconst snvData = this.snvArcsMapper.map(dataHolder.snvRingDataMap)\n\t\tif (snvData.length > 0) {\n\t\t\tthis.snvArcRing = new Ring(dataHolder.snvInnerRadius, this.settings.rings.snvRingWidth, snvData)\n\t\t}\n\n\t\tconst lohMapper = new LohArcMapper(\n\t\t\tdataHolder.lohInnerRadius,\n\t\t\tthis.settings.rings.lohRingWidth,\n\t\t\tthis.sampleName,\n\t\t\tthis.reference\n\t\t)\n\t\tconst lohData = lohMapper.map(dataHolder.lohData)\n\t\tif (lohData.length > 0) {\n\t\t\tthis.lohArcRing = new Ring(dataHolder.lohInnerRadius, this.settings.rings.lohRingWidth, lohData)\n\t\t}\n\n\t\tthis.cnvArcsMapper = new CnvArcsMapper(\n\t\t\tdataHolder.cnvInnerRadius,\n\t\t\tthis.settings.rings.cnvRingWidth,\n\t\t\tthis.settings,\n\t\t\tthis.sampleName,\n\t\t\tthis.reference,\n\t\t\tdataHolder.percentilePositive,\n\t\t\tdataHolder.percentileNegative,\n\t\t\tdataHolder.cappedCnvMaxAbsValue,\n\t\t\tdataHolder.cnvMaxPercentileAbs,\n\t\t\tthis.settings.cnv.unit,\n\t\t\tthis.settings.Disco.cnvRenderingType\n\t\t)\n\n\t\tconst cnvData = this.cnvArcsMapper.map(dataHolder.cnvData)\n\t\tif (cnvData.length > 0) {\n\t\t\tthis.cnvArcRing = new Ring(dataHolder.cnvInnerRadius, this.settings.rings.cnvRingWidth, cnvData)\n\t\t}\n\n\t\tif (\n\t\t\tthis.settings.Disco.mutationWaterfallPlot &&\n\t\t\tdataHolder.mutationWaterfallData?.length &&\n\t\t\tdataHolder.mutationWaterfallInnerRadius !== undefined &&\n\t\t\t//Added this check to prevent TypeScript error \"mutationWaterfallInnerRadius might be undefined\"\n\t\t\t(dataHolder.mutationWaterfallInnerRadius ?? 0) > 0 &&\n\t\t\tdataHolder.mutationWaterfallLogRange\n\t\t) {\n\t\t\tconst mutationWaterfallMapper = new MutationWaterfallMapper(\n\t\t\t\tdataHolder.mutationWaterfallInnerRadius,\n\t\t\t\tthis.settings.rings.mutationWaterfallRingWidth,\n\t\t\t\tthis.reference,\n\t\t\t\tdataHolder.mutationWaterfallLogRange,\n\t\t\t\tthis.settings.Disco.mutationWaterfallColor || '#4d4d4d'\n\t\t\t)\n\n\t\t\tconst waterfallData = mutationWaterfallMapper.map(dataHolder.mutationWaterfallData)\n\t\t\tif (waterfallData.length > 0) {\n\t\t\t\tthis.mutationWaterfallRing = new Ring(\n\t\t\t\t\tdataHolder.mutationWaterfallInnerRadius,\n\t\t\t\t\tthis.settings.rings.mutationWaterfallRingWidth,\n\t\t\t\t\twaterfallData\n\t\t\t\t)\n\t\t\t}\n\t\t}\n\n\t\tconst fusionMapper = new FusionMapper(dataHolder.fusionRadius, this.sampleName, this.reference)\n\n\t\tconst fusions = fusionMapper.map(dataHolder.fusionData)\n\n\t\tlet lohLegend: LohLegend | undefined\n\n\t\tif (this.settings.legend.lohLegendEnabled && dataHolder.lohMinValue && dataHolder.lohMaxValue) {\n\t\t\tlohLegend = new LohLegend(dataHolder.lohMinValue, dataHolder.lohMaxValue)\n\t\t}\n\n\t\tconst legend = new Legend(\n\t\t\tthis.settings.legend.snvTitle,\n\t\t\tthis.settings.legend.cnvTitle,\n\t\t\tthis.settings.legend.lohTitle,\n\t\t\tthis.settings.legend.fusionTitle,\n\t\t\tthis.settings.Disco.cnvPercentile,\n\t\t\tthis.settings.Disco.cnvCutoffMode,\n\t\t\tthis.snvArcsMapper ? this.snvArcsMapper.snvClassMap : new Map(),\n\t\t\tthis.cnvArcsMapper ? this.cnvArcsMapper.cnvClassMap : new Map(),\n\t\t\tthis.settings.Disco.cnvRenderingType,\n\t\t\tfusions.length > 0,\n\t\t\tthis.discoInteractions,\n\t\t\tlohLegend,\n\t\t\tthis.settings.Disco.mutationWaterfallPlot && this.mutationWaterfallRing\n\t\t\t\t? {\n\t\t\t\t\tcolor: this.settings.Disco.mutationWaterfallColor || '#4d4d4d',\n\t\t\t\t\tonColorChange: this.discoInteractions.onMutationWaterfallColorChange\n\t\t\t\t}\n\t\t\t\t: undefined\n\t\t)\n\n\t\tconst rings = new Rings(\n\t\t\tlabelsRing,\n\t\t\tchromosomesRing,\n\t\t\tthis.nonExonicArcRing,\n\t\t\tthis.snvArcRing,\n\t\t\tthis.cnvArcRing,\n\t\t\tthis.lohArcRing,\n\t\t\tthis.mutationWaterfallRing\n\t\t)\n\n\t\treturn new ViewModel(\n\t\t\tthis.settings,\n\t\t\trings,\n\t\t\tlegend,\n\t\t\tfusions,\n\t\t\tdataHolder,\n\t\t\tthis.genesetName,\n\t\t\tdata.filter(i => i.dt == dtsnvindel).length\n\t\t)\n\t}\n}\n", "import type ViewModel from '#plots/disco/viewmodel/ViewModel.ts'\nimport Reference from '#plots/disco/chromosome/Reference.ts'\nimport DataMapper from '#plots/disco/data/DataMapper.ts'\nimport type Settings from '#plots/disco/Settings.ts'\nimport ViewModelProvider from './ViewModelProvider.ts'\nimport type { DiscoInteractions } from '../interactions/DiscoInteractions.ts'\nimport { dtsnvindel, dtcnv, dtloh } from '#shared/common.js'\n\nexport class ViewModelMapper {\n\tstatic snvClassLayer = {\n\t\tM: 'exonic',\n\t\tE: 'exonic',\n\t\tF: 'exonic',\n\t\tN: 'exonic',\n\t\tS: 'exonic',\n\t\tD: 'exonic',\n\t\tI: 'exonic',\n\t\tP: 'exonic',\n\t\tL: 'exonic',\n\t\tUtr3: 'exonic',\n\t\tUtr5: 'exonic',\n\t\tProteinAltering: 'exonic',\n\t\tmnv: 'non-exonic',\n\t\tITD: 'non-exonic',\n\t\tinsertion: 'non-exonic',\n\t\tdeletion: 'non-exonic',\n\t\tIntron: 'non-exonic',\n\t\tX: 'non-exonic',\n\t\tnoncoding: 'non-exonic'\n\t}\n\n\tprivate settings: Settings\n\tprivate discoInteractions: DiscoInteractions\n\n\tconstructor(settings: Settings, discoInteractions: DiscoInteractions) {\n\t\t// the settings object retrieved is frozen. created\n\t\t// a mutable copy so ring dimensions can be adjusted at runtime\n\t\tthis.settings = JSON.parse(JSON.stringify(settings))\n\t\tthis.discoInteractions = discoInteractions\n\t}\n\n\tprivate applyRadius() {\n\t\tconst radius = this.settings.Disco.radius\n\t\tif (!radius) return\n\n\t\tconst scale = radius / this.settings.rings.labelLinesInnerRadius\n\n\t\tthis.settings.rings.labelLinesInnerRadius *= scale\n\t\tthis.settings.rings.labelsToLinesDistance *= scale\n\t\tthis.settings.rings.chromosomeInnerRadius *= scale\n\t\tthis.settings.rings.chromosomeWidth *= scale\n\t\tthis.settings.rings.nonExonicRingWidth *= scale\n\t\tthis.settings.rings.snvRingWidth *= scale\n\t\tthis.settings.rings.lohRingWidth *= scale\n\t\tthis.settings.rings.cnvRingWidth *= scale\n\t\tthis.settings.rings.mutationWaterfallRingWidth *= scale\n\t\tthis.settings.label.fontSize *= scale\n\t\tthis.settings.legend.fontSize *= scale\n\t}\n\n\tstatic computeDynamicRadius(data: Array<any>): number {\n\t\tlet ringCount = 0\n\t\tif (data.some(d => d.dt == dtsnvindel)) ringCount++\n\t\tif (data.some(d => d.dt == dtcnv)) ringCount++\n\t\tif (data.some(d => d.dt == dtloh)) ringCount++\n\n\t\tif (ringCount <= 1) return 200\n\t\tif (ringCount == 2) return 250\n\t\treturn 300\n\t}\n\n\tmap(opts: any): ViewModel {\n\t\tconst chrSizes = opts.args.genome.majorchr\n\n\t\t/** Remove hidden chromosomes */\n\t\tconst chromosomesOverride = {}\n\t\tfor (const chr of Object.keys(chrSizes)) {\n\t\t\tif (!this.settings.Disco.hiddenChromosomes.includes(chr)) {\n\t\t\t\tchromosomesOverride[chr] = chrSizes[chr]\n\t\t\t}\n\t\t}\n\n\t\tconst sampleName = opts.args.sampleName\n\n\t\tconst genome = opts.args.genome\n\n\t\tconst prioritizedGenes = genome?.geneset?.[0] ? genome.geneset[0].lst : []\n\n\t\tconst genesetName = genome?.geneset?.[0] ? genome.geneset[0].name : ''\n\n\t\tconst data: Array<any> = opts.args.data\n\n\t\tif (this.settings.Disco.autoRadius) {\n\t\t\tthis.settings.Disco.radius = ViewModelMapper.computeDynamicRadius(data)\n\t\t}\n\n\t\tthis.applyRadius()\n\n\t\tconst reference = new Reference(this.settings, chrSizes, chromosomesOverride)\n\n\t\tconst dataMapper = new DataMapper(this.settings, reference, sampleName, prioritizedGenes)\n\n\t\treturn new ViewModelProvider(\n\t\t\tthis.settings,\n\t\t\tdataMapper,\n\t\t\treference,\n\t\t\tsampleName,\n\t\t\tgenesetName,\n\t\t\tthis.discoInteractions\n\t\t).map(data)\n\t}\n}\n", "import type Legend from './Legend.ts'\nimport { CnvType } from '#plots/disco/cnv/CnvType.ts'\nimport { FusionLegend } from '#plots/disco/fusion/FusionLegend.ts'\nimport { CnvRenderingType } from '#plots/disco/cnv/CnvRenderingType.ts'\nimport { scaleLinear } from 'd3-scale'\n\nexport default class LegendJSONMapper {\n\tprivate cappedCnvMaxAbsValue: number\n\n\tconstructor(cappedCnvMaxAbsValue: number) {\n\t\tthis.cappedCnvMaxAbsValue = cappedCnvMaxAbsValue\n\t}\n\n\tmap(legend: Legend) {\n\t\tconst legendJSON: Array<any> = []\n\n\t\tlet order = 0\n\t\tif (legend.snvClassMap) {\n\t\t\tthis.mapSnv(legend, legendJSON, order++)\n\t\t}\n\n\t\tif (legend.cnvRenderingType == CnvRenderingType.heatmap) {\n\t\t\tthis.mapCnvHeatmap(legend, legendJSON, order++)\n\t\t} else if (legend.cnvRenderingType == CnvRenderingType.bar) {\n\t\t\tif (legend.cnvClassMap) {\n\t\t\t\tthis.mapCnvBar(legend, legendJSON, order++)\n\t\t\t}\n\t\t}\n\n\t\tif (legend.lohLegend) {\n\t\t\tthis.mapLoh(legend, legendJSON, order++)\n\t\t}\n\n\t\tif (legend.fusionLegend) {\n\t\t\tthis.mapFusion(legend, legendJSON, order++)\n\t\t}\n\n\t\tif (legend.mutationWaterfallLegend) {\n\t\t\tthis.mapMutationWaterfall(legend, legendJSON, order++)\n\t\t}\n\n\t\treturn legendJSON\n\t}\n\n\tprivate mapSnv(legend: Legend, legendJSON: Array<any>, order: number) {\n\t\tconst snvItems: Array<any> = []\n\n\t\tlet snvOrder = 0\n\n\t\tfor (const [snvKey, snvLegendElement] of legend.snvClassMap) {\n\t\t\tsnvItems.push({\n\t\t\t\ttermid: legend.snvTitle,\n\t\t\t\tkey: snvKey,\n\t\t\t\ttext: `${snvLegendElement.snvType} (${snvLegendElement.count})`,\n\t\t\t\tcolor: snvLegendElement.color,\n\t\t\t\torder: snvOrder++,\n\t\t\t\tborder: '1px solid #ccc'\n\t\t\t})\n\t\t}\n\n\t\tlegendJSON.push({\n\t\t\tname: legend.snvTitle,\n\t\t\torder: order,\n\t\t\titems: snvItems\n\t\t})\n\t}\n\n\tprivate mapCnvBar(legend: Legend, legendJSON: Array<any>, order: number) {\n\t\tif (!legend.cnvClassMap) return\n\t\tconst gain = legend.cnvClassMap.get(CnvType.Gain)\n\t\tconst loss = legend.cnvClassMap.get(CnvType.Loss)\n\t\tconst cap = legend.cnvClassMap.get(CnvType.Cap)\n\n\t\tif (gain && loss && cap) {\n\t\t\tlet cnvOrder = 0\n\t\t\tconst cnvItems: Array<any> = []\n\t\t\tif (gain.value > 0) {\n\t\t\t\tcnvItems.push({\n\t\t\t\t\ttermid: legend.cnvTitle,\n\t\t\t\t\tkey: CnvType.Gain,\n\t\t\t\t\ttext: `Max: ${gain.value}`,\n\t\t\t\t\tcolor: gain.color,\n\t\t\t\t\torder: cnvOrder++,\n\t\t\t\t\tborder: '1px solid #ccc'\n\t\t\t\t})\n\t\t\t}\n\n\t\t\tif (loss.value < 0) {\n\t\t\t\tcnvItems.push({\n\t\t\t\t\ttermid: legend.cnvTitle,\n\t\t\t\t\tkey: CnvType.Loss,\n\t\t\t\t\ttext: `Min: ${loss.value}`,\n\t\t\t\t\tcolor: loss.color,\n\t\t\t\t\torder: cnvOrder++,\n\t\t\t\t\tborder: '1px solid #ccc'\n\t\t\t\t})\n\t\t\t}\n\n\t\t\tcnvItems.push({\n\t\t\t\ttermid: legend.cnvTitle,\n\t\t\t\tkey: CnvType.Cap,\n\t\t\t\ttext: `Capping: ${cap.value}`,\n\t\t\t\tcolor: cap.color,\n\t\t\t\torder: cnvOrder++,\n\t\t\t\tborder: '1px solid #ccc'\n\t\t\t\t// ,\n\t\t\t\t// onClickCallback: this.onClickCallback\n\t\t\t})\n\n\t\t\tlegendJSON.push({\n\t\t\t\tname: legend.cnvTitle,\n\t\t\t\tid: 'sjpp-disco-cnv-legend',\n\t\t\t\torder: order,\n\t\t\t\titems: cnvItems\n\t\t\t})\n\t\t}\n\t}\n\n\tprivate mapCnvHeatmap(legend: Legend, legendJSON: Array<any>, order: number) {\n\t\tif (!legend.cnvClassMap) return\n\t\tconst gain = legend.cnvClassMap.get(CnvType.Gain)\n\t\tconst loss = legend.cnvClassMap.get(CnvType.Loss)\n\t\tconst cap = legend.cnvClassMap.get(CnvType.Cap)\n\n\t\tif (gain && loss && cap) {\n\t\t\tlet cnvOrder = 0\n\n\t\t\tconst cnvItems: Array<any> = []\n\t\t\tconst base = {\n\t\t\t\ttermid: legend.cnvTitle,\n\t\t\t\twidth: 100,\n\t\t\t\torder: cnvOrder++,\n\t\t\t\tisLegendItem: true,\n\t\t\t\tdt: 4\n\t\t\t}\n\t\t\tif (gain.value > 0 && loss.value < 0) {\n\t\t\t\t// Use a symmetric scale for the heatmap\n\t\t\t\t// Matches the logic for coloring the arcs in the heatmap\n\t\t\t\t// in CnvHeatmapRenderer.ts\n\t\t\t\tconst maxValue = Math.max(Math.abs(loss.value), gain.value)\n\t\t\t\tconst domain = [-maxValue, 0, maxValue]\n\t\t\t\tcnvItems.push(\n\t\t\t\t\tObject.assign(\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\tkey: CnvType.LossGain,\n\t\t\t\t\t\t\tdomain,\n\t\t\t\t\t\t\tscale: scaleLinear([-1, 0, 1], [loss.color, 'white', gain.color]),\n\t\t\t\t\t\t\tlabels: { left: 'Loss', right: 'Gain' },\n\t\t\t\t\t\t\tnumericInputs: {\n\t\t\t\t\t\t\t\tcutoffMode: legend.cnvCutoffMode,\n\t\t\t\t\t\t\t\tdefaultPercentile: legend.cnvPercentile,\n\t\t\t\t\t\t\t\tcallback: obj => legend.discoInteractions.colorScaleNumericInputsCallback(obj)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t},\n\t\t\t\t\t\tbase\n\t\t\t\t\t)\n\t\t\t\t)\n\t\t\t} else {\n\t\t\t\tif (gain.value > 0) {\n\t\t\t\t\tcnvItems.push(\n\t\t\t\t\t\tObject.assign(\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tkey: CnvType.Gain,\n\t\t\t\t\t\t\t\ttext: 'Copy number gain',\n\t\t\t\t\t\t\t\tdomain: [0, gain.value],\n\t\t\t\t\t\t\t\tscale: scaleLinear([0, 1], ['white', gain.color])\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\tbase\n\t\t\t\t\t\t)\n\t\t\t\t\t)\n\t\t\t\t}\n\t\t\t\tif (loss.value < 0) {\n\t\t\t\t\tcnvItems.push(\n\t\t\t\t\t\tObject.assign(\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tkey: CnvType.Loss,\n\t\t\t\t\t\t\t\ttext: 'Copy number loss',\n\t\t\t\t\t\t\t\tdomain: [loss.value, 0],\n\t\t\t\t\t\t\t\tscale: scaleLinear([0, 1], [loss.color, 'white'])\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\tbase\n\t\t\t\t\t\t)\n\t\t\t\t\t)\n\t\t\t\t}\n\t\t\t}\n\t\t\tlegendJSON.push({\n\t\t\t\tname: legend.cnvTitle,\n\t\t\t\torder: order,\n\t\t\t\tid: 'sjpp-disco-cnv-legend',\n\t\t\t\titems: cnvItems\n\t\t\t})\n\t\t}\n\t}\n\n\tprivate mapLoh(legend: Legend, legendJSON: Array<any>, order: number) {\n\t\tif (!legend.lohLegend) return\n\t\tconst lohItems: Array<any> = []\n\n\t\tlohItems.push({\n\t\t\ttermid: legend.lohTitle,\n\t\t\tkey: 'min',\n\t\t\ttext: 'min',\n\t\t\tcolor: legend.lohLegend.colorStartValue,\n\t\t\torder: 0,\n\t\t\tborder: '1px solid #ccc'\n\t\t})\n\n\t\tlohItems.push({\n\t\t\ttermid: legend.lohTitle,\n\t\t\tkey: 'max',\n\t\t\ttext: 'max',\n\t\t\tcolor: legend.lohLegend.colorEndValue,\n\t\t\torder: 1,\n\t\t\tborder: '1px solid #ccc'\n\t\t})\n\n\t\tlegendJSON.push({\n\t\t\tname: legend.lohTitle,\n\t\t\torder: order,\n\t\t\titems: lohItems\n\t\t})\n\t}\n\n\tprivate mapFusion(legend: Legend, legendJSON: Array<any>, order: number) {\n\t\tconst fusionItems: Array<any> = []\n\n\t\tfusionItems.push({\n\t\t\ttermid: legend.fusionTitle,\n\t\t\tkey: FusionLegend.Interchromosomal,\n\t\t\ttext: 'Interchromosomal',\n\t\t\tcolor: FusionLegend.Interchromosomal.valueOf(),\n\t\t\torder: 0,\n\t\t\tborder: '1px solid #ccc'\n\t\t})\n\n\t\tfusionItems.push({\n\t\t\ttermid: legend.fusionTitle,\n\t\t\tkey: FusionLegend.Intrachromosomal,\n\t\t\ttext: 'Intrachromosomal',\n\t\t\tcolor: FusionLegend.Intrachromosomal.valueOf(),\n\t\t\torder: 1,\n\t\t\tborder: '1px solid #ccc'\n\t\t})\n\n\t\tlegendJSON.push({\n\t\t\tname: legend.fusionTitle,\n\t\t\torder: order,\n\t\t\titems: fusionItems\n\t\t})\n\t}\n\n\tprivate mapMutationWaterfall(legend: Legend, legendJSON: Array<any>, order: number) {\n\t\tif (!legend.mutationWaterfallLegend) return\n\n\t\tconst waterfallItems: Array<any> = []\n\n\t\twaterfallItems.push({\n\t\t\ttermid: 'Mutation Waterfall Plot',\n\t\t\tkey: 'mutation-waterfall-color',\n\t\t\ttext: 'Dot color',\n\t\t\tcolor: legend.mutationWaterfallLegend.color,\n\t\t\torder: 0,\n\t\t\tcolorPicker: true,\n\t\t\tinputWidth: 28,\n\t\t\twidth: 0,\n\t\t\tonColorChange: legend.mutationWaterfallLegend.onColorChange\n\t\t})\n\n\t\twaterfallItems.push({\n\t\t\ttermid: 'Mutation Waterfall Plot',\n\t\t\tkey: 'mutation-waterfall-axis',\n\t\t\ttext: 'Axis: log10 intermutation distance',\n\t\t\torder: 1,\n\t\t\tskipIcon: true,\n\t\t\twidth: 0\n\t\t})\n\n\t\tlegendJSON.push({\n\t\t\tname: 'Mutation Waterfall Plot',\n\t\t\torder: order,\n\t\t\titems: waterfallItems\n\t\t})\n\t}\n}\n", "import type { SvgG } from '../../../types/d3'\nimport { Menu, renderTable } from '#dom'\nimport type { TableCell, TableColumn } from '#dom'\n\nexport type AlternativeCnvSet = {\n\tnameHtml?: string\n\tname?: string\n\tinuse?: boolean\n\tmlst: any[]\n\tattrs?: { [key: string]: string }\n}\n\nfunction parseSetLabel(set: AlternativeCnvSet, index: number) {\n\tlet text = set.name || `Set ${index + 1}`\n\tlet href: string | undefined\n\tlet target = '_blank'\n\n\tif (set.nameHtml) {\n\t\tconst parser = new DOMParser()\n\t\tconst doc = parser.parseFromString(set.nameHtml, 'text/html')\n\t\tconst anchor = doc.querySelector('a')\n\t\tif (anchor) {\n\t\t\thref = anchor.getAttribute('href') || undefined\n\t\t\ttarget = anchor.getAttribute('target') || '_blank'\n\t\t\ttext = anchor.textContent?.trim() || text\n\t\t} else {\n\t\t\ttext = doc.body.textContent?.trim() || text\n\t\t}\n\t}\n\n\treturn { text, href, target }\n}\n\n/**\n * Render the CNV source label and a control inside the legend. Clicking the\n * control will display a menu with a table to choose among the\n * available CNV data sets.\n *\n * @param legendG - legend <g> element to append the label and control to\n * @param datasets - list of alternative CNV data sets from the server\n * @param fontSize - font size used in the legend\n * @param onChange - callback fired with the index of the selected data set\n */\nexport function renderCnvSourceLegend(\n\tlegendG: SvgG,\n\tdatasets: AlternativeCnvSet[],\n\tfontSize: number,\n\tonChange: (index: number) => void\n) {\n\tif (!legendG || legendG.empty()) throw new Error('legendG is required')\n\tif (!datasets || datasets.length === 0) throw new Error('at least one dataset is required')\n\n\tlegendG.select('g.sjpp-cnv-source').remove()\n\n\tconst gBBox = legendG.node()!.getBBox()\n\tconst cnvSrcWrapper = legendG\n\t\t.append('g')\n\t\t.attr('class', 'sjpp-cnv-source')\n\t\t.attr('transform', `translate(${gBBox.width},${gBBox.y + fontSize})`)\n\n\tconst btnPaddingX = Math.round(fontSize * 0.8)\n\tconst btnHgt = Math.round(fontSize * 1.8)\n\n\tconst btnWrapper = cnvSrcWrapper\n\t\t.append('g')\n\t\t.attr('transform', `translate(${fontSize},${-btnHgt / 2})`)\n\t\t.style('cursor', 'pointer')\n\t\t.on('click', function (event: MouseEvent) {\n\t\t\tevent.stopPropagation()\n\t\t\tshowCnvMenu(this)\n\t\t})\n\n\tconst btnText = btnWrapper\n\t\t.append('text')\n\t\t.attr('x', 0)\n\t\t.attr('y', btnHgt / 2)\n\t\t.attr('font-size', fontSize)\n\t\t.attr('text-anchor', 'start')\n\t\t.attr('dominant-baseline', 'middle')\n\t\t.text('Select source \u25B2'.toUpperCase())\n\n\tconst textW = btnText.node() ? Math.ceil(btnText.node()!.getBBox().width) : 0\n\tconst btnWdt = textW + btnPaddingX * 2\n\n\tbtnWrapper\n\t\t.insert('rect', ':first-child')\n\t\t.attr('width', btnWdt)\n\t\t.attr('height', btnHgt)\n\t\t.attr('rx', 10)\n\t\t.attr('ry', 10)\n\t\t.style('fill', '#f2f2f2')\n\n\tbtnText.attr('x', btnWdt / 2).attr('text-anchor', 'middle')\n\n\tconst cnvMenu = new Menu({\n\t\tonHide: () => {\n\t\t\tbtnText.text('Select source \u25B2'.toUpperCase())\n\t\t}\n\t})\n\n\tfunction showCnvMenu(dom: Element) {\n\t\tbtnText.text('Select source \u25BC'.toUpperCase())\n\t\tcnvMenu.clear().showunder(dom)\n\n\t\tcnvMenu.d.append('div').text('Choose data source for CNV:').style('margin', '5px 5px 0 5px')\n\n\t\tconst tableHolder = cnvMenu.d.append('div').style('padding', '5px')\n\n\t\tconst { columns, rows } = buildTableData(datasets)\n\t\tconst [, activeIndex] = getActiveDataset(datasets)\n\n\t\trenderTable({\n\t\t\tcolumns,\n\t\t\trows,\n\t\t\tdiv: tableHolder,\n\t\t\tsingleMode: true,\n\t\t\tmaxWidth: '70vw',\n\t\t\tmaxHeight: '60vh',\n\t\t\tselectedRows: [activeIndex],\n\t\t\theader: { allowSort: false },\n\t\t\tnoButtonCallback: (rowIndex, node) => {\n\t\t\t\tconst inputIndex = Number(node?.value)\n\t\t\t\tconst selectedIndex = Number.isNaN(inputIndex) ? rowIndex : inputIndex\n\t\t\t\tif (!Number.isNaN(selectedIndex)) onChange(selectedIndex)\n\t\t\t\tcnvMenu.hide()\n\t\t\t}\n\t\t})\n\t}\n}\n\nfunction getActiveDataset(datasets) {\n\tlet currentIndex = datasets.findIndex(d => d.inuse)\n\tif (currentIndex == -1) currentIndex = 0\n\treturn [datasets[currentIndex], currentIndex]\n}\n\nfunction buildTableData(datasets: AlternativeCnvSet[]): { columns: TableColumn[]; rows: TableCell[][] } {\n\tconst attrKeys: string[] = []\n\tfor (const set of datasets) {\n\t\tif (!set.attrs) continue\n\t\tfor (const key of Object.keys(set.attrs)) {\n\t\t\tif (!attrKeys.includes(key)) attrKeys.push(key)\n\t\t}\n\t}\n\n\tconst columns: TableColumn[] = [{ label: 'Source' }]\n\tfor (const key of attrKeys) columns.push({ label: key })\n\n\tconst rows: TableCell[][] = datasets.map((set, index) => {\n\t\tconst sourceInfo = parseSetLabel(set, index)\n\t\tconst cells: TableCell[] = []\n\n\t\tif (set.nameHtml) cells.push({ html: set.nameHtml })\n\t\telse if (sourceInfo.href) cells.push({ value: sourceInfo.text, url: sourceInfo.href })\n\t\telse cells.push({ value: sourceInfo.text })\n\n\t\tfor (const key of attrKeys) {\n\t\t\tconst value = set.attrs?.[key]\n\t\t\tcells.push({ value: value ?? '' })\n\t\t}\n\n\t\treturn cells\n\t})\n\n\treturn { columns, rows }\n}\n", "import type Legend from './Legend.ts'\nimport { svgLegend, getMaxLabelWidth } from '#dom'\nimport LegendJSONMapper from './LegendJSONMapper.ts'\nimport { dtcnv } from '#shared/common.js'\nimport { renderCnvSourceLegend, type AlternativeCnvSet } from '../cnv/renderCnvSourceLegend.ts'\nimport type ViewModel from '../viewmodel/ViewModel.ts'\n\nexport default class LegendRenderer {\n\tprivate legendJSONMapper: LegendJSONMapper\n\tprivate fontSize: number\n\n\tconstructor(cappedCnvMaxAbsValue = 0, fontSize: number) {\n\t\tthis.fontSize = fontSize\n\t\tthis.legendJSONMapper = new LegendJSONMapper(cappedCnvMaxAbsValue)\n\t}\n\n\trender(\n\t\tholder: any,\n\t\tlegend: Legend,\n\t\txOffset: number,\n\t\tsvgw: number,\n\t\tsvgh: number,\n\t\tviewModel: ViewModel,\n\t\tonCnvSourceSelect: (index: number) => void\n\t) {\n\t\tconst svgLegendRenderer = svgLegend({\n\t\t\tholder: holder.append('g').attr('data-testid', 'sjpp_disco_plot_legend'),\n\t\t\trectFillFxn: d => d.color,\n\t\t\ticonStroke: '#aaa'\n\t\t})\n\t\tconst data = this.legendJSONMapper.map(legend)\n\n\t\tconst legendTitles = data.map(d => d.name.trim())\n\t\tconst maxLabelWidth = getMaxLabelWidth(holder, legendTitles)\n\n\t\tconst d = {\n\t\t\txOffset: maxLabelWidth + xOffset\n\t\t}\n\n\t\tsvgLegendRenderer(data, {\n\t\t\tsettings: Object.assign(\n\t\t\t\t{},\n\t\t\t\t{\n\t\t\t\t\tsvgw: svgw,\n\t\t\t\t\tsvgh: svgh,\n\t\t\t\t\tdimensions: d,\n\t\t\t\t\tfontsize: this.fontSize\n\t\t\t\t}\n\t\t\t)\n\t\t})\n\t\tconst altCnv: AlternativeCnvSet[] = viewModel.appState.args.alternativeDataByDt?.[dtcnv]\n\n\t\tif (altCnv && altCnv.length > 0) {\n\t\t\tconst legendG = holder.select('g[data-testid=\"sjpp_disco_plot_legend\"]')\n\t\t\tconst cnvLegendG = legendG.select('#sjpp-disco-cnv-legend')\n\n\t\t\tif (!legendG.empty()) {\n\t\t\t\t/** This shouldn't be necessary. It's reasonable to assume\n\t\t\t\t * a cnv legend group will exist if there is a cnvClassMap.*/\n\t\t\t\tconst add2G = cnvLegendG.empty() ? legendG : cnvLegendG\n\t\t\t\trenderCnvSourceLegend(add2G, altCnv, this.fontSize, onCnvSourceSelect)\n\t\t\t}\n\t\t}\n\t}\n}\n", "import * as d3 from 'd3'\nimport type IRenderer from '#plots/disco/IRenderer.ts'\nimport type Chromosome from './Chromosome.ts'\nimport MenuProvider from '#plots/disco/menu/MenuProvider.ts'\nimport { bplen } from '#shared/common.js'\n\nexport default class ChromosomesRenderer implements IRenderer {\n       private padAngle: number\n       private innerRadius: number\n       private outerRadius: number\n       private fontSize: number\n\n       constructor(\n               padAngle: number,\n               innerRadius: number,\n               outerRadius: number,\n               fontSize: number\n       ) {\n               this.padAngle = padAngle\n               this.innerRadius = innerRadius\n               this.outerRadius = outerRadius\n               this.fontSize = fontSize\n       }\n\n\trender(holder: any, elements: Array<Chromosome>) {\n\t\tconst pie = d3\n\t\t\t.pie<Chromosome>()\n\t\t\t.padAngle(this.padAngle)\n\t\t\t.value(d => d.size)\n\t\t\t.sort(null)\n\n\t\tconst arcData = pie(elements)\n\n\t\tconst arc = d3.arc<d3.PieArcDatum<number>>().innerRadius(this.innerRadius).outerRadius(this.outerRadius)\n\n\t\tconst arcs = holder.append('g').attr('data-testid', 'sjpp_chromosomes_arc_group')\n\n\t\tconst menu = MenuProvider.create()\n\n\t\tarcs\n\t\t\t.selectAll('path')\n\t\t\t.data(arcData)\n\t\t\t.enter()\n\t\t\t.append('path')\n\t\t\t.attr('d', arc)\n\t\t\t.attr('fill', 'black')\n\t\t\t.on('mousemove', (event: MouseEvent, d: d3.PieArcDatum<Chromosome>) => {\n\t\t\t\t// Get mouse pointer coordinates relative to the arcs group\n\t\t\t\tconst [x, y] = d3.pointer(event, arcs.node())\n\t\t\t\t// Convert Cartesian coordinates to polar angle (in radians)\n\t\t\t\tlet angle = Math.atan2(y, x) + Math.PI / 2\n\t\t\t\t// Normalize angle to be within [0, 2\u03C0]\n\t\t\t\tif (angle < 0) angle += 2 * Math.PI\n\t\t\t\t// Compute how far along this arc segment the angle falls (fraction between 0 and 1)\n\t\t\t\tconst frac = Math.max(0, Math.min(1, (angle - d.data.startAngle) / (d.data.endAngle - d.data.startAngle)))\n\t\t\t\t// Interpolate position along chromosome based on angle\n\t\t\t\tconst pos = Math.round(frac * d.data.size)\n\t\t\t\t// Update tooltip text with chromosome name and position (formatted with commas)\n\t\t\t\tmenu.d.html(`<span style=\"font-size:.8em\">chr${d.data.text}</span> ${bplen(pos)}`).style('padding', '5px')\n\t\t\t\t// Display tooltip at cursor position\n\t\t\t\tmenu.show(event.x, event.y)\n\t\t\t})\n\t\t\t.on('mouseenter', (event: MouseEvent) => {\n\t\t\t\t// When hovering over an arc, highlight it with an orange border\n\t\t\t\td3.select(event.currentTarget as SVGElement)\n\t\t\t\t\t.attr('stroke', 'orange')\n\t\t\t\t\t.attr('stroke-width', 1)\n\t\t\t})\n\t\t\t.on('mouseleave', event => {\n\t\t\t\t// Remove highlight and hide tooltip when mouse leaves the arc\n\t\t\t\td3.select(event.currentTarget as SVGElement)\n\t\t\t\t\t.attr('stroke', null)\n\t\t\t\t\t.attr('stroke-width', null)\n\t\t\t\tmenu.hide()\n\t\t\t})\n\n\t\tarcs\n\t\t\t.selectAll('text')\n\t\t\t.data(arcData)\n\t\t\t.enter()\n\t\t\t.append('text')\n\t\t\t// TODO extract all value and functions to Chromosomes\n\t\t\t.attr('transform', (d: d3.PieArcDatum<Chromosome>) => {\n\t\t\t\treturn `translate(${arc.centroid(<any>d)}) rotate(${(d.data.angle * 180) / Math.PI - 90})${\n\t\t\t\t\td.data.angle > Math.PI ? 'rotate(180)' : ''\n\t\t\t\t}`\n\t\t\t})\n                       .attr('dy', '0.35em')\n                       .attr('text-anchor', 'middle')\n                       .text((d: d3.PieArcDatum<Chromosome>) => d.data.text)\n                       .style('fill', 'white')\n                       .style('font-size', `${this.fontSize}px`)\n                       .style('padding', '500px')\n                       //prevents chromosome number from interfering with hover\n                       .style('pointer-events', 'none')\n                       .style('padding', '500px')\n\t}\n}\n", "import { fillbar } from '#dom'\nimport type Data from '#plots/disco/data/Data.ts'\n\nexport type ReadCountValue = string | number | undefined\nexport type VafEntry = {\n\tlabel: string\n\trefCount: ReadCountValue\n\taltCount: ReadCountValue\n}\n\nexport function getIntegerCount(v: ReadCountValue): number | null {\n\tif (Number.isInteger(v)) return v as number\n\tif (typeof v == 'string' && /^-?\\d+$/.test(v)) {\n\t\tconst n = Number(v)\n\t\tif (Number.isInteger(n)) return n\n\t}\n\treturn null\n}\n\nexport function hasValidReadCounts(refCountValue: ReadCountValue, altCountValue: ReadCountValue): boolean {\n\tconst refCount = getIntegerCount(refCountValue)\n\tconst altCount = getIntegerCount(altCountValue)\n\treturn refCount != null && altCount != null && refCount >= 0 && altCount >= 0 && refCount + altCount > 0\n}\n\nexport function getVafEntries(vafs: Data['vafs']): VafEntry[] {\n\tconst entries: VafEntry[] = []\n\tif (Array.isArray(vafs)) {\n\t\tfor (const vaf of vafs) {\n\t\t\tconst label = vaf?.id || vaf?.name\n\t\t\tconst refCount = vaf?.refCount\n\t\t\tconst altCount = vaf?.altCount\n\t\t\tif (!label || refCount == null || altCount == null) continue\n\t\t\tentries.push({ label, refCount, altCount })\n\t\t}\n\t}\n\treturn entries\n}\n\nexport function hasAnyValidVafEntry(vafs: Data['vafs']): boolean {\n\treturn getVafEntries(vafs).some(vaf => hasValidReadCounts(vaf.refCount, vaf.altCount))\n}\n\nexport function appendVafBar(td2: any, refCountValue: ReadCountValue, altCountValue: ReadCountValue, label = 'VAF') {\n\tconst refCount = getIntegerCount(refCountValue)\n\tconst altCount = getIntegerCount(altCountValue)\n\tif (refCount == null || altCount == null) return\n\n\tconst totalCount = refCount + altCount\n\tconst fraction = altCount / totalCount\n\tconst div = td2\n\t\t.append('div')\n\t\t.style('margin-left', '5px')\n\t\t.style('margin-top', '4px')\n\t\t.style('display', 'flex')\n\t\t.style('align-items', 'center')\n\t\t.style('gap', '6px')\n\n\tdiv.append('span').style('font-size', '0.8em').style('color', '#555').text(label)\n\tfillbar(div, { f: fraction, v1: altCount, v2: totalCount })\n}\n\nexport function appendVafBars(td2: any, vafs: Data['vafs']) {\n\tfor (const vaf of getVafEntries(vafs)) {\n\t\tif (!hasValidReadCounts(vaf.refCount, vaf.altCount)) continue\n\t\tappendVafBar(td2, vaf.refCount, vaf.altCount, vaf.label)\n\t}\n}\n", "import type IRenderer from '#plots/disco/IRenderer.ts'\nimport { select } from 'd3-selection'\nimport { line } from 'd3-shape'\nimport type Label from './Label.ts'\nimport MenuProvider from '#plots/disco/menu/MenuProvider.ts'\nimport type MutationTooltip from '#plots/disco/label/MutationTooltip.ts'\nimport type FusionTooltip from '#plots/disco/fusion/FusionTooltip.ts'\nimport { table2col } from '#dom/table2col'\nimport type CnvTooltip from '#plots/disco/cnv/CnvTooltip.ts'\nimport { appendVafBars, hasAnyValidVafEntry } from '#plots/disco/snv/vafTooltip.ts'\n\nexport default class LabelsRenderer implements IRenderer {\n\tprivate animationDuration: number\n\tprivate fontSize: number\n\tprivate geneClickListener: (gene: string, mnames: Array<string>) => void\n\n\tconstructor(\n\t\tanimationDuration: number,\n\t\tfontSize: number,\n\t\tgeneClickListener: (gene: string, mnames: Array<string>) => void\n\t) {\n\t\tthis.animationDuration = animationDuration\n\t\tthis.fontSize = fontSize\n\t\tthis.geneClickListener = geneClickListener\n\t}\n\n\trender(holder: any, elements: Array<Label>, collisions?: Array<Label>) {\n\t\tconst labelsG = holder.append('g')\n\n\t\tconst lineFunction = line<{ x: number; y: number }>()\n\t\t\t.x(point => point.x)\n\t\t\t.y(point => point.y)\n\n\t\tconst menu = MenuProvider.create()\n\n\t\tlabelsG\n\t\t\t.selectAll('.group')\n\t\t\t.data(elements)\n\t\t\t.enter()\n\t\t\t.append('g')\n\t\t\t.attr('class', 'group')\n\t\t\t.each((label: Label, i: number, nodes: HTMLDivElement[]) => {\n\t\t\t\tconst g = select(nodes[i])\n\t\t\t\tg.append('text')\n\t\t\t\t\t.attr('class', 'chord-text')\n\t\t\t\t\t.attr('dy', '.35em')\n\t\t\t\t\t.attr('transform', label.transform)\n\t\t\t\t\t.style('text-anchor', label.textAnchor)\n\t\t\t\t\t.style('font-size', `${this.fontSize}px`)\n\t\t\t\t\t.style('fill', label.color)\n\t\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t\t.text(label.text)\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tif (label.mutationsTooltip) {\n\t\t\t\t\t\t\tthis.geneClickListener(\n\t\t\t\t\t\t\t\tlabel.text,\n\t\t\t\t\t\t\t\tlabel.mutationsTooltip.map(value => value.mname)\n\t\t\t\t\t\t\t)\n\t\t\t\t\t\t}\n\t\t\t\t\t})\n\t\t\t\t\t.on('mouseover', (mouseEvent: MouseEvent) => {\n\t\t\t\t\t\tconst table = table2col({ holder: menu.d })\n\t\t\t\t\t\tthis.createTooltip(table, label)\n\t\t\t\t\t\tmenu.show(mouseEvent.x, mouseEvent.y)\n\t\t\t\t\t})\n\t\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\t\tmenu.clear()\n\t\t\t\t\t\tmenu.hide()\n\t\t\t\t\t})\n\n\t\t\t\tg.append('path')\n\t\t\t\t\t.attr('class', 'chord-tick')\n\t\t\t\t\t.datum(label.line.points)\n\t\t\t\t\t.style('stroke', label.color)\n\t\t\t\t\t.style('fill', 'none')\n\t\t\t\t\t.attr('d', lineFunction)\n\t\t\t})\n\n\t\tlabelsG.selectAll('.group').each((label: Label, i: number, nodes: HTMLDivElement[]) => {\n\t\t\tconst collision = collisions ? collisions.find(l => l.text === label.text) : undefined\n\t\t\tif (collision) {\n\t\t\t\tconst g = select(nodes[i])\n\t\t\t\tg.selectAll('.chord-text')\n\t\t\t\t\t.datum(collision)\n\t\t\t\t\t.transition()\n\t\t\t\t\t.duration(this.animationDuration)\n\t\t\t\t\t.attr('transform', collision.transform)\n\t\t\t\t\t.style('text-anchor', collision.textAnchor)\n\n\t\t\t\tg.selectAll('.chord-tick')\n\t\t\t\t\t.datum(collision.line.points)\n\t\t\t\t\t.transition()\n\t\t\t\t\t.duration(this.animationDuration)\n\t\t\t\t\t.style('fill', 'none')\n\t\t\t\t\t.attr('d', lineFunction)\n\t\t\t}\n\t\t})\n\t}\n\n\tcreateTooltip(table: any, label: Label) {\n\t\tif (label.mutationsTooltip) {\n\t\t\tconst [td1, td2] = table.addRow()\n\t\t\ttd1.text('Gene')\n\t\t\ttd2.append('span').style('margin-left', '5px').text(label.text)\n\n\t\t\tlabel.mutationsTooltip.forEach((mutation: MutationTooltip) => {\n\t\t\t\t{\n\t\t\t\t\tconst [td1, td2] = table.addRow()\n\n\t\t\t\t\ttd1.text('Mutation')\n\t\t\t\t\ttd2\n\t\t\t\t\t\t.append('span')\n\t\t\t\t\t\t.style('margin-left', '5px')\n\t\t\t\t\t\t.text(mutation.mname)\n\t\t\t\t\t\t.append('span')\n\t\t\t\t\t\t.style('margin-left', '5px')\n\t\t\t\t\t\t.style('color', mutation.color)\n\t\t\t\t\t\t.text(`${mutation.dataClass}`)\n\t\t\t\t\t\t.append('span')\n\t\t\t\t\t\t.style('margin-left', '5px')\n\t\t\t\t\t\t.style('color', 'black')\n\t\t\t\t\t\t.style('font-size', '0.8em')\n\t\t\t\t\t\t.text(` ${mutation.chr}:${mutation.position}`)\n\t\t\t\t\tif (hasAnyValidVafEntry(mutation.vafs)) {\n\t\t\t\t\t\tappendVafBars(td2, mutation.vafs)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t})\n\t\t}\n\n\t\tif (label.fusionTooltip) {\n\t\t\tconst [td1, td2] = table.addRow()\n\n\t\t\ttd1.text('Data type')\n\t\t\ttd2.append('span').text('Fusion transcript')\n\t\t\tlabel.fusionTooltip.forEach((fusionTooltip: FusionTooltip) => {\n\t\t\t\tconst [td1, td2] = table.addRow()\n\n\t\t\t\ttd1.text('Position')\n\t\t\t\ttd2.append('span').text(\n\t\t\t\t\t` ${fusionTooltip.geneA ? fusionTooltip.geneA : '?'} ${fusionTooltip.chrA}:${fusionTooltip.posA}\n\t\t\t\t\t\t${fusionTooltip.strandA == '+' ? 'forward' : 'reverse'} > ` +\n\t\t\t\t\t\t`${fusionTooltip.geneB ? fusionTooltip.geneB : '?'} ${fusionTooltip.chrB}:${fusionTooltip.posB} ${\n\t\t\t\t\t\t\tfusionTooltip.strandB == '+' ? 'forward' : 'reverse'\n\t\t\t\t\t\t} `\n\t\t\t\t)\n\t\t\t})\n\t\t}\n\n\t\tif (label.cnvTooltip) {\n\t\t\tlabel.cnvTooltip.forEach((cnv: CnvTooltip) => {\n\t\t\t\tconst [td1, td2] = table.addRow()\n\t\t\t\ttd1.text('CNV')\n\t\t\t\ttd2.append('span').style('margin-left', '5px').style('background-color', cnv.color).html('&nbsp;&nbsp;')\n\n\t\t\t\ttd2\n\t\t\t\t\t.append('span')\n\t\t\t\t\t.style('margin-left', '7.5px')\n\t\t\t\t\t.text(cnv.value)\n\t\t\t\t\t.append('span')\n\t\t\t\t\t.style('margin-left', '7.5px')\n\t\t\t\t\t.style('font-size', '0.8em')\n\t\t\t\t\t.text(`${cnv.chr}:${cnv.start}-${cnv.stop}`)\n\t\t\t})\n\t\t}\n\t}\n}\n", "import type Settings from './Settings'\nimport { copyMerge } from '#rx'\nimport { CnvRenderingType } from '#plots/disco/cnv/CnvRenderingType.ts'\n\nexport default function discoDefaults(overrides: any = {}, app?: any): Settings {\n\tconst hiddenChromosomes: string[] = []\n\t//TODO: Change skipChrM into Set to accept multiple chromosomes\n\tif (app?.vocabApi?.termdbConfig?.queries?.singleSampleMutation?.discoPlot?.skipChrM) {\n\t\thiddenChromosomes.push('chrM')\n\t}\n\n\tconst defaults = {\n\t\tdownloadImgName: 'disco.plot',\n\n\t\tDisco: {\n\t\t\tcenterText: null,\n\t\t\tcnvCapping: 5,\n\t\t\tisOpen: false,\n\t\t\tprioritizeGeneLabelsByGeneSets: false,\n\t\t\tshowPrioritizeGeneLabelsByGeneSets: false,\n\t\t\tshowGeneNames: true,\n\t\t\tmutationWaterfallPlot: false,\n\t\t\tmutationWaterfallColor: '#4d4d4d',\n\t\t\tcnvRenderingType: CnvRenderingType.heatmap,\n\t\t\tcnvPercentile: 90, // 90th percentile for removing outliers\n\t\t\tcnvCutoffMode: 'percentile',\n\t\t\tautoRadius: true,\n\t\t\tradius: 300,\n\t\t\tfusionOpacity: 1,\n\t\t\thiddenChromosomes\n\t\t},\n\n\t\trings: {\n\t\t\tnonExonicRingWidth: 20,\n\t\t\tsnvRingWidth: 20,\n\t\t\tlohRingWidth: 20,\n\t\t\tcnvRingWidth: 30,\n\t\t\tmutationWaterfallRingWidth: 35,\n\n\t\t\tsnvRingFilters: ['exonic'],\n\n\t\t\tchromosomeInnerRadius: 190,\n\t\t\tchromosomeWidth: 20,\n\n\t\t\tlabelLinesInnerRadius: 210,\n\t\t\tlabelsToLinesDistance: 30,\n\t\t\tlabelsToLinesGap: 2,\n\n\t\t\tnonExonicRingEnabled: true,\n\t\t\tnonExonicFilterValues: ['non-exonic']\n\t\t},\n\n\t\tverticalPadding: 0,\n\t\thorizontalPadding: 50,\n\n\t\tlayerScaler: 1,\n\t\tpadAngle: 0.002, //0.01, //0.04,\n\n\t\tlabel: {\n\t\t\tfontSize: 12,\n\t\t\tmaxDeltaAngle: 0.05,\n\t\t\tanimationDuration: 1000,\n\t\t\toverlapAngleFactor: 5 // 5 is set by testing, because label height is not known before rendering\n\t\t},\n\n\t\tcnv: {\n\t\t\tcapping: 5,\n\t\t\tpercentile: 80,\n\t\t\tampColor: '#D6683C',\n\t\t\tlossColor: '#67a9cf',\n\t\t\tcappedAmpColor: '#8B0000',\n\t\t\tcappedLossColor: '#00008B',\n\t\t\tunit: 'Unit'\n\t\t},\n\t\tsnv: {\n\t\t\tmaxMutationCount: 10000\n\t\t},\n\t\tlegend: {\n\t\t\tsnvTitle: 'SNV',\n\t\t\tcnvTitle: 'CNV',\n\t\t\tlohTitle: 'LOH',\n\t\t\tfusionTitle: 'SV', // Structural Variants (color by co-location)\n\t\t\tlohLegendEnabled: true,\n\t\t\tfontSize: 12,\n\t\t\trowHeight: 48\n\t\t},\n\n\t\tmenu: {\n\t\t\tpadding: 5\n\t\t}\n\t}\n\n\tif (overrides?.Disco?.radius != null && (overrides.Disco.radius > 1000 || overrides.Disco.radius < 200)) {\n\t\tconsole.log(`${overrides?.Disco?.radius} is greater or lower than the min and max for the radius`)\n\t}\n\n\treturn copyMerge(defaults, overrides)\n}\n", "import type IRenderer from '#plots/disco/IRenderer.ts'\nimport * as d3 from 'd3'\nimport type SnvArc from './SnvArc.ts'\nimport type Arc from '#plots/disco/arc/Arc.ts'\nimport MenuProvider from '#plots/disco/menu/MenuProvider.ts'\nimport { dtsnvindel } from '#shared/common.js'\nimport { table2col } from '#dom/table2col'\nimport { appendVafBars, hasAnyValidVafEntry } from './vafTooltip.ts'\n\nexport default class NonExonicSnvRenderer implements IRenderer {\n\tprivate geneClickListener: (gene: string, mnames: Array<string>) => void\n\n\tconstructor(geneClickListener: (gene: string, mnames: Array<string>) => void) {\n\t\tthis.geneClickListener = geneClickListener\n\t}\n\n\trender(holder: any, elements: Array<Arc>) {\n\t\tconst arcGenerator = d3.arc<SnvArc>()\n\n\t\tconst arcs = holder.append('g')\n\n\t\tconst menu = MenuProvider.create()\n\n\t\tarcs\n\t\t\t.selectAll('path')\n\t\t\t.data(elements)\n\t\t\t.enter()\n\t\t\t.append('path')\n\t\t\t.attr('d', (d: SnvArc) => arcGenerator(d))\n\t\t\t.attr('fill', (d: SnvArc) => d.color)\n\t\t\t.on('mouseover', (mouseEvent: MouseEvent, arc: SnvArc) => {\n\t\t\t\tconst table = table2col({ holder: menu.d })\n\t\t\t\tconst snv: any = structuredClone(arc)\n\t\t\t\tsnv.dt = dtsnvindel\n\t\t\t\tsnv.class = arc.dataClass\n\t\t\t\tsnv.gene = snv.text\n\n\t\t\t\t{\n\t\t\t\t\tconst [td1, td2] = table.addRow()\n\t\t\t\t\ttd1.text('Consequence')\n\t\t\t\t\ttd2.append('span').text(snv.mname)\n\t\t\t\t\ttd2\n\t\t\t\t\t\t.append('span')\n\t\t\t\t\t\t.style('margin-left', '5px')\n\t\t\t\t\t\t.style('color', snv.color)\n\t\t\t\t\t\t.style('font-size', '.8em')\n\t\t\t\t\t\t.text(snv.dataClass)\n\t\t\t\t}\n\t\t\t\t{\n\t\t\t\t\tconst [td1, td2] = table.addRow()\n\t\t\t\t\ttd1.text(snv.ref && snv.alt ? 'Mutation' : 'Position')\n\t\t\t\t\ttd2.append('span').text(`${snv.chr}:${snv.pos + 1} ${snv.ref && snv.alt ? snv.ref + '>' + snv.alt : ''}`)\n\t\t\t\t}\n\n\t\t\t\tif (snv.gene) {\n\t\t\t\t\tconst [td1, td2] = table.addRow()\n\t\t\t\t\ttd1.text('Gene')\n\t\t\t\t\ttd2.text(snv.gene)\n\t\t\t\t}\n\n\t\t\t\tif (snv.occurrence > 1) {\n\t\t\t\t\tconst [td1, td2] = table.addRow()\n\t\t\t\t\ttd1.text('Occurrence')\n\t\t\t\t\ttd2.text(snv.occurrence)\n\t\t\t\t}\n\t\t\t\tif (hasAnyValidVafEntry(arc.vafs)) {\n\t\t\t\t\tconst [td1, td2] = table.addRow()\n\t\t\t\t\ttd1.text('Read count')\n\t\t\t\t\tappendVafBars(td2, arc.vafs)\n\t\t\t\t}\n\n\t\t\t\tmenu.show(mouseEvent.x, mouseEvent.y)\n\t\t\t})\n\t\t\t.on('mouseout', () => {\n\t\t\t\tmenu.clear()\n\t\t\t\tmenu.hide()\n\t\t\t})\n\t\t\t.on('click', (mouseEvent: MouseEvent, arc: SnvArc) => {\n\t\t\t\tthis.geneClickListener(arc.text, [arc.mname])\n\t\t\t})\n\t}\n}\n", "import * as d3 from 'd3'\nimport type SnvArc from './SnvArc.ts'\nimport type IRenderer from '#plots/disco/IRenderer.ts'\nimport FullArcRenderer from '#plots/disco/arc/FullArcRenderer.ts'\nimport MenuProvider from '#plots/disco/menu/MenuProvider.ts'\nimport { dtsnvindel } from '#shared/common.js'\nimport { table2col } from '#dom/table2col'\nimport { appendVafBars, hasAnyValidVafEntry } from './vafTooltip.ts'\n\nexport default class SnvRenderer implements IRenderer {\n\tprivate svnWidth: number\n\n\tprivate geneClickListener: (gene: string, mnames: Array<string>) => void\n\n\tconstructor(svnWidth: number, geneClickListener: (gene: string, mnames: Array<string>) => void) {\n\t\tthis.svnWidth = svnWidth\n\n\t\tthis.geneClickListener = geneClickListener\n\t}\n\n\trender(holder: any, elements: Array<SnvArc>) {\n\t\tif (elements.length > 0) {\n\t\t\tconst svnInnerRadius = elements[0].innerRadius\n\t\t\tconst fullArcRenderer = new FullArcRenderer(svnInnerRadius, this.svnWidth, '#6464641A')\n\t\t\tfullArcRenderer.render(holder)\n\t\t}\n\n\t\tconst arcGenerator = d3.arc<SnvArc>()\n\n\t\tconst arcs = holder.append('g')\n\n\t\tconst menu = MenuProvider.create()\n\n\t\tarcs\n\t\t\t.selectAll('path')\n\t\t\t.data(elements)\n\t\t\t.enter()\n\t\t\t.append('path')\n\t\t\t.attr('d', (d: SnvArc) => arcGenerator(d))\n\t\t\t.attr('fill', (d: SnvArc) => d.color)\n\t\t\t.on('mouseover', (mouseEvent: MouseEvent, arc: SnvArc) => {\n\t\t\t\tconst table = table2col({ holder: menu.d })\n\t\t\t\tconst snv: any = structuredClone(arc)\n\t\t\t\tsnv.dt = dtsnvindel\n\t\t\t\tsnv.class = arc.dataClass\n\t\t\t\tsnv.gene = snv.text\n\n\t\t\t\t{\n\t\t\t\t\tconst [td1, td2] = table.addRow()\n\t\t\t\t\ttd1.text('Consequence')\n\t\t\t\t\ttd2.append('span').text(snv.mname)\n\t\t\t\t\ttd2\n\t\t\t\t\t\t.append('span')\n\t\t\t\t\t\t.style('margin-left', '5px')\n\t\t\t\t\t\t.style('color', snv.color)\n\t\t\t\t\t\t.style('font-size', '.8em')\n\t\t\t\t\t\t.text(snv.dataClass)\n\t\t\t\t}\n\t\t\t\t{\n\t\t\t\t\tconst [td1, td2] = table.addRow()\n\t\t\t\t\ttd1.text(snv.ref && snv.alt ? 'Mutation' : 'Position')\n\t\t\t\t\ttd2.append('span').text(`${snv.chr}:${snv.pos + 1} ${snv.ref && snv.alt ? snv.ref + '>' + snv.alt : ''}`)\n\t\t\t\t}\n\n\t\t\t\tif (snv.gene) {\n\t\t\t\t\tconst [td1, td2] = table.addRow()\n\t\t\t\t\ttd1.text('Gene')\n\t\t\t\t\ttd2.text(snv.gene)\n\t\t\t\t}\n\n\t\t\t\tif (snv.occurrence > 1) {\n\t\t\t\t\tconst [td1, td2] = table.addRow()\n\t\t\t\t\ttd1.text('Occurrence')\n\t\t\t\t\ttd2.text(snv.occurrence)\n\t\t\t\t}\n\n\t\t\t\tif (hasAnyValidVafEntry(arc.vafs)) {\n\t\t\t\t\tconst [td1, td2] = table.addRow()\n\t\t\t\t\ttd1.text('Read count')\n\t\t\t\t\tappendVafBars(td2, arc.vafs)\n\t\t\t\t}\n\n\t\t\t\tmenu.show(mouseEvent.x, mouseEvent.y)\n\t\t\t})\n\t\t\t.on('mouseout', () => {\n\t\t\t\tmenu.clear()\n\t\t\t\tmenu.hide()\n\t\t\t})\n\t\t\t.on('click', (mouseEvent: MouseEvent, arc: SnvArc) => {\n\t\t\t\tthis.geneClickListener(arc.text, [arc.mname])\n\t\t\t})\n\t}\n}\n", "import * as d3 from 'd3'\nimport type LohArc from './LohArc.ts'\nimport type IRenderer from '#plots/disco/IRenderer.ts'\nimport MenuProvider from '#plots/disco/menu/MenuProvider.ts'\nimport { dtloh } from '#shared/common.js'\nimport { table2col } from '#dom/table2col'\n\nexport default class LohRenderer implements IRenderer {\n\trender(holder: any, elements: Array<LohArc>) {\n\t\tconst arcGenerator = d3.arc<LohArc>()\n\n\t\tconst arcs = holder.append('g')\n\n\t\tconst menu = MenuProvider.create()\n\n\t\tarcs\n\t\t\t.selectAll('path')\n\t\t\t.data(elements)\n\t\t\t.enter()\n\t\t\t.append('path')\n\t\t\t.attr('d', (d: LohArc) => arcGenerator(d))\n\t\t\t.attr('fill', (d: LohArc) => d.color)\n\t\t\t.on('mouseover', (mouseEvent: MouseEvent, arc: LohArc) => {\n\t\t\t\tconst table = table2col({ holder: menu.d })\n\t\t\t\tconst loh: any = structuredClone(arc)\n\t\t\t\tloh.dt = dtloh\n\t\t\t\tloh.gene = loh.text\n\t\t\t\t{\n\t\t\t\t\tconst [td1, td2] = table.addRow()\n\t\t\t\t\ttd1.text('Data type')\n\t\t\t\t\ttd2.append('span').style('margin-left', '5px').text('Loss of Heterozygosity')\n\t\t\t\t}\n\n\t\t\t\tconst [td1, td2] = table.addRow()\n\t\t\t\ttd1.text('Position')\n\t\t\t\ttd2.append('span').text(`${arc.chr}:${arc.start}-${arc.stop}`)\n\n\t\t\t\tmenu.show(mouseEvent.x, mouseEvent.y)\n\t\t\t})\n\t\t\t.on('mouseout', () => {\n\t\t\t\tmenu.clear()\n\t\t\t\tmenu.hide()\n\t\t\t})\n\t}\n}\n", "import * as d3 from 'd3'\nimport type IRenderer from '#plots/disco/IRenderer.ts'\nimport type CnvArc from './CnvArc.ts'\nimport MenuProvider from '#plots/disco/menu/MenuProvider.ts'\nimport { dtcnv } from '#shared/common.js'\nimport { table2col } from '#dom/table2col'\n\nexport default class CnvBarRenderer implements IRenderer {\n\trender(holder: any, elements: Array<CnvArc>) {\n\t\tconst arcGenerator = d3.arc<CnvArc>()\n\n\t\t// Create a group for the arcs (actual CNV bars)\n\t\tconst arcs = holder.append('g')\n\t\t// Create a group for overlays used to highlight hovered bars\n\t\tconst hoverOverlay = holder\n\t\t\t.append('g')\n\t\t\t.attr('class', 'hover-overlay')\n\t\t\t// prevent highlighht from blocking thin CNVs\n\t\t\t.style('pointer-events', 'none')\n\n\t\tconst menu = MenuProvider.create()\n\n\t\tarcs\n\t\t\t.selectAll('path')\n\t\t\t.data(elements)\n\t\t\t.enter()\n\t\t\t.append('path')\n\t\t\t// Generate arc path for each CNV\n\t\t\t.attr('d', (d: CnvArc) => arcGenerator(d))\n\t\t\t// Fill with the CNV's specified color\n\t\t\t.attr('fill', (d: CnvArc) => d.color)\n\t\t\t// Start of highlight + tooltip behavior\n\t\t\t.on('mouseover', (mouseEvent: MouseEvent, arc: CnvArc) => {\n\t\t\t\t// Remove any existing overlay (e.g., from previous hover)\n\t\t\t\thoverOverlay.selectAll('*').remove()\n\t\t\t\t// Add a highlighted black stroke on top of the hovered arc\n\t\t\t\thoverOverlay\n\t\t\t\t\t.append('path')\n\t\t\t\t\t.datum(arc)\n\t\t\t\t\t.attr('d', arcGenerator(arc))\n\t\t\t\t\t.attr('fill', 'none')\n\t\t\t\t\t.attr('stroke', 'black')\n\t\t\t\t\t.attr('stroke-width', 1)\n\n\t\t\t\t// Prepare the CNV data for tooltip display\n\t\t\t\tconst cnv: any = structuredClone(arc)\n\t\t\t\tcnv.dt = dtcnv\n\t\t\t\tcnv.samples = [{ sample_id: arc.sampleName }]\n\t\t\t\tcnv.gene = cnv.text\n\n\t\t\t\t// Create a two-column table in the tooltip\n\t\t\t\tconst table = table2col({ holder: menu.d })\n\t\t\t\t// Add: Copy number change row\n\t\t\t\t{\n\t\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\t\tc1.text('CNV')\n\t\t\t\t\tc2.html(`<span style=\"background:${cnv.color}\">&nbsp;&nbsp;</span> ${cnv.value}`)\n\t\t\t\t}\n\t\t\t\t// Add: Position row\n\t\t\t\t{\n\t\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\t\tc1.text('Position')\n\t\t\t\t\tc2.text(cnv.chr + ':' + cnv.start + '-' + cnv.stop)\n\t\t\t\t}\n\t\t\t\t// Add: Unit value row\n\t\t\t\t{\n\t\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\t\tc1.text('Unit')\n\t\t\t\t\tc2.text(cnv.value)\n\t\t\t\t}\n\n\t\t\t\t// Show tooltip near the cursor\n\t\t\t\tmenu.show(mouseEvent.x, mouseEvent.y)\n\t\t\t})\n\t\t\t// Remove highlight and tooltip when mouse leaves\n\t\t\t.on('mouseout', () => {\n\t\t\t\thoverOverlay.selectAll('*').remove()\n\t\t\t\tmenu.clear()\n\t\t\t\tmenu.hide()\n\t\t\t})\n\t}\n}\n", "import type CnvArc from '#plots/disco/cnv/CnvArc.ts'\nimport * as d3 from 'd3'\nimport MenuProvider from '#plots/disco/menu/MenuProvider.ts'\nimport { table2col } from '#dom/table2col'\nimport { scaleLinear } from 'd3-scale'\nimport { dtcnv } from '#shared/common.js'\n\nexport class CnvHeatmapRenderer {\n\tprivate positivePercentile: number\n\tprivate negativePercentile: number\n\n\tconstructor(positivePercentile = 0, negativePercentile = 0) {\n\t\tthis.positivePercentile = positivePercentile\n\t\tthis.negativePercentile = negativePercentile\n\t}\n\n\trender(holder: any, elements: Array<CnvArc>) {\n\t\tconst arcGenerator = d3.arc<CnvArc>()\n\n\t\t// Group for actual heatmap CNV arcs\n\t\tconst arcs = holder.append('g')\n\n\t\t// Separate group for overlays on hover (not blocking interactions)\n\t\tconst hoverOverlay = holder.append('g').attr('class', 'hover-overlay').style('pointer-events', 'none')\n\n\t\tconst menu = MenuProvider.create()\n\n\t\tarcs\n\t\t\t.selectAll('path')\n\t\t\t.data(elements)\n\t\t\t.enter()\n\t\t\t.append('path')\n\t\t\t// Generate the arc shape for each CNV\n\t\t\t.attr('d', (d: CnvArc) => arcGenerator(d))\n\t\t\t// Fill using interpolated color based on CNV value and percentile range\n\t\t\t.attr('fill', (d: CnvArc) => this.getColor(d.color, d.value))\n\n\t\t\t// Hover event: show highlight stroke and tooltip\n\t\t\t.on('mouseenter', (mouseEvent: MouseEvent, arc: CnvArc) => {\n\t\t\t\t// Add highlight stroke over the hovered arc\n\t\t\t\thoverOverlay\n\t\t\t\t\t.append('path')\n\t\t\t\t\t.datum(arc)\n\t\t\t\t\t.attr('d', arcGenerator(arc))\n\t\t\t\t\t.attr('fill', 'none')\n\t\t\t\t\t.attr('stroke', 'black')\n\t\t\t\t\t.attr('stroke-width', 1)\n\n\t\t\t\t// Prepare data for tooltip\n\t\t\t\tconst table = table2col({ holder: menu.d })\n\t\t\t\tconst cnv: any = structuredClone(arc)\n\t\t\t\tcnv.dt = dtcnv\n\t\t\t\tcnv.samples = [{ sample_id: arc.sampleName }]\n\t\t\t\tcnv.gene = cnv.text\n\n\t\t\t\t// Row 1: Copy number change + colored square\n\t\t\t\t{\n\t\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\t\tc1.text('CNV')\n\t\t\t\t\t//Match the color shown in the tooltip to the heatmap\n\t\t\t\t\tc2.html(\n\t\t\t\t\t\t`<span style=\"background:${this.getColor(\n\t\t\t\t\t\t\tcnv.color,\n\t\t\t\t\t\t\tcnv.value\n\t\t\t\t\t\t)}; border:solid lightgrey 0.1px;\">&nbsp;&nbsp;</span> ${cnv.value}`\n\t\t\t\t\t)\n\t\t\t\t}\n\t\t\t\t// Row 2: Position\n\t\t\t\t{\n\t\t\t\t\tconst [c1, c2] = table.addRow()\n\t\t\t\t\tc1.text('Position')\n\t\t\t\t\tc2.text(cnv.chr + ':' + cnv.start + '-' + cnv.stop)\n\t\t\t\t}\n\n\t\t\t\t// Show tooltip near mouse\n\t\t\t\tmenu.show(mouseEvent.x, mouseEvent.y)\n\t\t\t})\n\n\t\t\t// Cleanup on hover out: remove highlight and hide tooltip\n\t\t\t.on('mouseleave', () => {\n\t\t\t\thoverOverlay.selectAll('*').remove()\n\t\t\t\tmenu.clear()\n\t\t\t\tmenu.hide()\n\t\t\t})\n\t}\n\n\t// Computes fill color using linear scale between -P80, 0, and +P80\n\tgetColor(color: string, value: number) {\n\t\t//For cnv values, use a zero-centered symmetric scale rather than the absolute values\n\t\tconst maxValue = Math.max(this.positivePercentile, Math.abs(this.negativePercentile))\n\t\treturn scaleLinear(\n\t\t\t[-maxValue, 0, maxValue],\n\t\t\t[color, 'white', color] // transitions to white in the middle\n\t\t).clamp(true)(value)\n\t}\n}\n", "import type IRenderer from '#plots/disco/IRenderer.ts'\nimport type MutationWaterfallPoint from './MutationWaterfallPoint.ts'\nimport MenuProvider from '#plots/disco/menu/MenuProvider.ts'\nimport { table2col } from '#dom/table2col'\nimport { bplen } from '#shared/common.js'\nimport { ticks } from 'd3-array'\n\nexport default class MutationWaterfallRenderer implements IRenderer {\n\tprivate dotRadius: number\n\n\tconstructor(dotRadius = 1.5) {\n\t\tthis.dotRadius = dotRadius\n\t}\n\n\trender(holder: any, elements: Array<MutationWaterfallPoint>) {\n\t\tif (!elements.length) return\n\n\t\tconst ringGroup = holder.append('g').attr('data-testid', 'sjpp_mutation_waterfall_ring')\n\t\tconst menu = MenuProvider.create()\n\n\t\tringGroup\n\t\t\t.append('g')\n\t\t\t.selectAll('circle')\n\t\t\t.data(elements)\n\t\t\t.enter()\n\t\t\t.append('circle')\n\t\t\t.attr('cx', d => Math.cos(d.startAngle - Math.PI / 2) * d.innerRadius)\n\t\t\t.attr('cy', d => Math.sin(d.startAngle - Math.PI / 2) * d.innerRadius)\n\t\t\t.attr('r', this.dotRadius)\n\t\t\t.attr('fill', d => d.color)\n\t\t\t.attr('opacity', 0.9)\n\t\t\t.on('mouseover', (event: MouseEvent, d: MutationWaterfallPoint) => {\n\t\t\t\tconst distance = Math.round(Math.pow(10, d.logDistance))\n\t\t\t\tmenu.clear()\n\t\t\t\tconst table = table2col({ holder: menu.d })\n\t\t\t\t{\n\t\t\t\t\tconst [td1, td2] = table.addRow()\n\t\t\t\t\ttd1.text('Intermutation distance')\n\t\t\t\t\ttd2.text(`${bplen(distance)}`)\n\t\t\t\t}\n\t\t\t\tmenu.show(event.x, event.y)\n\t\t\t})\n\t\t\t.on('mouseout', () => {\n\t\t\t\tmenu.clear()\n\t\t\t\tmenu.hide()\n\t\t\t})\n\n\t\tthis.renderAxis(ringGroup, elements[0])\n\t}\n\n\tprivate renderAxis(holder: any, referencePoint: MutationWaterfallPoint) {\n\t\tconst { ringInnerRadius, ringWidth, rangeMin, rangeMax } = referencePoint\n\t\tconst axisGroup = holder.append('g').attr('class', 'sjpp-waterfall-axis')\n\t\tconst topRadius = ringInnerRadius + ringWidth\n\n\t\taxisGroup\n\t\t\t.append('line')\n\t\t\t.attr('x1', 0)\n\t\t\t.attr('y1', -topRadius)\n\t\t\t.attr('x2', 0)\n\t\t\t.attr('y2', -ringInnerRadius)\n\t\t\t.attr('stroke', '#6e6e6e')\n\t\t\t.attr('stroke-width', 1)\n\n\t\tconst span = rangeMax - rangeMin || 1\n\t\tconst tickValues = rangeMax === rangeMin ? [rangeMin] : ticks(rangeMin, rangeMax, 4)\n\n\t\ttickValues.forEach(value => {\n\t\t\tconst ratio = (value - rangeMin) / span\n\t\t\tconst radius = ringInnerRadius + ringWidth * ratio\n\t\t\tconst y = -radius\n\t\t\taxisGroup.append('line').attr('x1', -4).attr('x2', 4).attr('y1', y).attr('y2', y).attr('stroke', '#6e6e6e')\n\n\t\t\tconst exponent = Math.round(value * 10) / 10\n\t\t\tconst formatted = Number.isInteger(exponent) ? `${exponent}` : exponent.toFixed(1)\n\t\t\taxisGroup\n\t\t\t\t.append('text')\n\t\t\t\t.attr('x', 6)\n\t\t\t\t.attr('y', y + 3)\n\t\t\t\t.style('font-size', '10px')\n\t\t\t\t.style('fill', '#4d4d4d')\n\t\t\t\t.text(`10^${formatted} bp`)\n\t\t})\n\t}\n}\n", "import { getCompInit } from '#rx'\nimport { DiscoRenderer } from './DiscoRenderer.ts'\nimport { DiscoInteractions } from './interactions/DiscoInteractions.ts'\nimport { ViewModelMapper } from './viewmodel/ViewModelMapper.ts'\nimport LegendRenderer from './legend/LegendRenderer.ts'\nimport ChromosomesRenderer from './chromosome/ChromosomesRenderer.ts'\nimport LabelsRenderer from './label/LabelsRenderer.ts'\nimport discoDefaults from './defaults.ts'\nimport NonExonicSnvRenderer from './snv/NonExonicSnvRenderer.ts'\nimport SnvRenderer from './snv/SnvRenderer.ts'\nimport LohRenderer from './loh/LohRenderer.ts'\nimport CnvBarRenderer from './cnv/CnvBarRenderer.ts'\nimport type IRenderer from './IRenderer.ts'\nimport { RingType } from './ring/RingType.ts'\nimport type Settings from './Settings.ts'\nimport { multiInit } from '../../rx'\nimport { topBarInit } from '../controls.btns'\nimport { configUiInit } from '../controls.config'\nimport { CnvHeatmapRenderer } from '#plots/disco/cnv/CnvHeatmapRenderer.ts'\nimport type ViewModel from '#plots/disco/viewmodel/ViewModel.ts'\nimport { CnvRenderingType } from '#plots/disco/cnv/CnvRenderingType.ts'\nimport { InvalidDataUI } from '#dom'\nimport { dtcnv, dtloh } from '#shared/common.js'\nimport MutationWaterfallRenderer from './waterfall/MutationWaterfallRenderer.ts'\n\nexport default class Disco {\n\tstatic type = 'Disco'\n\n\t// following attributes are required by rx\n\tprivate type: string\n\tprivate opts: any\n\tprivate state: any\n\tprivate id: any\n\tprivate app: any\n\tprivate features: any\n\tprivate isOpen: boolean\n\tprivate discoInteractions: DiscoInteractions\n\n\tprivate stateViewModelMapper?: ViewModelMapper\n\tprivate viewModel?: ViewModel\n\tprivate recreateViewModel = false\n\tprivate errorDiv: any\n\tprivate svgDiv: any\n\n\tconstructor(opts: any) {\n\t\tthis.type = 'Disco'\n\t\tthis.opts = opts\n\t\tthis.isOpen = false\n\t\tthis.discoInteractions = new DiscoInteractions(this)\n\t}\n\n\tasync init() {\n\t\tconst state = this.app.getState()\n\t\tconst settings = state.plots.find(p => p.id === this.id).settings\n\n\t\tthis.stateViewModelMapper = new ViewModelMapper(settings, this.discoInteractions)\n\t\tthis.viewModel = this.stateViewModelMapper.map(state)\n\n\t\tconst holder = this.opts.holder\n\t\tconst controlsHolder = holder.append('div').style('display', 'inline-block').style('vertical-align', 'top') // on the left\n\t\tconst mainDiv = holder.append('div').style('display', 'inline-block') // on the right\n\n\t\tconst topbar = controlsHolder.append('div')\n\t\tconst config_div = controlsHolder.append('div')\n\t\tconst configInputsOptions = this.getConfigInputsOptions(this.viewModel)\n\n\t\tthis.features = await multiInit({\n\t\t\ttopbar: topBarInit({\n\t\t\t\tapp: this.app,\n\t\t\t\tid: this.id,\n\t\t\t\t// TODO change the way svg is selected\n\t\t\t\tdownloadHandler: () =>\n\t\t\t\t\tthis.discoInteractions.downloadClickListener(holder.select('svg[id=\"sjpp_disco_plot\"]').node()),\n\t\t\t\tcallback: () => this.toggleVisibility(this.isOpen),\n\t\t\t\tisOpen: () => this.isOpen,\n\t\t\t\tholder: topbar\n\t\t\t}),\n\n\t\t\tconfig: configUiInit({\n\t\t\t\tapp: this.app,\n\t\t\t\tid: this.id,\n\t\t\t\tholder: config_div,\n\t\t\t\tisOpen: () => this.isOpen,\n\t\t\t\tinputs: configInputsOptions\n\t\t\t})\n\t\t})\n\n\t\tthis.errorDiv = mainDiv.append('div').attr('data-testid', 'sjpp-disco-errorDiv')\n\t\tthis.svgDiv = mainDiv.append('div').attr('data-testid', 'sjpp-disco-svgDiv')\n\t}\n\n\tprivate getConfigInputsOptions(viewModel: ViewModel) {\n\t\tconst configInputsOptions: Array<any> = []\n\n\t\tif (viewModel.settings.Disco.showPrioritizeGeneLabelsByGeneSets) {\n\t\t\tconst filterMutationsGenesCheckbox = [\n\t\t\t\t{\n\t\t\t\t\tboxLabel: viewModel.genesetName,\n\t\t\t\t\tlabel: `Filter mutations`,\n\t\t\t\t\ttype: 'checkbox',\n\t\t\t\t\tchartType: 'Disco',\n\t\t\t\t\tsettingsKey: 'prioritizeGeneLabelsByGeneSets',\n\t\t\t\t\ttitle: `Only show mutations for ${viewModel.genesetName} genes`\n\t\t\t\t}\n\t\t\t]\n\n\t\t\tconfigInputsOptions.push(...filterMutationsGenesCheckbox)\n\t\t}\n\n\t\tif (viewModel.cnvMaxValue !== 0 || viewModel.cnvMinValue !== 0) {\n\t\t\tconst cnvConfigInputOptions = [\n\t\t\t\t{\n\t\t\t\t\tboxLabel: '',\n\t\t\t\t\tlabel: 'CNV rendering type',\n\t\t\t\t\ttype: 'radio',\n\t\t\t\t\tchartType: 'Disco',\n\t\t\t\t\tsettingsKey: 'cnvRenderingType',\n\t\t\t\t\ttitle: 'CNV rendering type',\n\t\t\t\t\toptions: [\n\t\t\t\t\t\t{ label: 'Heatmap', value: CnvRenderingType.heatmap },\n\t\t\t\t\t\t{ label: 'Bar', value: CnvRenderingType.bar }\n\t\t\t\t\t]\n\t\t\t\t}\n\t\t\t]\n\t\t\tconfigInputsOptions.push(...cnvConfigInputOptions)\n\t\t}\n\n\t\tconfigInputsOptions.push({\n\t\t\tboxLabel: '',\n\t\t\tlabel: 'Show gene names',\n\t\t\ttype: 'checkbox',\n\t\t\tchartType: 'Disco',\n\t\t\tsettingsKey: 'showGeneNames',\n\t\t\ttitle: 'Show gene name labels on the outside of the plot'\n\t\t})\n\n\t\tconst genomeChr = this.app.opts.state.args.genome.majorchr\n\t\tconst chromosomeConfigOption = {\n\t\t\tlabel: 'Chromosomes',\n\t\t\ttitle: 'Chromosomes shown in the plot',\n\t\t\ttype: 'multiCheckbox',\n\t\t\tchartType: 'Disco',\n\t\t\tsettingsKey: 'hiddenChromosomes',\n\t\t\tstyle: {\n\t\t\t\tcolNum: 4\n\t\t\t},\n\t\t\toptions: Object.keys(genomeChr).map(c => ({ label: c, value: c })),\n\t\t\tprocessInput: (values: string[] = []) => {\n\t\t\t\t/** Show all chromosomes as checked by default but only\n\t\t\t\t * save to the state hidden (unchecked) chromosomes.\n\t\t\t\t * Allows for easier debugging, reduces user error when\n\t\t\t\t * embedding, and code clarity. */\n\t\t\t\tconst reverse = Object.keys(genomeChr).filter(c => !values.includes(c))\n\t\t\t\treturn reverse\n\t\t\t}\n\t\t}\n\n\t\tconfigInputsOptions.push(chromosomeConfigOption)\n\n\t\tconfigInputsOptions.push({\n\t\t\tboxLabel: '',\n\t\t\tlabel: 'Auto radius',\n\t\t\ttype: 'checkbox',\n\t\t\tchartType: 'Disco',\n\t\t\tsettingsKey: 'autoRadius',\n\t\t\ttitle: 'Automatically set the radius based on the number of data rings'\n\t\t})\n\n\t\tconst dimensionOptions = [\n\t\t\t{\n\t\t\t\tlabel: 'Radius',\n\t\t\t\ttitle: 'Set the radius of the entire plot, between 200 and 1000 pixels.',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'Disco',\n\t\t\t\tsettingsKey: 'radius',\n\t\t\t\tdebounceInterval: 500,\n\t\t\t\tstep: 25,\n\t\t\t\tmin: 200,\n\t\t\t\tmax: 1000,\n\t\t\t\tgetDisplayStyle: (plot: any) => (plot.settings.Disco.autoRadius ? 'none' : 'table-row')\n\t\t\t},\n\t\t\t{\n\t\t\t\tlabel: 'Fusion opacity',\n\t\t\t\ttitle: 'Adjust opacity of fusion arcs, between 0 and 1',\n\t\t\t\ttype: 'number',\n\t\t\t\tchartType: 'Disco',\n\t\t\t\tsettingsKey: 'fusionOpacity',\n\t\t\t\tstep: 0.01,\n\t\t\t\tmin: 0,\n\t\t\t\tmax: 1,\n\t\t\t\tdebounceInterval: 500\n\t\t\t}\n\t\t]\n\n\t\tconfigInputsOptions.push(...dimensionOptions)\n\t\tif (viewModel.canShowMutationWaterfallPlot && viewModel.snvDataLength > 0) {\n\t\t\tconfigInputsOptions.push({\n\t\t\t\tboxLabel: '',\n\t\t\t\tlabel: 'Mutation Waterfall Plot',\n\t\t\t\ttype: 'checkbox',\n\t\t\t\tchartType: 'Disco',\n\t\t\t\tsettingsKey: 'mutationWaterfallPlot',\n\t\t\t\ttitle: 'Render log10 intermutation distance ring for SNV/indel data'\n\t\t\t})\n\t\t}\n\t\treturn configInputsOptions\n\t}\n\n\tasync main(): Promise<void> {\n\t\t// run this only when this.state{} is set; cannot do this step in constructor()\n\t\tconst settings: Settings = this.state.settings\n\n\t\tthis.isOpen = settings.Disco.isOpen\n\n\t\tif (this.recreateViewModel) {\n\t\t\tthis.stateViewModelMapper = new ViewModelMapper(settings, this.discoInteractions)\n\t\t\tthis.viewModel = this.stateViewModelMapper.map(this.app.getState())\n\t\t}\n\t\tthis.recreateViewModel = true\n\n\t\tif (this.viewModel) {\n\t\t\t// TODO calculate viewModel.filteredSnvDataLength always\n\t\t\tthis.svgDiv.selectAll('*').remove() // todo not to need this\n\t\t\tconst appState = this.app.getState()\n\t\t\tthis.viewModel.svgDiv = this.svgDiv\n\t\t\tthis.viewModel.appState = appState\n\n\t\t\tfor (const name in this.features) {\n\t\t\t\tthis.features[name].update({ state: this.state, appState })\n\t\t\t}\n\n\t\t\tconst legendRenderer = new LegendRenderer(this.viewModel.cappedCnvMaxAbsValue, settings.label.fontSize)\n\n\t\t\tconst discoRenderer = new DiscoRenderer(\n\t\t\t\tthis.getRingRenderers(this.viewModel.settings, this.viewModel, this.discoInteractions.geneClickListener),\n\t\t\t\tlegendRenderer,\n\t\t\t\tthis.app.opts.state.args.genome\n\t\t\t)\n\n\t\t\tdiscoRenderer.render(this.svgDiv, this.viewModel, this.onCnvSourceSelect)\n\n\t\t\tif (this.viewModel.invalidDataInfo?.entries?.length) {\n\t\t\t\tInvalidDataUI.render(this.errorDiv, this.viewModel.invalidDataInfo)\n\t\t\t}\n\t\t}\n\t}\n\n\tgetState(appState: any) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tif (!config) return config\n\t\t// include args.data so updates rerender when mutation list changes\n\t\treturn { ...config, mlst: appState.args.data }\n\t}\n\n\tgetRingRenderers(\n\t\tsettings: Settings,\n\t\tviewModel: ViewModel,\n\t\tgeneClickListener: (gene: string, mnames: Array<string>) => void\n\t) {\n\t\tconst chromosomesRenderer = new ChromosomesRenderer(\n\t\t\tsettings.padAngle,\n\t\t\tsettings.rings.chromosomeInnerRadius,\n\t\t\tsettings.rings.chromosomeInnerRadius + settings.rings.chromosomeWidth,\n\t\t\tsettings.label.fontSize\n\t\t)\n\t\tconst labelsRenderer = new LabelsRenderer(\n\t\t\tsettings.label.animationDuration,\n\t\t\tsettings.label.fontSize,\n\t\t\tgeneClickListener\n\t\t)\n\t\tconst nonExonicSnvRenderer = new NonExonicSnvRenderer(geneClickListener)\n\t\tconst snvRenderer = new SnvRenderer(settings.rings.snvRingWidth, geneClickListener)\n\t\tconst cnvRenderer =\n\t\t\tsettings.Disco.cnvRenderingType === CnvRenderingType.heatmap\n\t\t\t\t? new CnvHeatmapRenderer(viewModel.positivePercentile, viewModel.negativePercentile)\n\t\t\t\t: new CnvBarRenderer()\n\t\tconst lohRenderer = new LohRenderer()\n\t\tconst mutationWaterfallRenderer = new MutationWaterfallRenderer()\n\n\t\tconst renderersMap: Map<RingType, IRenderer> = new Map()\n\t\trenderersMap.set(RingType.CHROMOSOME, chromosomesRenderer)\n\t\trenderersMap.set(RingType.LABEL, labelsRenderer)\n\t\trenderersMap.set(RingType.NONEXONICSNV, nonExonicSnvRenderer)\n\t\trenderersMap.set(RingType.SNV, snvRenderer)\n\t\trenderersMap.set(RingType.MUTATION_WATERFALL, mutationWaterfallRenderer)\n\t\trenderersMap.set(RingType.CNV, cnvRenderer)\n\t\trenderersMap.set(RingType.LOH, lohRenderer)\n\n\t\treturn renderersMap\n\t}\n\n\tprivate onCnvSourceSelect = (index: number) => {\n\t\tconst state = this.app.getState()\n\t\tconst args = state.args\n\t\tconst alt = args.alternativeDataByDt?.[dtcnv]\n\t\tif (!alt) return\n\t\tconst altClone = structuredClone(args.alternativeDataByDt)\n\t\taltClone[dtcnv].forEach((d, i) => (d.inuse = i === index))\n\t\tconst selected = altClone[dtcnv][index]\n\t\tselected.mlst.forEach((d: any) => (d.position = d.pos))\n\t\tconst baseData = args.data.filter((d: any) => d.dt != dtcnv && d.dt != dtloh)\n\t\tconst newData = baseData.concat(selected.mlst)\n\t\tthis.app.dispatch({\n\t\t\ttype: 'app_refresh',\n\t\t\tstate: { args: { ...args, data: newData, alternativeDataByDt: altClone } }\n\t\t})\n\t}\n\n\ttoggleVisibility(isOpen: boolean) {\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.opts.id,\n\t\t\tconfig: {\n\t\t\t\tsettings: {\n\t\t\t\t\tDisco: { isOpen: !isOpen }\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t}\n}\n\nexport const discoInit = getCompInit(Disco)\n\nexport const componentInit = discoInit\n\nexport async function getPlotConfig(opts: any, app: any) {\n\treturn {\n\t\tchartType: 'Disco',\n\t\tsubfolder: 'disco',\n\t\textension: 'ts',\n\t\tsettings: discoDefaults(opts.overrides, app)\n\t}\n}\n"],
+  "mappings": 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+}