@sjcrh/proteinpaint-client 2.183.0 → 2.183.1

package/dist/chunk-6ITDJ5UR.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../shared/utils/src/terms.js"],
-  "sourcesContent": ["import {\n\tdtgeneexpression,\n\tdtssgsea,\n\tdtdnamethylation,\n\tdtmetaboliteintensity,\n\tdtproteomeabundance,\n\tTermTypeGroups,\n\tdtTerms,\n} from \"./common.js\"\nimport { TermTypeGroups as TermTypeGroups2 } from \"./common.js\"\nconst ROOT_SAMPLE_TYPE = 1\nconst DEFAULT_SAMPLE_TYPE = 2\nconst NumericModes = {\n\tcontinuous: \"continuous\",\n\tdiscrete: \"discrete\",\n}\nconst CATEGORICAL = \"categorical\"\nconst CONDITION = \"condition\"\nconst DATE = \"date\"\nconst DNA_METHYLATION = \"dnaMethylation\"\nconst FLOAT = \"float\"\nconst GENE_VARIANT = \"geneVariant\"\nconst GENE_EXPRESSION = \"geneExpression\"\nconst ISOFORM_EXPRESSION = \"isoformExpression\"\nconst INTEGER = \"integer\"\nconst METABOLITE_INTENSITY = \"metaboliteIntensity\"\nconst MULTIVALUE = \"multivalue\"\nconst SAMPLELST = \"samplelst\"\nconst SINGLECELL_CELLTYPE = \"singleCellCellType\"\nconst SINGLECELL_GENE_EXPRESSION = \"singleCellGeneExpression\"\nconst SNP = \"snp\"\nconst SNP_LIST = \"snplst\"\nconst SNP_LOCUS = \"snplocus\"\nconst SSGSEA = \"ssGSEA\"\nconst SURVIVAL = \"survival\"\nconst TERM_COLLECTION = \"termCollection\"\nconst PROTEOME_ABUNDANCE = \"proteomeAbundance\"\nconst TermTypes = {\n\tGENE_VARIANT,\n\tGENE_EXPRESSION,\n\tISOFORM_EXPRESSION,\n\tSSGSEA,\n\tDNA_METHYLATION,\n\tCATEGORICAL,\n\tINTEGER,\n\tFLOAT,\n\tSNP,\n\tSNP_LIST,\n\tSNP_LOCUS,\n\tCONDITION,\n\tSURVIVAL,\n\tSAMPLELST,\n\tMETABOLITE_INTENSITY,\n\tPROTEOME_ABUNDANCE,\n\tSINGLECELL_CELLTYPE,\n\tSINGLECELL_GENE_EXPRESSION,\n\tMULTIVALUE,\n\tDATE,\n\tTERM_COLLECTION,\n}\nconst dtTermTypes = new Set(dtTerms.map((t) => t.type))\nfor (const dtTermType of dtTermTypes) {\n\tTermTypes[dtTermType.toUpperCase()] = dtTermType\n}\nconst TermTypes2Dt = {\n\t[GENE_EXPRESSION]: dtgeneexpression,\n\t[SSGSEA]: dtssgsea,\n\t[DNA_METHYLATION]: dtdnamethylation,\n\t[METABOLITE_INTENSITY]: dtmetaboliteintensity,\n\t[PROTEOME_ABUNDANCE]: dtproteomeabundance,\n}\nconst typeGroup = {\n\t[CATEGORICAL]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[CONDITION]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[FLOAT]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[INTEGER]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[SAMPLELST]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[SURVIVAL]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[DATE]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[MULTIVALUE]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[GENE_VARIANT]: TermTypeGroups.MUTATION_CNV_FUSION,\n\t[SNP]: TermTypeGroups.SNP,\n\t[SNP_LIST]: TermTypeGroups.SNP_LIST,\n\t[SNP_LOCUS]: TermTypeGroups.SNP_LOCUS,\n\t[GENE_EXPRESSION]: TermTypeGroups.GENE_EXPRESSION,\n\t[ISOFORM_EXPRESSION]: TermTypeGroups.ISOFORM_EXPRESSION,\n\t[SSGSEA]: TermTypeGroups.SSGSEA,\n\t[DNA_METHYLATION]: TermTypeGroups.DNA_METHYLATION,\n\t[METABOLITE_INTENSITY]: TermTypeGroups.METABOLITE_INTENSITY,\n\t[PROTEOME_ABUNDANCE]: TermTypeGroups.PROTEOME_ABUNDANCE,\n\t[TERM_COLLECTION]: TermTypeGroups.TERM_COLLECTION,\n\t[SINGLECELL_CELLTYPE]: TermTypeGroups.SINGLECELL_CELLTYPE,\n\t[SINGLECELL_GENE_EXPRESSION]: TermTypeGroups.SINGLECELL_GENE_EXPRESSION,\n}\nconst nonDictTypes = /* @__PURE__ */ new Set([\n\tSNP,\n\tSNP_LIST,\n\tSNP_LOCUS,\n\tGENE_EXPRESSION,\n\tISOFORM_EXPRESSION,\n\tSSGSEA,\n\tDNA_METHYLATION,\n\tGENE_VARIANT,\n\tMETABOLITE_INTENSITY,\n\tPROTEOME_ABUNDANCE,\n\tSINGLECELL_CELLTYPE,\n\tSINGLECELL_GENE_EXPRESSION,\n])\nfor (const dtTermType of dtTermTypes) {\n\tnonDictTypes.add(TermTypes[dtTermType.toUpperCase()])\n}\nconst numericTypes = /* @__PURE__ */ new Set([\n\tINTEGER,\n\tFLOAT,\n\tGENE_EXPRESSION,\n\tISOFORM_EXPRESSION,\n\tSSGSEA,\n\tDNA_METHYLATION,\n\tMETABOLITE_INTENSITY,\n\tPROTEOME_ABUNDANCE,\n\tSINGLECELL_GENE_EXPRESSION,\n\tDATE,\n])\nconst annoNumericTypes = /* @__PURE__ */ new Set([INTEGER, FLOAT, DATE])\nconst categoricalTypes = /* @__PURE__ */ new Set([CATEGORICAL, SNP])\nconst singleCellTerms = /* @__PURE__ */ new Set([\n\tSINGLECELL_CELLTYPE,\n\tSINGLECELL_GENE_EXPRESSION,\n])\nfunction isSingleCellTerm(term) {\n\tif (!term) return false\n\treturn singleCellTerms.has(term.type)\n}\nfunction isNumericTerm(term) {\n\tif (!term) return false\n\treturn numericTypes.has(term.type)\n}\nfunction isCategoricalTerm(term) {\n\tif (!term) return false\n\treturn categoricalTypes.has(term.type)\n}\nfunction isDictionaryType(type) {\n\treturn !isNonDictionaryType(type)\n}\nfunction isNonDictionaryType(type) {\n\tif (!type) throw new Error(\"Type is not defined\")\n\treturn nonDictTypes.has(type)\n}\nfunction isNumTermCollection(term) {\n\tif (!term || !term.type) throw new Error(\"Term or term type is not defined\")\n\treturn term.type === TERM_COLLECTION\n}\nfunction equals(t1, t2) {\n\tif (!t1) throw new Error(\"First term is not defined \")\n\tif (!t2) throw new Error(\"Second term is not defined \")\n\tif (t1.type !== t2.type) return false\n\tif (\n\t\tisDictionaryType(t1.type) &&\n\t\tisDictionaryType(t2.type) &&\n\t\tt1.type != SAMPLELST\n\t)\n\t\treturn t1.id === t2.id\n\tswitch (t1.type) {\n\t\tcase GENE_EXPRESSION:\n\t\t\treturn t1.gene == t2.gene\n\t\tcase ISOFORM_EXPRESSION:\n\t\t\treturn t1.isoform == t2.isoform\n\t\tcase SSGSEA:\n\t\t\treturn t1.id == t2.id\n\t\tcase DNA_METHYLATION:\n\t\t\treturn t1.chr == t2.chr && t1.start == t2.start && t1.stop == t2.stop\n\t\tcase METABOLITE_INTENSITY:\n\t\tcase PROTEOME_ABUNDANCE:\n\t\t\treturn t1.name == t2.name\n\t\tcase GENE_VARIANT:\n\t\t\treturn (\n\t\t\t\tt1.gene == t2.gene ||\n\t\t\t\t(t1.chr == t2.chr && t1.start == t2.start && t1.stop == t2.stop)\n\t\t\t)\n\t\t// TO DO: Add more cases\n\t\t// case SNP_LIST:\n\t\t// case SNP_LOCUS:\n\t\t// case SAMPLELST:\n\t\tdefault:\n\t\t\treturn false\n\t}\n}\nfunction getBin(lst, value) {\n\tlet bin = lst.findIndex(\n\t\t(b) =>\n\t\t\t(b.startunbounded && value < b.stop) ||\n\t\t\t(b.startunbounded && b.stopinclusive && value == b.stop)\n\t)\n\tif (bin == -1)\n\t\tbin = lst.findIndex(\n\t\t\t(b) =>\n\t\t\t\t(b.stopunbounded && value > b.start) ||\n\t\t\t\t(b.stopunbounded && b.startinclusive && value == b.start)\n\t\t)\n\tif (bin == -1)\n\t\tbin = lst.findIndex(\n\t\t\t(b) =>\n\t\t\t\t(value > b.start && value < b.stop) ||\n\t\t\t\t(b.startinclusive && value == b.start) ||\n\t\t\t\t(b.stopinclusive && value == b.stop)\n\t\t)\n\treturn bin\n}\nfunction getSampleType(term, ds) {\n\tif (!term) return null\n\tif (term.type && isNonDictionaryType(term.type)) return DEFAULT_SAMPLE_TYPE\n\tif (term.id) return ds.cohort.termdb.term2SampleType.get(term.id)\n\tif (term.type == \"samplelst\") {\n\t\tconst key = Object.keys(term.values)[0]\n\t\tconst sampleId = term.values[key].list[0]?.sampleId\n\t\tif (sampleId) return ds.sampleId2Type.get(Number(sampleId) || sampleId)\n\t\telse return DEFAULT_SAMPLE_TYPE\n\t}\n\treturn DEFAULT_SAMPLE_TYPE\n}\nfunction getParentType(types, ds) {\n\tif (Object.keys(ds.cohort.termdb.sampleTypes).length == 0) return null\n\tconst ids = Array.from(types)\n\tif (!ids || ids.length == 0) return null\n\tfor (const id of ids) {\n\t\tconst typeObj = ds.cohort.termdb.sampleTypes[id]\n\t\tif (!typeObj) continue\n\t\tif (typeObj.parent_id == null) return id\n\t\tif (ids.includes(typeObj.parent_id)) continue\n\t\telse return typeObj.parent_id\n\t}\n\treturn null\n}\nconst typeMap = {\n\tcategorical: \"Categorical\",\n\tcondition: \"Condition\",\n\tfloat: \"Numerical\",\n\tinteger: \"Numerical\",\n\tgeneExpression: \"Gene Expression\",\n\tisoformExpression: \"Isoform Expression\",\n\tssGSEA: \"Geneset Expression\",\n\tdnaMethylation: \"DNA Methylation\",\n\tgeneVariant: \"Gene Variant\",\n\tmetaboliteIntensity: \"Metabolite Intensity\",\n\tproteomeAbundance: \"Proteome Abundance\",\n\tmultivalue: \"Multi Value\",\n\tsingleCellGeneExpression: \"Single Cell, Gene Expression\",\n\tsingleCellCellType: \"Single Cell, Cell Type\",\n\tsnplocus: \"SNP Locus\",\n\tsnp: \"SNP\",\n\tsnplst: \"SNP List\",\n\ttermCollection: \"Term Collection\",\n}\nfunction termType2label(type) {\n\treturn typeMap[type] || \"Unknown term type\"\n}\nfunction getDateFromNumber(value) {\n\tconst year = Math.floor(value)\n\tconst january1st = new Date(year, 0, 1)\n\tconst totalDays = getDaysInYear(year)\n\tconst time = Math.round((value - year) * totalDays) * oneDayTime\n\tconst date = new Date(january1st.getTime() + time)\n\treturn date\n}\nconst oneDayTime = 24 * 60 * 60 * 1e3\nfunction getDateStrFromNumber(value) {\n\tconst date = getDateFromNumber(value)\n\treturn date.toLocaleDateString(\"en-US\", {\n\t\tyear: \"numeric\",\n\t\tmonth: \"long\",\n\t})\n}\nfunction getNumberFromDateStr(str) {\n\tconst date = new Date(str)\n\treturn getNumberFromDate(date)\n}\nfunction getNumberFromDate(date) {\n\tconst year = date.getFullYear()\n\tconst january1st = new Date(year, 0, 1)\n\tconst diffDays = (date.getTime() - january1st.getTime()) / oneDayTime\n\tconst daysTotal = getDaysInYear(year)\n\tconst decimal = diffDays / daysTotal\n\treturn year + decimal\n}\nfunction getDaysInYear(year) {\n\tconst isLeap = new Date(year, 1, 29).getMonth() === 1\n\tconst days = isLeap ? 366 : 365\n\treturn days\n}\nexport {\n\tCATEGORICAL,\n\tCONDITION,\n\tDATE,\n\tDEFAULT_SAMPLE_TYPE,\n\tDNA_METHYLATION,\n\tFLOAT,\n\tGENE_EXPRESSION,\n\tGENE_VARIANT,\n\tINTEGER,\n\tISOFORM_EXPRESSION,\n\tMETABOLITE_INTENSITY,\n\tMULTIVALUE,\n\tNumericModes,\n\tPROTEOME_ABUNDANCE,\n\tROOT_SAMPLE_TYPE,\n\tSAMPLELST,\n\tSINGLECELL_CELLTYPE,\n\tSINGLECELL_GENE_EXPRESSION,\n\tSNP,\n\tSNP_LIST,\n\tSNP_LOCUS,\n\tSSGSEA,\n\tSURVIVAL,\n\tTERM_COLLECTION,\n\tTermTypeGroups2 as TermTypeGroups,\n\tTermTypes,\n\tTermTypes2Dt,\n\tannoNumericTypes,\n\tdtTermTypes,\n\tequals,\n\tgetBin,\n\tgetDateFromNumber,\n\tgetDateStrFromNumber,\n\tgetDaysInYear,\n\tgetNumberFromDate,\n\tgetNumberFromDateStr,\n\tgetParentType,\n\tgetSampleType,\n\tisCategoricalTerm,\n\tisDictionaryType,\n\tisNonDictionaryType,\n\tisNumTermCollection,\n\tisNumericTerm,\n\tisSingleCellTerm,\n\tnumericTypes,\n\ttermType2label,\n\ttypeGroup,\n}\n"],
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-  "names": []
-}

package/dist/chunk-77ZJGPK2.js

@@ -1,289 +0,0 @@
-import {
-  getSortOptions
-} from "./chunk-5UMPBVA6.js";
-import {
-  defaultUiLabels,
-  fillTermWrapper
-} from "./chunk-OXJ2TWDO.js";
-import {
-  copyMerge
-} from "./chunk-MVTCBVSX.js";
-import {
-  isDictionaryType
-} from "./chunk-6ITDJ5UR.js";
-import {
-  CNVClasses,
-  dtcnv,
-  mclass,
-  mutationClasses,
-  proteinChangingMutations,
-  synonymousMutations,
-  truncatingMutations
-} from "./chunk-XYFDBYOY.js";
-
-// plots/matrix/matrix.config.js
-async function getPlotConfig(opts = {}, app) {
-  const controlLabels = structuredClone(defaultUiLabels);
-  const devicePixelRatio = opts.devicePixelRatio || window.devicePixelRatio;
-  const config = {
-    // data configuration
-    termgroups: [],
-    samplegroups: [],
-    divideBy: null,
-    legendValueFilter: {
-      isAtomic: true,
-      type: "tvslst",
-      in: true,
-      join: "and",
-      lst: []
-    },
-    legendGrpFilter: {
-      isAtomic: true,
-      type: "tvslst",
-      in: true,
-      join: "and",
-      lst: []
-    },
-    filter: {
-      isAtomic: true,
-      type: "tvslst",
-      in: true,
-      join: "and",
-      lst: []
-    },
-    // cnvCutoffs: {},
-    // rendering options
-    settings: {
-      matrix: {
-        svgCanvasSwitch: 1e3,
-        // the number of samples to trigger switching between svg and canvas
-        useMinPixelWidth: true,
-        // canvas may be hazy if false, but more accurately reflects column density
-        cellEncoding: "",
-        // can be "oncoprint" | "stacked" | "single"
-        margin: {
-          top: 10,
-          right: 5,
-          bottom: 20,
-          left: 50
-        },
-        // set any dataset-defined sample limits and sort priority, otherwise undefined
-        // put in settings, so that later may be overridden by a user
-        maxGenes: opts.settings?.maxGenes || 50,
-        maxSample: opts.settings?.maxSample || 1e3,
-        sampleNameFilter: "",
-        sortSamplesBy: "a",
-        sortPriority: void 0,
-        // will be filled-in
-        // sortByMutation: 'consequence', computed
-        // sortByCNV: true, computed
-        //sortOptions: getSortOptions(app.vocabApi.termdbConfig, controlLabels),
-        sortSampleGrpsBy: "name",
-        // 'hits' | 'name' | 'sampleCount'
-        sortSamplesTieBreakers: [{
-          $id: "sample",
-          sortSamples: {}
-          /*split: {char: '', index: 0}*/
-        }],
-        sortTermsBy: "sampleCount",
-        // or 'as listed'
-        // do not show number of samples at hiercluster gene row labels
-        samplecount4gene: opts.chartType == "hierCluster" ? "" : "abs",
-        //true, // 'abs' (default, previously true), 'pct', ''  (previously false)
-        geneVariantCountSamplesSkipMclass: [],
-        cellbg: "#ececec",
-        showGrid: "",
-        // false | 'pattern' | 'rect'
-        // whether to show these controls buttons
-        addMutationCNVButtons: false,
-        truncatingMutations,
-        proteinChangingMutations,
-        synonymousMutations,
-        mutationClasses,
-        CNVClasses,
-        gridStroke: "#fff",
-        outlineStroke: "#ccc",
-        beamStroke: "#f00",
-        colw: 0,
-        colwMin: 0.1 / devicePixelRatio,
-        colwMax: 16,
-        colspace: 1,
-        colgspace: 8,
-        colglabelpos: true,
-        collabelpos: "bottom",
-        collabelvisible: true,
-        collabelgap: 5,
-        collabelpad: 1,
-        collabelmaxchars: 32,
-        rowh: 18,
-        //use 0 to auto-compute row height, previous default=18,
-        rowhMin: 1,
-        rowhMax: 20,
-        rowspace: 1,
-        rowgspace: 8,
-        rowlabelpos: "left",
-        // | 'right'
-        rowlabelgap: 5,
-        rowlabelvisible: true,
-        rowlabelpad: 1,
-        rowlabelmaxchars: 32,
-        legendGrpLabelMaxChars: 26,
-        grpLabelFontSize: 12,
-        minLabelFontSize: 6,
-        maxLabelFontSize: 14,
-        transpose: false,
-        sampleLabelsToggle: opts.chartType === "hierCluster" ? "hide" : "auto",
-        // 'auto' | 'hide'
-        sampleLabelOffset: 120,
-        sampleGrpLabelOffset: 120,
-        sampleGrpLabelMaxChars: 32,
-        termLabelOffset: 80,
-        termGrpLabelOffset: 80,
-        termGrpLabelMaxChars: 32,
-        duration: 0,
-        zoomLevel: 1,
-        zoomCenterPct: 0,
-        zoomIndex: 0,
-        zoomGrpIndex: 0,
-        zoomMin: 0.5,
-        zoomIncrement: 0.1,
-        zoomStep: 1,
-        // renderedWMax should not be exposed as a user-input
-        // 60000 pixels is based on laptop and external monitor tests,
-        // when a canvas dataURL image in a zoomed-in matrix svg stops rendering
-        imgWMax: 6e4 / devicePixelRatio,
-        scrollHeight: 12,
-        controlLabels,
-        cnvUnit: "log2ratio",
-        ignoreCnvValues: false,
-        //will ignore numeric CNV values if true
-        barh: 32,
-        // default bar height for continuous terms,
-        // possible string entries:
-        // - "genesetEdit", for gene-centric embedders only like GDC OncoMatrix
-        // - may add other optional hints later
-        showHints: [],
-        // settings for a specific tw
-        twSpecificSettings: {},
-        oncoPrintSNVindelCellBorder: false,
-        // whether to show white cell border for SNVindel in oncoPrint mode
-        cnvValues: {
-          //Properties match the args for the ColorScales
-          //numericInput arg
-          cutoffMode: "percentile",
-          defaultPercentile: 99,
-          min: null,
-          max: null,
-          percentile: 99
-        }
-      }
-    }
-  };
-  const s = config.settings;
-  const fontsize = Math.max(s.matrix.rowh + s.matrix.rowspace - 3 * s.matrix.rowlabelpad, 12);
-  s.legend = {
-    ontop: false,
-    lineh: 25,
-    padx: 5,
-    padleft: 0,
-    //150,
-    padright: 20,
-    padbtm: 30,
-    fontsize,
-    iconh: fontsize - 2,
-    iconw: fontsize - 2,
-    hangleft: 1,
-    linesep: false
-  };
-  const overrides = app.vocabApi.termdbConfig.matrix || {};
-  copyMerge(config.settings.matrix, overrides.settings);
-  if (overrides.legendGrpFilter) config.legendGrpFilter = overrides.legendGrpFilter;
-  if (overrides.legendValueFilter) config.legendValueFilter = overrides.legendValueFilter;
-  if (overrides.filter) config.filter = overrides.filter;
-  if (opts.name) {
-    const data = await app.vocabApi.getMatrixByName(opts.name);
-    if (!data) throw "error from getMatrixByName()";
-    if (data.error) throw data.error;
-    copyMerge(config, data);
-  }
-  const os = opts?.settings?.matrix;
-  if (os) {
-    if ((os.sortSamplesBy == "custom" || os.sortSamplesBy == "asListed") && os.sortOptions?.custom.label == "against alteration type") {
-      os.sortSamplesBy = "a";
-    }
-    if (os.sortOptions) {
-      delete os.sortOptions.custom;
-      delete os.sortOptions.asListed;
-    }
-  }
-  copyMerge(config, opts);
-  const m = config.settings.matrix;
-  m.sortOptions = getSortOptions(app.vocabApi.termdbConfig, controlLabels, m);
-  m.duration = 0;
-  m.colw = 0;
-  if (m.sortSamplesBy != "asListed" && !m.sortOptions?.[m.sortSamplesBy]) m.sortSamplesBy = "a";
-  else if (["selectedTerms", "class", "dt", "hits"].includes(m.sortSamplesBy)) m.sortSamplesBy = "a";
-  if (m.samplecount4gene === true || m.samplecount4gene === 1) m.samplecount4gene = "abs";
-  if (window.location.hostname == "localhost") {
-    if (window.location.hash == "#canvas") m.svgCanvasSwitch = 0;
-  }
-  for (const grp of config.termgroups) {
-    const promises = [];
-    for (const tw of grp.lst) {
-      if (!tw.term?.type || isDictionaryType(tw.term.type)) {
-        if (!tw.id && tw.term.type != "samplelst" && tw.term.type != "termCollection") {
-          if (!tw.term.id) throw `missing tw.id and tw.term.id`;
-          tw.id = tw.term.id;
-        }
-        if (tw.term?.type != "samplelst" && tw.term?.type != "termCollection") delete tw.term;
-      }
-      promises.push(fillTermWrapper(tw, app.vocabApi));
-    }
-    grp.lst = await Promise.all(promises);
-  }
-  if (config.divideBy) config.divideBy = await fillTermWrapper(config.divideBy, app.vocabApi);
-  return config;
-}
-function setComputedConfig(config) {
-  const s = config.settings.matrix;
-  const allClasses = [...s.mutationClasses, ...s.CNVClasses];
-  s.filterByClass = { isAtomic: true };
-  for (const f of config.legendGrpFilter.lst) {
-    if (!f.dt) continue;
-    allClasses.filter((m) => f.dt.includes(mclass[m].dt)).forEach((key2) => {
-      s.filterByClass[key2] = "value";
-    });
-  }
-  for (const f of config.legendValueFilter.lst) {
-    if (!f.legendGrpName || f.tvs?.term?.type !== "geneVariant") continue;
-    if (f.tvs.values?.[0].mclasslst)
-      f.tvs.values[0].mclasslst.forEach((key2) => {
-        s.filterByClass[key2] = f.legendFilterType?.endsWith("_hard") ? "case" : "value";
-      });
-    else if (f.tvs.values)
-      f.tvs.values.forEach((v) => {
-        s.filterByClass[key] = "value";
-      });
-    else throw `unhandled tvs from legendValueFilter`;
-  }
-  s.hiddenVariants = Object.keys(s.filterByClass).filter((c) => c !== "isAtomic");
-  const hiddenCNVs = new Set(s.hiddenVariants.filter((key2) => mclass[key2]?.dt === dtcnv));
-  s.hiddenCNVs = [...hiddenCNVs];
-  s.showMatrixCNV = !hiddenCNVs.size ? "all" : hiddenCNVs.size == s.CNVClasses.length ? "none" : "bySelection";
-  s.allMatrixCNVHidden = hiddenCNVs.size == s.CNVClasses.length;
-  const hiddenMutations = new Set(s.hiddenVariants.filter((key2) => s.mutationClasses.find((k) => k === key2)));
-  s.hiddenMutations = [...hiddenMutations];
-  const PCset = new Set(s.proteinChangingMutations);
-  const TMset = new Set(s.truncatingMutations);
-  s.showMatrixMutation = !hiddenMutations.size ? "all" : hiddenMutations.size == s.mutationClasses.length ? "none" : hiddenMutations.size === s.mutationClasses.length - PCset.size && [...hiddenMutations].every((m) => !PCset.has(m)) ? "onlyPC" : hiddenMutations.size === s.mutationClasses.length - TMset.size && [...hiddenMutations].every((m) => !TMset.has(m)) ? "onlyTruncating" : "bySelection";
-  s.allMatrixMutationHidden = hiddenMutations.size == s.mutationClasses.length;
-  const tiebreakers = s.sortOptions.a?.sortPriority.find((sp) => sp.types.length == 1 && sp.types[0] == "geneVariant")?.tiebreakers || [];
-  s.sortByMutation = tiebreakers.find((tb) => tb.filter?.values[0]?.dt === 1)?.isOrdered ? "consequence" : "presence";
-  s.sortByCNV = tiebreakers.find((tb) => tb.filter?.values[0]?.dt === 4)?.disabled !== true;
-}
-
-export {
-  getPlotConfig,
-  setComputedConfig
-};
-//# sourceMappingURL=chunk-77ZJGPK2.js.map