@sjcrh/proteinpaint-client 2.193.0 → 2.195.0

package/dist/chunk-5TJQ6633.js

@@ -1,291 +0,0 @@
-import {
-  getSortOptions
-} from "./chunk-CDUNE45Q.js";
-import {
-  defaultUiLabels,
-  fillTermWrapper
-} from "./chunk-L7VDSIM7.js";
-import {
-  copyMerge
-} from "./chunk-M3J4MINX.js";
-import {
-  isDictionaryType
-} from "./chunk-IVXCWCKS.js";
-import {
-  CNVClasses,
-  dtcnv,
-  mclass,
-  mutationClasses,
-  proteinChangingMutations,
-  synonymousMutations,
-  truncatingMutations
-} from "./chunk-7KRS7L4U.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: [],
-        genesetEditUiVersion: "",
-        // '' | 'withTabs'
-        // 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-5TJQ6633.js.map

package/dist/chunk-5TJQ6633.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/matrix/matrix.config.js"],
-  "sourcesContent": ["import { copyMerge } from '#rx'\nimport { getSortOptions } from './matrix.sort'\nimport { fillTermWrapper } from '#termsetting'\nimport {\n\tmclass,\n\tdtcnv,\n\tproteinChangingMutations,\n\ttruncatingMutations,\n\tsynonymousMutations,\n\tmutationClasses,\n\tCNVClasses\n} from '#shared/common.js'\nimport { isDictionaryType } from '#shared/terms.js'\nimport { defaultUiLabels } from '#plots/PlotBase.js'\n\nexport async function getPlotConfig(opts = {}, app) {\n\tconst controlLabels = structuredClone(defaultUiLabels)\n\tconst devicePixelRatio = opts.devicePixelRatio || window.devicePixelRatio\n\tconst config = {\n\t\t// data configuration\n\t\ttermgroups: [],\n\t\tsamplegroups: [],\n\t\tdivideBy: null,\n\t\tlegendValueFilter: {\n\t\t\tisAtomic: true,\n\t\t\ttype: 'tvslst',\n\t\t\tin: true,\n\t\t\tjoin: 'and',\n\t\t\tlst: []\n\t\t},\n\t\tlegendGrpFilter: {\n\t\t\tisAtomic: true,\n\t\t\ttype: 'tvslst',\n\t\t\tin: true,\n\t\t\tjoin: 'and',\n\t\t\tlst: []\n\t\t},\n\t\tfilter: {\n\t\t\tisAtomic: true,\n\t\t\ttype: 'tvslst',\n\t\t\tin: true,\n\t\t\tjoin: 'and',\n\t\t\tlst: []\n\t\t},\n\t\t// cnvCutoffs: {},\n\n\t\t// rendering options\n\t\tsettings: {\n\t\t\tmatrix: {\n\t\t\t\tsvgCanvasSwitch: 1000, // the number of samples to trigger switching between svg and canvas\n\t\t\t\tuseMinPixelWidth: true, // canvas may be hazy if false, but more accurately reflects column density\n\t\t\t\tcellEncoding: '', // can be \"oncoprint\" | \"stacked\" | \"single\"\n\t\t\t\tmargin: {\n\t\t\t\t\ttop: 10,\n\t\t\t\t\tright: 5,\n\t\t\t\t\tbottom: 20,\n\t\t\t\t\tleft: 50\n\t\t\t\t},\n\t\t\t\t// set any dataset-defined sample limits and sort priority, otherwise undefined\n\t\t\t\t// put in settings, so that later may be overridden by a user\n\t\t\t\tmaxGenes: opts.settings?.maxGenes || 50,\n\t\t\t\tmaxSample: opts.settings?.maxSample || 1000,\n\n\t\t\t\tsampleNameFilter: '',\n\t\t\t\tsortSamplesBy: 'a',\n\t\t\t\tsortPriority: undefined, // will be filled-in\n\t\t\t\t// sortByMutation: 'consequence', computed\n\t\t\t\t// sortByCNV: true, computed\n\t\t\t\t//sortOptions: getSortOptions(app.vocabApi.termdbConfig, controlLabels),\n\t\t\t\tsortSampleGrpsBy: 'name', // 'hits' | 'name' | 'sampleCount'\n\t\t\t\tsortSamplesTieBreakers: [{ $id: 'sample', sortSamples: {} /*split: {char: '', index: 0}*/ }],\n\t\t\t\tsortTermsBy: 'sampleCount', // or 'as listed'\n\t\t\t\t// do not show number of samples at hiercluster gene row labels\n\t\t\t\tsamplecount4gene: opts.chartType == 'hierCluster' ? '' : 'abs', //true, // 'abs' (default, previously true), 'pct', ''  (previously false)\n\t\t\t\tgeneVariantCountSamplesSkipMclass: [],\n\t\t\t\tcellbg: '#ececec',\n\t\t\t\tshowGrid: '', // false | 'pattern' | 'rect'\n\t\t\t\t// whether to show these controls buttons\n\t\t\t\taddMutationCNVButtons: false,\n\t\t\t\ttruncatingMutations,\n\t\t\t\tproteinChangingMutations,\n\t\t\t\tsynonymousMutations,\n\t\t\t\tmutationClasses,\n\t\t\t\tCNVClasses,\n\t\t\t\tgridStroke: '#fff',\n\t\t\t\toutlineStroke: '#ccc',\n\t\t\t\tbeamStroke: '#f00',\n\t\t\t\tcolw: 0,\n\t\t\t\tcolwMin: 0.1 / devicePixelRatio,\n\t\t\t\tcolwMax: 16,\n\t\t\t\tcolspace: 1,\n\t\t\t\tcolgspace: 8,\n\t\t\t\tcolglabelpos: true,\n\t\t\t\tcollabelpos: 'bottom',\n\t\t\t\tcollabelvisible: true,\n\t\t\t\tcollabelgap: 5,\n\t\t\t\tcollabelpad: 1,\n\t\t\t\tcollabelmaxchars: 32,\n\t\t\t\trowh: 18, //use 0 to auto-compute row height, previous default=18,\n\t\t\t\trowhMin: 1,\n\t\t\t\trowhMax: 20,\n\t\t\t\trowspace: 1,\n\t\t\t\trowgspace: 8,\n\t\t\t\trowlabelpos: 'left', // | 'right'\n\t\t\t\trowlabelgap: 5,\n\t\t\t\trowlabelvisible: true,\n\t\t\t\trowlabelpad: 1,\n\t\t\t\trowlabelmaxchars: 32,\n\t\t\t\tlegendGrpLabelMaxChars: 26,\n\t\t\t\tgrpLabelFontSize: 12,\n\t\t\t\tminLabelFontSize: 6,\n\t\t\t\tmaxLabelFontSize: 14,\n\t\t\t\ttranspose: false,\n\t\t\t\tsampleLabelsToggle: opts.chartType === 'hierCluster' ? 'hide' : 'auto', // 'auto' | 'hide'\n\t\t\t\tsampleLabelOffset: 120,\n\t\t\t\tsampleGrpLabelOffset: 120,\n\t\t\t\tsampleGrpLabelMaxChars: 32,\n\t\t\t\ttermLabelOffset: 80,\n\t\t\t\ttermGrpLabelOffset: 80,\n\t\t\t\ttermGrpLabelMaxChars: 32,\n\t\t\t\tduration: 0,\n\t\t\t\tzoomLevel: 1,\n\t\t\t\tzoomCenterPct: 0,\n\t\t\t\tzoomIndex: 0,\n\t\t\t\tzoomGrpIndex: 0,\n\t\t\t\tzoomMin: 0.5,\n\t\t\t\tzoomIncrement: 0.1,\n\t\t\t\tzoomStep: 1,\n\t\t\t\t// renderedWMax should not be exposed as a user-input\n\t\t\t\t// 60000 pixels is based on laptop and external monitor tests,\n\t\t\t\t// when a canvas dataURL image in a zoomed-in matrix svg stops rendering\n\t\t\t\timgWMax: 60000 / devicePixelRatio,\n\t\t\t\tscrollHeight: 12,\n\t\t\t\tcontrolLabels,\n\t\t\t\tcnvUnit: 'log2ratio',\n\t\t\t\tignoreCnvValues: false, //will ignore numeric CNV values if true\n\n\t\t\t\tbarh: 32, // default bar height for continuous terms,\n\n\t\t\t\t// possible string entries:\n\t\t\t\t// - \"genesetEdit\", for gene-centric embedders only like GDC OncoMatrix\n\t\t\t\t// - may add other optional hints later\n\t\t\t\tshowHints: [],\n\t\t\t\tgenesetEditUiVersion: '', // '' | 'withTabs'\n\t\t\t\t// settings for a specific tw\n\t\t\t\ttwSpecificSettings: {},\n\t\t\t\toncoPrintSNVindelCellBorder: false, // whether to show white cell border for SNVindel in oncoPrint mode\n\t\t\t\tcnvValues: {\n\t\t\t\t\t//Properties match the args for the ColorScales\n\t\t\t\t\t//numericInput arg\n\t\t\t\t\tcutoffMode: 'percentile',\n\t\t\t\t\tdefaultPercentile: 99,\n\t\t\t\t\tmin: null,\n\t\t\t\t\tmax: null,\n\t\t\t\t\tpercentile: 99\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\tconst s = config.settings\n\tconst fontsize = Math.max(s.matrix.rowh + s.matrix.rowspace - 3 * s.matrix.rowlabelpad, 12)\n\n\ts.legend = {\n\t\tontop: false,\n\t\tlineh: 25,\n\t\tpadx: 5,\n\t\tpadleft: 0, //150,\n\t\tpadright: 20,\n\t\tpadbtm: 30,\n\t\tfontsize,\n\t\ticonh: fontsize - 2,\n\t\ticonw: fontsize - 2,\n\t\thangleft: 1,\n\t\tlinesep: false\n\t}\n\n\tconst overrides = app.vocabApi.termdbConfig.matrix || {}\n\tcopyMerge(config.settings.matrix, overrides.settings)\n\tif (overrides.legendGrpFilter) config.legendGrpFilter = overrides.legendGrpFilter\n\tif (overrides.legendValueFilter) config.legendValueFilter = overrides.legendValueFilter\n\tif (overrides.filter) config.filter = overrides.filter\n\n\tif (opts.name) {\n\t\t// name should be identifier of a premade plot from the datase; load data of the premade plot and override into config{}\n\t\tconst data = await app.vocabApi.getMatrixByName(opts.name)\n\t\tif (!data) throw 'error from getMatrixByName()'\n\t\tif (data.error) throw data.error\n\t\tcopyMerge(config, data)\n\t}\n\n\tconst os = opts?.settings?.matrix\n\tif (os) {\n\t\tif (\n\t\t\t(os.sortSamplesBy == 'custom' || os.sortSamplesBy == 'asListed') &&\n\t\t\tos.sortOptions?.custom.label == 'against alteration type'\n\t\t) {\n\t\t\tos.sortSamplesBy = 'a'\n\t\t}\n\t\tif (os.sortOptions) {\n\t\t\tdelete os.sortOptions.custom\n\t\t\tdelete os.sortOptions.asListed\n\t\t}\n\t}\n\n\t// may apply term-specific changes to the default object\n\tcopyMerge(config, opts)\n\tconst m = config.settings.matrix\n\tm.sortOptions = getSortOptions(app.vocabApi.termdbConfig, controlLabels, m)\n\t// harcode these overrides for now\n\tm.duration = 0\n\t// force auto-dimensions for colw\n\tm.colw = 0\n\t// support deprecated sortSamplesBy value from a saved session\n\tif (m.sortSamplesBy != 'asListed' && !m.sortOptions?.[m.sortSamplesBy]) m.sortSamplesBy = 'a'\n\telse if (['selectedTerms', 'class', 'dt', 'hits'].includes(m.sortSamplesBy)) m.sortSamplesBy = 'a'\n\tif (m.samplecount4gene === true || m.samplecount4gene === 1) m.samplecount4gene = 'abs'\n\t// support overrides in localhost\n\tif (window.location.hostname == 'localhost') {\n\t\tif (window.location.hash == '#canvas') m.svgCanvasSwitch = 0\n\t}\n\n\tfor (const grp of config.termgroups) {\n\t\tconst promises = []\n\t\t//grp.lst = JSON.parse(JSON.stringify(grp.lst))\n\t\tfor (const tw of grp.lst) {\n\t\t\t// may force the saved session to request the most up-to-data dictionary term data from server\n\t\t\t// TODO: should skip samplelst term here\n\t\t\tif (!tw.term?.type || isDictionaryType(tw.term.type)) {\n\t\t\t\tif (!tw.id && tw.term.type != 'samplelst' && tw.term.type != 'termCollection') {\n\t\t\t\t\tif (!tw.term.id) throw `missing tw.id and tw.term.id`\n\t\t\t\t\ttw.id = tw.term.id // tw.id will be used to rehydrate tw with new term data from server. tw.id will be deleted following rehydration.\n\t\t\t\t}\n\t\t\t\tif (tw.term?.type != 'samplelst' && tw.term?.type != 'termCollection') delete tw.term\n\t\t\t}\n\t\t\t/** If tw fails at this step, consider using structuredClone(tw) in\n\t\t\t * the config for app.dispatch() to make the tw mutable. Should\n\t\t\t * not fail from runpp(), only app.dispatch(). */\n\t\t\tpromises.push(fillTermWrapper(tw, app.vocabApi))\n\t\t}\n\t\tgrp.lst = await Promise.all(promises)\n\t}\n\tif (config.divideBy) config.divideBy = await fillTermWrapper(config.divideBy, app.vocabApi)\n\treturn config\n}\n\n// config: a hydrated matrix config object\nexport function setComputedConfig(config) {\n\tconst s = config.settings.matrix\n\tconst allClasses = [...s.mutationClasses, ...s.CNVClasses]\n\n\ts.filterByClass = { isAtomic: true }\n\tfor (const f of config.legendGrpFilter.lst) {\n\t\tif (!f.dt) continue\n\t\tallClasses\n\t\t\t.filter(m => f.dt.includes(mclass[m].dt))\n\t\t\t.forEach(key => {\n\t\t\t\ts.filterByClass[key] = 'value'\n\t\t\t})\n\t}\n\tfor (const f of config.legendValueFilter.lst) {\n\t\tif (!f.legendGrpName || f.tvs?.term?.type !== 'geneVariant') continue\n\t\tif (f.tvs.values?.[0].mclasslst)\n\t\t\tf.tvs.values[0].mclasslst.forEach(key => {\n\t\t\t\ts.filterByClass[key] = f.legendFilterType?.endsWith('_hard') ? 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'all'\n\t\t: hiddenMutations.size == s.mutationClasses.length\n\t\t? 'none'\n\t\t: hiddenMutations.size === s.mutationClasses.length - PCset.size && [...hiddenMutations].every(m => !PCset.has(m))\n\t\t? 'onlyPC'\n\t\t: hiddenMutations.size === s.mutationClasses.length - TMset.size && [...hiddenMutations].every(m => !TMset.has(m))\n\t\t? 'onlyTruncating'\n\t\t: 'bySelection'\n\ts.allMatrixMutationHidden = hiddenMutations.size == s.mutationClasses.length\n\n\tconst tiebreakers =\n\t\ts.sortOptions.a?.sortPriority.find(sp => sp.types.length == 1 && sp.types[0] == 'geneVariant')?.tiebreakers || []\n\n\t//Backwards compatibility fix for old saved sessions missing .isOrdered and/or .disabled\n\ts.sortByMutation = tiebreakers.find(tb => tb.filter?.values[0]?.dt === 1)?.isOrdered ? 'consequence' : 'presence'\n\n\ts.sortByCNV = tiebreakers.find(tb => tb.filter?.values[0]?.dt === 4)?.disabled !== true\n}\n"],
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-}

package/dist/chunk-5X5LI5YM.js

@@ -1,254 +0,0 @@
-import {
-  getMclassSorter,
-  getSampleGroupSorter,
-  getSampleSorter,
-  getTermSorter
-} from "./chunk-CDUNE45Q.js";
-import {
-  sample_match_termvaluesetting
-} from "./chunk-7IYJZZQI.js";
-import {
-  dtcnv,
-  dtfusionrna,
-  dtgeneexpression,
-  dtsnvindel
-} from "./chunk-7KRS7L4U.js";
-import {
-  __export
-} from "./chunk-HFNDKYVF.js";
-
-// plots/matrix/matrix.groups.js
-var matrix_groups_exports = {};
-__export(matrix_groups_exports, {
-  classifyValues: () => classifyValues,
-  getSampleGroups: () => getSampleGroups,
-  getSampleOrder: () => getSampleOrder,
-  getTermOrder: () => getTermOrder,
-  stackSiblingCellsByClass: () => stackSiblingCellsByClass
-});
-function getTermOrder(data) {
-  const s = this.settings.matrix;
-  this.termSorter = getTermSorter(this, s);
-  const termOrder = [];
-  let totalIndex = 0, visibleGrpIndex = 0, numClusterTerms = 0;
-  this.mclassSorter = getMclassSorter(this);
-  for (const [grpIndex, grp] of this.termGroups.entries()) {
-    const lst = [];
-    for (const [index, tw] of grp.lst.entries()) {
-      const counts = { samples: 0, hits: 0 };
-      const countedSamples = /* @__PURE__ */ new Set();
-      for (const sd of data.lst) {
-        if (countedSamples.has(sd.sample)) continue;
-        countedSamples.add(sd.sample);
-        const anno = sd[tw.$id];
-        if (anno) {
-          const { filteredValues, countedValues, renderedValues } = this.classifyValues(anno, tw, grp, s, sd);
-          anno.filteredValues = filteredValues;
-          anno.countedValues = countedValues;
-          anno.renderedValues = renderedValues;
-          if (anno.countedValues?.length) {
-            const v = tw.term.values?.[anno.value];
-            if (v?.uncountable) continue;
-            counts.samples += 1;
-            counts.hits += anno.countedValues.length;
-            if (tw.q?.mode == "continuous") {
-              const v2 = anno.value;
-              if (!("minval" in counts) || counts.minval > v2) counts.minval = v2;
-              if (!("maxval" in counts) || counts.maxval < v2) counts.maxval = v2;
-            }
-          }
-        }
-      }
-      if (grp.type != "hierCluster" || counts.samples) lst.push({ tw, counts, index });
-      if (grp.type == "hierCluster") numClusterTerms++;
-    }
-    const termSorter = grp.sortTermsBy || grp.type == "hierCluster" ? getTermSorter(this, s, grp) : this.termSorter;
-    const processedLst = lst.filter((t) => {
-      if ("minNumSamples" in t.tw) return t.tw.minNumSamples <= t.counts.samples;
-      if (!grp.settings) return true;
-      return !("minNumSamples" in grp.settings) || t.counts.samples >= grp.settings.minNumSamples;
-    }).sort(termSorter);
-    if (!processedLst.length) continue;
-    for (const [index, t] of processedLst.entries()) {
-      const { tw, counts } = t;
-      const ref = data.refs.byTermId[t.tw.$id] || {};
-      termOrder.push({
-        grp,
-        grpIndex,
-        visibleGrpIndex,
-        tw,
-        index,
-        // rendered index
-        lstIndex: t.index,
-        // as-listed index, before applying term filters
-        processedLst,
-        prevGrpTotalIndex: totalIndex,
-        totalIndex: totalIndex + index,
-        ref,
-        allCounts: counts
-        // note: term label will be assigned after sample counts are known
-        // label: t.tw.label || t.tw.term.name,
-      });
-    }
-    totalIndex += processedLst.length;
-    visibleGrpIndex += 1;
-  }
-  this.numTerms = termOrder.length;
-  this.numClusterTerms = numClusterTerms;
-  return termOrder;
-}
-function getSampleGroups(data) {
-  const s = this.settings.matrix;
-  const defaultSampleGrp = {
-    id: this.config.divideBy?.$id,
-    name: this.config.divideBy ? "Not annotated" : "",
-    lst: []
-  };
-  const sampleGroups = /* @__PURE__ */ new Map();
-  const term = this.config.divideBy?.term || {};
-  const $id = this.config.divideBy?.$id || "-";
-  const exclude = this.config.divideBy?.exclude || [];
-  const values = term.values || {};
-  const ref = data.refs.byTermId[$id] || {};
-  for (const row of data.lst) {
-    if ($id in row) {
-      const key = row[$id].key;
-      const name = key in values && values[key].label ? values[key].label : key;
-      if (!sampleGroups.has(key)) {
-        const grp = {
-          name: `${name}`,
-          // convert to a string
-          id: key,
-          lst: [],
-          tw: this.config.divideBy,
-          legendGroups: {},
-          isExcluded: exclude.includes(key)
-        };
-        if (ref.bins && s.sortSampleGrpsBy == "name") grp.order = ref.bins.findIndex((bin) => bin.name == key);
-        else delete grp.order;
-        sampleGroups.set(key, grp);
-      }
-      sampleGroups.get(key).lst.push(row);
-    } else {
-      defaultSampleGrp.lst.push(row);
-    }
-  }
-  const sampleGrpsArr = [...sampleGroups.values()];
-  const n = sampleGroups.size;
-  if (n > 100 && sampleGrpsArr.filter((sg) => sg.lst.length < 3).length > 0.8 * n) {
-    const l = s.controlLabels;
-    throw `Did not group ${l.samples} by "${term.name}": too many ${l.sample} groups (${n}), with the majority of groups having <= 2 ${l.samples} per group.`;
-  }
-  if (defaultSampleGrp.lst.length && !sampleGroups.size) {
-    sampleGroups.set(void 0, defaultSampleGrp);
-    sampleGrpsArr.push(...sampleGroups.values());
-  }
-  this.asListedSampleOrder = [];
-  for (const grp of sampleGrpsArr) {
-    this.asListedSampleOrder.push(...grp.lst.map((s2) => s2.sample));
-  }
-  const selectedDictTerms = this.termOrder.filter((t) => t.tw.sortSamples && t.tw.term.type != "geneVariant");
-  const noGrpSampleSorter = getSampleSorter(this, s, data.lst, {
-    skipSorter: (p, tw) => !p.types?.includes("geneVariant") && selectedDictTerms.find((t) => t.tw.$id === tw.$id)
-  });
-  const noGrpSampleOrder = data.lst.sort(noGrpSampleSorter);
-  const allowedSamples = noGrpSampleOrder.slice(0, s.maxSample);
-  const dataFilter = (d) => allowedSamples.includes(d);
-  const hitsPerSample = (t, c) => t + (typeof c == "object" && c.countedValues?.length ? 1 : 0);
-  const countHits = (total, d) => total + (Object.values(d).reduce(hitsPerSample, 0) ? 1 : 0);
-  const grpLstSampleSorter = getSampleSorter(this, s, data.lst);
-  for (const grp of sampleGrpsArr) {
-    grp.lst = grp.lst.filter(dataFilter);
-    grp.totalCountedValues = grp.lst.reduce(countHits, 0);
-    grp.lst.sort(grpLstSampleSorter);
-  }
-  const sampleGrpSorter = getSampleGroupSorter(this);
-  return sampleGrpsArr.sort(sampleGrpSorter);
-}
-function getSampleOrder(data) {
-  const s = this.settings.matrix;
-  this.visibleSampleGrps = /* @__PURE__ */ new Set();
-  const sampleOrder = [];
-  let total = 0, numHiddenGrps = 0;
-  for (const [grpIndex, grp] of this.sampleGroups.entries()) {
-    if (!grp.lst.length) continue;
-    if (grp.isExcluded) numHiddenGrps++;
-    let processedLst = grp.lst;
-    for (const [index, row] of processedLst.entries()) {
-      sampleOrder.push({
-        grp,
-        grpIndex: grpIndex - numHiddenGrps,
-        // : this.sampleGroups.length,
-        row,
-        index,
-        prevGrpTotalIndex: total,
-        totalIndex: total + index,
-        totalHtAdjustments: 0,
-        // may be required when transposed???
-        grpTotals: { htAdjustment: 0 },
-        // may be required when transposed???
-        processedLst
-      });
-    }
-    if (!grp.isExcluded) total += processedLst.length;
-    this.visibleSampleGrps.add(grp);
-  }
-  this.unfilteredSampleOrder = sampleOrder;
-  return sampleOrder.filter((so) => !so.grp.isExcluded);
-}
-function classifyValues(anno, tw, grp, s, sample) {
-  const values = "value" in anno ? [anno.value] : anno.values;
-  if (!values) return { filteredValues: null, countedValues: null, renderedValues: null };
-  const isSpecific = [tw.valueFilter || grp.valueFilter].filter((v) => v && true);
-  if (isSpecific.length && isSpecific[0].type !== "tvs" && isSpecific[0].type !== "tvslst")
-    throw `unknown matrix value filter type='${isSpecific.type}'`;
-  let filteredValues = !isSpecific.length ? values : values.filter((v) => sample_match_termvaluesetting(v, isSpecific[0], tw.term, sample));
-  const renderedValues = [];
-  if (tw.term.type == "geneVariant" && tw.q?.type == "values") {
-    filteredValues.sort(this.mclassSorter);
-    if (s.cellEncoding == "") renderedValues.push(...filteredValues);
-    else {
-      const sortedFilteredValues = [];
-      for (const dt of [dtcnv, dtsnvindel, dtfusionrna, dtgeneexpression]) {
-        const v = dt == dtgeneexpression ? filteredValues.find((v2) => v2.dt === dt) : filteredValues.find((v2) => v2.dt === dt && v2.class !== "WT" && v2.class !== "Blank");
-        if (v) renderedValues.push(v);
-        const oneDtV = filteredValues.filter((v2) => v2.dt === dt);
-        sortedFilteredValues.push(...oneDtV);
-      }
-      filteredValues = sortedFilteredValues;
-    }
-  } else {
-    renderedValues.push(...filteredValues);
-  }
-  return {
-    filteredValues,
-    countedValues: filteredValues.filter((v) => {
-      if (tw.term.type == "geneVariant") {
-        if (tw.q?.type == "predefined-groupset" || tw.q?.type == "custom-groupset") {
-          const groupset = tw.q.type == "predefined-groupset" ? tw.term.groupsetting.lst[tw.q.predefined_groupset_idx] : tw.q.customset;
-          if (!groupset) throw "groupset not found";
-          const group = groupset.groups[0];
-          if (v != group.name) return false;
-        } else {
-          if (v.class == "WT" || v.class == "Blank" || s.geneVariantCountSamplesSkipMclass.includes(v.class))
-            return false;
-        }
-      }
-      return true;
-    }),
-    renderedValues
-  };
-}
-function stackSiblingCellsByClass(a, b) {
-  return a.class === b.class ? 0 : a.class === "Blank" ? 1 : b.class == "Blank" ? -1 : a.class < b.class ? -1 : 1;
-}
-
-export {
-  getTermOrder,
-  getSampleGroups,
-  getSampleOrder,
-  classifyValues,
-  stackSiblingCellsByClass,
-  matrix_groups_exports
-};
-//# sourceMappingURL=chunk-5X5LI5YM.js.map