@sjcrh/proteinpaint-client 2.192.0 → 2.193.0

package/dist/chunk-BMS32SNA.js

@@ -1,37 +0,0 @@
-import {
-  addGeneSearchbox,
-  getGEunit
-} from "./chunk-KUZPTJJO.js";
-import {
-  Menu
-} from "./chunk-HYOEWQ5P.js";
-import {
-  TermTypes
-} from "./chunk-2U2CP2Y2.js";
-
-// termdb/handlers/geneExpression.ts
-var SearchHandler = class {
-  init(opts) {
-    this.callback = opts.callback;
-    this.app = opts.app;
-    const holder = opts.holder.append("div").style("padding", "10px 0px");
-    const geneSearch = addGeneSearchbox({
-      tip: new Menu({ padding: "0px" }),
-      genome: opts.genomeObj,
-      row: holder,
-      searchOnly: "gene",
-      callback: () => this.selectGene(geneSearch.geneSymbol)
-    });
-  }
-  async selectGene(gene) {
-    const unit = getGEunit(this.app.vocabApi);
-    const name = `${gene} ${unit}`;
-    if (!gene) throw new Error("No gene selected");
-    this.callback({ gene, name, type: TermTypes.GENE_EXPRESSION });
-  }
-};
-
-export {
-  SearchHandler
-};
-//# sourceMappingURL=chunk-BMS32SNA.js.map

package/dist/chunk-C4BCMAIK.js

@@ -1,188 +0,0 @@
-import {
-  __glob
-} from "./chunk-HFNDKYVF.js";
-
-// import("../plots/**/*.js") in plots/importPlot.js
-var globImport_plots_js = __glob({
-  "../plots/barchart.data.js": () => import("./barchart.data-ZWF6EVJH.js"),
-  "../plots/barchart.events.js": () => import("./barchart.events-XON2ANOC.js"),
-  "../plots/barchart.js": () => import("./barchart-MXSPTKV4.js"),
-  "../plots/bars.renderer.js": () => import("./bars.renderer-57KSYAAT.js"),
-  "../plots/bars.settings.js": () => import("./bars.settings-SDU7PZOS.js"),
-  "../plots/brainImaging.js": () => import("./brainImaging-P3AF3C5N.js"),
-  "../plots/controls.btns.js": () => import("./controls.btns-AP67YWKW.js"),
-  "../plots/controls.config.js": () => import("./controls.config-IBF5ILFP.js"),
-  "../plots/controls.js": () => import("./controls-7TDB75LK.js"),
-  "../plots/cuminc.js": () => import("./cuminc-CAHPKW7W.js"),
-  "../plots/dataDownload.js": () => import("./dataDownload-SOUCBKXM.js"),
-  "../plots/dictionary.js": () => import("./dictionary-RUT5VXDD.js"),
-  "../plots/dziviewer/plot.dzi.js": () => import("./plot.dzi-IA2SOFUD.js"),
-  "../plots/facet.js": () => import("./facet-T5ZX7ZGV.js"),
-  "../plots/gb/test/genomeBrowser.spec.js": () => import("./genomeBrowser.spec-EDILOQON.js"),
-  "../plots/geneExpression.js": () => import("./geneExpression-ZHQH6SNA.js"),
-  "../plots/geneORA.js": () => import("./geneORA-YLIRUMCZ.js"),
-  "../plots/geneset.js": () => import("./geneset-ACRMGBJO.js"),
-  "../plots/gsea.js": () => import("./gsea-2PQ5HNNT.js"),
-  "../plots/hierCluster.js": () => import("./hierCluster-H5HB7FPW.js"),
-  "../plots/importPlot.js": () => import("./importPlot-DQFWY5A7.js"),
-  "../plots/matrix.js": () => import("./matrix-7BFYR6QL.js"),
-  "../plots/matrix/hierCluster.config.js": () => import("./hierCluster.config-6UIJWCND.js"),
-  "../plots/matrix/hierCluster.interactivity.js": () => import("./hierCluster.interactivity-7MW6ZT6O.js"),
-  "../plots/matrix/hierCluster.js": () => import("./hierCluster-L3LCP2II.js"),
-  "../plots/matrix/hierCluster.renderers.js": () => import("./hierCluster.renderers-F34EVY5J.js"),
-  "../plots/matrix/matrix.cells.js": () => import("./matrix.cells-OTAXAJ4N.js"),
-  "../plots/matrix/matrix.cluster.js": () => import("./matrix.cluster-NU5CYRUT.js"),
-  "../plots/matrix/matrix.config.js": () => import("./matrix.config-AL4WSFZ7.js"),
-  "../plots/matrix/matrix.data.js": () => import("./matrix.data-BDHCSN2G.js"),
-  "../plots/matrix/matrix.dom.js": () => import("./matrix.dom-F7AN3QGE.js"),
-  "../plots/matrix/matrix.groups.js": () => import("./matrix.groups-MV2D2636.js"),
-  "../plots/matrix/matrix.interactivity.js": () => import("./matrix.interactivity-H7EJW3P2.js"),
-  "../plots/matrix/matrix.js": () => import("./matrix-USAB2CHO.js"),
-  "../plots/matrix/matrix.layout.js": () => import("./matrix.layout-7CAS2IBO.js"),
-  "../plots/matrix/matrix.legend.js": () => import("./matrix.legend-JDVG2JDF.js"),
-  "../plots/matrix/matrix.renderers.js": () => import("./matrix.renderers-PDR5FIBC.js"),
-  "../plots/matrix/matrix.serieses.js": () => import("./matrix.serieses-QVDS5HKK.js"),
-  "../plots/matrix/matrix.sort.js": () => import("./matrix.sort-HCK4CSTJ.js"),
-  "../plots/matrix/matrix.sorterUi.js": () => import("./matrix.sorterUi-XGBQOPG4.js"),
-  "../plots/matrix/test/hierCluster.integration.spec.js": () => import("./hierCluster.integration.spec-EVAPT2VF.js"),
-  "../plots/matrix/test/matrix.integration.spec.js": () => import("./matrix.integration.spec-DESORC2Y.js"),
-  "../plots/matrix/test/matrix.sort.unit.spec.js": () => import("./matrix.sort.unit.spec-2GC4E26N.js"),
-  "../plots/matrix/test/matrix.sorterUi.unit.spec.js": () => import("./matrix.sorterUi.unit.spec-BJQKDU2F.js"),
-  "../plots/matrix/test/oncomatrix.spec.js": () => import("./oncomatrix.spec-YGQYIUDT.js"),
-  "../plots/plot.brainImaging.js": () => import("./plot.brainImaging-6KVNPPMT.js"),
-  "../plots/plot.disco.js": () => import("./plot.disco-ZFH5RK6B.js"),
-  "../plots/plot.ssgq.js": () => import("./plot.ssgq-QARGQVKB.js"),
-  "../plots/regression.inputs.js": () => import("./regression.inputs-42LY4MEZ.js"),
-  "../plots/regression.inputs.term.js": () => import("./regression.inputs.term-TTUFFPG6.js"),
-  "../plots/regression.inputs.values.table.js": () => import("./regression.inputs.values.table-CJAPTSMS.js"),
-  "../plots/regression.js": () => import("./regression-DLPBCDZT.js"),
-  "../plots/regression.results.js": () => import("./regression.results-IA3C7SHR.js"),
-  "../plots/sampleView.js": () => import("./sampleView-CZF7U23I.js"),
-  "../plots/scatter/test/scatter.integration.spec.js": () => import("./scatter.integration.spec-CRMLFO4J.js"),
-  "../plots/singleCellPlot.js": () => import("./singleCellPlot-6EZ6JXCM.js"),
-  "../plots/stattable.js": () => import("./stattable-MDABSW3F.js"),
-  "../plots/survival/test/survival.integration.spec.js": () => import("./survival.integration.spec-EUAAALVW.js"),
-  "../plots/table.js": () => import("./table-MVX3IMAL.js"),
-  "../plots/test/barchart.integration.spec.js": () => import("./barchart.integration.spec-PJIENJGT.js"),
-  "../plots/test/cuminc.integration.spec.js": () => import("./cuminc.integration.spec-NNSQGBRI.js"),
-  "../plots/test/dataDownload.integration.spec.js": () => import("./dataDownload.integration.spec-C6TLWSSO.js"),
-  "../plots/test/expclust.gdc.spec.js": () => import("./expclust.gdc.spec-DTBFOXBC.js"),
-  "../plots/test/regression.integration.spec.js": () => import("./regression.integration.spec-UDA26OGS.js"),
-  "../plots/test/regression.spec.js": () => import("./regression.spec-HEXCL3QV.js"),
-  "../plots/test/sampleScatter.spec.js": () => import("./sampleScatter.spec-N6V4BQ5Q.js"),
-  "../plots/test/summary.integration.spec.js": () => import("./summary.integration.spec-SLIIM4HN.js"),
-  "../plots/test/violin.integration.spec.js": () => import("./violin.integration.spec-5CLYJSAR.js"),
-  "../plots/violin.interactivity.js": () => import("./violin.interactivity-KXVKTT22.js"),
-  "../plots/violin.js": () => import("./violin-NBZTGGYF.js"),
-  "../plots/violin.renderer.js": () => import("./violin.renderer-37OF6K7Q.js"),
-  "../plots/volcano/test/testData.js": () => import("./testData-LEJ53F2K.js"),
-  "../plots/wsiviewer/plot.wsi.js": () => import("./plot.wsi-C2DULA7U.js")
-});
-
-// plots/importPlot.js
-async function importPlot(chartType, notFoundMessage = "") {
-  switch (chartType) {
-    case "AIProjectAdmin":
-      return await import("./AIProjectAdmin-AEXQY5LY.js");
-    case "barchart":
-      return await import("./barchart-MXSPTKV4.js");
-    case "boxplot":
-      return await import("./BoxPlot-HDP3SIGU.js");
-    case "correlationVolcano":
-      return await import("./CorrelationVolcano-V2E566XL.js");
-    case "DEinput":
-      return await import("./DEinput-P2HOQC4Z.js");
-    case "dictionary":
-      return await import("./dictionary-RUT5VXDD.js");
-    case "differentialAnalysis":
-      return await import("./DifferentialAnalysis-2Z6BHS7A.js");
-    case "Disco":
-      return await import("./Disco-ZLC54X7T.js");
-    case "dmr":
-      return await import("./DmrPlot-OEJRGNI3.js");
-    case "DziViewer":
-      return await import("./DziViewer-6737GC22.js");
-    case "GeneExpInput":
-      return await import("./GeneExpInput-PWLPDLYT.js");
-    case "genomeBrowser":
-      return await import("./GB-2GHDD3MW.js");
-    case "grin2":
-      return await import("./grin2-GNB35CMF.js");
-    case "gsea":
-      return await import("./gsea-2PQ5HNNT.js");
-    case "imagePlot":
-      return await import("./imagePlot-RSFZ2OKD.js");
-    case "report":
-      return await import("./report-4CFOWNPJ.js");
-    case "runChart2":
-    //See frequencyChart
-    case "frequencyChart":
-      return await import("./RunChart2-SQ6TFOHD.js");
-    case "profileBarchart2":
-      return await import("./barchart2-HIKBGSSE.js");
-    case "profileForms":
-      return await import("./profileForms-Y6ZBMZWQ.js");
-    case "profileForms2":
-      return await import("./forms2-S5OGBFKL.js");
-    case "profilePlot":
-      return await import("./profilePlot-SVI3QKMD.js");
-    case "profilePolar2":
-      return await import("./polar2-3HS3QBU6.js");
-    case "profileRadar2":
-      return await import("./radar2-TTQZLARY.js");
-    case "profileRadarFacility2":
-      return await import("./radarFacility2-YGS56QUA.js");
-    case "proteinView":
-      return await import("./proteinView-YPFJSBL7.js");
-    case "numericDictTermCluster":
-      return await import("./numericDictTermCluster-WIVO33AV.js");
-    case "proteomeAbundance":
-      return await import("./proteomeAbundance-NQ4635NL.js");
-    case "animatedBubbleChart":
-      return await import("./animatedBubbleChart-Q6Z5W2UL.js");
-    case "brainRegions":
-      return await import("./brainRegions-YA2H2QOI.js");
-    case "geneRanking":
-      return await import("./geneRanking-JDJXNGEC.js");
-    case "ProteomeInput":
-      return await import("./ProteomeInput-AUXWUIWK.js");
-    case "sampleScatter":
-      return await import("./scatter-EY7HQVCO.js");
-    case "sc":
-      return await import("./SC-OWJ6LYIW.js");
-    case "summarizeCnvGeneexp":
-      return await import("./summarizeCnvGeneexp-LYVDZXXD.js");
-    case "summarizeGeneexpSurvival":
-      return await import("./summarizeGeneexpSurvival-Y52TGAHF.js");
-    case "summarizeMutationDiagnosis":
-      return await import("./summarizeMutationDiagnosis-HZKXHOOQ.js");
-    case "summarizeMutationSurvival":
-      return await import("./summarizeMutationSurvival-TU7TQYFQ.js");
-    case "summarizeMutationCnv":
-      return await import("./summarizeMutationCnv-6EEJT3PV.js");
-    case "summaryInput":
-      return await import("./summaryInput-6HROPKCE.js");
-    case "summary":
-      return await import("./summary-4QQZUAMU.js");
-    case "survival":
-      return await import("./survival-QSL2KDKD.js");
-    case "table":
-      return await import("./table-MVX3IMAL.js");
-    case "violin":
-      return await import("./violin-NBZTGGYF.js");
-    case "volcano":
-      return await import("./Volcano-XHDH6UN7.js");
-    case "WSISamplesPlot":
-      return await import("./WsiSamplesPlot-YUOAWG2A.js");
-    case "WSIViewer":
-      return await import("./WSIViewer-WT2QV747.js");
-    default:
-      if (notFoundMessage) throw notFoundMessage;
-      return await globImport_plots_js(`../plots/${chartType}.js`);
-  }
-}
-
-export {
-  importPlot
-};
-//# sourceMappingURL=chunk-C4BCMAIK.js.map

package/dist/chunk-C4BCMAIK.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/importPlot.js"],
-  "sourcesContent": ["export async function importPlot(chartType, notFoundMessage = '') {\n\t// TODO: move to dynamic import of exact plot names here, instead of string-pattern,\n\t// so that the bundler does not have to guess code file extension, directory names and letter casing\n\tswitch (chartType) {\n\t\tcase 'AIProjectAdmin':\n\t\t\treturn await import('./aiProjectAdmin/AIProjectAdmin.ts')\n\n\t\tcase 'barchart':\n\t\t\treturn await import(`./barchart.js`)\n\n\t\tcase 'boxplot':\n\t\t\treturn await import(`./boxplot/BoxPlot.ts`)\n\n\t\tcase 'correlationVolcano':\n\t\t\treturn await import(`./corrVolcano/CorrelationVolcano.ts`)\n\n\t\tcase 'DEinput':\n\t\t\treturn await import(`./DEinput.ts`)\n\n\t\tcase 'dictionary':\n\t\t\treturn await import(`./dictionary.js`)\n\n\t\tcase 'differentialAnalysis':\n\t\t\treturn await import(`./diffAnalysis/DifferentialAnalysis.ts`)\n\n\t\tcase 'Disco':\n\t\t\treturn await import('./disco/Disco.ts')\n\n\t\tcase 'dmr':\n\t\t\treturn await import('./dmr/DmrPlot.ts')\n\n\t\tcase 'DziViewer':\n\t\t\treturn await import(`./dziviewer/DziViewer.ts`)\n\n\t\tcase 'GeneExpInput':\n\t\t\treturn await import(`./GeneExpInput.ts`)\n\n\t\tcase 'genomeBrowser':\n\t\t\treturn await import('./gb/GB.ts')\n\n\t\tcase 'grin2':\n\t\t\treturn await import('./grin2/grin2')\n\n\t\tcase 'gsea':\n\t\t\treturn await import(`./gsea.js`)\n\n\t\tcase 'imagePlot':\n\t\t\treturn await import('./imagePlot.ts')\n\n\t\tcase 'report':\n\t\t\treturn await import(`./report/report.ts`)\n\n\t\tcase 'runChart2': //See frequencyChart\n\t\tcase 'frequencyChart':\n\t\t\treturn await import(`./runChart2/RunChart2.ts`)\n\n\t\tcase 'profileBarchart2':\n\t\t\treturn await import('./profile/barchart2.ts')\n\n\t\tcase 'profileForms':\n\t\t\treturn await import('./profile/profileForms.ts')\n\n\t\tcase 'profileForms2':\n\t\t\treturn await import('./profile/forms2.ts')\n\n\t\tcase 'profilePlot':\n\t\t\treturn await import('./profile/profilePlot.ts')\n\n\t\tcase 'profilePolar2':\n\t\t\treturn await import('./profile/polar2.ts')\n\n\t\tcase 'profileRadar2':\n\t\t\treturn await import('./profile/radar2.ts')\n\n\t\tcase 'profileRadarFacility2':\n\t\t\treturn await import('./profile/radarFacility2.ts')\n\n\t\tcase 'proteinView':\n\t\t\treturn await import(`./proteinView.ts`)\n\n\t\tcase 'numericDictTermCluster':\n\t\t\treturn await import(`./numericDictTermCluster.ts`)\n\n\t\tcase 'proteomeAbundance':\n\t\t\treturn await import(`./proteomeAbundance.ts`)\n\n\t\tcase 'animatedBubbleChart':\n\t\t\treturn await import(`./animatedBubbleChart.ts`)\n\n\t\tcase 'brainRegions':\n\t\t\treturn await import('./brainRegions.ts')\n\n\t\tcase 'geneRanking':\n\t\t\treturn await import(`./geneRanking.ts`)\n\n\t\tcase 'ProteomeInput':\n\t\t\treturn await import('./ProteomeInput.ts')\n\n\t\tcase 'sampleScatter':\n\t\t\treturn await import(`./scatter/scatter.js`)\n\n\t\tcase 'sc':\n\t\t\treturn await import('./sc/SC.ts')\n\n\t\tcase 'summarizeCnvGeneexp':\n\t\t\treturn await import(`./summarizeCnvGeneexp.ts`)\n\n\t\tcase 'summarizeGeneexpSurvival':\n\t\t\treturn await import(`./summarizeGeneexpSurvival.ts`)\n\n\t\tcase 'summarizeMutationDiagnosis':\n\t\t\treturn await import(`./summarizeMutationDiagnosis.ts`)\n\n\t\tcase 'summarizeMutationSurvival':\n\t\t\treturn await import(`./summarizeMutationSurvival.ts`)\n\n\t\tcase 'summarizeMutationCnv':\n\t\t\treturn await import(`./summarizeMutationCnv.ts`)\n\n\t\tcase 'summaryInput':\n\t\t\treturn await import(`./summaryInput.ts`)\n\n\t\tcase 'summary':\n\t\t\treturn await import(`./summary.ts`)\n\n\t\tcase 'survival':\n\t\t\treturn await import(`./survival/survival.js`)\n\n\t\tcase 'table':\n\t\t\treturn await import(`./table.js`)\n\n\t\tcase 'violin':\n\t\t\treturn await import(`./violin.js`)\n\n\t\tcase 'volcano':\n\t\t\treturn await import(`./volcano/Volcano.ts`)\n\n\t\tcase 'WSISamplesPlot':\n\t\t\treturn await import('./wsisamples/WsiSamplesPlot.ts')\n\n\t\tcase 'WSIViewer':\n\t\t\treturn await import('./wsiviewer/WSIViewer.ts')\n\n\t\tdefault:\n\t\t\t// temporary option to force an error, to bypass the default filename matching\n\t\t\tif (notFoundMessage) throw notFoundMessage\n\n\t\t\t// TODO: should always throw here once all chart types are handled separately as cases;\n\t\t\t// the pattern matching below is problematic because:\n\t\t\t// - it matches non-plot code file names\n\t\t\t// - it assumes a non-typescript, .js file extension\n\t\t\t// - it doesn't handle plot code that are organized under its own subdirectory\n\t\t\treturn await import(`../plots/${chartType}.js`)\n\t}\n}\n"],
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-}

package/dist/chunk-CJPGYPI3.js

@@ -1,291 +0,0 @@
-import {
-  getSortOptions
-} from "./chunk-WXSRK3XR.js";
-import {
-  defaultUiLabels,
-  fillTermWrapper
-} from "./chunk-KUZPTJJO.js";
-import {
-  copyMerge
-} from "./chunk-M3J4MINX.js";
-import {
-  isDictionaryType
-} from "./chunk-2U2CP2Y2.js";
-import {
-  CNVClasses,
-  dtcnv,
-  mclass,
-  mutationClasses,
-  proteinChangingMutations,
-  synonymousMutations,
-  truncatingMutations
-} from "./chunk-ZF6HNVYD.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-CJPGYPI3.js.map

package/dist/chunk-CTQH7LQ6.js

@@ -1,31 +0,0 @@
-import {
-  IN_frame,
-  OUT_frame
-} from "./chunk-ZF6HNVYD.js";
-
-// src/spliceevent.exonskip.getdefault.js
-function spliceevent_exonskip_getdefault_default(events) {
-  let evt2showidx = 0;
-  for (let i = 1; i < events.length; i++) {
-    const e = events[i];
-    const e2show = events[evt2showidx];
-    if (e.isskipexon && e2show.isaltexon) {
-      evt2showidx = i;
-      continue;
-    }
-    if (e.frame == OUT_frame && e2show.framenocheck) {
-      evt2showidx = i;
-      continue;
-    }
-    if (e.frame == IN_frame && e2show.frame != IN_frame) {
-      evt2showidx = i;
-      continue;
-    }
-  }
-  return evt2showidx;
-}
-
-export {
-  spliceevent_exonskip_getdefault_default
-};
-//# sourceMappingURL=chunk-CTQH7LQ6.js.map