@sjcrh/proteinpaint-client 2.208.0 → 2.210.0

package/dist/chunk-DFT2PAIU.js

@@ -1,243 +0,0 @@
-import {
-  keyupEnter
-} from "./chunk-QJ3HYZH3.js";
-import {
-  get_bin_label,
-  get_bin_range_equation
-} from "./chunk-VMRO6DMC.js";
-import {
-  toStoredUnit,
-  toUserUnit
-} from "./chunk-W5J3LTYS.js";
-
-// termsetting/handlers/NumCustomBinEditor.ts
-var NumCustomBinEditor = class {
-  constructor(editHandler) {
-    this.dom = {};
-    this.editHandler = editHandler;
-    this.opts = editHandler.opts;
-    this.tw = editHandler.tw;
-    this.termsetting = editHandler.termsetting;
-  }
-  /* bin boundaries are stored in the term's own unit but entered and shown in its user-facing one.
-  both are identity functions unless the term declares valueConversion{} */
-  toDisplay(v) {
-    return toUserUnit(v, this.tw.term);
-  }
-  toStored(v) {
-    return toStoredUnit(v, this.tw.term);
-  }
-  async render(div) {
-    this.tw = this.editHandler.tw;
-    const isRemounting = !!this.dom.inputsDiv && this.editHandler.dom.binsDiv?.node().contains(this.dom.inputsDiv.node());
-    if (!isRemounting) this.q = this.getDefaultQ();
-    await this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
-    if (isRemounting) return;
-    if (this.dom.inputsDiv) {
-      this.dom.inputsDiv.remove();
-      delete this.dom.inputsDiv;
-    }
-    this.dom.inputsDiv = div.append("div").style("display", "flex").style("width", "100%");
-    this.renderCustomBinInputs();
-  }
-  getBoundaryOpts() {
-    return {
-      values: this.q.lst.slice(1).map((bin) => ({ x: this.toDisplay(bin.startunbounded ? bin.stop : bin.start), isDraggable: true })),
-      // the dragged value arrives in display units, matching what the textarea holds
-      callback: (d, value) => {
-        const boundaryValues = this.q.lst.slice(1).map((d2) => "start" in d2 ? this.toDisplay(d2.start) : "");
-        boundaryValues[d.index] = value;
-        this.dom.customBinBoundaryInput.property("value", boundaryValues.join("\n"));
-        this.handleInputChange("drag");
-        return 0;
-      }
-    };
-  }
-  getDefaultQ() {
-    if (this.tw.q.mode == "discrete" && this.tw.q.type == "custom-bin") {
-      const copy = JSON.parse(JSON.stringify(this.tw.q));
-      copy.lst.forEach((bin) => {
-        if (!bin.label) bin.label = get_bin_label(bin, this.tw.q, this.tw.term.valueConversion);
-        bin.range = get_bin_range_equation(bin, this.tw.q, this.tw.term.valueConversion);
-      });
-      return copy;
-    }
-    const { min, max } = this.editHandler.handler.density_data;
-    const defaultCustomBoundary = (
-      /* when no sample is annotated by this term,
-      minvalue and maxvalue are both null
-      setting defaultCustomBoundary to arbitrary "0" will allow existing UI to work
-      but remains to be evaluated if is really okay to use 0
-      */
-      !Number.isFinite(min) || !Number.isFinite(max) ? 0 : (
-        // minvalue and maxvalue is valid number
-        max != min ? min + (max - min) / 2 : max
-      )
-    );
-    const firstBin = {
-      startunbounded: true,
-      startinclusive: false,
-      stopinclusive: false,
-      stop: +defaultCustomBoundary.toFixed(this.tw.term.type == "integer" ? 0 : 2)
-    };
-    const lastBin = {
-      stopunbounded: true,
-      startinclusive: true,
-      stopinclusive: false,
-      start: +defaultCustomBoundary.toFixed(this.tw.term.type == "integer" ? 0 : 2)
-    };
-    return {
-      mode: "discrete",
-      type: "custom-bin",
-      lst: [
-        // Type '{ label: any; range: any; startunbounded: boolean; startinclusive: boolean; stopinclusive: boolean; stop: number; }' is not assignable to type 'StartUnboundedBin | FullyBoundedBin'.
-        // Property 'start' is missing in type '{ label: any; range: any; startunbounded: boolean; startinclusive: boolean; stopinclusive: boolean; stop: number; }' but required in type 'FullyBoundedBin'.
-        {
-          ...firstBin,
-          label: get_bin_label(firstBin, this.tw.q, this.tw.term.valueConversion),
-          range: get_bin_range_equation(firstBin, this.tw.q, this.tw.term.valueConversion)
-        },
-        {
-          ...lastBin,
-          label: get_bin_label(lastBin, this.tw.q, this.tw.term.valueConversion),
-          range: get_bin_range_equation(lastBin, this.tw.q, this.tw.term.valueConversion)
-        }
-        //satisfies StopUnboundedBin
-      ]
-    };
-  }
-  /******************* Functions for Numerical Custom size bins *******************/
-  renderCustomBinInputs() {
-    const q = this.q;
-    const boundaryDiv = this.dom.inputsDiv.append("div").style("margin-right", "20px");
-    this.dom.rangeAndLabelDiv = this.dom.inputsDiv.append("div");
-    boundaryDiv.append("div").style("margin-bottom", "5px").style("color", "rgb(136, 136, 136)").text("Bin boundaries");
-    this.dom.customBinBoundaryInput = boundaryDiv.append("textarea").style("width", "100px").style("height", "70px").text(
-      q.lst.slice(1).map((d) => "start" in d ? this.toDisplay(d.start) : "").join("\n")
-    ).on("change", () => this.handleInputChange()).on("keyup", async (event) => {
-      if (!keyupEnter(event) && event.key != 8 && event.key != "Enter") return;
-      if (!this.dom.inputsDiv.selectAll("input").node().value) return;
-      this.handleInputChange();
-    });
-    boundaryDiv.append("div").style("font-size", ".6em").style("margin-left", "1px").style("color", "#858585").html("Enter numeric values </br>seperated by ENTER");
-    this.renderBoundaryInputDivs();
-  }
-  renderBoundaryInputDivs() {
-    const data = this.q.lst;
-    const holder = this.dom.rangeAndLabelDiv;
-    holder.selectAll("*").remove();
-    const grid = holder.append("div").style("display", "grid").style("grid-template-columns", "auto auto").style("column-gap", "20px").style("align-items", "center");
-    grid.append("div").style("margin-bottom", "3px").style("color", "rgb(136, 136, 136)").text("Range");
-    grid.append("div").style("margin-bottom", "3px").style("color", "rgb(136, 136, 136)").text("Bin label");
-    for (const d of data) {
-      grid.append("div").attr("name", "range").html(d.range);
-      grid.append("div").append("input").attr("type", "text").style("margin", "2px 0px").property("value", d.label).on("change", function() {
-        d.label = this.value;
-      });
-    }
-    this.dom.customBinRanges = this.dom.inputsDiv.selectAll('div[name="range"]').data(data);
-    this.dom.customBinLabelInput = this.dom.inputsDiv.selectAll("input").data(data);
-  }
-  handleInputChange(eventType = "") {
-    const self = this.tw;
-    const inputs = this.dom.inputsDiv.selectAll("input");
-    inputs.property("value", "");
-    const data = this.processCustomBinInputs();
-    if (data == void 0) {
-      return;
-    }
-    if (self.q.hiddenValues) this.tw.q.hiddenValues = self.q.hiddenValues;
-    if (this.binsChanged(data, this.q.lst)) {
-      this.q.lst = data;
-    }
-    this.renderBoundaryInputDivs();
-    if (eventType != "drag") this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
-  }
-  binsChanged(data, qlst) {
-    if (data.length != qlst.length) return true;
-    if (Object.keys(data[0]).length !== Object.keys(qlst[0]).length) return true;
-    for (const [i, bin] of qlst.entries()) {
-      for (const k of Object.keys(bin)) {
-        if (bin[k] && bin[k] !== data[i][k]) {
-          return true;
-        }
-      }
-    }
-    return false;
-  }
-  processCustomBinInputs() {
-    const self = this.termsetting;
-    const startinclusive = this.editHandler.boundaryInclusion == "startinclusive";
-    const stopinclusive = this.editHandler.boundaryInclusion == "stopinclusive";
-    const inputs = this.dom.inputsDiv.node().querySelectorAll("input");
-    const inputData = this.dom.customBinBoundaryInput.property("value").split("\n").filter((d) => d != "" && !isNaN(d));
-    const trackBins = new Set(inputData);
-    if (!trackBins.size) return this.tw.q.lst;
-    const sortedBins = Array.from(trackBins).map((v) => this.toStored(Number(v))).sort((a, b) => a - b);
-    const data = [
-      // first bin: StartUnbounded type
-      {
-        startunbounded: true,
-        stop: sortedBins[0],
-        startinclusive: false,
-        stopinclusive,
-        label: inputs[0].value
-      }
-    ];
-    if (!data[0].label) data[0].label = get_bin_label(data[0], self.q, self.term.valueConversion);
-    if (!data[0].range) data[0].range = get_bin_range_equation(data[0], self.q, self.term.valueConversion);
-    for (const [i, d] of sortedBins.entries()) {
-      let bin;
-      const label = inputs[i + 1]?.value || "";
-      if (i !== trackBins.size - 1) {
-        bin = {
-          start: +d,
-          startinclusive,
-          stopinclusive,
-          stop: sortedBins[i + 1],
-          label
-          //range: ''
-        };
-      } else {
-        bin = {
-          start: +d,
-          startinclusive,
-          stopinclusive: false,
-          stopunbounded: true,
-          label
-          //range: ''
-        };
-      }
-      if (bin.label === "" || bin.label === void 0) bin.label = get_bin_label(bin, self.q, self.term.valueConversion);
-      if (bin.range === "" || bin.range === void 0)
-        bin.range = get_bin_range_equation(bin, self.q, self.term.valueConversion);
-      data.push(bin);
-    }
-    return data;
-  }
-  getEditedQ(destroyDom = true) {
-    const lst = this.processCustomBinInputs();
-    if (destroyDom) {
-      for (const name of Object.keys(this.dom)) {
-        this.dom[name].remove();
-        delete this.dom[name];
-      }
-    }
-    return {
-      mode: "discrete",
-      type: "custom-bin",
-      lst
-    };
-  }
-  undoEdits() {
-    this.q = this.getDefaultQ();
-    this.dom.inputsDiv.selectAll("*").remove();
-    this.renderCustomBinInputs();
-    this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
-  }
-};
-
-export {
-  NumCustomBinEditor
-};
-//# sourceMappingURL=chunk-DFT2PAIU.js.map

package/dist/chunk-DMWOK4DS.js

@@ -1,178 +0,0 @@
-import {
-  __glob
-} from "./chunk-HS5PO5ZQ.js";
-
-// import("../plots/**/*.js") in plots/importPlot.js
-var globImport_plots_js = __glob({
-  "../plots/controls.btns.js": () => import("./controls.btns-BYM4DON4.js"),
-  "../plots/controls.config.js": () => import("./controls.config-NELL5HY5.js"),
-  "../plots/controls.js": () => import("./controls-ZPQ6SXD2.js"),
-  "../plots/dictionary.js": () => import("./dictionary-WSDD6TFI.js"),
-  "../plots/gb/test/genomeBrowser.spec.js": () => import("./genomeBrowser.spec-7PZCNBL3.js"),
-  "../plots/geneExpression.js": () => import("./geneExpression-EMLVPVNK.js"),
-  "../plots/geneORA.js": () => import("./geneORA-CIAFQQWB.js"),
-  "../plots/geneset.js": () => import("./geneset-RCIP2GZH.js"),
-  "../plots/hierCluster.js": () => import("./hierCluster-AV5NO2GW.js"),
-  "../plots/importPlot.js": () => import("./importPlot-7FISAQKR.js"),
-  "../plots/matrix.js": () => import("./matrix-DX4W5XMX.js"),
-  "../plots/matrix/hierCluster.config.js": () => import("./hierCluster.config-4MBWG6RZ.js"),
-  "../plots/matrix/hierCluster.interactivity.js": () => import("./hierCluster.interactivity-6PJE64PF.js"),
-  "../plots/matrix/hierCluster.js": () => import("./hierCluster-W2MVN34V.js"),
-  "../plots/matrix/hierCluster.renderers.js": () => import("./hierCluster.renderers-RWDQ5SHY.js"),
-  "../plots/matrix/matrix.cells.js": () => import("./matrix.cells-BLULUGSZ.js"),
-  "../plots/matrix/matrix.cluster.js": () => import("./matrix.cluster-RH4BOM5F.js"),
-  "../plots/matrix/matrix.config.js": () => import("./matrix.config-Z3LWYH74.js"),
-  "../plots/matrix/matrix.data.js": () => import("./matrix.data-73HY7Y2V.js"),
-  "../plots/matrix/matrix.dom.js": () => import("./matrix.dom-2SA43BPT.js"),
-  "../plots/matrix/matrix.groups.js": () => import("./matrix.groups-NOUMYNFY.js"),
-  "../plots/matrix/matrix.interactivity.js": () => import("./matrix.interactivity-YHDIO5A2.js"),
-  "../plots/matrix/matrix.js": () => import("./matrix-S34ITAPJ.js"),
-  "../plots/matrix/matrix.layout.js": () => import("./matrix.layout-25HYKUF2.js"),
-  "../plots/matrix/matrix.legend.js": () => import("./matrix.legend-IMK7DH4V.js"),
-  "../plots/matrix/matrix.renderers.js": () => import("./matrix.renderers-3RZRN6HO.js"),
-  "../plots/matrix/matrix.serieses.js": () => import("./matrix.serieses-ZTVHQ7QA.js"),
-  "../plots/matrix/matrix.sort.js": () => import("./matrix.sort-EDXHT6NZ.js"),
-  "../plots/matrix/matrix.sorterUi.js": () => import("./matrix.sorterUi-3DRNHG5Z.js"),
-  "../plots/matrix/test/hierCluster.integration.spec.js": () => import("./hierCluster.integration.spec-JUIBIUKH.js"),
-  "../plots/matrix/test/matrix.integration.spec.js": () => import("./matrix.integration.spec-VTXYJ46U.js"),
-  "../plots/matrix/test/matrix.sort.unit.spec.js": () => import("./matrix.sort.unit.spec-LSNY7PHU.js"),
-  "../plots/matrix/test/matrix.sorterUi.unit.spec.js": () => import("./matrix.sorterUi.unit.spec-GNIIWGRJ.js"),
-  "../plots/matrix/test/matrix.unit.spec.js": () => import("./matrix.unit.spec-7A6ZFRXI.js"),
-  "../plots/matrix/test/oncomatrix.spec.js": () => import("./oncomatrix.spec-6X2WAHL7.js"),
-  "../plots/plot.brainImaging.js": () => import("./plot.brainImaging-JGDLKLR7.js"),
-  "../plots/plot.disco.js": () => import("./plot.disco-TPMXTTZK.js"),
-  "../plots/plot.ssgq.js": () => import("./plot.ssgq-KIZIOZIF.js"),
-  "../plots/singleCellPlot.js": () => import("./singleCellPlot-Q6INE54V.js"),
-  "../plots/stattable.js": () => import("./stattable-BD64SFYV.js"),
-  "../plots/survival/test/survival.integration.spec.js": () => import("./survival.integration.spec-OJUPTY5N.js"),
-  "../plots/table.js": () => import("./table-YCTSMLQL.js"),
-  "../plots/test/expclust.gdc.spec.js": () => import("./expclust.gdc.spec-46HDKH2Q.js"),
-  "../plots/test/summary.integration.spec.js": () => import("./summary.integration.spec-SSLTLVNW.js"),
-  "../plots/volcano/test/testData.js": () => import("./testData-DRM5HWQB.js")
-});
-
-// plots/importPlot.js
-async function importPlot(chartType, notFoundMessage = "") {
-  switch (chartType) {
-    case "aggMatrixInput":
-      return await import("./AggMatrixInput-NJHU4FU2.js");
-    case "aggregateMatrix":
-      return await import("./AggregateMatrix-IBWOJWOC.js");
-    case "animatedBubbleChart":
-      return await import("./animatedBubbleChart-X53PR73H.js");
-    case "brainImaging":
-      return await import("./brainImaging-KSTJQJAB.js");
-    case "brainRegions":
-      return await import("./brainRegions-WCRMMSK4.js");
-    case "barchart":
-      return await import("./barchart-TWMOUZFL.js");
-    case "boxplot":
-      return await import("./BoxPlot-ZIVA55SK.js");
-    case "bubbleHeatmap":
-      return await import("./bubbleHeatmap-4YOQ3BAB.js");
-    case "cellTypeBubbleHeatmap":
-      return await import("./cellTypeBubbleHeatmap-O6YZ2RW4.js");
-    case "correlationVolcano":
-      return await import("./CorrelationVolcano-33I4FC44.js");
-    case "cuminc":
-      return await import("./Cuminc-WKY35UGV.js");
-    case "dataDownload":
-      return await import("./dataDownload-NSDY4MSL.js");
-    case "DEinput":
-      return await import("./DEinput-YU3W72K7.js");
-    case "dictionary":
-      return await import("./dictionary-WSDD6TFI.js");
-    case "differentialAnalysis":
-      return await import("./DifferentialAnalysis-SHMQHWJL.js");
-    case "Disco":
-      return await import("./Disco-OZY5GW2Z.js");
-    case "dmr":
-      return await import("./DmrPlot-QKUX5XUW.js");
-    case "facet":
-      return await import("./facet-3EONZDDE.js");
-    case "GeneExpInput":
-      return await import("./GeneExpInput-XEFUTLFU.js");
-    case "geneRanking":
-      return await import("./geneRanking-JRAU6FMJ.js");
-    case "genomeBrowser":
-      return await import("./GB-ZYH7PGHT.js");
-    case "geomap":
-      return await import("./Geomap-GEK7UEDU.js");
-    case "grin2":
-      return await import("./grin2-YYBB5XJK.js");
-    case "gsea":
-      return await import("./GSEA-VQTD4MLY.js");
-    case "imagePlot":
-      return await import("./imagePlot-XLDQNUJA.js");
-    case "numericDictTermCluster":
-      return await import("./numericDictTermCluster-XPKEYXD7.js");
-    case "profileBarchart2":
-      return await import("./barchart2-CV7RMMRG.js");
-    case "profileForms":
-      return await import("./profileForms-BJRNB2ZF.js");
-    case "profilePlot":
-      return await import("./profilePlot-DDO53C4T.js");
-    case "profilePolar2":
-      return await import("./polar2-LA4MSRRN.js");
-    case "profileRadar2":
-      return await import("./radar2-RTVUJ3AN.js");
-    case "profileRadarFacility2":
-      return await import("./radarFacility2-ZGLZ5AKM.js");
-    case "proteinView":
-      return await import("./proteinView-NFUR42XQ.js");
-    case "proteomeAbundance":
-      return await import("./proteomeAbundance-NH3Y4YC7.js");
-    case "proteomeCohortCompare":
-      return await import("./proteomeCohortCompare-OZVF3X66.js");
-    case "ProteomeInput":
-      return await import("./ProteomeInput-IKEXPCGV.js");
-    case "regression":
-      return await import("./Regression-6F6YP3AX.js");
-    case "report":
-      return await import("./report-37W5OXUM.js");
-    case "runChart2":
-    //See frequencyChart
-    case "frequencyChart":
-      return await import("./RunChart2-CVRPXQH5.js");
-    case "sampleView":
-      return await import("./sampleView-BDC2WPH7.js");
-    case "sampleScatter":
-      return await import("./scatter-ZOWFPGIS.js");
-    case "sc":
-      return await import("./SC-FPXVXBXF.js");
-    case "studyCatalog":
-      return await import("./studyCatalog-6BOWO4PO.js");
-    case "summarizeCnvGeneexp":
-      return await import("./summarizeCnvGeneexp-AMLYJIPU.js");
-    case "summarizeGeneexpSurvival":
-      return await import("./summarizeGeneexpSurvival-IDM7T333.js");
-    case "summarizeMutationDiagnosis":
-      return await import("./summarizeMutationDiagnosis-XZJ4JLW2.js");
-    case "summarizeMutationSurvival":
-      return await import("./summarizeMutationSurvival-ABJ5RL4L.js");
-    case "summarizeMutationCnv":
-      return await import("./summarizeMutationCnv-R6SYSJQC.js");
-    case "summaryInput":
-      return await import("./summaryInput-SJOZETRP.js");
-    case "summary":
-      return await import("./summary-NVYCTE6P.js");
-    case "survival":
-      return await import("./survival-DVG6Y2FV.js");
-    case "table":
-      return await import("./table-YCTSMLQL.js");
-    case "violin":
-      return await import("./Violin-BAS6DQHL.js");
-    case "volcano":
-      return await import("./Volcano-FCCWUMX7.js");
-    case "wsi":
-      return await import("./Wsi-3YTFABWG.js");
-    default:
-      if (notFoundMessage) throw notFoundMessage;
-      return await globImport_plots_js(`../plots/${chartType}.js`);
-  }
-}
-
-export {
-  importPlot
-};
-//# sourceMappingURL=chunk-DMWOK4DS.js.map

package/dist/chunk-E7NVJ44Z.js

@@ -1,263 +0,0 @@
-import {
-  Matrix
-} from "./chunk-3WYUHDDP.js";
-import {
-  hierCluster_renderers_exports
-} from "./chunk-BPGZUNLL.js";
-import {
-  hierCluster_interactivity_exports
-} from "./chunk-BGVGN73F.js";
-import {
-  filterJoin,
-  getNormalRoot
-} from "./chunk-QJ3HYZH3.js";
-import {
-  clusterMethodLst,
-  distanceMethodLst,
-  dofetch3
-} from "./chunk-VMRO6DMC.js";
-import {
-  TermTypes2Dt,
-  dictionaryNumericTypes
-} from "./chunk-GMRIEUBW.js";
-import {
-  colorScaleMap
-} from "./chunk-4EZLVENZ.js";
-import {
-  deepEqual,
-  getCompInit
-} from "./chunk-WINIL2KN.js";
-import {
-  extent,
-  linear
-} from "./chunk-4OLM3KSB.js";
-
-// plots/matrix/hierCluster.js
-var HierCluster = class _HierCluster extends Matrix {
-  static type = "hierCluster";
-  constructor(opts) {
-    super(opts);
-    this.type = _HierCluster.type;
-    this.chartType = _HierCluster.type;
-  }
-  async init(appState) {
-    await super.init(appState);
-    this.maySetSandboxHeader(appState);
-    this.hcClipId = this.seriesClipId + "-hc";
-    this.dom.hcClipRect = this.dom.svg.select("defs").append("clipPath").attr("id", this.hcClipId).attr("clipPathUnits", "userSpaceOnUse").append("rect").attr("display", "block");
-    this.dom.topDendrogram = this.dom.svg.insert("g", "g").attr("clip-path", `url(#${this.hcClipId})`).append("g").attr("class", "sjpp-matrix-dendrogram").attr("data-testid", "hierCluster_top_dendrogram").on("click", (event) => {
-      const clickedClusterId = this.getClusterFromTopDendrogram(event);
-      if (clickedClusterId) {
-        this.clickedClusterIds = this.getAllChildrenClusterIds(clickedClusterId);
-        this.clickedClusterIds.push(clickedClusterId);
-        const clickedCluster = this.hierClusterData.clustering.col.mergedClusters.get(clickedClusterId);
-        const clickedClusterSampleNames = clickedCluster.children.map((c) => c.name);
-        this.addSelectedSamplesOptions(clickedClusterSampleNames, event);
-      } else {
-        delete this.clickedClusterIds;
-      }
-      if (this.clickedLeftClusterIds) {
-        delete this.clickedLeftClusterIds;
-        this.plotDendrogramHclust();
-      } else this.plotDendrogramHclust("top");
-    });
-    this.dom.leftDendrogram = this.dom.svg.insert("g", "g").attr("class", "sjpp-matrix-dendrogram").attr("data-testid", "hierCluster_left_dendrogram").on("click", (event) => {
-      const clickedLeftClusterId = this.getClusterFromLeftDendrogram(event);
-      if (clickedLeftClusterId) {
-        this.clickedLeftClusterIds = this.getAllChildrenClusterIds(clickedLeftClusterId, true);
-        this.clickedLeftClusterIds.push(clickedLeftClusterId);
-        const clickedLeftCluster = this.hierClusterData.clustering.row.mergedClusters.get(clickedLeftClusterId);
-        const clickedLeftClusterRowsNames = clickedLeftCluster.children.map((c) => c.name);
-        this.addSelectedRowsOptions(clickedLeftClusterRowsNames, event);
-      } else {
-        delete this.clickedLeftClusterIds;
-      }
-      if (this.clickedClusterIds) {
-        delete this.clickedClusterIds;
-        this.plotDendrogramHclust();
-      } else this.plotDendrogramHclust("left");
-    });
-  }
-  async setHierClusterData(_data = {}) {
-    this.prevServerData = this.currServerData;
-    const [d, twlst] = await this.requestData({});
-    if (d.error) throw d.error;
-    this.currServerData = structuredClone(d);
-    if (!deepEqual(this.prevServerData, this.currServerData)) {
-      delete this.clickedClusterIds;
-      delete this.clickedLeftClusterIds;
-    }
-    const s = this.settings.hierCluster;
-    if (!d.clustering) {
-      if (d.gene) {
-        throw `Cannot do clustering: data is only available for 1 gene (${d.gene}). Try again by adding more genes.`;
-      }
-    }
-    this.hierClusterData = d;
-    const c = this.hierClusterData.clustering;
-    this.setHierColorScale(c);
-    const samples = {};
-    for (const [i, column] of c.col.order.entries()) {
-      samples[column.name] = { sample: column.name };
-      for (const [j, row] of c.row.order.entries()) {
-        const tw = twlst.find((tw2) => tw2.$id === row.name || tw2.id === row.name);
-        const value = c.matrix[j][i];
-        samples[column.name][tw.$id] = {
-          key: tw.term.name,
-          values: [
-            {
-              sample: column.name,
-              dt: TermTypes2Dt[this.state.config.dataType],
-              label: s.termGroupName,
-              // gene: tw.term.name,
-              // chr: tw.term.chr,
-              // pos: `${tw.term.start}-${tw.term.stop}`,
-              value
-              // the color will be computed in matrix.cells, so that
-              // it can get updated even when there are no nonsetting state diff
-            }
-          ]
-        };
-      }
-    }
-    this.hcTermNameOrder = this.settings.hierCluster.sortClusterRows == "asListed" ? twlst.map((t) => t.term.name) : this.settings.hierCluster.sortClusterRows == "byName" ? twlst.map((t) => t.term.name).sort() : dictionaryNumericTypes.has(this.config.dataType) ? c.row.order.map((row) => twlst.find((t) => t.$id == row.name || t.term.id == row.name)?.term.name) : c.row.order.map((row) => twlst.find((t) => t.$id == row.name)?.term.name);
-    if (this.hcTermNameOrder.includes(void 0)) throw `unable to map row.name to term.name`;
-    this.hcTermSorter = (a, b) => {
-      const i = this.hcTermNameOrder.indexOf(a.tw.term.name);
-      const j = this.hcTermNameOrder.indexOf(b.tw.term.name);
-      if (i == -1 && j == -1) return 0;
-      if (i == -1) return 1;
-      if (j == -1) return -1;
-      return i - j;
-    };
-    this.hcSampleNameOrder = c.col.order.map((col) => col.name);
-    this.hcSampleSorter = (a, b) => {
-      const i = this.hcSampleNameOrder.indexOf(a.sample);
-      const j = this.hcSampleNameOrder.indexOf(b.sample);
-      if (i == -1 && j == -1) return 0;
-      if (i == -1) return 1;
-      if (j == -1) return -1;
-      return i - j;
-    };
-    const byTermId = {};
-    for (const tw of twlst) {
-      if (d.byTermId?.[tw.term.name]) byTermId[tw.$id] = d.byTermId[tw.term.name];
-    }
-    this.hierClusterSamples = {
-      refs: { byTermId, bySampleId: d.bySampleId },
-      lst: c.col.order.map((c2) => samples[c2.name]),
-      samples,
-      removedHierClusterTerms: d.removedHierClusterTerms
-    };
-  }
-  async requestData() {
-    const body = this.currRequestOpts?.hierCluster || this.getHCRequestBody(this.state);
-    const twlst = this.hcTermGroup.lst;
-    const data = await dofetch3("termdb/cluster", { body, signal: this.api.getAbortSignal?.() });
-    return [data, twlst];
-  }
-  getHCRequestBody(state) {
-    this.hcTermGroup = this.config.termgroups.find((grp) => grp.type == "hierCluster") || this.termOrder?.find((t) => t.grp.type == "hierCluster")?.grp;
-    const s = state.config.settings.hierCluster;
-    const dictionaryLegendFilter = {
-      type: "tvslst",
-      in: true,
-      join: "and",
-      lst: state.config.legendValueFilter.lst.filter((f) => !f.tvs.legendFilterType)
-    };
-    const terms = this.getClusterRowTermsAsParameter();
-    if (!terms.length) throw "no data";
-    if (!clusterMethodLst.find((i) => i.value == s.clusterMethod)) throw "Invalid cluster method";
-    if (!distanceMethodLst.find((i) => i.value == s.distanceMethod)) throw "Invalid distance method";
-    const body = {
-      genome: state.vocab.genome,
-      dslabel: state.vocab.dslabel,
-      dataType: state.config.dataType,
-      clusterMethod: s.clusterMethod,
-      distanceMethod: s.distanceMethod,
-      zScoreTransformation: s.zScoreTransformation,
-      terms,
-      filter: getNormalRoot(filterJoin([state.filter, dictionaryLegendFilter])),
-      filter0: state.filter0
-    };
-    if (state.config.dataType == "proteomeAbundance") {
-      body.proteomeDetails = {
-        organism: state.config.proteomeDetails?.organism,
-        assay: state.config.proteomeDetails?.assay,
-        cohort: state.config.proteomeDetails?.cohort
-      };
-    }
-    return body;
-  }
-  combineData() {
-    if (!this.hierClusterSamples) return;
-    const d = this.data;
-    const removedHierClusterTerms = this.hierClusterSamples.removedHierClusterTerms;
-    const samples = {};
-    const lst = [];
-    for (const sampleId in this.hierClusterSamples.samples) {
-      const s = this.hierClusterSamples.samples[sampleId];
-      samples[sampleId] = s;
-      lst.push(s);
-      if (sampleId in d.samples) Object.assign(s, d.samples[sampleId]);
-      const _ref_ = this.hierClusterSamples.refs.bySampleId[sampleId] || {};
-      if (!s._ref_) s._ref_ = _ref_;
-      else Object.assign(s._ref_, _ref_);
-    }
-    const t = this.hierClusterSamples.refs.byTermId;
-    for (const $id of Object.keys(t)) {
-      d.refs.byTermId[$id] = Object.assign({}, d.refs.byTermId[$id] || {}, t[$id]);
-    }
-    this.data = { samples, lst, refs: d.refs, removedHierClusterTerms };
-  }
-  setHierColorScale(c) {
-    const hc = this.settings.hierCluster;
-    const scale = linear(colorScaleMap[hc.colorScale].domain, colorScaleMap[hc.colorScale].range).clamp(true);
-    const globalMinMaxes = [];
-    for (const row of c.matrix) {
-      globalMinMaxes.push(...extent(row));
-    }
-    const absMax = Math.min(hc.zScoreCap, Math.max(...extent(globalMinMaxes).map(Math.abs)));
-    const [min, max] = hc.zScoreTransformation ? [-absMax, absMax] : [Math.min(...globalMinMaxes), Math.max(...globalMinMaxes)];
-    this.hierClusterValues = { scale, min, max };
-  }
-  getValueColor(value) {
-    const hc = this.settings.hierCluster;
-    if (hc.zScoreTransformation) {
-      const zScoreCap = this.settings.hierCluster.zScoreCap;
-      return this.hierClusterValues.scale((value - -zScoreCap) / (zScoreCap * 2));
-    } else {
-      return this.hierClusterValues.scale(value / this.hierClusterValues.max);
-    }
-  }
-  /* returns list of gene terms as request parameter, e.g. {gene,chr,start,stop}
-  	request parameter only need term but not tw, as it will simply fetch continuous sample values on terms without transform
-  
-  	use of this function is unfortunate because:
-  		the incomplete migration of {name} to {gene} for gene-based term
-  		geneset edit ui is hardcoded to return {name}
-  		existing plot states contain {name}
-  
-  	!!! migration instruction !!!
-  	- term.name is for display only, if a term is gene-based, it has term.gene=str
-  	- a geneVariant term can be based on a genomic range (and not a gene), in that case it won't have term.gene and cannot be used where gene is expected, e.g. gene-based clustering analysis
-  
-  	*/
-  getClusterRowTermsAsParameter() {
-    const lst = this.hcTermGroup.lst.map(this.opts.app.vocabApi.getTwMinCopy);
-    lst.sort((a, b) => a.term.name < b.term.name ? -1 : 1);
-    return lst;
-  }
-};
-for (const methods of [hierCluster_renderers_exports, hierCluster_interactivity_exports]) {
-  for (const methodName in methods) HierCluster.prototype[methodName] = methods[methodName];
-}
-var hierClusterInit = getCompInit(HierCluster);
-var componentInit = hierClusterInit;
-
-export {
-  HierCluster,
-  hierClusterInit,
-  componentInit
-};
-//# sourceMappingURL=chunk-E7NVJ44Z.js.map