@sjcrh/proteinpaint-client 2.206.0 → 2.207.0

package/dist/cellTypeBubbleHeatmap-DXPLFT5U.js

@@ -1,278 +0,0 @@
-import {
-  LegendCircleReference,
-  PlotBase,
-  addGeneSearchbox
-} from "./chunk-Q5SK3U2T.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-54KC7DAB.js";
-import "./chunk-N7DVQTPC.js";
-import {
-  Menu
-} from "./chunk-ELJX3QIQ.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import {
-  dofetch3
-} from "./chunk-RPDVFM7E.js";
-import "./chunk-M4XXKTH2.js";
-import "./chunk-5ILEFNXJ.js";
-import "./chunk-IZUYLFOX.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import {
-  linear,
-  sqrt
-} from "./chunk-4OLM3KSB.js";
-import "./chunk-FXQXCOII.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// plots/cellTypeBubbleHeatmap.ts
-var defaultConfig = { chartType: "cellTypeBubbleHeatmap" };
-var CELL_W = 84;
-var CELL_H = 60;
-var ROW_LABEL_W = 74;
-var GROUP_LABEL_H = 22;
-var GENO_LABEL_H = 40;
-var COL_LABEL_H = GROUP_LABEL_H + GENO_LABEL_H;
-var MIN_DOT_R = 8;
-var MAX_DOT_R = 22;
-var NEG_LOG_FDR_CAP = 10;
-var COLOR_NEG = "#762a83";
-var COLOR_ZERO = "#f7f7f7";
-var COLOR_POS = "#2166ac";
-var CellTypeBubbleHeatmap = class _CellTypeBubbleHeatmap extends PlotBase {
-  constructor(opts, api) {
-    super(opts, api);
-    this.currentIsoform = "";
-    this.type = _CellTypeBubbleHeatmap.type;
-  }
-  static {
-    this.type = "cellTypeBubbleHeatmap";
-  }
-  async init() {
-    const holder = this.opts.holder.append("div").style("padding", "10px");
-    this.dom = {
-      holder,
-      body: holder.append("div"),
-      tip: new Menu({ padding: "" }),
-      header: this.opts.header
-    };
-    if (this.dom.header) this.dom.header.html("Cell-type Bubble Heatmap");
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) throw `No plot with id='${this.id}' found`;
-    return { config };
-  }
-  async main() {
-    const gene = this.state.config?.gene;
-    if (!gene) throw new Error("cellTypeBubbleHeatmap: gene is missing");
-    if (this.dom.header) this.dom.header.text(`Cell-type Bubble Heatmap: ${gene}`);
-    const body = {
-      genome: this.app.opts.state.vocab.genome,
-      dslabel: this.app.opts.state.vocab.dslabel,
-      gene
-    };
-    const data = await dofetch3("termdb/cellTypeBubbleHeatmap", { body });
-    if (data.error) throw data.error;
-    this.data = data;
-    this.dom.body.selectAll("*").remove();
-    const isoformIds = Object.keys(data.isoforms);
-    if (isoformIds.length === 0) {
-      this.dom.body.append("div").style("padding", "20px").style("color", "#666").text(`No data found for gene "${gene}" in any cohort DAPfile.`);
-      return;
-    }
-    this.currentIsoform = isoformIds[0];
-    const isoBlock = this.dom.body.append("div").style("margin-bottom", "12px");
-    isoBlock.append("span").style("font-weight", "bold").text("Isoform: ");
-    if (isoformIds.length > 1) {
-      const sel = isoBlock.append("select").style("margin-left", "5px").style("padding", "3px 6px").on("change", () => {
-        this.currentIsoform = sel.node().value;
-        this.renderGrid();
-      });
-      sel.selectAll("option").data(isoformIds).enter().append("option").attr("value", (d) => d).text((d) => `${data.isoforms[d].gene_name} \u2014 ${d}`);
-    } else {
-      isoBlock.append("span").style("margin-left", "5px").text(`${data.isoforms[this.currentIsoform].gene_name} \u2014 ${this.currentIsoform}`);
-    }
-    this.gridHolder = this.dom.body.append("div");
-    this.renderGrid();
-  }
-  renderGrid() {
-    const data = this.data;
-    const selectedIsoform = this.currentIsoform;
-    const threshold = data.fdrThreshold;
-    this.gridHolder.selectAll("*").remove();
-    const container = this.gridHolder.append("div").style("display", "flex").style("gap", "24px").style("align-items", "flex-start").style("flex-wrap", "wrap");
-    const isoformData = data.isoforms[selectedIsoform];
-    if (!isoformData) return;
-    const columns = data.columns;
-    const rows = data.rows;
-    const nCols = columns.length;
-    const nRows = rows.length;
-    const negLogFdr = (fdr) => fdr > 0 ? Math.min(-Math.log10(fdr), NEG_LOG_FDR_CAP) : NEG_LOG_FDR_CAP;
-    const cellOf = (colKey, rowKey) => isoformData.data[colKey]?.[rowKey];
-    let maxAbs = 0;
-    const thresholdNegLog = negLogFdr(threshold);
-    let maxNegLog = thresholdNegLog;
-    for (const col of columns) {
-      for (const row of rows) {
-        const s = cellOf(col.key, row.key);
-        if (!s) continue;
-        const v = Math.abs(s.log2FC);
-        if (v > maxAbs) maxAbs = v;
-        const nl = negLogFdr(s.fdr);
-        if (nl > maxNegLog) maxNegLog = nl;
-      }
-    }
-    if (maxAbs === 0) maxAbs = 1;
-    if (maxNegLog <= thresholdNegLog) maxNegLog = thresholdNegLog + 1;
-    const colorScale = linear().domain([-maxAbs, 0, maxAbs]).range([COLOR_NEG, COLOR_ZERO, COLOR_POS]).clamp(true);
-    const sizeScale = sqrt().domain([thresholdNegLog, maxNegLog]).range([MIN_DOT_R, MAX_DOT_R]).clamp(true);
-    const gridW = ROW_LABEL_W + nCols * CELL_W + 20;
-    const gridH = COL_LABEL_H + nRows * CELL_H + 20;
-    const svg = container.append("svg").attr("width", gridW).attr("height", gridH).style("flex", "0 0 auto");
-    const grid = svg.append("g");
-    let c = 0;
-    while (c < nCols) {
-      const cellType = columns[c].cellType;
-      let end = c;
-      while (end + 1 < nCols && columns[end + 1].cellType === cellType) end++;
-      const xStart = ROW_LABEL_W + c * CELL_W;
-      const xEnd = ROW_LABEL_W + (end + 1) * CELL_W;
-      const xMid = (xStart + xEnd) / 2;
-      grid.append("text").attr("x", xMid).attr("y", GROUP_LABEL_H - 7).attr("text-anchor", "middle").attr("font-size", "13px").attr("font-weight", "bold").text(cellType);
-      grid.append("line").attr("x1", xStart + 4).attr("y1", GROUP_LABEL_H - 3).attr("x2", xEnd - 4).attr("y2", GROUP_LABEL_H - 3).attr("stroke", "#bbb").attr("stroke-width", 1);
-      c = end + 1;
-    }
-    for (let col = 0; col < nCols; col++) {
-      const cx = ROW_LABEL_W + col * CELL_W + CELL_W / 2;
-      grid.append("text").attr("x", cx).attr("y", COL_LABEL_H - 14).attr("text-anchor", "middle").attr("font-size", "12px").attr("font-weight", "600").text(columns[col].genotype);
-    }
-    for (let r = 0; r < nRows; r++) {
-      const cy = COL_LABEL_H + r * CELL_H + CELL_H / 2;
-      grid.append("text").attr("x", ROW_LABEL_W - 12).attr("y", cy).attr("text-anchor", "end").attr("dominant-baseline", "central").attr("font-size", "13px").attr("font-weight", "bold").text(rows[r].label);
-    }
-    for (let r = 0; r < nRows; r++) {
-      for (let col = 0; col < nCols; col++) {
-        const x0 = ROW_LABEL_W + col * CELL_W;
-        const y0 = COL_LABEL_H + r * CELL_H;
-        grid.append("rect").attr("x", x0).attr("y", y0).attr("width", CELL_W).attr("height", CELL_H).attr("fill", "none").attr("stroke", "#eee").attr("stroke-width", 1);
-        const s = cellOf(columns[col].key, rows[r].key);
-        if (!s) continue;
-        const cx = x0 + CELL_W / 2;
-        const cy = y0 + CELL_H / 2;
-        grid.append("circle").attr("cx", cx).attr("cy", cy).attr("r", sizeScale(negLogFdr(s.fdr))).attr("fill", colorScale(s.log2FC)).attr("stroke", "#888").attr("stroke-width", 0.8).style("opacity", s.significant ? 1 : 0.35).on(
-          "mouseover",
-          (event) => this.showCellTip(event, isoformData.gene_name, selectedIsoform, columns[col], rows[r], s)
-        ).on("mouseout", () => this.dom.tip.hide());
-      }
-    }
-    this.renderLegend(container, colorScale, maxAbs, threshold, maxNegLog);
-  }
-  fmtFdr(v) {
-    return v >= 1e-4 ? v.toFixed(4) : v.toExponential(2);
-  }
-  showCellTip(event, geneName, isoform, col, row, s) {
-    this.dom.tip.clear().show(event.clientX, event.clientY);
-    const t = this.dom.tip.d.append("div").style("padding", "8px").style("font-size", "13px");
-    t.append("div").style("font-weight", "bold").style("margin-bottom", "4px").text(`${geneName} \u2014 ${isoform}`);
-    t.append("div").text(`Cell type: ${col.cellType}`);
-    t.append("div").text(`Genotype: ${col.genotype}`);
-    t.append("div").text(`Timepoint: ${row.label}`);
-    t.append("div").text(`Protein: ${s.id}`);
-    t.append("div").text(`log\u2082FC: ${s.log2FC.toFixed(3)}`);
-    t.append("div").text(`FDR: ${this.fmtFdr(s.fdr)}${s.significant ? "" : " (n.s.)"}`);
-    t.append("div").style("color", "#666").style("margin-top", "4px").text("Color = log\u2082FC (blue up / purple down). Size = \u2212log\u2081\u2080 FDR.");
-  }
-  renderLegend(container, colorScale, maxAbs, threshold, maxNegLog) {
-    const legend = container.append("div").style("display", "flex").style("flex-direction", "column").style("gap", "16px").style("padding", "8px 0").style("min-width", "180px").style("max-width", "260px");
-    const colorBlock = legend.append("div");
-    colorBlock.append("div").style("font-weight", "bold").style("font-size", "13px").style("margin-bottom", "6px").text("log\u2082FC");
-    const cW = 22;
-    const cH = 130;
-    const cSvg = colorBlock.append("svg").attr("width", cW + 80).attr("height", cH + 16);
-    const gid = `ctbh-grad-${this.id}`;
-    const grad = cSvg.append("defs").append("linearGradient").attr("id", gid).attr("x1", "0").attr("y1", "0").attr("x2", "0").attr("y2", "1");
-    const steps = 10;
-    for (let i = 0; i <= steps; i++) {
-      const t = i / steps;
-      grad.append("stop").attr("offset", `${t * 100}%`).attr("stop-color", colorScale(maxAbs * (1 - 2 * t)));
-    }
-    cSvg.append("rect").attr("x", 0).attr("y", 8).attr("width", cW).attr("height", cH).style("fill", `url(#${gid})`).attr("stroke", "#999");
-    const cScale = linear().domain([maxAbs, -maxAbs]).range([8, cH + 8]);
-    for (const tick of [maxAbs, maxAbs / 2, 0, -maxAbs / 2, -maxAbs]) {
-      const y = cScale(tick);
-      cSvg.append("line").attr("x1", cW).attr("y1", y).attr("x2", cW + 5).attr("y2", y).attr("stroke", "#666");
-      cSvg.append("text").attr("x", cW + 8).attr("y", y).attr("dominant-baseline", "central").attr("font-size", "10px").text(`${tick > 0 ? "+" : ""}${tick.toFixed(2)}`);
-    }
-    colorBlock.append("div").style("font-size", "11px").style("color", "#666").style("margin-top", "2px").text("blue = up (+), purple = down (\u2212)");
-    const sizeBlock = legend.append("div");
-    sizeBlock.append("div").style("font-weight", "bold").style("font-size", "13px").style("margin-bottom", "6px").text("Dot size: significance (\u2212log\u2081\u2080 FDR)");
-    const sSvg = sizeBlock.append("svg");
-    const sG = sSvg.append("g");
-    new LegendCircleReference({
-      g: sG,
-      inputMin: 0,
-      inputMax: MAX_DOT_R * 2,
-      minRadius: MIN_DOT_R,
-      maxRadius: MAX_DOT_R,
-      minLabel: Number(Math.min(-Math.log10(threshold), NEG_LOG_FDR_CAP).toFixed(1)),
-      maxLabel: Number(maxNegLog.toFixed(1))
-    });
-    const sPad = 4;
-    const sBox = sG.node().getBBox();
-    sG.attr("transform", `translate(${sPad - sBox.x}, ${sPad - sBox.y})`);
-    sSvg.attr("width", Math.ceil(sBox.width + 2 * sPad)).attr("height", Math.ceil(sBox.height + 2 * sPad));
-    const notes = legend.append("div").style("font-size", "11px").style("color", "#666").style("line-height", "1.5").style("max-width", "240px").style("overflow-wrap", "break-word");
-    notes.append("div").text(
-      `Color = log\u2082FC (blue up, purple down). Dot size = significance, \u2212log\u2081\u2080 FDR; the smallest size marks the FDR < ${threshold} cutoff. Non-significant dots (FDR \u2265 ${threshold}) are faded.`
-    );
-    notes.append("div").style("margin-top", "4px").text("An empty cell means the cohort was not assayed (e.g. OPC has no 4m) or the protein was not detected.");
-  }
-};
-var componentInit = getCompInit(CellTypeBubbleHeatmap);
-async function getPlotConfig(opts) {
-  const config = structuredClone(defaultConfig);
-  if (!opts.gene) throw new Error("cellTypeBubbleHeatmap requires opts.gene");
-  return copyMerge(config, opts);
-}
-function makeChartBtnMenu(holder, chartsInstance) {
-  const row = holder.append("div").style("padding", "5px");
-  row.append("span").style("font-weight", "bold").text("Enter a gene name:");
-  const geneSearch = addGeneSearchbox({
-    row,
-    genome: chartsInstance.app.opts.genome,
-    tip: new Menu({ padding: "0px" }),
-    searchOnly: "gene",
-    callback: async () => {
-      if (!geneSearch.geneSymbol) throw new Error("A valid gene selection is required");
-      chartsInstance.dom.tip.hide();
-      chartsInstance.app.dispatch({
-        type: "plot_create",
-        config: {
-          chartType: "cellTypeBubbleHeatmap",
-          gene: geneSearch.geneSymbol
-        }
-      });
-    }
-  });
-}
-export {
-  componentInit,
-  getPlotConfig,
-  makeChartBtnMenu
-};
-//# sourceMappingURL=cellTypeBubbleHeatmap-DXPLFT5U.js.map

package/dist/chunk-2BQ572SL.js

@@ -1,102 +0,0 @@
-import {
-  getPlotConfig
-} from "./chunk-FTLCINDC.js";
-import {
-  fillTermWrapper
-} from "./chunk-Q5SK3U2T.js";
-import {
-  dictionaryNumericTypes,
-  numericTypes
-} from "./chunk-5ILEFNXJ.js";
-import {
-  copyMerge
-} from "./chunk-WINIL2KN.js";
-
-// plots/matrix/hierCluster.config.js
-async function getPlotConfig2(opts = {}, app) {
-  opts.chartType = "hierCluster";
-  if (dictionaryNumericTypes.has(opts.dataType) || opts.dataType == "numericDictTerm") {
-    const grp = opts.termgroups?.find((g) => g.type == "hierCluster");
-    for (const tw of grp?.lst || []) tw.q = { ...tw.q, mode: "continuous" };
-  }
-  const config = await getPlotConfig(opts, app);
-  delete config.genes;
-  if (config.dataType == "numericDictTerm") {
-    const lst = config.termgroups?.find((g) => g.type == "hierCluster")?.lst;
-    config.dataType = lst?.[0]?.term?.type || "float";
-  }
-  config.settings.hierCluster = {
-    /* type of data used for clustering
-    exciting todo: (to introduce new dt values)
-    - gene dependency
-    - numeric dic term
-    - non-gene genomic stuff that resolves into numeric quantities (cpg meth)
-    - metabolite
-    */
-    dataType: config.dataType,
-    // adjust the default group name based on automatically detected term types
-    // Done in matrix.cells.js: setHierClusterCellProps
-    // termGroupName: 'Expression',
-    clusterSamples: true,
-    clusterRows: true,
-    clusterMethod: "average",
-    // complete
-    distanceMethod: "euclidean",
-    zScoreCap: 5,
-    zScoreTransformation: true,
-    xDendrogramHeight: 100,
-    yDendrogramHeight: 200,
-    colorScale: "blueWhiteRed"
-  };
-  const overrides = app.vocabApi.termdbConfig.hierCluster || {};
-  const numericDictTermClusterOverrides = dictionaryNumericTypes.has(config.dataType) && app.vocabApi.termdbConfig.numericDictTermCluster ? app.vocabApi.termdbConfig.numericDictTermCluster : {};
-  copyMerge(
-    config.settings.hierCluster,
-    overrides.settings,
-    opts.settings?.hierCluster || {},
-    numericDictTermClusterOverrides.settings
-  );
-  {
-    const c = config.settings.hierCluster.colorScale;
-    if (!c) throw "colorScale missing";
-  }
-  config.settings.matrix.collabelpos = "top";
-  const termGroupName = config.settings.hierCluster.termGroupName;
-  const hcTermGroup = config.termgroups.find((g) => g.type == "hierCluster" || g.name == termGroupName) || {
-    name: termGroupName
-  };
-  hcTermGroup.type = "hierCluster";
-  if (!hcTermGroup.lst?.length) {
-    if (!Array.isArray(opts.terms)) throw "opts.terms[] not array (may show geneset edit ui)";
-    const promises = [];
-    for (const i of opts.terms) {
-      const tw = i.term ? i : { term: i };
-      if (!tw.term.type) {
-        if (config.dataType && numericTypes.has(config.dataType)) {
-          tw.term.type = config.dataType;
-        } else {
-          throw `term type missing and cannot be assigned by dataType '${config.dataType}'`;
-        }
-      } else if (!numericTypes.has(tw.term.type)) {
-        throw "term type is not numeric";
-      } else if (config.dataType && !canTermBeInHierGrp(config.dataType, tw.term.type)) {
-        throw `cannot have term type ${tw.term.type} in ${config.dataType} term group`;
-      }
-      if (dictionaryNumericTypes.has(tw.term.type)) tw.q = { ...tw.q, mode: "continuous" };
-      promises.push(fillTermWrapper(tw, app.vocabApi));
-    }
-    hcTermGroup.lst = await Promise.all(promises);
-    if (config.termgroups.indexOf(hcTermGroup) == -1) config.termgroups.unshift(hcTermGroup);
-  }
-  config.settings.matrix.maxSample = 1e5;
-  return config;
-}
-function canTermBeInHierGrp(grpType, twType) {
-  if (dictionaryNumericTypes.has(grpType) && dictionaryNumericTypes.has(twType)) return true;
-  return twType == grpType;
-}
-
-export {
-  getPlotConfig2 as getPlotConfig
-};
-//# sourceMappingURL=chunk-2BQ572SL.js.map

package/dist/chunk-2DQIQYY3.js

@@ -1,103 +0,0 @@
-import {
-  SearchHandler,
-  fillTermWrapper,
-  table2col,
-  termsettingInit
-} from "./chunk-Q5SK3U2T.js";
-
-// plots/summarizeMutationDiagnosis.ts
-async function makeChartBtnMenu(holder, chartsInstance) {
-  let dictTw;
-  {
-    const t = chartsInstance.app.vocabApi.termdbConfig.defaultTw4correlationPlot?.disease;
-    if (!t) throw "defaultTw4correlationPlot missing";
-    dictTw = structuredClone(t);
-    await fillTermWrapper(dictTw, chartsInstance.app.vocabApi);
-  }
-  const table = table2col({
-    holder: holder.append("div"),
-    margin: "0px 10px 10px 10px",
-    cellPadding: "10px"
-  });
-  {
-    const [td1, td2] = table.addRow();
-    td1.text("Mutation Variable");
-    const searchDiv = td2.append("div");
-    const geneSearchInst = new SearchHandler();
-    geneSearchInst.init({
-      holder: searchDiv,
-      app: chartsInstance.app,
-      // required to supply "opts.app.vocabApi" for the search ui
-      genomeObj: chartsInstance.app.opts.genome,
-      msg: "Hit ENTER to launch plot.",
-      /* the geneTw below is used as it comes, so a grouping the user built for this gene
-      elsewhere can be offered here, see keepsQ in client/termdb/TermTypeSearch.ts */
-      keepsQ: true,
-      callback: async (geneTw) => {
-        await fillTermWrapper(geneTw, chartsInstance.app.vocabApi);
-        launchPlot({
-          tw1: dictTw,
-          tw2: geneTw,
-          chartsInstance,
-          holder
-        });
-      }
-    });
-    searchDiv.style("padding", "0px 0px 5px 0px");
-  }
-  {
-    const [td1, td2] = table.addRow();
-    td1.text("Compare Mutations Against");
-    const pillDiv = td2.append("div"), waitDiv = td2.append("div").style("font-size", ".7em").text("LOADING ...");
-    const pill = await termsettingInit({
-      menuOptions: "{edit,replace}",
-      /** presumably this usecase let it restrict to dictionary term ui, and hide genomic queries
-      target="filter" works for gdc since in gdc ds it is overriding filter to dict
-      but is not a general fix for non-gdc ds, which Replace menu will launch genomic+dict options
-      maybe this is okay for non-gdc ds as the default dictTw is meaningful
-      */
-      usecase: { target: "filter" },
-      vocabApi: chartsInstance.app.vocabApi,
-      holder: pillDiv,
-      callback: async (tw) => {
-        waitDiv.text("LOADING ...");
-        try {
-          await pill.main(tw);
-          dictTw = tw;
-          waitDiv.text("Click to edit/replace the variable before searching gene.");
-        } catch (e) {
-          waitDiv.text("Error: " + (e.message || e));
-        }
-      }
-    });
-    try {
-      await fillTermWrapper(dictTw, chartsInstance.app.vocabApi);
-      await pill.main(dictTw);
-      waitDiv.text("Click to edit/replace the variable before searching gene.");
-    } catch (e) {
-      waitDiv.text("Error: " + (e.message || e));
-    }
-  }
-}
-function launchPlot({ tw1, tw2, chartsInstance, holder }) {
-  const chart = {
-    config: {
-      chartType: tw1?.term?.type == "survival" ? "survival" : "summary",
-      // TODO define sandbox header with gene+term name
-      term: tw1,
-      term2: tw2
-    }
-  };
-  chartsInstance.plotCreate(chart);
-  holder.selectAll("*").remove();
-  holder.append("div").style("margin", "20px").text("LOADING CHART ...");
-  setTimeout(() => {
-    holder.style("display", "none");
-  }, 1e3);
-}
-
-export {
-  makeChartBtnMenu,
-  launchPlot
-};
-//# sourceMappingURL=chunk-2DQIQYY3.js.map

package/dist/chunk-2POQWEK6.js

@@ -1,134 +0,0 @@
-import {
-  addGeneSearchbox,
-  isoformSelect,
-  pickCollectionFraction,
-  sayerror
-} from "./chunk-Q5SK3U2T.js";
-import {
-  Menu
-} from "./chunk-ELJX3QIQ.js";
-import {
-  dofetch3
-} from "./chunk-RPDVFM7E.js";
-import {
-  ISOFORM_EXPRESSION,
-  getColors
-} from "./chunk-IZUYLFOX.js";
-
-// termdb/handlers/isoformExpression.ts
-var SearchHandler = class {
-  constructor() {
-    this.currentGene = null;
-  }
-  init(opts) {
-    this.callback = opts.callback;
-    this.app = opts.app;
-    this.termCollectionSelectionMode = opts.termCollectionSelectionMode;
-    const holder = opts.holder.append("div").style("padding", "10px 0px");
-    this.dom = {
-      errDiv: holder.append("div").style("margin", "5px 0px").style("display", "none")
-    };
-    const geneSearch = addGeneSearchbox({
-      tip: new Menu({ padding: "0px" }),
-      genome: opts.genomeObj,
-      row: holder,
-      searchOnly: "gene",
-      callback: async () => {
-        try {
-          this.dom.errDiv.style("display", "none");
-          if (!geneSearch.geneSymbol) throw new Error("No gene selected");
-          if (geneSearch.geneSymbol === this.currentGene) return;
-          this.currentGene = geneSearch.geneSymbol;
-          if (this.dom.isoformDiv) this.dom.isoformDiv.remove();
-          this.dom.isoformDiv = holder.append("div");
-          await this.showIsoforms(geneSearch.geneSymbol, opts.genomeObj);
-        } catch (e) {
-          this.dom.errDiv.style("display", "block");
-          sayerror(this.dom.errDiv, "Error: " + (e instanceof Error ? e.message : String(e)));
-        }
-      }
-    });
-  }
-  async showIsoforms(gene, genomeObj) {
-    if (!gene) throw new Error("No gene selected");
-    const data = await dofetch3("genelookup", { body: { genome: genomeObj.name, input: gene, deep: 1 } });
-    if (!data.gmlst?.length) throw new Error(`No isoforms found for ${gene}`);
-    const enstCandidates = data.gmlst.filter((gm) => gm.isoform?.startsWith("ENST"));
-    if (enstCandidates.length === 0) throw new Error(`No Ensembl transcript isoforms found for ${gene}`);
-    const { available } = await dofetch3("termdb/isoformAvailability", {
-      body: {
-        genome: genomeObj.name,
-        dslabel: this.app.vocabApi.vocab.dslabel,
-        isoforms: enstCandidates.map((gm) => gm.isoform)
-      }
-    });
-    const availableSet = new Set(available || []);
-    const enstModels = enstCandidates.filter((gm) => availableSet.has(gm.isoform));
-    if (enstModels.length === 0) throw new Error(`No isoforms with data found for ${gene}`);
-    if (gene !== this.currentGene) return;
-    const div = this.dom.isoformDiv;
-    div.append("div").style("margin-bottom", "8px").style("opacity", 0.65).text(`${gene} \u2014 select isoform(s):`);
-    isoformSelect({
-      holder: div,
-      allgm: enstModels,
-      multiSelect: true,
-      // a single checked isoform yields an individual term, 2+ yield a collection
-      getSubmitLabel: (selectedCount) => selectedCount === 1 ? "Select One Isoform" : `Create Collection (${selectedCount})`,
-      onMultiSelect: (selected) => {
-        if (selected.length === 1) {
-          this.selectIsoform(selected[0].isoform, gene);
-        } else {
-          this.selectCollection(selected, gene);
-        }
-      }
-    });
-  }
-  getUnit() {
-    return this.app.vocabApi.termdbConfig.queries.isoformExpression?.unit || "TPM";
-  }
-  selectIsoform(isoform, gene) {
-    const name = `${isoform} ${this.getUnit()}`;
-    this.callback({ isoform, gene, name, type: ISOFORM_EXPRESSION });
-  }
-  selectCollection(gms, gene) {
-    const unit = this.getUnit();
-    const termlst = gms.map((gm) => ({
-      id: gm.isoform,
-      name: gm.isoform,
-      type: ISOFORM_EXPRESSION,
-      isoform: gm.isoform
-    }));
-    const colorScale = getColors(termlst.length);
-    const term = {
-      type: "termCollection",
-      isCustom: true,
-      memberType: "numeric",
-      name: `${gene} Isoforms (${unit})`,
-      termlst,
-      propsByTermId: Object.fromEntries(termlst.map((term2) => [term2.id, { color: colorScale(term2.id) }])),
-      isleaf: true
-    };
-    if (this.termCollectionSelectionMode === "fraction") {
-      if (!this.dom?.isoformDiv) throw new Error("isoform result holder is missing");
-      this.dom.fractionDiv?.remove();
-      this.dom.fractionDiv = this.dom.isoformDiv.append("div").style("margin-top", "10px");
-      pickCollectionFraction({
-        holder: this.dom.fractionDiv,
-        term,
-        callback: (tw) => this.callback(tw)
-      });
-      return;
-    }
-    this.callback(term);
-  }
-};
-function filterIsoforms(gmlst, availableItems) {
-  const itemSet = new Set(availableItems);
-  return gmlst.filter((gm) => gm.isoform?.startsWith("ENST") && (itemSet.size === 0 || itemSet.has(gm.isoform)));
-}
-
-export {
-  SearchHandler,
-  filterIsoforms
-};
-//# sourceMappingURL=chunk-2POQWEK6.js.map