@sjcrh/proteinpaint-client 2.181.0 → 2.182.0

package/dist/chunk-LLPFFNLV.js

@@ -1,526 +0,0 @@
-import {
-  matrix_layout_exports
-} from "./chunk-AG6HVFQY.js";
-import {
-  matrix_serieses_exports
-} from "./chunk-FP5VKE3Z.js";
-import {
-  matrix_legend_exports
-} from "./chunk-U3UR3U3F.js";
-import {
-  matrix_groups_exports
-} from "./chunk-O64UTRAC.js";
-import {
-  setComputedConfig
-} from "./chunk-N46WTUX7.js";
-import {
-  setMatrixDom
-} from "./chunk-IC7SUXJD.js";
-import {
-  setInteractivity
-} from "./chunk-QXCVG66S.js";
-import {
-  setRenderers
-} from "./chunk-BQLC6QOH.js";
-import {
-  MatrixCluster
-} from "./chunk-A5TSPTYC.js";
-import {
-  MatrixControls
-} from "./chunk-TTSNECVD.js";
-import {
-  matrix_data_exports
-} from "./chunk-NBMJ2UMA.js";
-import {
-  PlotBase,
-  TwRouter,
-  getCombinedTermFilter,
-  rebaseGroupFilter,
-  routedTermTypes,
-  sayerror,
-  svgLegend
-} from "./chunk-XZZLEHWC.js";
-import {
-  copyMerge,
-  deepEqual,
-  getCompInit
-} from "./chunk-MVTCBVSX.js";
-import {
-  dt2label,
-  mclass,
-  morigin
-} from "./chunk-ZLH4PJKX.js";
-import {
-  convertUnits
-} from "./chunk-TV74I3Y5.js";
-import {
-  select_default
-} from "./chunk-NDWTN4U5.js";
-
-// plots/matrix/matrix.xtw.ts
-var addons;
-async function getTermGroups(termgroups, app) {
-  const termGroups = structuredClone(termgroups);
-  if (!addons)
-    addons = {
-      QualTWValues: discreteAddons,
-      QualTWPredefinedGS: discreteAddons,
-      QualTWCustomGS: discreteAddons,
-      NumTWRegularBin: discreteAddons,
-      NumTWCustomBin: discreteAddons,
-      NumTWCont: continuousAddons,
-      TermCollectionTWCont: TermCollectionContAddons
-    };
-  const opts = {
-    vocabApi: app.vocabApi,
-    addons
-  };
-  for (const [origIndex, tG] of termGroups.entries()) {
-    tG.origIndex = origIndex;
-    if (tG.type == "hierCluster") continue;
-    const xtwlst = [];
-    for (const tw of tG.lst) {
-      const inputTw = tw.getTw?.() || tw;
-      xtwlst.push(
-        inputTw.type in opts.addons && routedTermTypes.has(inputTw.term.type) ? await TwRouter.init(inputTw, opts) : inputTw
-      );
-    }
-    tG.lst = xtwlst;
-  }
-  return termGroups;
-}
-var discreteAddons = {
-  setCellProps: {
-    value: function(cell, anno, value, s, t, self2, width, height, dx, dy, i) {
-      const tw = this.getTw();
-      const key = anno.key;
-      const values = tw.term.values || {};
-      cell.label = "label" in anno ? anno.label : values[key]?.label ? values[key].label : key;
-      const tw$id = tw.$id;
-      cell.fill = self2.config.settings.matrix.twSpecificSettings?.[tw$id]?.[key]?.color || anno.color || values[anno.key]?.color || self2.data.refs.byTermId?.[tw$id]?.bins?.find((b) => anno.key == b.name)?.color;
-      cell.order = t.ref.bins ? t.ref.bins.findIndex((bin) => bin.name == key) : 0;
-      cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-      cell.y = height * i;
-      const group = tw.legend?.group || tw$id;
-      return { ref: t.ref, group, value: key, entry: { key, label: cell.label, fill: cell.fill } };
-    }
-  }
-};
-var continuousAddons = {
-  setCellProps: {
-    value: function(cell, anno, value, s, t, self2, width, height, dx, dy, i) {
-      const tw = this.getTw();
-      const key = anno.key;
-      const values = tw.term.values || {};
-      cell.label = "label" in anno ? anno.label : values[key]?.label ? values[key].label : key;
-      cell.fill = anno.color || values[anno.key]?.color;
-      const tw$id = tw.$id;
-      const twSpecificSettings = self2.config.settings.matrix.twSpecificSettings;
-      if (!twSpecificSettings[tw$id]) twSpecificSettings[tw$id] = {};
-      const twSettings = twSpecificSettings[tw$id];
-      if (!twSettings.contBarH) twSettings.contBarH = s.barh;
-      if (!("gap" in twSettings)) twSettings.contBarGap = 4;
-      const specialValue = tw.term.values?.[cell.key];
-      if (specialValue?.uncomputable) {
-        cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-        cell.y = height * i;
-        cell.height = twSettings.contBarH;
-        cell.fill = "transparent";
-        cell.label = specialValue.label;
-        const group = tw.legend?.group || tw.$id;
-        return {
-          ref: t.ref,
-          group,
-          value: specialValue.label || specialValue.key,
-          entry: { key, label: cell.label, fill: cell.fill }
-        };
-      }
-      cell.fill = self2.config.settings.matrix.twSpecificSettings?.[tw$id]?.contBarColor || "#555";
-      if (s.transpose) {
-        cell.height = t.scale(cell.key);
-        cell.x = twSettings.contBarGap;
-      } else {
-        const vc = cell.term.valueConversion;
-        let renderV = vc ? cell.key * vc.scaleFactor : cell.key;
-        if (this.q.convert2ZScore) {
-          renderV = (renderV - t.mean) / t.std;
-          cell.fill = renderV > 0 ? "#FF6666" : "#6666FF";
-          cell.zscoreLabel = ` (Z-score: ${renderV.toFixed(2)})`;
-        }
-        cell.label = "label" in anno ? anno.label : values[key]?.label ? values[key].label : this.term.unit ? `${cell.key.toFixed(2)} ${this.term.unit}` : cell.key.toFixed(2);
-        cell.height = renderV >= 0 ? t.scales.pos(renderV) : t.scales.neg(renderV);
-        cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-        cell.y = renderV >= 0 ? t.counts.posMaxHt + twSettings.contBarGap - cell.height : t.counts.posMaxHt + twSettings.contBarGap;
-        cell.convertedValueLabel = !vc ? "" : convertUnits(cell.key, vc.fromUnit, vc.toUnit, vc.scaleFactor);
-      }
-    }
-  }
-};
-var TermCollectionContAddons = {
-  setCellProps: {
-    value: function(cell, anno, value, s, t, self2, width, height, dx, _dy, _i) {
-      const tw = this.getTw();
-      const twSpecificSettings = self2.config.settings.matrix.twSpecificSettings;
-      if (!twSpecificSettings[tw.$id]) twSpecificSettings[tw.$id] = {};
-      const twSettings = twSpecificSettings[tw.$id];
-      if (!twSettings.contBarH) twSettings.contBarH = s.barh;
-      if (!("gap" in twSettings)) twSettings.contBarGap = 4;
-      const isNegative = value.value < 0;
-      if (isNegative) {
-        cell.height = t.scales.neg ? t.scales.neg(value.value) - t.scales.neg(0) : 0;
-        cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-        const cumulativeHeight = t.scales.neg ? t.scales.neg(value.pre_val_sum) - t.scales.neg(0) : 0;
-        cell.y = t.counts.posMaxHt + twSettings.contBarGap + (t.scales.neg ? t.scales.neg(0) : 0) + cumulativeHeight;
-      } else {
-        cell.height = t.scales.pos(value.value) - t.scales.pos(0);
-        cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-        const cumulativeHeight = t.scales.pos(value.pre_val_sum) - t.scales.pos(0);
-        cell.y = t.counts.posMaxHt + twSettings.contBarGap - t.scales.pos(0) - cumulativeHeight - cell.height;
-      }
-      cell.label = value.label;
-      cell.fill = twSettings[value.label]?.color || value.color || tw.term.propsByTermId?.[value.label]?.color;
-      cell.value = value.value;
-      return {
-        ref: t.ref,
-        group: tw.$id,
-        value: value.label,
-        order: -1,
-        entry: { key: value.label, label: value.label, fill: cell.fill }
-      };
-    }
-  }
-};
-
-// plots/matrix/matrix.js
-var Matrix = class _Matrix extends PlotBase {
-  static type = "matrix";
-  configTermKeys = ["termgroups.lst", "divideBy"];
-  constructor(opts) {
-    super(opts);
-    this.type = _Matrix.type;
-    this.holderTitle = "Sample Matrix";
-    this.optionalFeatures = JSON.parse(sessionStorage.getItem("optionalFeatures") || `{}`)?.matrix || [];
-    setInteractivity(this);
-    setRenderers(this);
-  }
-  async init(appState) {
-    const opts = this.opts;
-    if (opts.reactsTo) this.reactsTo = opts.reactsTo;
-    this.setDom = setMatrixDom;
-    this.setDom(opts);
-    this.config = appState.plots.find((p) => p.id === this.id);
-    this.settings = Object.assign({}, this.config.settings.matrix);
-    this.computed = {};
-    if (this.dom.header) this.dom.header.html(this.config.preBuiltPlotTitle || this.holderTitle);
-    this.setControls(appState);
-    this.clusterRenderer = new MatrixCluster({ holder: this.dom.cluster, app: this.app, parent: this });
-    this.legendRenderer = svgLegend({
-      holder: this.dom.legendG,
-      rectFillFxn: (d) => d.color,
-      iconStroke: "#aaa",
-      handlers: {
-        legend: {
-          click: this.legendClick
-        }
-      },
-      settings: {
-        isExcludedAttr: "isExcluded"
-      },
-      note: "CLICK A ROW LABEL OR ITEM TO APPLY FILTERING"
-    });
-    this.customTipApi = this.dom.tip.getCustomApi({
-      d: this.dom.menubody,
-      clear: (event) => {
-        if (event?.target) this.dom.menutop.style("display", "none");
-        this.dom.menubody.selectAll("*").remove();
-        return this.customTipApi;
-      },
-      show: () => {
-        this.dom.menubody.style("display", "block");
-      },
-      hide: () => {
-      }
-    });
-    this.setPill(appState);
-    const commonKeys = { mclass, dt2label, morigin };
-    for (const k in commonKeys) {
-      const v = commonKeys[k];
-      this[k] = copyMerge({}, v, appState.termdbConfig[k] || {}, appState.termdbConfig.matrix?.[k] || {});
-    }
-  }
-  setControls(appState) {
-    this.controlsRenderer = new MatrixControls(
-      {
-        app: this.app,
-        id: this.id,
-        parent: this,
-        holder: this.dom.controls,
-        getSvg: () => this.dom.svg.node()
-      },
-      appState
-    );
-  }
-  // reactsTo(action) {
-  // 	// note: a parent app or 'plot' component is expected to already have
-  // 	// a comprehensive reactsTo() call to filter the actions for this component,
-  // 	// so only farther selective action filters should be applied here as needed
-  // 	return true
-  // }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    const filter0 = appState.termfilter.filter0;
-    this.prevFilter0 = this.state?.filter0;
-    const parentConfig = appState.plots.find((p) => p.id === this.parentId);
-    const termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter);
-    return {
-      isVisible: true,
-      config,
-      filter: termfilter.filter,
-      filter0,
-      // read-only, invisible filter currently only used for gdc dataset
-      hasVerifiedToken: this.app.vocabApi.hasVerifiedToken(),
-      tokenVerificationMessage: this.app.vocabApi.tokenVerificationMessage,
-      vocab: appState.vocab,
-      termdbConfig: appState.termdbConfig,
-      clusterMethod: config.settings.hierCluster?.clusterMethod,
-      distanceMethod: config.settings.hierCluster?.distanceMethod,
-      clusterSamples: config.settings.hierCluster?.clusterSamples,
-      clusterRows: config.settings.hierCluster?.clusterRows,
-      zScoreTransformation: config.settings.hierCluster?.zScoreTransformation,
-      nav: appState.nav,
-      groups: rebaseGroupFilter(appState)
-    };
-  }
-  async main() {
-    try {
-      this.config = await this.getMutableConfig();
-      if (this.mayRequireToken()) return;
-      const termGroups = await getTermGroups(this.config.termgroups, this.app);
-      const prevTranspose = this.settings.transpose;
-      Object.assign(this.settings, structuredClone(this.config.settings), this.controlsRenderer.getSettings());
-      this.dom.loadingDiv.selectAll("*").remove();
-      this.dom.loadingDiv.html("").style("display", "").style("position", "relative").style("left", "45%");
-      this.dom.svg.style("opacity", 0.1).style("pointer-events", "none");
-      delete this.clickedClusterIds;
-      delete this.clickedLeftClusterIds;
-      try {
-        setComputedConfig(this.config);
-        const promises = [];
-        if (this.setHierClusterData) promises.push(this.setHierClusterData());
-        promises.push(this.setData());
-        this.dom.loadingDiv.html("Processing data ...");
-        await Promise.all(promises);
-        const warnings = this.data.warnings.join("\n");
-        this.dom.warningDiv.style("display", warnings.length ? "" : "none").html(warnings);
-        this.applyLegendValueFilter();
-        if (this.combineData) this.combineData();
-        this.app.save({ type: "plot_edit", id: this.id, config: this.config });
-      } catch (e) {
-        if (e == "no data") {
-          this.showNoMatchingDataMessage();
-          return;
-        } else if (this.app.isAbortError(e)) {
-          return;
-        } else {
-          this.dom.svg.style("display", "none");
-          throw e;
-        }
-      }
-      this.termGroups = termGroups;
-      this.dom.loadingDiv.html("Updating ...").style("display", "");
-      this.termOrder = this.getTermOrder(this.data);
-      this.sampleGroups = this.getSampleGroups(this.hierClusterSamples || this.data);
-      this.sampleOrder = this.getSampleOrder(this.data);
-      this.setLayout();
-      if (this.setHierColorScale) this.setHierColorScale(this.hierClusterData.clustering);
-      if (!this.sampleOrder?.length) {
-        this.showNoMatchingDataMessage();
-      }
-      this.controlsRenderer.main();
-      this.serieses = this.getSerieses(this.data);
-      this.dom.loadingDiv.html("Rendering ...");
-      if (this.plotDendrogramHclust) this.plotDendrogramHclust();
-      this.render();
-      this.mayDisplayCohortMessage();
-      this.dom.svg.style("display", "").style("opacity", 1).style("pointer-events", "");
-      const [xGrps, yGrps] = !this.settings.matrix.transpose ? ["sampleGrps", "termGrps"] : ["termGrps", "sampleGrps"];
-      const d = this.dimensions;
-      this.clusterRenderer.main({
-        settings: this.settings.matrix,
-        xGrps: this[xGrps],
-        yGrps: this[yGrps],
-        dimensions: d
-      });
-      this.legendRenderer(this.legendData, {
-        settings: Object.assign({}, this.settings.legend, {
-          svgw: Math.max(400, d.mainw + d.xOffset - this.settings.matrix.margin.right),
-          svgh: d.mainh + d.yOffset,
-          dimensions: d,
-          padleft: this.settings.legend.padleft
-          //+ d.xOffset
-        })
-      });
-      await this.adjustSvgDimensions(prevTranspose);
-      this.controlsRenderer.main();
-      if (this.data.removedHierClusterTerms) {
-        for (const r of this.data.removedHierClusterTerms) {
-          sayerror(this.dom.errorDiv, r.text + ": " + r.lst.join(", "));
-        }
-      }
-    } catch (e) {
-      const message = this.app.vocabApi.tokenVerificationMessage;
-      this.mayRequireToken(message);
-      if (!message) {
-        this.app.tip.hide();
-        this.dom.loadingDiv.style("display", "none");
-        throw e;
-      }
-    }
-    this.resetInteractions();
-  }
-  showNoMatchingDataMessage() {
-    this.forcedSampleCount = 0;
-    this.dom.svg.style("opacity", 1e-3).style("display", "none");
-    if (this.termOrder && this.dimensions) this.controlsRenderer.main({ sampleCount: 0 });
-    this.dom.loadingDiv.html("");
-    const div = this.dom.loadingDiv.append("div").style("display", "inline-block").style("text-align", "center").style("position", "relative").style("left", "-150px");
-    div.append("div").style("margin", "5px 10px").html("No matching cohort sample data for the current gene list.");
-    if (this.settings.matrix.showHints?.includes("genesetEdit")) {
-      const div1 = div.append("div").style("margin", "5px 10px");
-      div1.append("span").html("You may change the selected cohort,");
-      if (this.config.legendGrpFilter?.lst.length || this.config.legendValueFilter?.lst.length) {
-        const cnvBtn = this.controlsRenderer.btns.filter((d) => d.label == "CNV")?.node();
-        if (cnvBtn) {
-          div1.append("br");
-          div1.append("span").html("show hidden ");
-          div1.append("span").html("CNV").style("cursor", "pointer").style("text-decoration", "underline").on("click", () => {
-            cnvBtn.click();
-          });
-        }
-        const mutationBtn = this.controlsRenderer.btns.filter((d) => d.label == "Mutation")?.node();
-        if (cnvBtn && mutationBtn) div1.append("span").html(" or ");
-        if (mutationBtn) {
-          div1.append("span").style("cursor", "pointer").style("text-decoration", "underline").html("Mutation").on("click", () => {
-            mutationBtn.click();
-          });
-        }
-        if (cnvBtn || mutationBtn) div1.append("span").html(" data,");
-      }
-      div1.append("br");
-      div1.append("span").html("or edit the gene list from the ");
-      div1.append("span").style("cursor", "pointer").style("text-decoration", "underline").html("Gene Set Edit Group menu.").on("click", () => {
-        const GenesBtn = this.controlsRenderer.btns.filter((d) => d.label == "Genes")?.node().click();
-        const i = setInterval(() => {
-          const editBtn = this.app.tip.d.selectAll("button").filter(function() {
-            return this.innerHTML == "Edit Group";
-          }).node();
-          if (editBtn) {
-            editBtn.click();
-            clearInterval(i);
-          }
-        }, 100);
-      });
-    }
-    this.dom.svg.style("display", "none");
-  }
-  mayDisplayCohortMessage() {
-    const msg = !this.prevFilter0 || deepEqual(this.state.filter0, this.prevFilter0) ? "" : "The gene list is persisted across cohorts.";
-    if (msg) {
-      this.dom.loadingDiv.html("");
-      const div = this.dom.loadingDiv.append("div").style("display", "inline-block").style("text-align", "center").style("position", "relative").style("left", "-150px");
-      div.append("div").html(msg);
-      if (this.settings.matrix.showHints?.includes("genesetEdit")) {
-        const div1 = div.append("div");
-        div1.append("span").html(" You may edit the gene list from the ");
-        div1.append("span").style("cursor", "pointer").style("text-decoration", "underline").html("Gene Set Edit Group menu.").on("click", () => {
-          const GenesBtn = this.controlsRenderer.btns.filter((d) => d.label == "Genes")?.node().click();
-          const i = setInterval(() => {
-            const editBtn = this.app.tip.d.selectAll("button").filter(function() {
-              return this.innerHTML == "Edit Group";
-            }).node();
-            if (editBtn) {
-              editBtn.click();
-              clearInterval(i);
-            }
-          }, 100);
-        });
-      }
-    }
-    this.dom.loadingDiv.style("display", msg ? "" : "none");
-  }
-  sampleKey(s) {
-    return s.row.sample;
-  }
-  sampleLabel(s) {
-    return s.label || s.row._ref_.label || "";
-  }
-  sampleGrpKey(s) {
-    return s.grp.name;
-  }
-  sampleGrpLabel(s) {
-    return s.grp.label || s.grp.name || "";
-  }
-  termKey(t) {
-    return t.tw.$id;
-  }
-  termLabel(t) {
-    return t.label;
-  }
-  termGrpKey(t) {
-    return t.grp.name;
-  }
-  termGrpLabel(t) {
-    return t.grp.label || t.grp.name || [{ text: "\u22EE", dx: 3, cls: "sjpp-exclude-svg-download" }];
-  }
-  destroy() {
-    select_default(window).on(`resize.sjpp-${self.id}`, null);
-  }
-};
-for (const m of [matrix_data_exports, matrix_groups_exports, matrix_layout_exports, matrix_serieses_exports, matrix_legend_exports]) {
-  for (const methodName in m) {
-    Matrix.prototype[methodName] = m[methodName];
-  }
-}
-var matrixInit = getCompInit(Matrix);
-var componentInit = matrixInit;
-function makeChartBtnMenu(holder, chartsInstance) {
-  chartsInstance.dom.tip.clear();
-  const menuDiv = holder.append("div");
-  if (chartsInstance.state.termdbConfig.matrixplots) {
-    for (const plot of chartsInstance.state.termdbConfig.matrixplots) {
-      menuDiv.append("button").style("margin", "10px").style("padding", "10px 15px").style("border-radius", "20px").style("border-color", "#ededed").style("display", "inline-block").text(plot.name).on("click", async () => {
-        chartsInstance.dom.tip.hide();
-        const config = await chartsInstance.app.vocabApi.getMatrixByName(plot.name);
-        config.preBuiltPlotTitle = plot.name;
-        chartsInstance.app.dispatch({
-          type: "plot_create",
-          config
-        });
-      });
-    }
-  }
-  const chart = {
-    clickTo: chartsInstance.showTree_selectlst,
-    chartType: "matrix",
-    usecase: { target: "matrix", detail: "termgroups" },
-    processSelection: (lst) => {
-      return [
-        {
-          name: "",
-          lst: lst.map((term) => {
-            return { term };
-          })
-        }
-      ];
-    }
-  };
-  chartsInstance.showTree_selectlst(chart);
-}
-
-export {
-  Matrix,
-  matrixInit,
-  componentInit,
-  makeChartBtnMenu
-};
-//# sourceMappingURL=chunk-LLPFFNLV.js.map

package/dist/chunk-LRV4VWRF.js

@@ -1,94 +0,0 @@
-import {
-  addGeneSearchbox,
-  sayerror
-} from "./chunk-XZZLEHWC.js";
-import {
-  Menu
-} from "./chunk-2SRMRC6L.js";
-import {
-  dofetch3
-} from "./chunk-QEHUEG4X.js";
-import {
-  ISOFORM_EXPRESSION
-} from "./chunk-2UWHV2SB.js";
-
-// termdb/handlers/isoformExpression.ts
-var SearchHandler = class {
-  constructor() {
-    this.currentGene = null;
-  }
-  init(opts) {
-    this.callback = opts.callback;
-    this.app = opts.app;
-    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.message || 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 an isoform:`);
-    for (const gm of enstModels) {
-      const row = div.append("div").style("padding", "2px 0").style("cursor", "pointer");
-      const label = row.append("label").style("cursor", "pointer");
-      const checkbox = label.append("input").attr("type", "checkbox").attr("name", "isoformSelect").style("cursor", "pointer").on("change", () => {
-        div.selectAll("input[name=isoformSelect]").property("checked", false);
-        checkbox.property("checked", true);
-        this.selectIsoform(gm.isoform, gene);
-      });
-      const defaultTag = gm.isdefault ? " (default)" : "";
-      label.append("span").style("margin-left", "6px").text(`${gm.isoform}${defaultTag}`);
-    }
-  }
-  selectIsoform(isoform, gene) {
-    const unit = this.app.vocabApi.termdbConfig.queries.isoformExpression?.unit || "Isoform Expression";
-    const name = `${isoform} ${unit}`;
-    this.callback({ isoform, gene, name, type: ISOFORM_EXPRESSION });
-  }
-};
-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-LRV4VWRF.js.map

package/dist/chunk-LRV4VWRF.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../termdb/handlers/isoformExpression.ts"],
-  "sourcesContent": ["import { Menu, addGeneSearchbox, sayerror } from '#dom'\nimport { dofetch3 } from '#common/dofetch'\nimport { ISOFORM_EXPRESSION } from '#shared/terms.js'\n\nexport class SearchHandler {\n\tcallback: any\n\tapp: any\n\tdom: any\n\tcurrentGene: string | null = null\n\n\tinit(opts) {\n\t\tthis.callback = opts.callback\n\t\tthis.app = opts.app\n\t\tconst holder = opts.holder.append('div').style('padding', '10px 0px')\n\t\tthis.dom = {\n\t\t\terrDiv: holder.append('div').style('margin', '5px 0px').style('display', 'none')\n\t\t}\n\n\t\tconst geneSearch = addGeneSearchbox({\n\t\t\ttip: new Menu({ padding: '0px' }),\n\t\t\tgenome: opts.genomeObj,\n\t\t\trow: holder,\n\t\t\tsearchOnly: 'gene',\n\t\t\tcallback: async () => {\n\t\t\t\ttry {\n\t\t\t\t\tthis.dom.errDiv.style('display', 'none')\n\t\t\t\t\tif (!geneSearch.geneSymbol) throw new Error('No gene selected')\n\t\t\t\t\t// guard against duplicate fires for the same gene\n\t\t\t\t\tif (geneSearch.geneSymbol === this.currentGene) return\n\t\t\t\t\tthis.currentGene = geneSearch.geneSymbol\n\t\t\t\t\t// isoformDiv is created after the search box so results appear below\n\t\t\t\t\tif (this.dom.isoformDiv) this.dom.isoformDiv.remove()\n\t\t\t\t\tthis.dom.isoformDiv = holder.append('div')\n\t\t\t\t\tawait this.showIsoforms(geneSearch.geneSymbol, opts.genomeObj)\n\t\t\t\t} catch (e: any) {\n\t\t\t\t\tthis.dom.errDiv.style('display', 'block')\n\t\t\t\t\tsayerror(this.dom.errDiv, 'Error: ' + (e.message || e))\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t}\n\n\tasync showIsoforms(gene: string, genomeObj: any) {\n\t\tif (!gene) throw new Error('No gene selected')\n\n\t\t// deep lookup to get all isoforms for this gene\n\t\tconst data = await dofetch3('genelookup', { body: { genome: genomeObj.name, input: gene, deep: 1 } })\n\t\tif (!data.gmlst?.length) throw new Error(`No isoforms found for ${gene}`)\n\n\t\t// filter to ENST isoforms, then check which have data via server-side lookup\n\t\tconst enstCandidates = data.gmlst.filter((gm: any) => gm.isoform?.startsWith('ENST'))\n\t\tif (enstCandidates.length === 0) throw new Error(`No Ensembl transcript isoforms found for ${gene}`)\n\n\t\tconst { available } = await dofetch3('termdb/isoformAvailability', {\n\t\t\tbody: {\n\t\t\t\tgenome: genomeObj.name,\n\t\t\t\tdslabel: this.app.vocabApi.vocab.dslabel,\n\t\t\t\tisoforms: enstCandidates.map((gm: any) => gm.isoform)\n\t\t\t}\n\t\t})\n\t\tconst availableSet = new Set(available || [])\n\t\tconst enstModels = enstCandidates.filter((gm: any) => availableSet.has(gm.isoform))\n\t\tif (enstModels.length === 0) throw new Error(`No isoforms with data found for ${gene}`)\n\n\t\t// bail if the user already searched a different gene while we were fetching\n\t\tif (gene !== this.currentGene) return\n\n\t\tconst div = this.dom.isoformDiv\n\t\tdiv.append('div').style('margin-bottom', '8px').style('opacity', 0.65).text(`${gene} \u2014 select an isoform:`)\n\n\t\tfor (const gm of enstModels) {\n\t\t\tconst row = div.append('div').style('padding', '2px 0').style('cursor', 'pointer')\n\t\t\tconst label = row.append('label').style('cursor', 'pointer')\n\t\t\tconst checkbox = label\n\t\t\t\t.append('input')\n\t\t\t\t.attr('type', 'checkbox')\n\t\t\t\t.attr('name', 'isoformSelect')\n\t\t\t\t.style('cursor', 'pointer')\n\t\t\t\t.on('change', () => {\n\t\t\t\t\t// uncheck all others \u2014 single selection for now\n\t\t\t\t\tdiv.selectAll('input[name=isoformSelect]').property('checked', false)\n\t\t\t\t\tcheckbox.property('checked', true)\n\t\t\t\t\tthis.selectIsoform(gm.isoform, gene)\n\t\t\t\t})\n\n\t\t\tconst defaultTag = gm.isdefault ? ' (default)' : ''\n\t\t\tlabel.append('span').style('margin-left', '6px').text(`${gm.isoform}${defaultTag}`)\n\t\t}\n\t}\n\n\tselectIsoform(isoform: string, gene: string) {\n\t\tconst unit = this.app.vocabApi.termdbConfig.queries.isoformExpression?.unit || 'Isoform Expression'\n\t\tconst name = `${isoform} ${unit}`\n\t\tthis.callback({ isoform, gene, name, type: ISOFORM_EXPRESSION })\n\t}\n}\n\n/** Filter gene models to ENST isoforms that exist in the available items list.\n *  If availableItems is empty, all ENST isoforms are returned (no filtering). */\nexport function filterIsoforms(gmlst: any[], availableItems: string[]) {\n\tconst itemSet = new Set(availableItems)\n\treturn gmlst.filter((gm: any) => gm.isoform?.startsWith('ENST') && (itemSet.size === 0 || itemSet.has(gm.isoform)))\n}\n"],
-  "mappings": ";;;;;;;;;;;;;;;AAIO,IAAM,gBAAN,MAAoB;AAAA,EAApB;AAIN,uBAA6B;AAAA;AAAA,EAE7B,KAAK,MAAM;AACV,SAAK,WAAW,KAAK;AACrB,SAAK,MAAM,KAAK;AAChB,UAAM,SAAS,KAAK,OAAO,OAAO,KAAK,EAAE,MAAM,WAAW,UAAU;AACpE,SAAK,MAAM;AAAA,MACV,QAAQ,OAAO,OAAO,KAAK,EAAE,MAAM,UAAU,SAAS,EAAE,MAAM,WAAW,MAAM;AAAA,IAChF;AAEA,UAAM,aAAa,iBAAiB;AAAA,MACnC,KAAK,IAAI,KAAK,EAAE,SAAS,MAAM,CAAC;AAAA,MAChC,QAAQ,KAAK;AAAA,MACb,KAAK;AAAA,MACL,YAAY;AAAA,MACZ,UAAU,YAAY;AACrB,YAAI;AACH,eAAK,IAAI,OAAO,MAAM,WAAW,MAAM;AACvC,cAAI,CAAC,WAAW,WAAY,OAAM,IAAI,MAAM,kBAAkB;AAE9D,cAAI,WAAW,eAAe,KAAK,YAAa;AAChD,eAAK,cAAc,WAAW;AAE9B,cAAI,KAAK,IAAI,WAAY,MAAK,IAAI,WAAW,OAAO;AACpD,eAAK,IAAI,aAAa,OAAO,OAAO,KAAK;AACzC,gBAAM,KAAK,aAAa,WAAW,YAAY,KAAK,SAAS;AAAA,QAC9D,SAAS,GAAQ;AAChB,eAAK,IAAI,OAAO,MAAM,WAAW,OAAO;AACxC,mBAAS,KAAK,IAAI,QAAQ,aAAa,EAAE,WAAW,EAAE;AAAA,QACvD;AAAA,MACD;AAAA,IACD,CAAC;AAAA,EACF;AAAA,EAEA,MAAM,aAAa,MAAc,WAAgB;AAChD,QAAI,CAAC,KAAM,OAAM,IAAI,MAAM,kBAAkB;AAG7C,UAAM,OAAO,MAAM,SAAS,cAAc,EAAE,MAAM,EAAE,QAAQ,UAAU,MAAM,OAAO,MAAM,MAAM,EAAE,EAAE,CAAC;AACpG,QAAI,CAAC,KAAK,OAAO,OAAQ,OAAM,IAAI,MAAM,yBAAyB,IAAI,EAAE;AAGxE,UAAM,iBAAiB,KAAK,MAAM,OAAO,CAAC,OAAY,GAAG,SAAS,WAAW,MAAM,CAAC;AACpF,QAAI,eAAe,WAAW,EAAG,OAAM,IAAI,MAAM,4CAA4C,IAAI,EAAE;AAEnG,UAAM,EAAE,UAAU,IAAI,MAAM,SAAS,8BAA8B;AAAA,MAClE,MAAM;AAAA,QACL,QAAQ,UAAU;AAAA,QAClB,SAAS,KAAK,IAAI,SAAS,MAAM;AAAA,QACjC,UAAU,eAAe,IAAI,CAAC,OAAY,GAAG,OAAO;AAAA,MACrD;AAAA,IACD,CAAC;AACD,UAAM,eAAe,IAAI,IAAI,aAAa,CAAC,CAAC;AAC5C,UAAM,aAAa,eAAe,OAAO,CAAC,OAAY,aAAa,IAAI,GAAG,OAAO,CAAC;AAClF,QAAI,WAAW,WAAW,EAAG,OAAM,IAAI,MAAM,mCAAmC,IAAI,EAAE;AAGtF,QAAI,SAAS,KAAK,YAAa;AAE/B,UAAM,MAAM,KAAK,IAAI;AACrB,QAAI,OAAO,KAAK,EAAE,MAAM,iBAAiB,KAAK,EAAE,MAAM,WAAW,IAAI,EAAE,KAAK,GAAG,IAAI,4BAAuB;AAE1G,eAAW,MAAM,YAAY;AAC5B,YAAM,MAAM,IAAI,OAAO,KAAK,EAAE,MAAM,WAAW,OAAO,EAAE,MAAM,UAAU,SAAS;AACjF,YAAM,QAAQ,IAAI,OAAO,OAAO,EAAE,MAAM,UAAU,SAAS;AAC3D,YAAM,WAAW,MACf,OAAO,OAAO,EACd,KAAK,QAAQ,UAAU,EACvB,KAAK,QAAQ,eAAe,EAC5B,MAAM,UAAU,SAAS,EACzB,GAAG,UAAU,MAAM;AAEnB,YAAI,UAAU,2BAA2B,EAAE,SAAS,WAAW,KAAK;AACpE,iBAAS,SAAS,WAAW,IAAI;AACjC,aAAK,cAAc,GAAG,SAAS,IAAI;AAAA,MACpC,CAAC;AAEF,YAAM,aAAa,GAAG,YAAY,eAAe;AACjD,YAAM,OAAO,MAAM,EAAE,MAAM,eAAe,KAAK,EAAE,KAAK,GAAG,GAAG,OAAO,GAAG,UAAU,EAAE;AAAA,IACnF;AAAA,EACD;AAAA,EAEA,cAAc,SAAiB,MAAc;AAC5C,UAAM,OAAO,KAAK,IAAI,SAAS,aAAa,QAAQ,mBAAmB,QAAQ;AAC/E,UAAM,OAAO,GAAG,OAAO,IAAI,IAAI;AAC/B,SAAK,SAAS,EAAE,SAAS,MAAM,MAAM,MAAM,mBAAmB,CAAC;AAAA,EAChE;AACD;AAIO,SAAS,eAAe,OAAc,gBAA0B;AACtE,QAAM,UAAU,IAAI,IAAI,cAAc;AACtC,SAAO,MAAM,OAAO,CAAC,OAAY,GAAG,SAAS,WAAW,MAAM,MAAM,QAAQ,SAAS,KAAK,QAAQ,IAAI,GAAG,OAAO,EAAE;AACnH;",
-  "names": []
-}