@sjcrh/proteinpaint-client 2.185.0 → 2.186.0

package/dist/chunk-Q3J3F2NU.js

@@ -0,0 +1,205 @@
+import {
+  DownloadMenu,
+  ListSamples,
+  filterJoin,
+  getFilterItemByTag,
+  renderTable
+} from "./chunk-2YC6ZVE4.js";
+import {
+  niceNumLabels
+} from "./chunk-X4NI4JLQ.js";
+import {
+  SINGLECELL_GENE_EXPRESSION
+} from "./chunk-EGWVYY7K.js";
+
+// plots/violin.interactivity.js
+function setInteractivity(self) {
+  self.getChartImages = function() {
+    const charts = [];
+    for (const [key, chart] of Object.entries(self.data.charts)) {
+      const title = self.getChartTitle(chart.chartId);
+      const name = `${self.config.term.term.name}  ${title}`;
+      const chartDiv = chart.chartDiv;
+      charts.push({ name, svg: chartDiv.select("svg") });
+    }
+    return charts;
+  };
+  self.download = function(event) {
+    if (!self.state) return;
+    const name2svg = self.getChartImages();
+    const dm = new DownloadMenu(name2svg, self.config.term.term.name);
+    dm.show(event.clientX, event.clientY, event.target);
+  };
+  self.displayLabelClickMenu = function(t1, t2, plot, event) {
+    if (!t2) return;
+    if (self.config.term.term.type == SINGLECELL_GENE_EXPRESSION) return;
+    const label = t1.q.mode === "continuous" ? "term2" : "term";
+    const options = [];
+    if (this.app.getState().nav.header_mode !== "only_buttons")
+      options.push({
+        label: `Add filter: ${plot.label.split(",")[0]}`,
+        testid: "sjpp-violinLabOpt-addf",
+        callback: getAddFilterCallback(self, plot)
+      });
+    options.push({
+      label: `Hide: ${plot.label}`,
+      testid: "sjpp-violinLabOpt-hide",
+      callback: () => {
+        const term = self.config[label];
+        const isHidden = true;
+        self.app.dispatch({
+          type: "plot_edit",
+          id: self.id,
+          config: {
+            [label]: {
+              isAtomic: true,
+              term: term.term,
+              q: getUpdatedQfromClick(plot, term, isHidden)
+            }
+          }
+        });
+      }
+    });
+    if (self.state.displaySampleIds && self.state.hasVerifiedToken) {
+      options.push({
+        label: `List samples`,
+        testid: "sjpp-violinLabOpt-list",
+        callback: async () => {
+          const [start, end] = [self.data.min, self.data.max];
+          await self.callListSamples(event, plot, start, end);
+        }
+      });
+    }
+    self.displayMenu(event, options);
+  };
+  self.displayBrushMenu = function(t1, t2, self2, plot, event, scale, isH) {
+    const selection = event.selection;
+    const [start, end] = isH ? [scale.invert(selection[0]), scale.invert(selection[1])] : [scale.invert(selection[1]), scale.invert(selection[0])];
+    const options = [];
+    if (this.app.getState().nav.header_mode === "with_tabs")
+      options.push({
+        label: `Add filter`,
+        testid: "sjpp-violinBrushOpt-addf",
+        callback: getAddFilterCallback(self2, plot, start, end)
+      });
+    if (self2.state.displaySampleIds && self2.state.hasVerifiedToken) {
+      options.push({
+        label: `List samples`,
+        testid: "sjpp-violinBrushOpt-list",
+        callback: async () => self2.callListSamples(event.sourceEvent, plot, start, end)
+      });
+    }
+    self2.displayMenu(event.sourceEvent, options, start, end);
+  };
+  self.displayMenu = function(event, options, start, end) {
+    const tip = self.dom.clicktip.clear().show(event.clientX, event.clientY);
+    const isBrush = start != null && end != null;
+    if (isBrush) {
+      const [niceStart, niceEnd] = self.config.term.term.type == "integer" ? [Math.round(start), Math.round(end)] : niceNumLabels([start, end]);
+      tip.d.append("div").style("margin", "10px").text(`From ${niceStart} to ${niceEnd}`);
+    }
+    tip.d.append("div").selectAll("div").data(options).enter().append("div").attr("class", "sja_menuoption sja_sharp_border").attr("data-testid", (d) => d.testid).text((d) => d.label).on("click", async (event2, d) => {
+      if (event2.target._clicked) return;
+      event2.target._clicked = true;
+      event2.target.textContent = "Loading...";
+      await d.callback();
+      tip.hide();
+    });
+  };
+  self.getSampleList = function(plot, start, end) {
+    const { term, term2, term0 } = self.config;
+    const bins = self.data.bins;
+    const rangeStart = start !== void 0 ? start : null;
+    const rangeStop = end !== void 0 ? end : null;
+    const ls = new ListSamples({
+      app: self.app,
+      termfilter: self.state.termfilter,
+      term,
+      term2,
+      term0,
+      plot,
+      bins,
+      start: rangeStart,
+      end: rangeStop
+    });
+    return ls;
+  };
+  self.callListSamples = async function(event, plot, start, end) {
+    const ls = self.getSampleList(plot, start, end);
+    const data = await ls.getData();
+    const [rows, columns] = ls.setTableData(data);
+    const tip = self.dom.sampletabletip;
+    tip.clear().show(event.clientX, event.clientY, false);
+    renderTable({
+      rows,
+      columns,
+      div: tip.d,
+      showLines: true,
+      maxHeight: "40vh",
+      resize: true,
+      dataTestId: "sjpp-listsampletable"
+    });
+  };
+  self.labelHideLegendClicking = function(t2, plot) {
+    self.dom.legendDiv.selectAll(".sjpp-htmlLegend").on("click", (event) => {
+      event.stopPropagation();
+      const d = event.target.__data__;
+      const termNum = t2?.term.type === "condition" || t2?.term.type === "samplelst" || t2?.term.type === "categorical" || (t2?.term.type === "float" || t2?.term.type === "integer") && self.config.term?.q.mode === "continuous" ? "term2" : "term";
+      const term = self.config[termNum];
+      if (t2) {
+        for (const key of Object.keys(term?.q?.hiddenValues)) {
+          if (d.text === key) {
+            delete term.q.hiddenValues[key];
+          }
+        }
+        const isHidden = false;
+        self.app.dispatch({
+          type: "plot_edit",
+          id: self.id,
+          config: {
+            [termNum]: {
+              isAtomic: true,
+              term: term.term,
+              q: getUpdatedQfromClick(plot, term, isHidden)
+            }
+          }
+        });
+      }
+    }).on("mouseover", (event) => {
+      const q = event.target.__data__;
+      if (q === void 0) return;
+      if (q.isHidden === true && q.isClickable === true) {
+        self.dom.hovertip.clear().show(event.clientX, event.clientY).d.append("span").text("Click to unhide plot");
+      }
+    }).on("mouseout", function() {
+      self.dom.hovertip.hide();
+    });
+  };
+}
+function getAddFilterCallback(self, plot, rangeStart, rangeStop) {
+  const ls = self.getSampleList(plot, rangeStart, rangeStop);
+  return () => {
+    const filterUiRoot = getFilterItemByTag(self.state.termfilter.filter, "filterUiRoot");
+    const filter = filterJoin([filterUiRoot, ls.tvslst]);
+    filter.tag = "filterUiRoot";
+    self.app.dispatch({
+      type: "filter_replace",
+      filter
+    });
+  };
+}
+function getUpdatedQfromClick(plot, term, isHidden = false) {
+  const label = plot.label;
+  const valueId = term?.term?.values ? term?.term?.values?.[label]?.label : label;
+  const id = !valueId ? label : valueId;
+  const q = term.q;
+  if (!q.hiddenValues) q.hiddenValues = {};
+  if (isHidden) q.hiddenValues[id] = 1;
+  else delete q.hiddenValues[id];
+  return q;
+}
+
+export {
+  setInteractivity
+};
+//# sourceMappingURL=chunk-Q3J3F2NU.js.map

package/dist/chunk-RYCOJY7M.js

@@ -0,0 +1,188 @@
+import {
+  __glob
+} from "./chunk-HFNDKYVF.js";
+
+// import("../plots/**/*.js") in plots/importPlot.js
+var globImport_plots_js = __glob({
+  "../plots/alphaGenome.js": () => import("./alphaGenome-F3W7GJQ5.js"),
+  "../plots/barchart.data.js": () => import("./barchart.data-MVVKPDLE.js"),
+  "../plots/barchart.events.js": () => import("./barchart.events-UQUSSRXB.js"),
+  "../plots/barchart.js": () => import("./barchart-HHFCBOZE.js"),
+  "../plots/bars.renderer.js": () => import("./bars.renderer-JHCZDSM6.js"),
+  "../plots/bars.settings.js": () => import("./bars.settings-SDU7PZOS.js"),
+  "../plots/brainImaging.js": () => import("./brainImaging-MTQTXNNL.js"),
+  "../plots/controls.btns.js": () => import("./controls.btns-3V7SNQT3.js"),
+  "../plots/controls.config.js": () => import("./controls.config-PRXVODCM.js"),
+  "../plots/controls.js": () => import("./controls-N4MPSNO4.js"),
+  "../plots/cuminc.js": () => import("./cuminc-JJHXW55V.js"),
+  "../plots/dataDownload.js": () => import("./dataDownload-OFB7TYDB.js"),
+  "../plots/dictionary.js": () => import("./dictionary-BSKN37CP.js"),
+  "../plots/dziviewer/plot.dzi.js": () => import("./plot.dzi-ZGLOVJJN.js"),
+  "../plots/facet.js": () => import("./facet-2W5SBPGP.js"),
+  "../plots/gb/test/genomeBrowser.spec.js": () => import("./genomeBrowser.spec-VPAKTUJF.js"),
+  "../plots/geneExpression.js": () => import("./geneExpression-WF56ODMZ.js"),
+  "../plots/geneORA.js": () => import("./geneORA-33FK2YOS.js"),
+  "../plots/geneset.js": () => import("./geneset-4C6ZLVMN.js"),
+  "../plots/gsea.js": () => import("./gsea-PE5WZ5ZI.js"),
+  "../plots/hierCluster.js": () => import("./hierCluster-FH6YJHRT.js"),
+  "../plots/importPlot.js": () => import("./importPlot-OWKXSK77.js"),
+  "../plots/matrix.js": () => import("./matrix-SPEDEB3J.js"),
+  "../plots/matrix/hierCluster.config.js": () => import("./hierCluster.config-M57ZIWMB.js"),
+  "../plots/matrix/hierCluster.interactivity.js": () => import("./hierCluster.interactivity-CDBAJXOY.js"),
+  "../plots/matrix/hierCluster.js": () => import("./hierCluster-IFM5I5QN.js"),
+  "../plots/matrix/hierCluster.renderers.js": () => import("./hierCluster.renderers-FWOV4Q47.js"),
+  "../plots/matrix/matrix.cells.js": () => import("./matrix.cells-KEIOXJQ7.js"),
+  "../plots/matrix/matrix.cluster.js": () => import("./matrix.cluster-NU5CYRUT.js"),
+  "../plots/matrix/matrix.config.js": () => import("./matrix.config-XB6WFXUY.js"),
+  "../plots/matrix/matrix.data.js": () => import("./matrix.data-QGCGFLD7.js"),
+  "../plots/matrix/matrix.dom.js": () => import("./matrix.dom-KGXRCCKU.js"),
+  "../plots/matrix/matrix.groups.js": () => import("./matrix.groups-HBPLZ2QX.js"),
+  "../plots/matrix/matrix.interactivity.js": () => import("./matrix.interactivity-OWMHUJCX.js"),
+  "../plots/matrix/matrix.js": () => import("./matrix-62CN2KXR.js"),
+  "../plots/matrix/matrix.layout.js": () => import("./matrix.layout-27QB6MWK.js"),
+  "../plots/matrix/matrix.legend.js": () => import("./matrix.legend-UCL7HM26.js"),
+  "../plots/matrix/matrix.renderers.js": () => import("./matrix.renderers-EPXES5E4.js"),
+  "../plots/matrix/matrix.serieses.js": () => import("./matrix.serieses-S2TJ3E6P.js"),
+  "../plots/matrix/matrix.sort.js": () => import("./matrix.sort-CFA4UWBJ.js"),
+  "../plots/matrix/matrix.sorterUi.js": () => import("./matrix.sorterUi-FT7K5664.js"),
+  "../plots/matrix/test/hierCluster.integration.spec.js": () => import("./hierCluster.integration.spec-Z64RL7MC.js"),
+  "../plots/matrix/test/matrix.integration.spec.js": () => import("./matrix.integration.spec-NN7OR5XM.js"),
+  "../plots/matrix/test/matrix.sort.unit.spec.js": () => import("./matrix.sort.unit.spec-NBT5FSZ6.js"),
+  "../plots/matrix/test/matrix.sorterUi.unit.spec.js": () => import("./matrix.sorterUi.unit.spec-QKGUE4RR.js"),
+  "../plots/matrix/test/oncomatrix.spec.js": () => import("./oncomatrix.spec-NALJBPYS.js"),
+  "../plots/plot.brainImaging.js": () => import("./plot.brainImaging-2Z3TOO6J.js"),
+  "../plots/plot.disco.js": () => import("./plot.disco-4JAEIAYK.js"),
+  "../plots/plot.ssgq.js": () => import("./plot.ssgq-IHUILM43.js"),
+  "../plots/regression.inputs.js": () => import("./regression.inputs-2AMJCJ3L.js"),
+  "../plots/regression.inputs.term.js": () => import("./regression.inputs.term-D6D2QEUB.js"),
+  "../plots/regression.inputs.values.table.js": () => import("./regression.inputs.values.table-M3IPLGDJ.js"),
+  "../plots/regression.js": () => import("./regression-TIR5D354.js"),
+  "../plots/regression.results.js": () => import("./regression.results-YD5S74YS.js"),
+  "../plots/sampleView.js": () => import("./sampleView-B5TM7JOW.js"),
+  "../plots/scatter/test/scatter.integration.spec.js": () => import("./scatter.integration.spec-TS4PNRLX.js"),
+  "../plots/singleCellPlot.js": () => import("./singleCellPlot-3YFUYA2Y.js"),
+  "../plots/stattable.js": () => import("./stattable-XXEIFPGM.js"),
+  "../plots/survival/test/survival.integration.spec.js": () => import("./survival.integration.spec-FS7V4OXK.js"),
+  "../plots/table.js": () => import("./table-ISOQOI6C.js"),
+  "../plots/test/barchart.integration.spec.js": () => import("./barchart.integration.spec-OF3MWFQ5.js"),
+  "../plots/test/cuminc.integration.spec.js": () => import("./cuminc.integration.spec-IXS2UO2O.js"),
+  "../plots/test/dataDownload.integration.spec.js": () => import("./dataDownload.integration.spec-4HWDQO4C.js"),
+  "../plots/test/expclust.gdc.spec.js": () => import("./expclust.gdc.spec-SGECIILQ.js"),
+  "../plots/test/profile.spec.js": () => import("./profile.spec-TOITKBBZ.js"),
+  "../plots/test/regression.integration.spec.js": () => import("./regression.integration.spec-ROUSXLMH.js"),
+  "../plots/test/regression.spec.js": () => import("./regression.spec-4OXBBTNO.js"),
+  "../plots/test/sampleScatter.spec.js": () => import("./sampleScatter.spec-LECMFMI2.js"),
+  "../plots/test/summary.integration.spec.js": () => import("./summary.integration.spec-XXU362UQ.js"),
+  "../plots/test/violin.integration.spec.js": () => import("./violin.integration.spec-5EW6PLJX.js"),
+  "../plots/violin.interactivity.js": () => import("./violin.interactivity-RI4RURGO.js"),
+  "../plots/violin.js": () => import("./violin-KGGTUQFF.js"),
+  "../plots/violin.renderer.js": () => import("./violin.renderer-EWU2IFZE.js"),
+  "../plots/volcano/test/testData.js": () => import("./testData-LEJ53F2K.js"),
+  "../plots/wsiviewer/plot.wsi.js": () => import("./plot.wsi-3GISVBDH.js")
+});
+
+// plots/importPlot.js
+async function importPlot(chartType, notFoundMessage = "") {
+  switch (chartType) {
+    case "AIProjectAdmin":
+      return await import("./AIProjectAdmin-ROSQHK6Q.js");
+    case "barchart":
+      return await import("./barchart-HHFCBOZE.js");
+    case "boxplot":
+      return await import("./BoxPlot-CU7MEBH7.js");
+    case "correlationVolcano":
+      return await import("./CorrelationVolcano-OE4R2GS3.js");
+    case "DEinput":
+      return await import("./DEinput-PRIAIBFH.js");
+    case "dictionary":
+      return await import("./dictionary-BSKN37CP.js");
+    case "differentialAnalysis":
+      return await import("./DifferentialAnalysis-UWTYK7NU.js");
+    case "Disco":
+      return await import("./Disco-IL6REGSA.js");
+    case "dmr":
+      return await import("./DmrPlot-DDP53T3F.js");
+    case "DziViewer":
+      return await import("./DziViewer-DDUK2RLO.js");
+    case "GeneExpInput":
+      return await import("./GeneExpInput-ZWBC226P.js");
+    case "genomeBrowser":
+      return await import("./GB-F4LMYMHF.js");
+    case "grin2":
+      return await import("./grin2-AJFEBD43.js");
+    case "gsea":
+      return await import("./gsea-PE5WZ5ZI.js");
+    case "imagePlot":
+      return await import("./imagePlot-NFEE6IGV.js");
+    case "report":
+      return await import("./report-ETNALKTY.js");
+    case "runChart2":
+    //See frequencyChart
+    case "frequencyChart":
+      return await import("./RunChart2-7DOXOFXV.js");
+    case "profileBarchart":
+      return await import("./profileBarchart-Z4SYIYBE.js");
+    case "profileBarchart2":
+      return await import("./barchart2-XRMPCBBU.js");
+    case "profileForms":
+      return await import("./profileForms-RA7XQ2QT.js");
+    case "profilePlot":
+      return await import("./profilePlot-4BM3XZVK.js");
+    case "profilePolar":
+      return await import("./polar-4AUAZHBV.js");
+    case "profilePolar2":
+      return await import("./polar2-SRD4WWXU.js");
+    case "profileRadar":
+      return await import("./profileRadar-EYBESEPI.js");
+    case "profileRadar2":
+      return await import("./radar2-I6FN5SUX.js");
+    case "profileRadarFacility":
+      return await import("./profileRadarFacility-FZYTFM26.js");
+    case "profileRadarFacility2":
+      return await import("./radarFacility2-GVK7PT3V.js");
+    case "proteinView":
+      return await import("./proteinView-F6XKT2A5.js");
+    case "numericDictTermCluster":
+      return await import("./numericDictTermCluster-DOD66G3A.js");
+    case "proteomeAbundance":
+      return await import("./proteomeAbundance-65R6M4YQ.js");
+    case "sampleScatter":
+      return await import("./scatter-ETOZ722F.js");
+    case "sc":
+      return await import("./SC-APZRV4H6.js");
+    case "summarizeCnvGeneexp":
+      return await import("./summarizeCnvGeneexp-GCHNKTIU.js");
+    case "summarizeGeneexpSurvival":
+      return await import("./summarizeGeneexpSurvival-R2RYQZ3M.js");
+    case "summarizeMutationDiagnosis":
+      return await import("./summarizeMutationDiagnosis-3JUY75LM.js");
+    case "summarizeMutationSurvival":
+      return await import("./summarizeMutationSurvival-VYLRWTCF.js");
+    case "summarizeMutationCnv":
+      return await import("./summarizeMutationCnv-LB2BIYRL.js");
+    case "summaryInput":
+      return await import("./summaryInput-OZHZG3PV.js");
+    case "summary":
+      return await import("./summary-2QQ72IEQ.js");
+    case "survival":
+      return await import("./survival-EBD4DHO7.js");
+    case "table":
+      return await import("./table-ISOQOI6C.js");
+    case "violin":
+      return await import("./violin-KGGTUQFF.js");
+    case "volcano":
+      return await import("./Volcano-X4ZWK644.js");
+    case "WSISamplesPlot":
+      return await import("./WsiSamplesPlot-3522VRB5.js");
+    case "WSIViewer":
+      return await import("./WSIViewer-E247ELKN.js");
+    default:
+      if (notFoundMessage) throw notFoundMessage;
+      return await globImport_plots_js(`../plots/${chartType}.js`);
+  }
+}
+
+export {
+  importPlot
+};
+//# sourceMappingURL=chunk-RYCOJY7M.js.map

package/dist/chunk-RYCOJY7M.js.map

@@ -0,0 +1,7 @@
+{
+  "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 'profileBarchart':\n\t\t\treturn await import('./profile/profileBarchart.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 'profilePlot':\n\t\t\treturn await import('./profile/profilePlot.ts')\n\n\t\tcase 'profilePolar':\n\t\t\treturn await import('./profile/polar.ts')\n\n\t\tcase 'profilePolar2':\n\t\t\treturn await import('./profile/polar2.ts')\n\n\t\tcase 'profileRadar':\n\t\t\treturn await import('./profile/profileRadar.ts')\n\n\t\tcase 'profileRadar2':\n\t\t\treturn await import('./profile/radar2.ts')\n\n\t\tcase 'profileRadarFacility':\n\t\t\treturn await import('./profile/profileRadarFacility.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 '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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+  "names": []
+}

package/dist/chunk-RZBV6474.js

@@ -0,0 +1,117 @@
+import {
+  addGeneSearchbox,
+  isoformSelect,
+  sayerror
+} from "./chunk-2YC6ZVE4.js";
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.js";
+import {
+  dofetch3
+} from "./chunk-I55NLUCQ.js";
+import {
+  ISOFORM_EXPRESSION
+} from "./chunk-EGWVYY7K.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 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,
+      submitLabel: "Create Collection",
+      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} ${this.getUnit()}`;
+    this.callback({ isoform, gene, name, type: ISOFORM_EXPRESSION });
+  }
+  selectCollection(gms, gene) {
+    const unit = this.getUnit();
+    const termlst = gms.map((gm) => ({
+      id: gm.isoform,
+      name: gm.isoform,
+      type: ISOFORM_EXPRESSION,
+      isoform: gm.isoform
+    }));
+    this.callback({
+      type: "termCollection",
+      isCustom: true,
+      memberType: "numeric",
+      name: `${gene} Isoforms (${unit})`,
+      termlst,
+      propsByTermId: {},
+      isleaf: true
+    });
+  }
+};
+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-RZBV6474.js.map