@sjcrh/proteinpaint-client 2.182.0 → 2.182.1

package/dist/summarizeCnvGeneexp-FTL2MGAJ.js

@@ -1,158 +0,0 @@
-import {
-  launchPlot
-} from "./chunk-KSFSM46X.js";
-import {
-  addGeneSearchbox,
-  fillTermWrapper,
-  make_one_checkbox,
-  table2col
-} from "./chunk-7FEHI46K.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-XD6BFNMR.js";
-import {
-  Menu
-} from "./chunk-2SRMRC6L.js";
-import "./chunk-TCPU43TU.js";
-import "./chunk-XDI4UFCZ.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-5EF5U7MX.js";
-import "./chunk-IQIXGTQV.js";
-import "./chunk-UCLS2SVB.js";
-import "./chunk-MVTCBVSX.js";
-import "./chunk-F6V4AYWP.js";
-import "./chunk-5OHXYXLD.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-DVDDXOWT.js";
-import "./chunk-6MSCYO7K.js";
-import "./chunk-22NJUYET.js";
-import "./chunk-MDL2HG3N.js";
-import {
-  dtcnv
-} from "./chunk-IGEQI6MR.js";
-import "./chunk-BEWDIM6H.js";
-import "./chunk-IH7ILDJS.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-SEEYV6P2.js";
-import {
-  select_default
-} from "./chunk-NDWTN4U5.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-
-// plots/summarizeCnvGeneexp.ts
-var tip = new Menu({ padding: "0px" });
-async function makeChartBtnMenu(holder, chartsInstance) {
-  let expTw, cnvTw, cnvGeneSameAsExp = true, expSearchPrompt, cnvTableRow;
-  make_one_checkbox({
-    holder: holder.append("div").style("margin", "20px 10px 5px 15px"),
-    labeltext: "Use Same Gene For CNV",
-    checked: true,
-    callback: async (checked) => {
-      cnvGeneSameAsExp = checked;
-      await updateUi();
-    }
-  });
-  const table = table2col({
-    holder: holder.append("div"),
-    margin: "10px",
-    cellPadding: "10px"
-  });
-  {
-    const [td1, td2] = table.addRow();
-    td1.text("Search Gene For Expression");
-    const searchDiv = td2.append("div");
-    expSearchPrompt = td2.append("div").style("font-size", ".7em");
-    const result = addGeneSearchbox({
-      row: searchDiv,
-      tip,
-      searchOnly: "gene",
-      genome: chartsInstance.app.opts.genome,
-      callback: async () => {
-        expSearchPrompt.text("LOADING ...");
-        try {
-          expTw = { term: { gene: result.geneSymbol, type: "geneExpression" }, q: {} };
-          await updateUi();
-          if (cnvGeneSameAsExp) launch();
-          expSearchPrompt.text("");
-        } catch (e) {
-          expSearchPrompt.text("Error: " + (e.message || e));
-          console.log(e.stack);
-        }
-      }
-    });
-  }
-  {
-    const [td1, td2] = table.addRow();
-    cnvTableRow = select_default(td1.node().parentNode);
-    td1.text("Search Gene for CNV");
-    const searchDiv = td2.append("div");
-    const cnvSearchPrompt = td2.append("div").style("font-size", ".7em");
-    const result = addGeneSearchbox({
-      row: searchDiv,
-      tip,
-      searchOnly: "gene",
-      genome: chartsInstance.app.opts.genome,
-      callback: async () => {
-        cnvSearchPrompt.text("LOADING ...");
-        try {
-          cnvTw = await fillGvTw(result.geneSymbol, dtcnv);
-          await updateUi();
-          cnvSearchPrompt.text("");
-        } catch (e) {
-          cnvSearchPrompt.text("Error: " + (e.message || e));
-          if (e.stack) console.log(e.stack);
-        }
-      }
-    });
-  }
-  const submitBtn = holder.append("button").text("Launch Plot").style("margin", "0px 15px 15px 15px").property("disabled", true).on("click", launch);
-  async function updateUi() {
-    if (cnvGeneSameAsExp) {
-      if (expTw) {
-        cnvTw = await fillGvTw(expTw.term.gene, dtcnv);
-      }
-    }
-    cnvTableRow.style("display", cnvGeneSameAsExp ? "none" : "");
-    expSearchPrompt.text(cnvGeneSameAsExp ? "Hit ENTER to launch plot." : "");
-    submitBtn.style("display", cnvGeneSameAsExp ? "none" : "").property("disabled", !expTw || !cnvTw);
-  }
-  updateUi();
-  async function fillGvTw(geneSymbol, dt) {
-    const name = geneSymbol;
-    const tw = {
-      term: {
-        id: name,
-        name,
-        genes: [
-          {
-            kind: "gene",
-            id: name,
-            gene: name,
-            name,
-            type: "geneVariant"
-          }
-        ],
-        type: "geneVariant"
-      },
-      q: { type: "predefined-groupset", dtLst: [dt] }
-    };
-    await fillTermWrapper(tw, chartsInstance.app.vocabApi);
-    return tw;
-  }
-  function launch() {
-    if (!expTw || !cnvTw) throw "either tw is missing";
-    launchPlot({
-      tw1: expTw,
-      tw2: cnvTw,
-      chartsInstance,
-      holder
-    });
-  }
-}
-export {
-  makeChartBtnMenu
-};
-//# sourceMappingURL=summarizeCnvGeneexp-FTL2MGAJ.js.map

package/dist/summarizeCnvGeneexp-FTL2MGAJ.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/summarizeCnvGeneexp.ts"],
-  "sourcesContent": ["import { table2col, addGeneSearchbox, make_one_checkbox, Menu } from '#dom'\nimport { dtcnv } from '#shared/common.js'\nimport { select } from 'd3-selection'\nimport { launchPlot } from './summarizeMutationDiagnosis'\nimport { fillTermWrapper } from '#termsetting'\n\n/*\nsame design as summarizeMutationDiagnosis.ts\n*/\n\nconst tip = new Menu({ padding: '0px' })\n\nexport async function makeChartBtnMenu(holder, chartsInstance) {\n\t//////////////////// modifiable variables ////////////////////\n\n\tlet expTw, // stores geneexp tw. overwritten by gene search\n\t\tcnvTw, // stores cnv tw\n\t\t/* important flag, true/false is set by toggling checkbox\n\t\t- true\n\t\t\tcnvTw uses same gene as expTw\n\t\t\tno submit btn needed. on exp gene search will create plot\n\t\t- false\n\t\t\tshow geneVariant search box\n\t\t\tshow submit btn. btn only enabled when both exp and cnv tws are set\n\t\t*/\n\t\tcnvGeneSameAsExp = true,\n\t\texpSearchPrompt, // <div> under exp gene search to show prompt\n\t\tcnvTableRow // <tr> of cnv selector. hidden when cnvGeneSameAsExp is true\n\n\t////////////////////        make ui        ////////////////////\n\n\tmake_one_checkbox({\n\t\tholder: holder.append('div').style('margin', '20px 10px 5px 15px'),\n\t\tlabeltext: 'Use Same Gene For CNV',\n\t\tchecked: true,\n\t\tcallback: async checked => {\n\t\t\tcnvGeneSameAsExp = checked\n\t\t\tawait updateUi()\n\t\t}\n\t})\n\n\tconst table = table2col({\n\t\tholder: holder.append('div'),\n\t\tmargin: '10px',\n\t\tcellPadding: '10px'\n\t})\n\n\t// gene expression variable\n\t{\n\t\tconst [td1, td2] = table.addRow()\n\t\ttd1.text('Search Gene For Expression')\n\t\tconst searchDiv = td2.append('div') // must create both before calling add box\n\t\texpSearchPrompt = td2.append('div').style('font-size', '.7em')\n\t\tconst result = addGeneSearchbox({\n\t\t\trow: searchDiv,\n\t\t\ttip,\n\t\t\tsearchOnly: 'gene',\n\t\t\tgenome: chartsInstance.app.opts.genome!,\n\t\t\tcallback: async () => {\n\t\t\t\texpSearchPrompt.text('LOADING ...')\n\t\t\t\ttry {\n\t\t\t\t\texpTw = { term: { gene: result.geneSymbol, type: 'geneExpression' }, q: {} }\n\t\t\t\t\tawait updateUi()\n\t\t\t\t\tif (cnvGeneSameAsExp) launch()\n\t\t\t\t\texpSearchPrompt.text('')\n\t\t\t\t} catch (e: any) {\n\t\t\t\t\texpSearchPrompt.text('Error: ' + (e.message || e))\n\t\t\t\t\tconsole.log(e.stack)\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t}\n\n\t// cnv variable\n\t{\n\t\tconst [td1, td2] = table.addRow()\n\t\tcnvTableRow = select(td1.node().parentNode)\n\t\ttd1.text('Search Gene for CNV')\n\t\tconst searchDiv = td2.append('div') // must create both before calling add box\n\t\tconst cnvSearchPrompt = td2.append('div').style('font-size', '.7em')\n\t\tconst result = addGeneSearchbox({\n\t\t\trow: searchDiv,\n\t\t\ttip,\n\t\t\tsearchOnly: 'gene',\n\t\t\tgenome: chartsInstance.app.opts.genome!,\n\t\t\tcallback: async () => {\n\t\t\t\tcnvSearchPrompt.text('LOADING ...')\n\t\t\t\ttry {\n\t\t\t\t\tcnvTw = await fillGvTw(result.geneSymbol, dtcnv)\n\t\t\t\t\tawait updateUi()\n\t\t\t\t\tcnvSearchPrompt.text('')\n\t\t\t\t} catch (e: any) {\n\t\t\t\t\tcnvSearchPrompt.text('Error: ' + (e.message || e))\n\t\t\t\t\tif (e.stack) console.log(e.stack)\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t}\n\n\tconst submitBtn = holder\n\t\t.append('button')\n\t\t.text('Launch Plot')\n\t\t.style('margin', '0px 15px 15px 15px')\n\t\t.property('disabled', true) // enable when both exp and cnv tws are set\n\t\t.on('click', launch)\n\n\t////////////////////        helpers        ////////////////////\n\n\tasync function updateUi() {\n\t\tif (cnvGeneSameAsExp) {\n\t\t\tif (expTw) {\n\t\t\t\tcnvTw = await fillGvTw(expTw.term.gene, dtcnv)\n\t\t\t}\n\t\t}\n\t\tcnvTableRow.style('display', cnvGeneSameAsExp ? 'none' : '')\n\t\texpSearchPrompt.text(cnvGeneSameAsExp ? 'Hit ENTER to launch plot.' : '')\n\t\tsubmitBtn.style('display', cnvGeneSameAsExp ? 'none' : '').property('disabled', !expTw || !cnvTw)\n\t}\n\n\tupdateUi()\n\n\tasync function fillGvTw(geneSymbol, dt) {\n\t\tconst name = geneSymbol\n\t\tconst tw: any = {\n\t\t\tterm: {\n\t\t\t\tid: name,\n\t\t\t\tname,\n\t\t\t\tgenes: [\n\t\t\t\t\t{\n\t\t\t\t\t\tkind: 'gene',\n\t\t\t\t\t\tid: name,\n\t\t\t\t\t\tgene: name,\n\t\t\t\t\t\tname,\n\t\t\t\t\t\ttype: 'geneVariant'\n\t\t\t\t\t}\n\t\t\t\t],\n\t\t\t\ttype: 'geneVariant'\n\t\t\t},\n\t\t\tq: { type: 'predefined-groupset', dtLst: [dt] }\n\t\t}\n\t\tawait fillTermWrapper(tw, chartsInstance.app.vocabApi)\n\t\treturn tw\n\t}\n\n\tfunction launch() {\n\t\tif (!expTw || !cnvTw) throw 'either tw is missing'\n\t\tlaunchPlot({\n\t\t\ttw1: expTw,\n\t\t\ttw2: cnvTw,\n\t\t\tchartsInstance,\n\t\t\tholder\n\t\t})\n\t}\n}\n"],
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-  "names": []
-}

package/dist/summarizeGeneexpSurvival-DDIF4UW6.js

@@ -1,105 +0,0 @@
-import {
-  t0_t2_defaultQ
-} from "./chunk-SPAIFVM2.js";
-import {
-  launchPlot
-} from "./chunk-KSFSM46X.js";
-import "./chunk-KISFQDQE.js";
-import "./chunk-V2OJLJSK.js";
-import {
-  addGeneSearchbox,
-  fillTermWrapper,
-  table2col,
-  termsettingInit
-} from "./chunk-7FEHI46K.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-XD6BFNMR.js";
-import {
-  Menu
-} from "./chunk-2SRMRC6L.js";
-import "./chunk-TCPU43TU.js";
-import "./chunk-XDI4UFCZ.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-5EF5U7MX.js";
-import "./chunk-IQIXGTQV.js";
-import "./chunk-UCLS2SVB.js";
-import "./chunk-MVTCBVSX.js";
-import "./chunk-F6V4AYWP.js";
-import "./chunk-5OHXYXLD.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-DVDDXOWT.js";
-import "./chunk-6MSCYO7K.js";
-import "./chunk-22NJUYET.js";
-import "./chunk-MDL2HG3N.js";
-import "./chunk-IGEQI6MR.js";
-import "./chunk-BEWDIM6H.js";
-import "./chunk-IH7ILDJS.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-SEEYV6P2.js";
-import "./chunk-NDWTN4U5.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-
-// plots/summarizeGeneexpSurvival.ts
-var tip = new Menu({ padding: "0px" });
-async function makeChartBtnMenu(holder, chartsInstance) {
-  let dictTw;
-  {
-    const t = chartsInstance.app.vocabApi.termdbConfig.defaultTw4correlationPlot?.survival;
-    if (!t) throw "defaultTw4correlationPlot missing";
-    dictTw = structuredClone(t);
-    await fillTermWrapper(dictTw, chartsInstance.app.vocabApi);
-  }
-  const table = table2col({
-    holder: holder.append("div"),
-    margin: "10px",
-    cellPadding: "10px"
-  });
-  {
-    const [td1, td2] = table.addRow();
-    td1.text("Search Gene For Expression");
-    const searchDiv = td2.append("div");
-    const loadingDiv = td2.append("div").style("display", "none").style("margin", "5px").style("font-size", ".7em").text("LOADING ...");
-    const result = addGeneSearchbox({
-      row: searchDiv,
-      tip,
-      searchOnly: "gene",
-      genome: chartsInstance.app.opts.genome,
-      callback: async () => {
-        loadingDiv.style("display", "block");
-        const expTw = { term: { gene: result.geneSymbol, type: "geneExpression" } };
-        await fillTermWrapper(expTw, chartsInstance.app.vocabApi, t0_t2_defaultQ);
-        launchPlot({
-          tw1: dictTw,
-          tw2: expTw,
-          chartsInstance,
-          holder
-        });
-      }
-    });
-  }
-  {
-    const [td1, td2] = table.addRow();
-    td1.text("Compare Expression Against");
-    const pillDiv = td2.append("div");
-    const pill = await termsettingInit({
-      usecase: { target: "survival", detail: "term" },
-      // limit to survival terms
-      vocabApi: chartsInstance.app.vocabApi,
-      holder: pillDiv,
-      callback: async (tw) => {
-        await pill.main(tw);
-        dictTw = tw;
-      }
-    });
-    await fillTermWrapper(dictTw, chartsInstance.app.vocabApi);
-    await pill.main(dictTw);
-  }
-}
-export {
-  makeChartBtnMenu
-};
-//# sourceMappingURL=summarizeGeneexpSurvival-DDIF4UW6.js.map

package/dist/summarizeGeneexpSurvival-DDIF4UW6.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/summarizeGeneexpSurvival.ts"],
-  "sourcesContent": ["import { addGeneSearchbox, Menu, table2col } from '#dom'\nimport { termsettingInit, fillTermWrapper } from '#termsetting'\nimport { launchPlot } from './summarizeMutationDiagnosis'\nimport { t0_t2_defaultQ } from './survival/survival'\n\n/*\nduplicates code from summarizeMutationDiagnosis, with minute changes\n*/\nconst tip = new Menu({ padding: '0px' })\n\nexport async function makeChartBtnMenu(holder, chartsInstance) {\n\tlet dictTw // the variable stores a copy of ds-supplied default tw and will be overwriten by pill update\n\t{\n\t\t// always require a default term and does not allow it to be deleted from pill to simplify ui logic\n\t\tconst t = chartsInstance.app.vocabApi.termdbConfig.defaultTw4correlationPlot?.survival\n\t\tif (!t) throw 'defaultTw4correlationPlot missing'\n\t\tdictTw = structuredClone(t)\n\t\tawait fillTermWrapper(dictTw, chartsInstance.app.vocabApi)\n\t}\n\n\t// 2-col table to organize input ui\n\tconst table = table2col({\n\t\tholder: holder.append('div'),\n\t\tmargin: '10px',\n\t\tcellPadding: '10px'\n\t})\n\n\t{\n\t\tconst [td1, td2] = table.addRow()\n\t\ttd1.text('Search Gene For Expression')\n\t\tconst searchDiv = td2.append('div')\n\t\tconst loadingDiv = td2\n\t\t\t.append('div')\n\t\t\t.style('display', 'none')\n\t\t\t.style('margin', '5px')\n\t\t\t.style('font-size', '.7em')\n\t\t\t.text('LOADING ...')\n\t\tconst result = addGeneSearchbox({\n\t\t\trow: searchDiv,\n\t\t\ttip,\n\t\t\tsearchOnly: 'gene',\n\t\t\tgenome: chartsInstance.app.opts.genome!,\n\t\t\tcallback: async () => {\n\t\t\t\tloadingDiv.style('display', 'block')\n\t\t\t\tconst expTw: any = { term: { gene: result.geneSymbol, type: 'geneExpression' } }\n\t\t\t\tawait fillTermWrapper(expTw, chartsInstance.app.vocabApi, t0_t2_defaultQ)\n\t\t\t\tlaunchPlot({\n\t\t\t\t\ttw1: dictTw,\n\t\t\t\t\ttw2: expTw,\n\t\t\t\t\tchartsInstance,\n\t\t\t\t\tholder\n\t\t\t\t})\n\t\t\t}\n\t\t})\n\t}\n\n\t{\n\t\tconst [td1, td2] = table.addRow()\n\t\ttd1.text('Compare Expression Against')\n\n\t\t// create both pill and wait divs first, then await pill.main(), so the loading text can display while waiting for pill.main()\n\t\tconst pillDiv = td2.append('div')\n\n\t\tconst pill = await termsettingInit({\n\t\t\tusecase: { target: 'survival', detail: 'term' }, // limit to survival terms\n\t\t\tvocabApi: chartsInstance.app.vocabApi,\n\t\t\tholder: pillDiv,\n\t\t\tcallback: async tw => {\n\t\t\t\tawait pill.main(tw)\n\t\t\t\tdictTw = tw\n\t\t\t}\n\t\t})\n\n\t\tawait fillTermWrapper(dictTw, chartsInstance.app.vocabApi) // required before calling pill.main()\n\t\tawait pill.main(dictTw)\n\t}\n}\n"],
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package/dist/summarizeMutationCnv-L3GL5YDY.js

@@ -1,159 +0,0 @@
-import {
-  launchPlot
-} from "./chunk-KSFSM46X.js";
-import {
-  addGeneSearchbox,
-  fillTermWrapper,
-  make_one_checkbox,
-  table2col
-} from "./chunk-7FEHI46K.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-XD6BFNMR.js";
-import {
-  Menu
-} from "./chunk-2SRMRC6L.js";
-import "./chunk-TCPU43TU.js";
-import "./chunk-XDI4UFCZ.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-5EF5U7MX.js";
-import "./chunk-IQIXGTQV.js";
-import "./chunk-UCLS2SVB.js";
-import "./chunk-MVTCBVSX.js";
-import "./chunk-F6V4AYWP.js";
-import "./chunk-5OHXYXLD.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-DVDDXOWT.js";
-import "./chunk-6MSCYO7K.js";
-import "./chunk-22NJUYET.js";
-import "./chunk-MDL2HG3N.js";
-import {
-  dtcnv,
-  dtsnvindel
-} from "./chunk-IGEQI6MR.js";
-import "./chunk-BEWDIM6H.js";
-import "./chunk-IH7ILDJS.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-SEEYV6P2.js";
-import {
-  select_default
-} from "./chunk-NDWTN4U5.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-
-// plots/summarizeMutationCnv.ts
-var tip = new Menu({ padding: "0px" });
-async function makeChartBtnMenu(holder, chartsInstance) {
-  let mutTw, cnvTw, cnvGeneSameAsMut = true, mutSearchPrompt, cnvTableRow;
-  make_one_checkbox({
-    holder: holder.append("div").style("margin", "20px 10px 5px 15px"),
-    labeltext: "Use Same Gene For CNV",
-    checked: true,
-    callback: async (checked) => {
-      cnvGeneSameAsMut = checked;
-      await updateUi();
-    }
-  });
-  const table = table2col({
-    holder: holder.append("div"),
-    margin: "10px",
-    cellPadding: "10px"
-  });
-  {
-    const [td1, td2] = table.addRow();
-    td1.text("Search Gene for Mutation");
-    const searchDiv = td2.append("div");
-    mutSearchPrompt = td2.append("div").style("font-size", ".7em");
-    const result = addGeneSearchbox({
-      row: searchDiv,
-      tip,
-      searchOnly: "gene",
-      genome: chartsInstance.app.opts.genome,
-      callback: async () => {
-        mutSearchPrompt.text("LOADING ...");
-        try {
-          mutTw = await fillGvTw(result.geneSymbol, dtsnvindel);
-          await updateUi();
-          if (cnvGeneSameAsMut) launch();
-          mutSearchPrompt.text("");
-        } catch (e) {
-          mutSearchPrompt.text("Error: " + (e.message || e));
-          if (e.stack) console.log(e.stack);
-        }
-      }
-    });
-  }
-  {
-    const [td1, td2] = table.addRow();
-    cnvTableRow = select_default(td1.node().parentNode);
-    td1.text("Search Gene for CNV");
-    const searchDiv = td2.append("div");
-    const cnvSearchPrompt = td2.append("div").style("font-size", ".7em");
-    const result = addGeneSearchbox({
-      row: searchDiv,
-      tip,
-      searchOnly: "gene",
-      genome: chartsInstance.app.opts.genome,
-      callback: async () => {
-        cnvSearchPrompt.text("LOADING ...");
-        try {
-          cnvTw = await fillGvTw(result.geneSymbol, dtcnv);
-          await updateUi();
-          cnvSearchPrompt.text("");
-        } catch (e) {
-          cnvSearchPrompt.text("Error: " + (e.message || e));
-          if (e.stack) console.log(e.stack);
-        }
-      }
-    });
-  }
-  const submitBtn = holder.append("button").text("Launch Plot").style("margin", "0px 15px 15px 15px").property("disabled", true).on("click", launch);
-  async function updateUi() {
-    if (cnvGeneSameAsMut) {
-      if (mutTw) {
-        cnvTw = await fillGvTw(mutTw.term.id, dtcnv);
-      }
-    }
-    cnvTableRow.style("display", cnvGeneSameAsMut ? "none" : "");
-    mutSearchPrompt.text(cnvGeneSameAsMut ? "Hit ENTER to launch plot." : "");
-    submitBtn.style("display", cnvGeneSameAsMut ? "none" : "").property("disabled", !mutTw || !cnvTw);
-  }
-  updateUi();
-  async function fillGvTw(geneSymbol, dt) {
-    const name = geneSymbol;
-    const tw = {
-      term: {
-        id: name,
-        name,
-        genes: [
-          {
-            kind: "gene",
-            id: name,
-            gene: name,
-            name,
-            type: "geneVariant"
-          }
-        ],
-        type: "geneVariant"
-      },
-      q: { type: "predefined-groupset", dtLst: [dt] }
-    };
-    await fillTermWrapper(tw, chartsInstance.app.vocabApi);
-    return tw;
-  }
-  function launch() {
-    if (!mutTw || !cnvTw) throw "either tw is missing";
-    launchPlot({
-      tw1: mutTw,
-      tw2: cnvTw,
-      chartsInstance,
-      holder
-    });
-  }
-}
-export {
-  makeChartBtnMenu
-};
-//# sourceMappingURL=summarizeMutationCnv-L3GL5YDY.js.map

package/dist/summarizeMutationCnv-L3GL5YDY.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/summarizeMutationCnv.ts"],
-  "sourcesContent": ["import { table2col, addGeneSearchbox, make_one_checkbox, Menu } from '#dom'\nimport { dtsnvindel, dtcnv } from '#shared/common.js'\nimport { select } from 'd3-selection'\nimport { launchPlot } from './summarizeMutationDiagnosis'\nimport { fillTermWrapper } from '#termsetting'\n\n/*\nsimilar design as summarizeCnvGeneexp.ts\n*/\n\nconst tip = new Menu({ padding: '0px' })\n\nexport async function makeChartBtnMenu(holder, chartsInstance) {\n\t//////////////////// modifiable variables ////////////////////\n\n\tlet mutTw, // stores mutation tw. overwritten by gene search\n\t\tcnvTw, // stores cnv tw\n\t\t/* important flag, true/false is set by toggling checkbox\n\t\t- true\n\t\t\tcnvTw uses same gene as mutTw\n\t\t\tno submit btn needed. on mutation gene search will create plot\n\t\t- false\n\t\t\tshow both mutation gene search and cnv gene search\n\t\t\tshow submit btn. btn only enabled when both exp and cnv tws are set\n\t\t*/\n\t\tcnvGeneSameAsMut = true,\n\t\tmutSearchPrompt, // <div> under mutation gene search to show prompt\n\t\tcnvTableRow // <tr> of cnv selector. hidden when cnvGeneSameAsMut is true\n\n\t////////////////////        make ui        ////////////////////\n\n\tmake_one_checkbox({\n\t\tholder: holder.append('div').style('margin', '20px 10px 5px 15px'),\n\t\tlabeltext: 'Use Same Gene For CNV',\n\t\tchecked: true,\n\t\tcallback: async checked => {\n\t\t\tcnvGeneSameAsMut = checked\n\t\t\tawait updateUi()\n\t\t}\n\t})\n\n\tconst table = table2col({\n\t\tholder: holder.append('div'),\n\t\tmargin: '10px',\n\t\tcellPadding: '10px'\n\t})\n\n\t// mutation variable\n\t{\n\t\tconst [td1, td2] = table.addRow()\n\t\ttd1.text('Search Gene for Mutation')\n\t\tconst searchDiv = td2.append('div') // must create both before calling add box\n\t\tmutSearchPrompt = td2.append('div').style('font-size', '.7em')\n\t\tconst result = addGeneSearchbox({\n\t\t\trow: searchDiv,\n\t\t\ttip,\n\t\t\tsearchOnly: 'gene',\n\t\t\tgenome: chartsInstance.app.opts.genome!,\n\t\t\tcallback: async () => {\n\t\t\t\tmutSearchPrompt.text('LOADING ...')\n\t\t\t\ttry {\n\t\t\t\t\tmutTw = await fillGvTw(result.geneSymbol, dtsnvindel)\n\t\t\t\t\tawait updateUi()\n\t\t\t\t\tif (cnvGeneSameAsMut) launch()\n\t\t\t\t\tmutSearchPrompt.text('')\n\t\t\t\t} catch (e: any) {\n\t\t\t\t\tmutSearchPrompt.text('Error: ' + (e.message || e))\n\t\t\t\t\tif (e.stack) console.log(e.stack)\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t}\n\n\t// cnv variable\n\t{\n\t\tconst [td1, td2] = table.addRow()\n\t\tcnvTableRow = select(td1.node().parentNode)\n\t\ttd1.text('Search Gene for CNV')\n\t\tconst searchDiv = td2.append('div') // must create both before calling add box\n\t\tconst cnvSearchPrompt = td2.append('div').style('font-size', '.7em')\n\t\tconst result = addGeneSearchbox({\n\t\t\trow: searchDiv,\n\t\t\ttip,\n\t\t\tsearchOnly: 'gene',\n\t\t\tgenome: chartsInstance.app.opts.genome!,\n\t\t\tcallback: async () => {\n\t\t\t\tcnvSearchPrompt.text('LOADING ...')\n\t\t\t\ttry {\n\t\t\t\t\tcnvTw = await fillGvTw(result.geneSymbol, dtcnv)\n\t\t\t\t\tawait updateUi()\n\t\t\t\t\tcnvSearchPrompt.text('')\n\t\t\t\t} catch (e: any) {\n\t\t\t\t\tcnvSearchPrompt.text('Error: ' + (e.message || e))\n\t\t\t\t\tif (e.stack) console.log(e.stack)\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t}\n\n\tconst submitBtn = holder\n\t\t.append('button')\n\t\t.text('Launch Plot')\n\t\t.style('margin', '0px 15px 15px 15px')\n\t\t.property('disabled', true) // enable when both exp and cnv tws are set\n\t\t.on('click', launch)\n\n\t////////////////////        helpers        ////////////////////\n\n\tasync function updateUi() {\n\t\tif (cnvGeneSameAsMut) {\n\t\t\tif (mutTw) {\n\t\t\t\tcnvTw = await fillGvTw(mutTw.term.id, dtcnv)\n\t\t\t}\n\t\t}\n\t\tcnvTableRow.style('display', cnvGeneSameAsMut ? 'none' : '')\n\t\tmutSearchPrompt.text(cnvGeneSameAsMut ? 'Hit ENTER to launch plot.' : '')\n\t\tsubmitBtn.style('display', cnvGeneSameAsMut ? 'none' : '').property('disabled', !mutTw || !cnvTw)\n\t}\n\n\tupdateUi()\n\n\tasync function fillGvTw(geneSymbol, dt) {\n\t\tconst name = geneSymbol\n\t\tconst tw: any = {\n\t\t\tterm: {\n\t\t\t\tid: name,\n\t\t\t\tname,\n\t\t\t\tgenes: [\n\t\t\t\t\t{\n\t\t\t\t\t\tkind: 'gene',\n\t\t\t\t\t\tid: name,\n\t\t\t\t\t\tgene: name,\n\t\t\t\t\t\tname,\n\t\t\t\t\t\ttype: 'geneVariant'\n\t\t\t\t\t}\n\t\t\t\t],\n\t\t\t\ttype: 'geneVariant'\n\t\t\t},\n\t\t\tq: { type: 'predefined-groupset', dtLst: [dt] }\n\t\t}\n\t\tawait fillTermWrapper(tw, chartsInstance.app.vocabApi)\n\t\treturn tw\n\t}\n\n\tfunction launch() {\n\t\tif (!mutTw || !cnvTw) throw 'either tw is missing'\n\t\tlaunchPlot({\n\t\t\ttw1: mutTw,\n\t\t\ttw2: cnvTw,\n\t\t\tchartsInstance,\n\t\t\tholder\n\t\t})\n\t}\n}\n"],
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-}

package/dist/summarizeMutationDiagnosis-LALOJTHV.js

@@ -1,38 +0,0 @@
-import {
-  launchPlot,
-  makeChartBtnMenu
-} from "./chunk-KSFSM46X.js";
-import "./chunk-7FEHI46K.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-XD6BFNMR.js";
-import "./chunk-2SRMRC6L.js";
-import "./chunk-TCPU43TU.js";
-import "./chunk-XDI4UFCZ.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-5EF5U7MX.js";
-import "./chunk-IQIXGTQV.js";
-import "./chunk-UCLS2SVB.js";
-import "./chunk-MVTCBVSX.js";
-import "./chunk-F6V4AYWP.js";
-import "./chunk-5OHXYXLD.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-DVDDXOWT.js";
-import "./chunk-6MSCYO7K.js";
-import "./chunk-22NJUYET.js";
-import "./chunk-MDL2HG3N.js";
-import "./chunk-IGEQI6MR.js";
-import "./chunk-BEWDIM6H.js";
-import "./chunk-IH7ILDJS.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-SEEYV6P2.js";
-import "./chunk-NDWTN4U5.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  launchPlot,
-  makeChartBtnMenu
-};
-//# sourceMappingURL=summarizeMutationDiagnosis-LALOJTHV.js.map

package/dist/summarizeMutationSurvival-TSNTSOBZ.js

@@ -1,97 +0,0 @@
-import {
-  launchPlot
-} from "./chunk-KSFSM46X.js";
-import {
-  SearchHandler,
-  fillTermWrapper,
-  table2col,
-  termsettingInit
-} from "./chunk-7FEHI46K.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-XD6BFNMR.js";
-import "./chunk-2SRMRC6L.js";
-import "./chunk-TCPU43TU.js";
-import "./chunk-XDI4UFCZ.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-5EF5U7MX.js";
-import "./chunk-IQIXGTQV.js";
-import "./chunk-UCLS2SVB.js";
-import "./chunk-MVTCBVSX.js";
-import "./chunk-F6V4AYWP.js";
-import "./chunk-5OHXYXLD.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-DVDDXOWT.js";
-import "./chunk-6MSCYO7K.js";
-import "./chunk-22NJUYET.js";
-import "./chunk-MDL2HG3N.js";
-import "./chunk-IGEQI6MR.js";
-import "./chunk-BEWDIM6H.js";
-import "./chunk-IH7ILDJS.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-SEEYV6P2.js";
-import "./chunk-NDWTN4U5.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-
-// plots/summarizeMutationSurvival.ts
-async function makeChartBtnMenu(holder, chartsInstance) {
-  let dictTw;
-  {
-    const t = chartsInstance.app.vocabApi.termdbConfig.defaultTw4correlationPlot?.survival;
-    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,
-      genomeObj: chartsInstance.app.opts.genome,
-      app: chartsInstance.app,
-      // required to supply "opts.app.vocabApi" for the search ui
-      msg: "Hit ENTER to launch plot.",
-      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");
-    const pill = await termsettingInit({
-      usecase: { target: "survival", detail: "term" },
-      // limit to survival terms
-      vocabApi: chartsInstance.app.vocabApi,
-      holder: pillDiv,
-      callback: async (tw) => {
-        await pill.main(tw);
-        dictTw = tw;
-      }
-    });
-    await fillTermWrapper(dictTw, chartsInstance.app.vocabApi);
-    await pill.main(dictTw);
-  }
-}
-export {
-  makeChartBtnMenu
-};
-//# sourceMappingURL=summarizeMutationSurvival-TSNTSOBZ.js.map

package/dist/summary-YRHVS64T.js

@@ -1,47 +0,0 @@
-import {
-  componentInit,
-  getPlotConfig,
-  mayAdjustConfig,
-  summaryInit
-} from "./chunk-AZYDW5T7.js";
-import "./chunk-GW7DHJYH.js";
-import "./chunk-MXI3NXRB.js";
-import "./chunk-2OSEZCWZ.js";
-import "./chunk-UBGTQMOO.js";
-import "./chunk-TN5GSG34.js";
-import "./chunk-7FEHI46K.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-XD6BFNMR.js";
-import "./chunk-2SRMRC6L.js";
-import "./chunk-TCPU43TU.js";
-import "./chunk-XDI4UFCZ.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-5EF5U7MX.js";
-import "./chunk-IQIXGTQV.js";
-import "./chunk-UCLS2SVB.js";
-import "./chunk-MVTCBVSX.js";
-import "./chunk-F6V4AYWP.js";
-import "./chunk-5OHXYXLD.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-DVDDXOWT.js";
-import "./chunk-6MSCYO7K.js";
-import "./chunk-22NJUYET.js";
-import "./chunk-MDL2HG3N.js";
-import "./chunk-IGEQI6MR.js";
-import "./chunk-BEWDIM6H.js";
-import "./chunk-IH7ILDJS.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-SEEYV6P2.js";
-import "./chunk-NDWTN4U5.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  componentInit,
-  getPlotConfig,
-  mayAdjustConfig,
-  summaryInit
-};
-//# sourceMappingURL=summary-YRHVS64T.js.map