@sjcrh/proteinpaint-client 2.185.0 → 2.186.0

package/dist/leftlabel.sample-NS2TBANH.js

@@ -1,257 +0,0 @@
-import {
-  displaySampleTable,
-  getFilterName,
-  makelabel
-} from "./chunk-4ZCR6CPK.js";
-import "./chunk-SKMFMGCD.js";
-import "./chunk-PXYYICV7.js";
-import "./chunk-UOOMFM7K.js";
-import "./chunk-V2OJLJSK.js";
-import "./chunk-AQ4OP4GR.js";
-import "./chunk-MSW7OS2O.js";
-import {
-  Tabs,
-  fillbar,
-  filterInit,
-  getNormalRoot,
-  renderTable
-} from "./chunk-YWUVCXFS.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-3QBZ2Y77.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-KWM6B3NL.js";
-import "./chunk-UCLS2SVB.js";
-import "./chunk-6ZCHECOT.js";
-import "./chunk-MVTCBVSX.js";
-import "./chunk-2K5DSRBJ.js";
-import {
-  violinRenderer
-} from "./chunk-X4NI4JLQ.js";
-import "./chunk-L4QG7XZE.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-UWYCEYML.js";
-import "./chunk-7UHUOC6F.js";
-import "./chunk-ZYY54HBU.js";
-import "./chunk-EGWVYY7K.js";
-import "./chunk-AMYSEKPF.js";
-import "./chunk-TV74I3Y5.js";
-import "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-
-// mds3/leftlabel.sample.js
-function makeSampleLabel(data, tk, block, laby) {
-  if (!tk.leftlabels.doms.samples) {
-    tk.leftlabels.doms.samples = makelabel(tk, block, laby);
-  }
-  if (data.sampleTotalNumber) {
-    tk.leftlabels.doms.samples.attr("class", "sja_clbtext2").style("opacity", 1).text(`${data.sampleTotalNumber} sample${data.sampleTotalNumber > 1 ? "s" : ""}`).attr("data-testid", "sjpp_mds3tk_samples_label").on("click", async (event) => {
-      tk.menutip.clear().showunder(event.target);
-      await mayShowSummary(tk, block);
-      const buttonrow = tk.menutip.d.append("div").style("margin", "10px");
-      menu_listSamples(buttonrow, data, tk, block);
-    });
-  } else {
-    tk.leftlabels.doms.samples.text("No samples").attr("class", "").style("opacity", 0.5).on("click", null);
-  }
-}
-function makeSampleFilterLabel(data, tk, block, laby) {
-  if (!tk.leftlabels.doms.filterObj) {
-    tk.leftlabels.doms.filterObj = makelabel(tk, block, laby);
-    tk.leftlabels.doms.filterObj.attr("data-testid", "sjpp_mds3tk_leftlabel_samplefilter");
-  }
-  tk.leftlabels.doms.filterObj.text(getFilterName(tk.filterObj)).on("click", async (event) => {
-    tk.menutip.clear().showunder(event.target);
-    const arg = {
-      holder: tk.menutip.d.append("div").style("margin", "10px"),
-      vocabApi: tk.mds.termdb.vocabApi,
-      callback: (f) => {
-        tk.filterObj = f;
-        tk.load();
-      }
-    };
-    mayAddGetCategoryArgs(arg, block);
-    filterInit(arg).main(tk.filterObj);
-  });
-}
-function mayAddGetCategoryArgs(arg, block) {
-  if (block.usegm) {
-    arg.getCategoriesArguments = { currentGeneNames: [block.usegm.name] };
-  } else {
-    arg.getCategoriesArguments = { rglst: structuredClone(block.rglst) };
-  }
-}
-async function mayShowSummary(tk, block) {
-  if (!tk.mds.variant2samples.twLst) {
-    return;
-  }
-  const div = tk.menutip.d.append("div").style("margin", "10px");
-  const wait = div.append("div").text("Loading...");
-  try {
-    const { summary } = await tk.mds.getSamples({ isSummary: true });
-    tk.leftlabels.__samples_data = summary;
-    wait.remove();
-    await showSummary4terms(summary, div.append("div").attr("data-testid", "sja_mds3samplesummarydiv"), tk, block);
-  } catch (e) {
-    wait.text(`Error: ${e.message || e}`);
-    if (e.stack) console.log(e.stack);
-  }
-}
-async function showSummary4terms(data, div, tk, block) {
-  const tabs = [];
-  for (const { termid, numbycategory } of data) {
-    tabs.push({
-      label: tk.mds.variant2samples.twLst.find((i) => i.term.id == termid).term.name + (numbycategory ? `<span style="font-size:.8em;float:right;margin-left: 5px;">n=${numbycategory.length}</span>` : ""),
-      keydownCallback: function(event) {
-        setTimeout(() => {
-          const tr = this.contentHolder.select("tbody").select("tr").node();
-          if (!tr) return;
-          tr.focus();
-        }, 100);
-      }
-    });
-  }
-  new Tabs({
-    holder: div,
-    tabsPosition: "vertical",
-    linePosition: "right",
-    tabs
-  }).main();
-  for (const [i, d] of data.entries()) {
-    const holder = tabs[i].contentHolder.style("padding-left", "20px");
-    if (d.numbycategory) {
-      holder.append("div").text("Click a category to create new track.").style("margin-bottom", "10px").style("font-size", ".8em").style("opacity", 0.5);
-      showSummary4oneTerm(d.termid, holder, d.numbycategory, tk, block);
-      continue;
-    }
-    if (d.density_data) {
-      if (!Number.isFinite(d.density_data.min) || !Number.isFinite(d.density_data.max)) {
-        holder.append("div").text("No data");
-        continue;
-      }
-      holder.append("div").text("Select a range to create new track.").style("margin-bottom", "10px").style("font-size", ".8em").style("opacity", 0.5);
-      showDensity4oneTerm(d.termid, holder, d, tk, block);
-      continue;
-    }
-    throw "unknown summary data";
-  }
-}
-function showSummary4oneTerm(termid, div, numbycategory, tk, block) {
-  const tw = tk.mds.variant2samples.twLst.find((i) => i.term.id == termid);
-  if (!tw) throw "showSummary4oneTerm(): tw not found from variant2samples.twLst";
-  const rows = [];
-  for (const [category_key, count, total] of numbycategory) {
-    const row = [
-      { value: tw.term.values?.[category_key]?.label || category_key },
-      { html: total == void 0 ? "" : fillbar(null, { f: count / total, v1: count, v2: total }) },
-      { html: count + (total ? ' <span style="font-size:.8em">/ ' + total + "</span>" : "") }
-    ];
-    rows.push(row);
-  }
-  renderTable({
-    div,
-    rows,
-    columns: [
-      {
-        nowrap: true
-        // to force all category values to show in one line without wrap. otherwise they wrap and column width appears fixed
-      },
-      {},
-      {}
-    ],
-    showHeader: false,
-    singleMode: true,
-    noRadioBtn: true,
-    noButtonCallback: (i) => {
-      clickCategory(numbycategory[i][0]);
-    }
-  });
-  async function clickCategory(category) {
-    tk.menutip.clear();
-    const term = await tk.mds.termdb.vocabApi.getterm(termid);
-    if (!term.values || Object.keys(term.values).length == 0) {
-      term.values = {};
-      for (const c of numbycategory) {
-        term.values[c[0]] = { label: c[0], samplecount: c[1] };
-      }
-    }
-    const tvs = {
-      type: "tvs",
-      tvs: { term, values: [{ key: category }] }
-    };
-    createSubTk(tk, block, tvs);
-  }
-}
-function getNewFilter(tk, tvs) {
-  if (tk.filterObj) {
-    return getNormalRoot({
-      type: "tvslst",
-      join: "and",
-      in: true,
-      lst: [tk.filterObj, tvs]
-    });
-  }
-  return {
-    type: "tvslst",
-    in: true,
-    join: "",
-    lst: [tvs]
-  };
-}
-async function showDensity4oneTerm(termid, div, data, tk, block) {
-  const term = await tk.mds.termdb.vocabApi.getterm(termid);
-  const callback = async (range) => {
-    tk.menutip.clear();
-    const tvs = {
-      type: "tvs",
-      tvs: { term, ranges: [{ start: range.range_start, stop: range.range_end }] }
-    };
-    createSubTk(tk, block, tvs);
-  };
-  const vr = new violinRenderer({
-    holder: div,
-    rd: data.density_data,
-    width: 400,
-    height: 100,
-    radius: 8,
-    callback,
-    scaleFactor: term.valueConversion ? term.valueConversion.scaleFactor : 1
-  });
-  vr.render();
-}
-function createSubTk(tk, block, tvs) {
-  const tk2 = block.block_addtk_template(tk.duplicateTk(getNewFilter(tk, tvs)));
-  tk2.subtk = true;
-  block.tk_load(tk2);
-}
-function menu_listSamples(buttonrow, data, tk, block) {
-  buttonrow.append("div").text(`List ${data.sampleTotalNumber} sample${data.sampleTotalNumber > 1 ? "s" : ""}`).attr("class", "sja_menuoption sja_mds3_slb_sampletablebtn").attr("data-testid", "sjpp-mds3-list-samples-option").on("click", async () => {
-    tk.menutip.clear();
-    const wait = tk.menutip.d.append("div").text("Loading...").style("margin", "15px");
-    try {
-      const { samples } = await tk.mds.getSamples();
-      await displaySampleTable(samples, {
-        div: tk.menutip.d,
-        tk,
-        block
-      });
-      wait.remove();
-    } catch (e) {
-      wait.text(e.message || e);
-      console.log(e);
-    }
-  });
-}
-export {
-  makeSampleFilterLabel,
-  makeSampleLabel
-};
-//# sourceMappingURL=leftlabel.sample-NS2TBANH.js.map

package/dist/lollipop-W6NOHHCP.js

@@ -1,166 +0,0 @@
-import {
-  block_init_default
-} from "./chunk-ENP4FLOX.js";
-import {
-  addGeneSearchbox,
-  first_genetrack_tolist
-} from "./chunk-YWUVCXFS.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-3QBZ2Y77.js";
-import {
-  Menu
-} from "./chunk-HYOEWQ5P.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-KWM6B3NL.js";
-import "./chunk-UCLS2SVB.js";
-import {
-  dofetch3
-} from "./chunk-6ZCHECOT.js";
-import "./chunk-MVTCBVSX.js";
-import "./chunk-2K5DSRBJ.js";
-import "./chunk-X4NI4JLQ.js";
-import "./chunk-L4QG7XZE.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-UWYCEYML.js";
-import "./chunk-7UHUOC6F.js";
-import "./chunk-ZYY54HBU.js";
-import "./chunk-EGWVYY7K.js";
-import "./chunk-AMYSEKPF.js";
-import "./chunk-TV74I3Y5.js";
-import "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-
-// gdc/lollipop.js
-var tip = new Menu({ padding: "" });
-async function init(arg, holder, genomes) {
-  const useGenome = arg.genome || "hg38";
-  const useDslabel = arg.dslabel || "GDC";
-  const genome = genomes[useGenome];
-  if (!genome) throw useGenome + " missing";
-  if (arg.geneSearch4GDCmds3.onloadalltk_always && typeof arg.geneSearch4GDCmds3.onloadalltk_always != "function")
-    throw "arg.geneSearch4GDCmds3.onloadalltk_always not function";
-  if (arg.geneSearch4GDCmds3.postRender && typeof arg.geneSearch4GDCmds3.postRender != "function")
-    throw "arg.geneSearch4GDCmds3.postRender not function";
-  holder.selectAll(".sja_lollipop_holder").remove();
-  const mainDiv = holder.append("div").attr("class", "sja_lollipop_holder");
-  const geneInputDiv = mainDiv.append("div").style("margin-left", "20px");
-  geneInputDiv.append("div").text(
-    arg.geneSearch4GDCmds3.hardcodeCnvOnly ? `To view ${useDslabel} CNV segments over a gene or region, enter genomic position (chr11:108195437-108267444), dbSNP accesion, or gene name (MYC).` : `To view ${useDslabel} mutations on a gene, enter one of gene symbol (MYC), alias (c-Myc), GENCODE accession (ENSG00000136997, ENST00000621592), or RefSeq accession (NM_002467).`
-  );
-  const graphDiv = mainDiv.append("div").attr("class", "sja_geneSearch4GDCmds3_blockdiv");
-  const searchOpt = {
-    genome,
-    tip,
-    row: geneInputDiv,
-    callback: launchView,
-    geneSymbol: arg.geneSymbol,
-    triggerSearch: arg.geneSymbol && arg.geneSearch4GDCmds3?.hardcodeCnvOnly == true,
-    hideInputBeforeCallback: arg.geneSearch4GDCmds3?.hardcodeCnvOnly == true
-  };
-  if (!arg.geneSearch4GDCmds3.hardcodeCnvOnly) {
-    searchOpt.searchOnly = "gene";
-  }
-  const coordInput = addGeneSearchbox(searchOpt);
-  let userSelection;
-  await arg.geneSearch4GDCmds3.postRender?.({ tip });
-  if (arg.state) {
-    if (arg.state.userSelection) launchView(false, arg.state.userSelection);
-    delete arg.state;
-  }
-  async function launchView(triggeredByInput = true, userSelection2) {
-    const pa = {
-      // param for instantiating block
-      genome,
-      holder: graphDiv,
-      gmmode: "exon only",
-      nobox: 1,
-      hide_dsHandles: arg.hide_dsHandles,
-      onloadalltk_always: arg.geneSearch4GDCmds3.onloadalltk_always
-    };
-    if (arg.tracks) {
-      pa.tklst = arg.tracks;
-    } else {
-      const tk = {
-        type: "mds3",
-        dslabel: useDslabel,
-        allow2selectSamples: arg.allow2selectSamples,
-        filter0: arg.filter0
-      };
-      pa.tklst = [tk];
-      if (arg.geneSearch4GDCmds3.hardcodeCnvOnly) {
-        tk.hardcodeCnvOnly = 1;
-        delete pa.gmmode;
-        first_genetrack_tolist(pa.genome, pa.tklst);
-      }
-    }
-    if (userSelection2) {
-      if (arg.geneSearch4GDCmds3.hardcodeCnvOnly) {
-        if (typeof userSelection2 != "object") throw "userSelection not object when pa.block is true";
-        pa.chr = userSelection2.chr;
-        pa.start = userSelection2.start;
-        pa.stop = userSelection2.stop;
-        if (!pa.chr || !Number.isInteger(pa.start) || !Number.isInteger(pa.stop))
-          throw "userSelection not {chr,start,stop}";
-      } else {
-        if (typeof userSelection2 != "string") throw "userSelection should be string when pa.block is not true";
-        pa.query = userSelection2;
-      }
-    } else {
-      if (arg.geneSearch4GDCmds3.hardcodeCnvOnly) {
-        if (!coordInput.chr || !Number.isInteger(coordInput.start) || !Number.isInteger(coordInput.stop)) {
-          if (triggeredByInput) throw "coordInput.chr/start/stop missing";
-        }
-        pa.chr = coordInput.chr;
-        pa.start = coordInput.start;
-        pa.stop = coordInput.stop;
-      } else {
-        if (!coordInput.geneSymbol) {
-          if (triggeredByInput) throw "coordInput.geneSymbol missing";
-        }
-        const gmlst = (await dofetch3(`genelookup?deep=1&input=${coordInput.geneSymbol}&genome=${useGenome}`)).gmlst;
-        if (!Array.isArray(gmlst) || gmlst.length == 0) throw "gmlst is not non-empty array";
-        pa.query = getSelectedIsoform(coordInput, gmlst);
-        if (gmlst.some((i) => i.coding)) pa.gmmode = "protein";
-      }
-    }
-    graphDiv.selectAll("*").remove();
-    if (!arg.geneSearch4GDCmds3.hardcodeCnvOnly) return await block_init_default(pa);
-    const _ = await import("./block-IGBB4BJH.js");
-    return new _.Block(pa);
-  }
-  const api = {
-    update: (_arg) => {
-      Object.assign(arg, _arg);
-      launchView(false);
-    },
-    getState: () => ({ userSelection })
-  };
-  return api;
-}
-function getSelectedIsoform(coordInput, gmlst) {
-  if (coordInput.fromWhat) {
-    if (gmlst.some((i) => i.isoform.toUpperCase() == coordInput.fromWhat.toUpperCase())) {
-      return coordInput.fromWhat;
-    }
-    if (coordInput.fromWhat.toUpperCase().startsWith("ENSG")) {
-      for (const i of gmlst) {
-        if (i.isdefault && i.isoform.startsWith("ENST")) return i.isoform;
-      }
-    }
-  }
-  const defaultIsoform = gmlst.find((i) => i.isdefault);
-  if (defaultIsoform) return defaultIsoform.isoform;
-  return gmlst[0].isoform;
-}
-export {
-  init
-};
-//# sourceMappingURL=lollipop-W6NOHHCP.js.map

package/dist/lollipop-W6NOHHCP.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../gdc/lollipop.js"],
-  "sourcesContent": ["import { addGeneSearchbox, Menu } from '#dom'\nimport { first_genetrack_tolist } from '../common/1stGenetk'\nimport { dofetch3 } from '#common/dofetch'\nimport blockinit from '#src/block.init'\n\n/*\n************* GDC view ********************\ndesigned to work for lollipop & cnv apps in GDC Analysis Tools Framework\nhttps://github.com/NCI-GDC/gdc-frontend-framework/blob/develop/packages/portal-proto/src/features/proteinpaint/ProteinPaintWrapper.tsx\n\ntest with:\n\thttp://localhost:3000/example.gdc.html\n\thttp://localhost:3000/example.mds3.numeric.html\n\nto launch gdc lollipop:\n\trunpp({ geneSearch4GDCmds3:true })\nto launch gdc cnv tool:\n\trunpp({\n\t\tgeneSearch4GDCmds3:{\n\t\t\thardcodeCnvOnly:1\n\t\t}\n\t})\n\n\n************* Non-GDC view ********************\nlaunch as:\n\trunpp({ geneSearch4GDCmds3:true, genome:'xx', dslabel:'yy' })\n\n\n*************  parameters  ********************\narg = {}\n\t// this is the runpp() argument object\n\tgeneSearch4GDCmds3:{}\n\t\t.postRender()\n\t\t.onloadalltk_always() }\n\t\t\t// optional callbacks for testing\n\t\t.hardcodeCnvOnly:1\n\t\t\t// if true, launches cnv tool (gene search box allows searching both gene/coord and yields coord)\n\t.allow2selectSamples:{}\n\t\t// pass to mds3 tk object to enable sample selection\n\t.filter0\n\t\t// hidden gdc cohort filter, passed to tk obj\n\t.geneSymbol:str\n\t\t// default gene to fill into search box\n\t.state{}\n\t\t// for auto updating app on GFF cohort change\n\t.tracks[]\n\t\t// for future use, allows to add extra annotation tracks in addition to mds3\n\n\t.genome:str\n\t.dslabel:str\n\t\t// allow to work for non-gdc ds\n\nholder\ngenomes = { hg38 : {} }\n\n\n*************  returns  ********************\napi object. required to work with react wrapper\n*/\n\nconst tip = new Menu({ padding: '' })\n\nexport async function init(arg, holder, genomes) {\n\tconst useGenome = arg.genome || 'hg38'\n\tconst useDslabel = arg.dslabel || 'GDC'\n\tconst genome = genomes[useGenome]\n\tif (!genome) throw useGenome + ' missing'\n\tif (arg.geneSearch4GDCmds3.onloadalltk_always && typeof arg.geneSearch4GDCmds3.onloadalltk_always != 'function')\n\t\tthrow 'arg.geneSearch4GDCmds3.onloadalltk_always not function'\n\tif (arg.geneSearch4GDCmds3.postRender && typeof arg.geneSearch4GDCmds3.postRender != 'function')\n\t\tthrow 'arg.geneSearch4GDCmds3.postRender not function'\n\n\t// assume that there will only be one main div within a given holder\n\tholder.selectAll('.sja_lollipop_holder').remove()\n\tconst mainDiv = holder.append('div').attr('class', 'sja_lollipop_holder')\n\n\t// first row, gene search\n\tconst geneInputDiv = mainDiv.append('div').style('margin-left', '20px')\n\tgeneInputDiv\n\t\t.append('div')\n\t\t.text(\n\t\t\targ.geneSearch4GDCmds3.hardcodeCnvOnly\n\t\t\t\t? `To view ${useDslabel} CNV segments over a gene or region, enter genomic position (chr11:108195437-108267444), dbSNP accesion, or gene name (MYC).`\n\t\t\t\t: `To view ${useDslabel} mutations on a gene, enter one of gene symbol (MYC), alias (c-Myc), GENCODE accession (ENSG00000136997, ENST00000621592), or RefSeq accession (NM_002467).`\n\t\t)\n\n\t// second row, display graph\n\tconst graphDiv = mainDiv.append('div').attr('class', 'sja_geneSearch4GDCmds3_blockdiv')\n\n\tconst searchOpt = {\n\t\tgenome,\n\t\ttip,\n\t\trow: geneInputDiv,\n\t\tcallback: launchView,\n\t\tgeneSymbol: arg.geneSymbol,\n\t\ttriggerSearch: arg.geneSymbol && arg.geneSearch4GDCmds3?.hardcodeCnvOnly == true,\n\t\thideInputBeforeCallback: arg.geneSearch4GDCmds3?.hardcodeCnvOnly == true\n\t}\n\tif (!arg.geneSearch4GDCmds3.hardcodeCnvOnly) {\n\t\t// not in cnv mode; is in lollipop mode to show coding ssm over gene coding exons, apply this flag\n\t\tsearchOpt.searchOnly = 'gene'\n\t}\n\tconst coordInput = addGeneSearchbox(searchOpt)\n\n\t/**********************\n\tmust declare this variable first then call postRender(), other wise it can crash for accessing variable before initialization...\n\tsaves user-selected isoform (string) or region ({chr/start/stop}) from <input>;\n\ton cohort change, this value will be used so the lollipop of the same gene can be auto updated\n\t**********************/\n\tlet userSelection\n\n\tawait arg.geneSearch4GDCmds3.postRender?.({ tip }) // supports testing\n\n\tif (arg.state) {\n\t\t// this is only present when the app auto updates from GFF cohort change\n\t\tif (arg.state.userSelection) launchView(false, arg.state.userSelection)\n\t\tdelete arg.state\n\t}\n\n\t/**************\n\tparameters:\n\t\ttriggeredByInput\n\t\t\tif true, func is called on user selecting something from <input>\n\t\t\tif false, is from api.update()\n\t\tuserSelection\n\t\t\twhen user selects from <input>, this is undefined\n\t\t\totherwise is from api.update()\n\t***************/\n\tasync function launchView(triggeredByInput = true, userSelection) {\n\t\tconst pa = {\n\t\t\t// param for instantiating block\n\t\t\tgenome,\n\t\t\tholder: graphDiv,\n\t\t\tgmmode: 'exon only',\n\t\t\tnobox: 1,\n\t\t\thide_dsHandles: arg.hide_dsHandles,\n\t\t\tonloadalltk_always: arg.geneSearch4GDCmds3.onloadalltk_always\n\t\t}\n\t\tif (arg.tracks) {\n\t\t\tpa.tklst = arg.tracks\n\t\t} else {\n\t\t\t// generate mds3 tk\n\t\t\tconst tk = {\n\t\t\t\ttype: 'mds3',\n\t\t\t\tdslabel: useDslabel,\n\t\t\t\tallow2selectSamples: arg.allow2selectSamples,\n\t\t\t\tfilter0: arg.filter0\n\t\t\t}\n\t\t\tpa.tklst = [tk]\n\t\t\tif (arg.geneSearch4GDCmds3.hardcodeCnvOnly) {\n\t\t\t\ttk.hardcodeCnvOnly = 1\n\t\t\t\t// also block is in genome browser mode\n\t\t\t\tdelete pa.gmmode\n\t\t\t\tfirst_genetrack_tolist(pa.genome, pa.tklst)\n\t\t\t}\n\t\t}\n\n\t\tif (userSelection) {\n\t\t\t// recovering from gff cohort change\n\t\t\tif (arg.geneSearch4GDCmds3.hardcodeCnvOnly) {\n\t\t\t\tif (typeof userSelection != 'object') throw 'userSelection not object when pa.block is true'\n\t\t\t\tpa.chr = userSelection.chr\n\t\t\t\tpa.start = userSelection.start\n\t\t\t\tpa.stop = userSelection.stop\n\t\t\t\tif (!pa.chr || !Number.isInteger(pa.start) || !Number.isInteger(pa.stop))\n\t\t\t\t\tthrow 'userSelection not {chr,start,stop}'\n\t\t\t} else {\n\t\t\t\tif (typeof userSelection != 'string') throw 'userSelection should be string when pa.block is not true'\n\t\t\t\tpa.query = userSelection\n\t\t\t}\n\t\t} else {\n\t\t\t// user selected gene/region from <input>\n\t\t\tif (arg.geneSearch4GDCmds3.hardcodeCnvOnly) {\n\t\t\t\tif (!coordInput.chr || !Number.isInteger(coordInput.start) || !Number.isInteger(coordInput.stop)) {\n\t\t\t\t\tif (triggeredByInput) throw 'coordInput.chr/start/stop missing' // ??\n\t\t\t\t}\n\t\t\t\tpa.chr = coordInput.chr\n\t\t\t\tpa.start = coordInput.start\n\t\t\t\tpa.stop = coordInput.stop\n\t\t\t} else {\n\t\t\t\tif (!coordInput.geneSymbol) {\n\t\t\t\t\tif (triggeredByInput) throw 'coordInput.geneSymbol missing' // ??\n\t\t\t\t\t// updates of arg.filter0 should still render\n\t\t\t\t}\n\t\t\t\t// a bit inefficient but must retrieve all gene models to find out if any is coding or all are noncoding\n\t\t\t\tconst gmlst = (await dofetch3(`genelookup?deep=1&input=${coordInput.geneSymbol}&genome=${useGenome}`)).gmlst\n\t\t\t\tif (!Array.isArray(gmlst) || gmlst.length == 0) throw 'gmlst is not non-empty array'\n\t\t\t\tpa.query = getSelectedIsoform(coordInput, gmlst)\n\t\t\t\tif (gmlst.some(i => i.coding)) pa.gmmode = 'protein'\n\t\t\t}\n\t\t}\n\n\t\tgraphDiv.selectAll('*').remove()\n\n\t\t// launch protein view\n\t\tif (!arg.geneSearch4GDCmds3.hardcodeCnvOnly) return await blockinit(pa) // does it need to return?\n\t\t// launch genome browser view\n\t\tconst _ = await import('../src/block')\n\t\treturn new _.Block(pa)\n\t}\n\n\tconst api = {\n\t\tupdate: _arg => {\n\t\t\tObject.assign(arg, _arg)\n\t\t\tlaunchView(false)\n\t\t},\n\t\tgetState: () => ({ userSelection })\n\t}\n\treturn api\n}\n\nfunction getSelectedIsoform(coordInput, gmlst) {\n\tif (coordInput.fromWhat) {\n\t\t// .fromWhat=str is input string user typed into <input>, check if it is isoform\n\t\tif (gmlst.some(i => i.isoform.toUpperCase() == coordInput.fromWhat.toUpperCase())) {\n\t\t\t// user has input isoform accession, use it\n\t\t\treturn coordInput.fromWhat\n\t\t}\n\t\t// user input does not match with isoform\n\t\tif (coordInput.fromWhat.toUpperCase().startsWith('ENSG')) {\n\t\t\t// user input looks like a gencode gene accession\n\t\t\t// find the ENST default isoform that matches with it\n\t\t\tfor (const i of gmlst) {\n\t\t\t\tif (i.isdefault && i.isoform.startsWith('ENST')) return i.isoform\n\t\t\t}\n\t\t}\n\t\t// user input is not isoform or ENSG (should be symbol or alias) continue with below\n\t}\n\n\tconst defaultIsoform = gmlst.find(i => i.isdefault)\n\tif (defaultIsoform) return defaultIsoform.isoform\n\treturn gmlst[0].isoform\n}\n"],
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