@sjcrh/proteinpaint-client 2.216.0 → 2.217.0

package/dist/tp.ui-EMWJCGRX.js

@@ -1,1449 +0,0 @@
-import {
-  blocklazyload
-} from "./chunk-42II4FNQ.js";
-import {
-  bulkin,
-  content2flag
-} from "./chunk-L4ORRHDP.js";
-import "./chunk-L2TWQXK2.js";
-import {
-  getsjcharts
-} from "./chunk-MKAF2BHB.js";
-import {
-  block_init_default
-} from "./chunk-YZO7NVZW.js";
-import "./chunk-SZ2VC2I2.js";
-import {
-  appear2 as appear,
-  disappear2 as disappear,
-  export_data,
-  filetypeselect,
-  font,
-  newpane,
-  sayerror
-} from "./chunk-FIFNXVTS.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-N2FCAFJH.js";
-import "./chunk-OH33WT6Q.js";
-import {
-  Menu
-} from "./chunk-CNFTQSNE.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import {
-  init_bulk_flag
-} from "./chunk-5MHE7AIV.js";
-import "./chunk-6WYKPBZI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-DBOJ3TMI.js";
-import {
-  dtcloss,
-  dtdel,
-  dtitd,
-  dtnloss,
-  dtsnvindel,
-  json_default,
-  mclass,
-  mclasscnvgain,
-  mclasscnvloss,
-  mclassfusionrna,
-  mclasssv,
-  mclassutr3,
-  mclassutr5
-} from "./chunk-EZFO5UYD.js";
-import "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// src/tp.classes.js
-function tp_classes_default(cohort, button, folder) {
-  let nothing = true;
-  for (const k in cohort.dsset) {
-    nothing = false;
-  }
-  if (nothing) {
-    button.remove();
-    folder.remove();
-    return null;
-  }
-  const cbreakdown = /* @__PURE__ */ new Map();
-  let totalcount = 0;
-  for (const dskey in cohort.dsset) {
-    const data = cohort.dsset[dskey].bulkdata;
-    if (!data) continue;
-    const class2count = /* @__PURE__ */ new Map();
-    const svstr = /* @__PURE__ */ new Set();
-    const fusionstr = /* @__PURE__ */ new Set();
-    for (const n in data) {
-      for (const m of data[n]) {
-        const c = m.class;
-        if (c == mclasssv) {
-          svstr.add((m.sample ? m.sample : "") + "." + (m.sampletype ? m.sampletype : "") + JSON.stringify(m.pairlst));
-          continue;
-        }
-        if (c == mclassfusionrna) {
-          fusionstr.add(
-            (m.sample ? m.sample : "") + "." + (m.sampletype ? m.sampletype : "") + JSON.stringify(m.pairlst)
-          );
-          continue;
-        }
-        totalcount++;
-        if (!class2count.has(c)) {
-          class2count.set(c, 0);
-        }
-        class2count.set(c, class2count.get(c) + 1);
-      }
-    }
-    if (svstr.size) {
-      class2count.set(mclasssv, svstr.size);
-      totalcount += svstr.size;
-    }
-    if (fusionstr.size) {
-      class2count.set(mclassfusionrna, fusionstr.size);
-      totalcount += fusionstr.size;
-    }
-    cbreakdown.set(dskey, class2count);
-  }
-  button.html(totalcount + ' <span style="font-size:.8em">VARIANTS</span>').attr("aria-label", "A summary of variant hits from all genes, in descending order.");
-  const table = folder.append("table").style("margin-right", "20px");
-  const trup = table.append("tr");
-  const trdown = table.append("tr");
-  const showclst = (lst, holder, number) => {
-    holder.selectAll("*").remove();
-    for (const i of lst) {
-      const d = holder.append("div").style("margin", "10px");
-      d.append("span").attr("class", "sja_mcdot").style("background-color", i.color).style("padding", "2px 5px").style("margin-right", "5px").html(number ? i.count : "&nbsp;&nbsp;");
-      d.append("span").style("color", i.color).text(i.label);
-    }
-  };
-  const ds2clst = {};
-  for (const [dskey, class2count] of cbreakdown) {
-    const lst = [];
-    for (const [k, count] of class2count) {
-      const mc = mclass[k];
-      if (mc.dt == dtsnvindel || mc.dt == dtitd || mc.dt == dtdel || mc.dt == dtnloss || mc.dt == dtcloss) {
-        lst.push({
-          key: k,
-          label: mc.label,
-          color: mc.color,
-          count
-        });
-      }
-    }
-    lst.sort((a, b) => b.count - a.count);
-    for (const thisclass of [mclasscnvloss, mclasscnvgain, mclasssv, mclassfusionrna]) {
-      if (class2count.has(thisclass)) {
-        const c = mclass[thisclass];
-        lst.push({
-          key: thisclass,
-          label: c.label,
-          color: c.color,
-          count: class2count.get(thisclass)
-        });
-      }
-    }
-    ds2clst[dskey] = lst;
-    const cholder = trdown.append("td").attr("valign", "top").attr("shownumber", 0);
-    showclst(lst, cholder, true);
-    const td = trup.append("td").style("border-bottom", "solid 1px #ccc").style("padding", "5px 10px").style("color", "#858585").style("font-size", ".8em").text(cohort.dsset[dskey].label);
-    td.append("button").style("margin", "5px").text("Hide number").on("click", (event) => {
-      const number = cholder.attr("shownumber") == "1";
-      showclst(lst, cholder, number);
-      cholder.attr("shownumber", number ? "0" : "1");
-      event.target.innerHTML = number ? "Hide number" : "Show number";
-    });
-  }
-  return totalcount ? ds2clst : null;
-}
-
-// src/tp.gene.geneexpression.js
-function tp_getgeneexpression(arg) {
-  Promise.resolve().then(() => {
-    if (!arg.gene) throw { message: "gene name missing" };
-    if (!arg.genome) throw { message: "genome name missing" };
-    if (arg.hostURL == void 0) throw { message: "no hostURL" };
-    if (!arg.loadgeneexpressionfromofficialds) throw { message: "loadgeneexpressionfromofficialds missing" };
-    if (!arg.loadgeneexpressionfromofficialds.dataset) throw { message: "dataset missing from loadgeneexpressionfromofficialds" };
-    const par = {
-      genome: arg.genome,
-      dsname: arg.loadgeneexpressionfromofficialds.dataset,
-      expressiononly: 1,
-      genename: arg.gene,
-      jwt: arg.jwt
-    };
-    return fetch(new Request(arg.hostURL + "/dsdata", {
-      method: "POST",
-      body: JSON.stringify(par)
-    })).then((data) => {
-      return data.json();
-    }).then((data) => {
-      if (data.error) throw { message: data.error };
-      if (!data.data) throw { message: "cannot get data" };
-      return data.data;
-    });
-  }).then((data) => {
-    for (let i = 0; i < data.length; i++) {
-      const par = {
-        data: data[i].lst,
-        expp: data[i].config,
-        genename: arg.gene,
-        presize: {
-          x: arg.x + 40 * i,
-          y: arg.y + 40 * i,
-          width: 350,
-          height: 650
-        }
-      };
-      import("./ep-DFBBKNXP.js").then((p) => {
-        new p.default(par);
-      });
-    }
-  }).catch((err) => {
-    const pane = newpane({ x: arg.x || 600, y: arg.y || 80 });
-    pane.body.append("p").text("Error getting gene expression: " + err);
-  });
-}
-
-// src/tp.gene.js
-var tip = new Menu();
-function tp_gene_default(cohort, ds2clst, butt, folder, defaulthide, host) {
-  if (!ds2clst) return null;
-  const hostURL = host || "";
-  const union = {};
-  let genelst = [];
-  for (const k in cohort.dsset) {
-    for (const gn in cohort.dsset[k].bulkdata) {
-      if (!(gn in union)) {
-        union[gn] = { mcount: 0, isoform: {} };
-        genelst.push(gn);
-      }
-      union[gn].mcount += cohort.dsset[k].bulkdata[gn].length;
-      for (const m of cohort.dsset[k].bulkdata[gn]) {
-        const i = m.isoform;
-        if (!i) continue;
-        union[gn].isoform[i] = 1;
-      }
-    }
-  }
-  let genelimit = Math.min(100, genelst.length);
-  const noncodingclass = /* @__PURE__ */ new Set(["Intron", "P", "S", "E", mclassutr3, mclassutr5]);
-  const gene2import = {};
-  const ds2import = {};
-  let usenoncoding = true, importsilent = false;
-  butt.html(genelst.length + ' <span style="font-size:.8em">GENES</span>').attr("aria-label", "A summary table of gene by variant type, order by number of hits in descending order.");
-  const errdiv = folder.append("div");
-  const sayerror2 = (m) => {
-    sayerror(errdiv, m);
-  };
-  const toprow = folder.append("div").style("margin-bottom", "8px");
-  toprow.append("button").style("margin-right", "10px").text("Configure").on("click", () => {
-    if (optiondiv.style("display") == "block") {
-      disappear(optiondiv);
-    } else {
-      appear(optiondiv);
-    }
-  });
-  toprow.append("button").style("margin-right", "10px").text("Download").on("click", () => {
-    const txt = dotable();
-    export_data("Gene summary", [{ text: txt }]);
-  });
-  toprow.append("input").attr("type", "search").attr("size", 10).attr("placeholder", "Find gene").style("margin", "0px 20px 0px 5px").on("keyup", (event) => {
-    let n = event.target.value;
-    if (n == "") {
-      tip.hide();
-      return;
-    }
-    if (cohort.geneToUpper) {
-      n = n.toUpperCase();
-    }
-    if (event.code == "Enter") {
-      tip.hide();
-      event.target.value = "";
-      if (n in union) {
-        paintgene(n);
-      }
-      return;
-    }
-    const hit = [];
-    for (const gn in union) {
-      if (gn.indexOf(n) == 0) {
-        hit.push({ name: gn, count: union[gn].mcount });
-      }
-    }
-    if (hit.length == 0) {
-      tip.hide();
-      return;
-    }
-    hit.sort((a, b) => b.count - a.count);
-    tip.clear().showunder(event.target);
-    for (let i = 0; i < Math.min(30, hit.length); i++) {
-      const n2 = hit[i].name;
-      const row = tip.d.append("div").attr("class", "sja_menuoption_y").on("click", () => {
-        paintgene(n2);
-      });
-      row.append("span").text(n2);
-      row.append("span").style("font-size", ".7em").text(hit[i].count);
-    }
-  });
-  toprow.append("a").attr("href", "https://docs.google.com/document/d/1NrH1H-FUWJtEKLk69V-k8uaYHOr9YO2obM9ZLZslEQ0/edit?usp=sharing").attr("target", "_blank").text("Help");
-  const secondrow = folder.append("div").style("border", "solid 1px #ccc").style("margin", "10px 0px");
-  const optiondiv = secondrow.append("div").style("display", "none").style("background-color", "#f1f1f1");
-  const scrolltoppad = 140;
-  const scrollholder = secondrow.append("div").style("padding-top", scrolltoppad + "px").style("position", "relative");
-  const scrolldiv = scrollholder.append("div").style("overflow-y", "scroll").style("height", "400px").style("resize", "vertical");
-  const table = scrolldiv.append("table").style("border-spacing", "1px").style("border-collapse", "separate");
-  const oprow1 = optiondiv.append("div").style("padding", "10px").style("border-bottom", "dashed 1px #ccc");
-  const oprow2 = optiondiv.append("div").style("padding", "10px").style("border-bottom", "dashed 1px #ccc");
-  const oprow3 = optiondiv.append("div").style("padding", "10px").style("border-bottom", "dashed 1px #ccc");
-  const gcsays = oprow1.append("span").style("padding-right", "10px").text("Showing " + (genelimit < genelst.length ? "top " + genelimit + " genes" : "all genes"));
-  oprow1.append("button").text("more").on("click", () => {
-    genelimit = Math.min(genelst.length, genelimit + 10);
-    gcsays.text("Showing " + (genelimit < genelst.length ? "top " + genelimit : "all genes"));
-    dotable();
-  });
-  oprow1.append("button").text("less").on("click", () => {
-    genelimit = Math.max(1, genelimit - 10);
-    gcsays.text("Showing " + (genelimit < genelst.length ? "top " + genelimit : "all genes"));
-    dotable();
-  });
-  oprow2.append("span").text("Show subset").style("padding-right", "10px");
-  const genesetta = oprow2.append("textarea").attr("rows", 1).attr("cols", 20).attr("placeholder", "enter gene names").style("margin-right", "10px");
-  oprow2.append("button").text("Submit").on("click", () => {
-    const v = genesetta.property("value").trim();
-    if (v == "") return;
-    const lst = v.split(/[\s\t\n]+/), good = [], nomatch = [];
-    for (const s of lst) {
-      if (s == "") continue;
-      const n = cohort.geneToUpper ? s.trim().toUpperCase() : s.trim();
-      if (n in union) {
-        good.push(n);
-      } else {
-        nomatch.push(s);
-      }
-    }
-    if (nomatch.length) {
-      sayerror2("No match found for " + nomatch.join(", "));
-    }
-    if (good.length == 0) return;
-    genelst = good;
-    genelimit = good.length;
-    dotable();
-  });
-  oprow2.append("button").text("Use default").on("click", () => {
-    genelst = [];
-    for (const n in union) {
-      genelst.push(n);
-    }
-    genelimit = Math.min(100, genelst.length);
-    dotable();
-  });
-  oprow3.append("span").html("Noncoding mutation visibility:&nbsp;");
-  const oprow3select = oprow3.append("select").on("change", () => {
-    usenoncoding = !usenoncoding;
-    for (const dat of attrlst) {
-      if (!dat.atlst) {
-        continue;
-      }
-      for (const at of dat.atlst) {
-        if (!at.ismclass) continue;
-        if (usenoncoding) {
-          at.hide = false;
-          continue;
-        }
-        at.hide = noncodingclass.has(at.key);
-      }
-    }
-    dotable();
-  });
-  oprow3select.append("option").text("show").attr("value", "y");
-  oprow3select.append("option").text("hide").attr("value", "n");
-  oprow3.append("p").style("font-size", ".8em").style("color", "#858585").text("Including: silent, splice_region, exon, UTR, and intron.");
-  const hassamplelst = [];
-  for (const k in cohort.dsset) {
-    const d = cohort.dsset[k];
-    if (d.hassample) {
-      hassamplelst.push(d);
-    }
-  }
-  if (hassamplelst.length) {
-    const oprow5 = optiondiv.append("div").style("padding", "10px").style("border-bottom", "dashed 1px #ccc");
-    oprow5.append("span").html("Gene recurrence (# of samples for each gene):&nbsp;");
-    for (const ds of hassamplelst) {
-      oprow5.append("button").text(hassamplelst.length == 1 ? "show" : ds.label).on("click", (event) => {
-        const bars = [];
-        for (const gene of genelst) {
-          const hash = {};
-          let samplecount = 0;
-          if (gene in ds.bulkdata) {
-            for (const m of ds.bulkdata[gene]) {
-              if (!usenoncoding && noncodingclass.has(m.class)) return;
-              if (!(m.sample in hash)) {
-                hash[m.sample] = 1;
-                samplecount++;
-              }
-            }
-          }
-          bars.push({
-            name: gene,
-            size: samplecount
-          });
-        }
-        const pos = event.target.getBoundingClientRect();
-        barplot(bars, "#76B38C", "Number of samples" + (usenoncoding ? "" : ", excluding noncoding mutations"), pos);
-      });
-    }
-    const oprow6 = optiondiv.append("div").style("padding", "10px").style("border-bottom", "dashed 1px #ccc");
-    oprow6.append("span").html("Mutation burden (# mutations for each sample):&nbsp;");
-    for (const ds of hassamplelst) {
-      oprow6.append("button").text(hassamplelst.length == 1 ? "show" : ds.label).on("click", (event) => {
-        const samplehash = {};
-        for (const g in ds.bulkdata) {
-          for (const m of ds.bulkdata[g]) {
-            const n = m.sample;
-            if (n) {
-              if (!usenoncoding && noncodingclass.has(m.class)) continue;
-              if (!(n in samplehash)) {
-                samplehash[n] = 0;
-              }
-              samplehash[n]++;
-            }
-          }
-        }
-        const bars = [];
-        for (const n in samplehash) {
-          bars.push({
-            name: n,
-            size: samplehash[n]
-          });
-        }
-        const pos = event.target.getBoundingClientRect();
-        barplot(bars, "#76B38C", "Mutation burden" + (usenoncoding ? "" : ", excluding noncoding mutations"), pos);
-      });
-    }
-  }
-  const oprow7 = optiondiv.append("div").style("padding", "10px").style("border-bottom", "dashed 1px #ccc").text("Click on a column header to rank genes.");
-  const attrlst = [
-    {
-      label: "Name",
-      isgenename: true
-    }
-  ];
-  let firstsort = true;
-  let dscount = 0;
-  for (const dsname in cohort.dsset) {
-    dscount++;
-    const thisds = {
-      name: cohort.dsset[dsname].label,
-      atlst: [
-        {
-          label: "# mutation",
-          get: (gn) => {
-            if (!(gn in cohort.dsset[dsname].bulkdata)) return 0;
-            if (usenoncoding) {
-              return cohort.dsset[dsname].bulkdata[gn].length;
-            }
-            let c = 0;
-            for (const i of cohort.dsset[dsname].bulkdata[gn]) {
-              if (!noncodingclass.has(i.class)) c++;
-            }
-            return c;
-          },
-          rotate: true,
-          descend: true,
-          sort: firstsort
-          //secondsort:true, // secondary, so to keep order persistant when sorting on classes with many genes having same number in sorted class
-        }
-      ]
-    };
-    firstsort = false;
-    if (cohort.dsset[dsname].hassample) {
-      thisds.atlst.push({
-        label: "# sample",
-        get: (gn) => {
-          if (!(gn in cohort.dsset[dsname].bulkdata)) return 0;
-          const set = /* @__PURE__ */ new Set();
-          for (const m of cohort.dsset[dsname].bulkdata[gn]) {
-            if (!usenoncoding && noncodingclass.has(m.class)) continue;
-            if (!m.sample) continue;
-            set.add(m.sample);
-          }
-          return set.size;
-        },
-        rotate: true,
-        descend: true
-      });
-    }
-    for (const c of ds2clst[dsname]) {
-      c.ismclass = true;
-      c.get = (gn) => {
-        if (!(gn in cohort.dsset[dsname].bulkdata)) return 0;
-        let total = 0;
-        for (const m of cohort.dsset[dsname].bulkdata[gn]) {
-          if (m.class == c.key) total++;
-        }
-        return total;
-      };
-      c.rotate = true;
-      c.descend = true;
-      thisds.atlst.push(c);
-    }
-    attrlst.push(thisds);
-  }
-  const dotable = () => {
-    let sortkey = null, sortkey2 = null;
-    for (const a of attrlst) {
-      if (a.hide) continue;
-      if (a.atlst) {
-        for (const b of a.atlst) {
-          if (b.hide) continue;
-          if (b.sort) {
-            sortkey = b;
-            continue;
-          }
-          if (b.secondsort) {
-            sortkey2 = b;
-            continue;
-          }
-        }
-        continue;
-      }
-      if (a.sort) {
-        sortkey = a;
-        continue;
-      }
-      if (a.secondsort) {
-        sortkey2 = a;
-      }
-    }
-    if (sortkey) {
-      genelst.sort((a, b) => {
-        if (sortkey.isgenename) {
-          if (a < b) {
-            return sortkey.descend ? 1 : -1;
-          }
-          return sortkey.descend ? -1 : 1;
-        }
-        const i = sortkey.get(a), j = sortkey.get(b);
-        if (typeof i == "string") {
-          if (i < j) {
-            return sortkey.descend ? 1 : -1;
-          }
-          return sortkey.descend ? -1 : 1;
-        }
-        if (i == j) {
-          if (sortkey2) {
-            const i2 = sortkey2.get(a), j2 = sortkey2.get(b);
-            if (i2 == j2) {
-              if (a in gene2import) {
-                if (!(b in gene2import)) return -1;
-              } else if (b in gene2import) {
-                return 1;
-              }
-            } else {
-              return j2 - i2;
-            }
-          } else {
-            if (a in gene2import) {
-              if (!(b in gene2import)) return -1;
-            } else if (b in gene2import) {
-              return 1;
-            }
-          }
-          return a < b ? -1 : 1;
-        }
-        return sortkey.descend ? j - i : i - j;
-      });
-    }
-    const importclass = {};
-    let hasimport = false;
-    for (const dsname in ds2import) {
-      hasimport = true;
-      const classcount = {};
-      for (let i = 0; i < genelimit; i++) {
-        const gene = genelst[i];
-        if (gene in gene2import && dsname in gene2import[gene]) {
-          for (const c in gene2import[gene][dsname].class) {
-            if (!(c in classcount)) {
-              classcount[c] = 0;
-            }
-            classcount[c] += gene2import[gene][dsname].class[c];
-          }
-        }
-      }
-      const clst = [];
-      for (const c in classcount) {
-        clst.push({
-          class: c,
-          n: classcount[c]
-        });
-      }
-      clst.sort((a, b) => b.n - a.n);
-      importclass[dsname] = clst;
-    }
-    const impspace = "solid 10px white";
-    table.selectAll("*").remove();
-    const tr1 = table.append("tr");
-    tr1.append("td").style("height", "0px").style("padding", "0px");
-    tr1.append("td").style("height", "0px").style("padding", "0px");
-    for (const ds of attrlst) {
-      if (!ds.atlst) continue;
-      let spannum = 0;
-      for (const a of ds.atlst) {
-        if (!a.hide) spannum++;
-      }
-      tr1.append("td").attr("colspan", spannum).style("text-align", "center").style("border-right", impspace).append("div").style("position", "absolute").style("top", "1px").style("border-bottom", dscount > 1 ? "solid 1px black" : "").text(dscount > 1 ? ds.name : "");
-    }
-    for (const dsname in ds2import) {
-      const td = tr1.append("td").attr("colspan", 2 + importclass[dsname].length).style("border-right", impspace).append("div").style("top", "2px").style("position", "absolute").style("color", cohort.genome.datasets[dsname].color).style("border-bottom", "solid 1px " + cohort.genome.datasets[dsname].color);
-      td.append("span").text(
-        cohort.genome.datasets[dsname].label + (ds2import[dsname].totalsample ? ", " + ds2import[dsname].totalsample + " total samples" : "")
-      );
-      td.append("div").style("position", "absolute").style("right", "0px").style("top", "-5px").attr("class", "sja_clb").html("&#10005;").on("click", () => {
-        delete ds2import[dsname];
-        for (const n in gene2import) {
-          delete gene2import[n][dsname];
-        }
-        dotable();
-      });
-    }
-    const exportlines = [];
-    const exportheader = [];
-    const tr2 = table.append("tr");
-    tr2.append("td").style("height", "0px").style("padding", "0px");
-    for (const a of attrlst) {
-      if (a.hide) continue;
-      let lst = [];
-      if (a.atlst) {
-        lst = a.atlst;
-      } else {
-        lst = [a];
-      }
-      let td;
-      for (const at of lst) {
-        if (at.hide) continue;
-        td = tr2.append("td").attr("class", "sja_clbtext").style("font-size", ".8em").style("height", "0px").style("padding", "0px").style("color", at.color ? at.color : "black").style("white-space", "nowrap");
-        td.append("div").html(
-          at.rotate ? at.sort ? (at.descend ? "&#9664;" : "&#9654;") + " " + at.label : at.label : at.label + (at.sort ? " " + (at.descend ? "&#9662;" : "&#9652;") : "")
-        ).style("position", "absolute").style("top", scrolltoppad - 25 + "px").style("transform", at.rotate ? "translate(-3px,0px) rotate(-90deg)" : "").style("width", at.rotate ? "25px" : "auto").on("click", () => {
-          const ps = at.sort;
-          for (const a2 of attrlst) {
-            if (a2.atlst) {
-              for (const b of a2.atlst) {
-                b.sort = false;
-              }
-            } else {
-              a2.sort = false;
-            }
-          }
-          at.sort = true;
-          if (ps) {
-            at.descend = !at.descend;
-          }
-          dotable();
-        });
-        exportheader.push(at.label + (a.name ? "." + a.name : ""));
-      }
-      td.style("border-right", impspace);
-    }
-    for (const dsname in ds2import) {
-      tr2.append("td").style("font-size", ".8em").style("height", "0px").style("padding", "0px").style("white-space", "nowrap").append("div").html("# mutation").style("position", "absolute").style("top", scrolltoppad - 25 + "px").style("transform", "translate(-3px,0px) rotate(-90deg)").style("width", "25px");
-      exportheader.push(dsname + ".#mutation");
-      tr2.append("td").style("font-size", ".8em").style("height", "0px").style("padding", "0px").style("white-space", "nowrap").append("div").html("# sample").style("position", "absolute").style("top", scrolltoppad - 25 + "px").style("transform", "translate(-3px,0px) rotate(-90deg)").style("width", "25px");
-      exportheader.push(dsname + ".#sample");
-      let td;
-      for (const cls of importclass[dsname]) {
-        td = tr2.append("td").style("font-size", "80%").style("overflow-y", "hidden").style("height", "0px").style("padding", "0px").style("color", mclass[cls.class].color).style("white-space", "nowrap");
-        td.append("div").html(mclass[cls.class].label).style("position", "absolute").style("top", scrolltoppad - 25 + "px").style("transform", "translate(-3px,0px) rotate(-90deg)").style("width", "25px");
-        exportheader.push(dsname + "." + mclass[cls.class].label);
-      }
-      if (td) {
-        td.style("border-right", impspace);
-      }
-    }
-    exportlines.push(exportheader.join("	"));
-    for (let i = 0; i < genelimit; i++) {
-      const gene = genelst[i];
-      const exportline = [gene];
-      const tr = table.append("tr");
-      tr.append("td").text(i + 1).style("font-size", ".7em").style("text-align", "right");
-      for (const at of attrlst) {
-        if (at.hide) continue;
-        if (at.isgenename) {
-          tr.append("td").text(genelst[i]).attr("class", "sja_menuoption_y").style("color", "black").style("display", "table-cell").on("click", () => {
-            paintgene(genelst[i]);
-          });
-          continue;
-        }
-        let td;
-        for (const bt of at.atlst) {
-          if (bt.hide) continue;
-          td = tr.append("td").style("color", "black").style("background-color", "#f1f1f1");
-          const m = bt.get(gene);
-          if (typeof m == "number") {
-            if (bt.color) {
-              if (m > 0) {
-                td.style("text-align", "center").append("span").attr("class", "sja_mcdot").style("background-color", bt.color).html(m > 1 ? m : "&nbsp;");
-              } else {
-                td.append("span").attr("class", "sja_mcdot").style("margin", "0px 4px").html("&nbsp;");
-              }
-            } else {
-              td.text(m);
-            }
-          } else {
-            td.text(m);
-          }
-          exportline.push(m);
-        }
-        td.style("border-right", impspace);
-      }
-      for (const dsname in ds2import) {
-        let sample = 0, total = 0, classsum = {}, notexist = true, pending = false;
-        if (gene in gene2import) {
-          const ipd = gene2import[gene][dsname];
-          if (!ipd) continue;
-          notexist = false;
-          if (ipd.pending) {
-            pending = true;
-            continue;
-          }
-          sample += ipd.sample;
-          total += ipd.total;
-          for (const c in ipd.class) {
-            if (!(c in classsum)) {
-              classsum[c] = 0;
-            }
-            classsum[c] += ipd.class[c];
-          }
-        }
-        if (notexist) {
-          tr.append("td").attr("colspan", 2 + importclass[dsname].length);
-          continue;
-        }
-        if (pending) {
-          tr.append("td").attr("colspan", 2 + importclass[dsname].length).text("loading ...");
-          continue;
-        }
-        tr.append("td").text(total).style("background-color", "#f1f1f1");
-        exportline.push(total);
-        tr.append("td").text(sample).style("background-color", "#f1f1f1");
-        exportline.push(sample);
-        let td;
-        for (const cls of importclass[dsname]) {
-          td = tr.append("td").style("text-align", "center").style("background-color", "#f1f1f1");
-          const _count = classsum[cls.class];
-          if (_count) {
-            td.append("span").attr("class", "sja_mcdot").style("background-color", mclass[cls.class].color).html(_count > 1 ? _count : "&nbsp;");
-          } else {
-            td.append("span").attr("class", "sja_mcdot").style("margin", "0px 4px").html("&nbsp;");
-          }
-          exportline.push(_count);
-        }
-        td.style("border-right", impspace);
-      }
-      exportlines.push(exportline.join("	"));
-    }
-    return exportlines.join("\n");
-  };
-  dotable();
-  function paintgene(gene) {
-    if (!(gene in union)) return;
-    tip.hide();
-    const dslst = [];
-    for (const k in cohort.dsset) {
-      dslst.push(k);
-    }
-    let pane;
-    for (const isoform in union[gene].isoform) {
-      if (!pane) {
-        pane = newpane({ x: 100, y: 100 });
-      }
-      block_init_default({
-        hostURL,
-        jwt: cohort.jwt,
-        holder: pane.body,
-        genome: cohort.genome,
-        query: isoform,
-        nopopup: true,
-        dataset: dslst
-      });
-    }
-    if (cohort.loadgeneexpressionfromofficialds) {
-      tp_getgeneexpression({
-        gene,
-        genome: cohort.genome.name,
-        loadgeneexpressionfromofficialds: cohort.loadgeneexpressionfromofficialds,
-        hostURL: cohort.hostURL,
-        jwt: cohort.jwt,
-        x: 1e3,
-        y: 80
-      });
-    }
-  }
-}
-async function barplot(bars, color, label, pos) {
-  const barplot2 = await import("./plot.barplot-VAJLAU7H.js");
-  return barplot2.default(bars, color, label, pos);
-}
-
-// src/tp.pathway.js
-var tip2 = new Menu();
-
-// src/hcmap.js
-function inithcmap(hm, holder) {
-  const err = (m) => {
-    sayerror(holder, m);
-  };
-  if (!hm.metadata) return err("no metadata");
-  const mdh = hm.metadata;
-  const legendholder = holder.append("div").style("display", "inline-block").style("border", "solid 1px #ccc").style("margin", "20px").style("padding", "20px");
-  const svg = holder.append("svg");
-  if (!hm.text) return err("text missing");
-  const lines = hm.text.trim().split("\n");
-  hm.samples = [];
-  const l = lines[0].split("	");
-  for (let i = 2; i < l.length; i++) {
-    hm.samples.push(l[i]);
-  }
-  if (hm.samples.length == 0) return err("no column names");
-  hm.items = [];
-  for (let i = 1; i < lines.length; i++) {
-    const l2 = lines[i].split("	");
-    const type = l2[0];
-    const md = mdh[type];
-    if (!md) return err("invalid data type " + type);
-    const name = l2[1];
-    const lst = [];
-    for (let j = 2; j < l2.length; j++) {
-      const vlst = l2[j].split(";");
-      const colorlst = [];
-      for (const v of vlst) {
-        if (!md[v]) {
-          return err("invalid value " + v + " at " + name + " and " + hm.samples[j - 2]);
-        }
-        colorlst.push(md[v].color);
-      }
-      lst.push(colorlst);
-    }
-    hm.items.push({
-      name,
-      type,
-      lst
-    });
-  }
-  hm.geneonrow = true;
-  if (!hm.rowh) {
-    hm.rowh = 20;
-  }
-  if (!hm.colw) {
-    hm.colw = 20;
-  }
-  if (!hm.rowspace) {
-    hm.rowspace = 2;
-  }
-  if (!hm.colspace) {
-    hm.colspace = 2;
-  }
-  if (!hm.rowlabtickspace) {
-    hm.rowlabtickspace = 4;
-  }
-  if (!hm.collabtickspace) {
-    hm.collabtickspace = 4;
-  }
-  if (!hm.rowtick) {
-    hm.rowtick = 5;
-  }
-  if (!hm.coltick) {
-    hm.coltick = 5;
-  }
-  render(hm, svg, legendholder, err);
-}
-function render(hm, svg, legendholder, err) {
-  const mdh = hm.metadata;
-  for (const key in mdh) {
-    for (const value in mdh[key]) {
-      const o = mdh[key][value];
-      if (!o.label) return err(".label missing for metadata " + key + "[" + value + "]");
-      if (!o.color) return err(".color missing for metadata " + key + "[" + value + "]");
-    }
-  }
-  for (const key in mdh) {
-    const d1 = legendholder.append("div").style("display", "inline-block").style("margin", "20px").style("vertical-align", "top");
-    d1.append("div").text(key).style("margin", "5px 3px").style("font-weight", "bold");
-    const d2 = d1.append("div").style("margin", "3px");
-    for (const v in mdh[key]) {
-      const o = mdh[key][v];
-      const row = d2.append("div").style("margin", "3px");
-      row.append("div").style("display", "inline-block").style("background-color", o.color).style("width", "14px").style("height", "14px").style("margin-right", "10px");
-      row.append("span").text(o.label);
-    }
-  }
-  const rowlabfontsize = hm.rowh - 3, collabfontsize = hm.colw - 3;
-  let labels = [];
-  for (const i of hm.items) {
-    labels.push(i.name);
-  }
-  let genenamewidth = 0;
-  for (const n of labels) {
-    svg.append("text").text(n).attr("font-size", hm.geneonrow ? rowlabfontsize : collabfontsize).attr("font-family", font).each(function() {
-      genenamewidth = Math.max(genenamewidth, this.getBBox().width);
-    }).remove();
-  }
-  let samplenamewidth = 0;
-  for (const n of hm.samples) {
-    svg.append("text").text(n).attr("font-size", hm.geneonrow ? collabfontsize : rowlabfontsize).attr("font-family", font).each(function() {
-      samplenamewidth = Math.max(samplenamewidth, this.getBBox().width);
-    }).remove();
-  }
-  const rowlabw = hm.geneonrow ? genenamewidth : samplenamewidth;
-  const collabh = hm.geneonrow ? samplenamewidth : genenamewidth;
-  const mapwidth = hm.samples.length * (hm.colw + hm.colspace) - hm.colspace;
-  const mapheight = hm.items.length * (hm.rowh + hm.rowspace) - hm.rowspace;
-  svg.attr("width", rowlabw + hm.rowlabtickspace + hm.rowtick + mapwidth + 100).attr("height", collabh + hm.collabtickspace + hm.coltick + mapheight);
-  const originx = rowlabw + hm.rowlabtickspace + hm.rowtick;
-  const originy = collabh + hm.collabtickspace + hm.coltick;
-  let y = originy;
-  for (const item of hm.items) {
-    const g = svg.append("g").attr("transform", "translate(" + (originx - hm.rowlabtickspace - hm.rowtick) + "," + (y + hm.rowh / 2) + ")");
-    g.append("text").text(item.name).attr("font-size", rowlabfontsize).attr("font-family", font).attr("fill", "black").attr("text-anchor", "end").attr("dominant-baseline", "central");
-    g.append("line").attr("stroke", "black").attr("shape-rendering", "crispEdges").attr("x1", hm.rowlabtickspace).attr("x2", hm.rowlabtickspace + hm.rowtick);
-    y += hm.rowh + hm.rowspace;
-  }
-  let x = originx;
-  for (const sample of hm.samples) {
-    const g = svg.append("g").attr("transform", "translate(" + (x + hm.colw / 2) + "," + collabh + ")");
-    g.append("text").text(sample).attr("font-size", collabfontsize).attr("font-family", font).attr("fill", "black").attr("dominant-baseline", "central").attr("transform", "rotate(-90)");
-    g.append("line").attr("stroke", "black").attr("shape-rendering", "crispEdges").attr("y1", hm.collabtickspace).attr("y2", hm.collabtickspace + hm.coltick);
-    x += hm.colw + hm.colspace;
-  }
-  y = originy;
-  for (const item of hm.items) {
-    let x2 = originx;
-    for (let i = 0; i < hm.samples.length; i++) {
-      const sample = hm.samples[i];
-      const g = svg.append("g").attr("transform", "translate(" + (x2 + hm.colw / 2) + "," + (y + hm.rowh / 2) + ")");
-      const pieceh = hm.rowh / item.lst[i].length;
-      const colorlst = item.lst[i];
-      for (let j = 0; j < colorlst.length; j++) {
-        const v = colorlst[j];
-        g.append("rect").attr("x", -hm.colw / 2).attr("y", -hm.rowh / 2 + j * pieceh).attr("width", hm.colw).attr("height", pieceh).attr("fill", v).attr("shape-rendering", "crispEdges");
-      }
-      x2 += hm.colw + hm.colspace;
-    }
-    y += hm.rowh + hm.rowspace;
-  }
-  svg.append("rect").attr("x", originx).attr("y", originy).attr("width", hm.samples.length * (hm.colw + hm.colspace) - hm.colspace).attr("height", hm.items.length * (hm.rowh + hm.rowspace) - hm.rowspace).attr("stroke", "black").attr("fill", "none").attr("shape-rendering", "crispEdges");
-}
-
-// src/tp.e2pca.js
-function tp_e2pca_default(cohort, folder) {
-  for (const obj of cohort.e2pca.list) {
-    const holder = folder.append("div").style("display", "inline-block").style("margin", "20px").style("vertical-align", "top");
-    if (cohort.e2pca.list.length > 1) {
-      holder.style("border", "solid 1px #ededed");
-    }
-    if (obj.name) {
-      holder.append("div").text(obj.name).style("background-color", "#f1f1f1").style("padding", "5px 10px");
-    }
-    const toprow = holder.append("div").style("margin", "20px");
-    json_default(cohort.hostURL + "/textfile").post(JSON.stringify({ file: obj.vectorfile, jwt: cohort.jwt }), (data) => {
-      if (data.error) {
-        sayerror(holder, "Error getting vector file: " + data.error);
-        return;
-      }
-      import("./e2pca-545GHJWM.js").then((p) => {
-        const [err, numdata2plot] = p.e2pca_plot({
-          holder,
-          toprow,
-          text: data.text,
-          mdanno: cohort.patientannotation,
-          obj
-        });
-        if (err) {
-          sayerror(holder, "Error: " + err);
-          return;
-        }
-        p.e2pca_genesearchui({
-          holder: toprow,
-          numdata2plot,
-          hostURL: cohort.hostURL,
-          jwt: cohort.jwt,
-          obj,
-          callback: () => {
-            boxplot4sampleannotation(cohort, obj);
-          }
-        });
-        if (cohort.patientannotation) {
-          obj.boxplotdiv = holder.append("div");
-          const div = toprow.append("div").style("display", "inline-block").style("margin-left", "10px");
-          metadataselector4pca(cohort, obj, div);
-        }
-      });
-    });
-  }
-}
-function boxplot4sampleannotation(cohort, obj) {
-  if (!cohort.patientannotation) {
-    return;
-  }
-  if (!obj.expressiondata) {
-    return;
-  }
-  if (!obj.usetermkey) {
-    obj.usetermkey = cohort.patientannotation.metadata[0].key;
-  }
-  let term = null;
-  for (const t of cohort.patientannotation.metadata) {
-    if (t.key == obj.usetermkey) {
-      term = t;
-      break;
-    }
-  }
-  if (!term) {
-    sayerror(obj.boxplotdiv, "invalid term key " + obj.usetermkey);
-    return;
-  }
-  const samplegroups = [];
-  for (const v of term.values) {
-    samplegroups.push({
-      valuekey: v.key,
-      label: v.label,
-      color: v.color,
-      samples: []
-    });
-  }
-  let minv = obj.expressiondata[0].value;
-  let maxv = obj.expressiondata[0].value;
-  const noattrsamples = [];
-  for (const s of obj.expressiondata) {
-    minv = Math.min(minv, s.value);
-    maxv = Math.max(maxv, s.value);
-    if (!cohort.patientannotation.annotation[s.sample]) {
-      noattrsamples.push(s);
-      continue;
-    }
-    const valuekey = cohort.patientannotation.annotation[s.sample][obj.usetermkey];
-    if (valuekey == void 0) {
-      noattrsamples.push(s);
-      continue;
-    }
-    for (const sg of samplegroups) {
-      if (sg.valuekey == valuekey) {
-        sg.samples.push(s);
-        break;
-      }
-    }
-  }
-  if (noattrsamples.length) {
-    samplegroups.push({
-      label: "unannotated",
-      color: "#858585",
-      samples: noattrsamples
-    });
-  }
-  obj.boxplotdiv.selectAll("*").remove();
-  import("./plot.boxplot-PT3BUNVT.js").then((p) => {
-    const err = p.default({
-      list: samplegroups,
-      holder: obj.boxplotdiv,
-      axislabel: obj.searchedgene
-    });
-    if (err) {
-      sayerror(obj.boxplotdiv, "Boxplot: " + err);
-    }
-  });
-}
-function metadataselector4pca(cohort, obj, holder) {
-  const tip3 = new Menu({ border: "", padding: "" });
-  const noannocolor = "#858585";
-  holder.append("span").text("Choose metadata").attr("class", "sja_clbtext").on("click", (event) => {
-    tip3.clear();
-    tip3.showunder(event.target);
-    for (const term of cohort.patientannotation.metadata) {
-      tip3.d.append("div").attr("class", "sja_menuoption").text(term.label).on("click", () => {
-        obj.usetermkey = term.key;
-        tip3.hide();
-        obj.circles.attr("fill", (d) => {
-          const a = cohort.patientannotation.annotation[d.sample];
-          if (!a) return noannocolor;
-          const valuekey = a[term.key];
-          if (!valuekey) return noannocolor;
-          const b = cohort.patientannotation.mdh[term.key].values[valuekey];
-          if (!b) {
-            console.error("invalid value key: " + valuekey + " at term: " + term.key);
-            return noannocolor;
-          }
-          return b.color;
-        });
-        obj.legendholder.selectAll("*").remove();
-        obj.legendholder.append("div").style("margin-bottom", "5px").text(term.label).style("font-weight", "bold");
-        for (const v of term.values) {
-          const row = obj.legendholder.append("div").style("margin-bottom", "3px");
-          row.append("span").attr("class", "sja_mcdot").style("background-color", v.color).style("margin-right", "5px").html("&nbsp;");
-          row.append("span").text(v.label);
-        }
-        if (obj.expressiondata) {
-          boxplot4sampleannotation(cohort, obj);
-        }
-      });
-    }
-  });
-}
-
-// src/tp.ui.js
-async function tpui(cohort, holder, hostURL, app = { callbacks: { sjcharts: {} } }) {
-  const debugmode = app.debugmode;
-  if (debugmode) {
-    window.cohort = cohort;
-  }
-  if (!("hostURL" in cohort)) cohort.hostURL = hostURL;
-  if (cohort.headerhtml) {
-    holder.append("div").html(cohort.headerhtml);
-  }
-  let personcount = 0;
-  for (const pn in cohort.p2st) {
-    personcount++;
-    for (const st in cohort.p2st[pn]) {
-      const s = cohort.p2st[pn][st];
-      s.sampletype = st;
-      s.patientname = pn;
-      s.cohort = cohort;
-    }
-  }
-  const table = holder.append("table").style("margin-top", "20px");
-  const tr0 = table.append("tr");
-  cohort.__tdleft = tr0.append("td").style("vertical-align", "top").style("padding-right", "20px");
-  cohort.__tdright = tr0.append("td").style("vertical-align", "top");
-  if (cohort.hide_navigation) {
-    cohort.__tdleft.style("display", "none");
-  }
-  if (!cohort.hide_addnewfile) {
-    const [butt1, folder1] = makefolder(cohort);
-    folder1.style("background-color", "#f4f4f4").style("margin", "0px 20px 20px 0px").style("padding", "20px");
-    butt1.html('&#43; <span style="font-size:.8em">NEW FILE</span>');
-    const saydiv = folder1.append("p");
-    const filediv = folder1.append("div");
-    const fileui = () => {
-      filediv.selectAll("*").remove();
-      filediv.append("span").html("Select data type&nbsp;");
-      const typeselect = filetypeselect(filediv).style("margin-right", "20px");
-      const butt = filediv.append("input").attr("type", "file").on("change", (event) => {
-        saydiv.text("");
-        const file = event.target.files[0];
-        if (!file) {
-          fileui();
-          return;
-        }
-        if (file.size == 0) {
-          saydiv.text("Wrong file: " + file.name);
-          fileui();
-          return;
-        }
-        const reader = new FileReader();
-        reader.onload = (event2) => {
-          saydiv.text(file.name + " loaded.");
-          const flag = init_bulk_flag(cohort.genome.name);
-          if (!flag) {
-            saydiv.text("should not happen");
-            fileui();
-            return;
-          }
-          const error0 = content2flag(event2.target.result, typeselect.node().selectedIndex, flag);
-          if (error0) {
-            saydiv.text("Error with " + file.name + ": " + error0);
-            fileui();
-            return;
-          }
-          let ds = null;
-          for (const k in cohort.dsset) {
-            ds = cohort.dsset[k];
-            break;
-          }
-          if (!ds) {
-            saydiv.text("no dataset in cohort, this should not happen");
-            fileui();
-            return;
-          }
-          const error1 = bulkin({
-            flag,
-            cohort,
-            flag2thisds: ds
-          });
-          if (error1) {
-            saydiv.text("Error with " + file.name + ": " + error1);
-            fileui();
-            return;
-          }
-          if (flag.good == 0) {
-            saydiv.text(file.name + ": no data loaded");
-            fileui();
-            return;
-          }
-          saydiv.text("");
-          fileui();
-          holder.selectAll("*").remove();
-          tpui(cohort, holder, hostURL);
-        };
-        reader.onerror = function() {
-          saydiv.text("Error reading file " + file.name);
-          fileui();
-          return;
-        };
-        saydiv.text("Parsing file " + file.name + " ...");
-        reader.readAsText(file, "utf8");
-      });
-    };
-    fileui();
-  }
-  const [butt2, folder2] = makefolder(cohort);
-  const ds2clst = tp_classes_default(cohort, butt2, folder2);
-  const hassamplelst = [];
-  const hasdiseaselst = [];
-  for (const k in cohort.dsset) {
-    const ds = cohort.genome.datasets[k];
-    if (ds.hassample) {
-      hassamplelst.push(k);
-    }
-    if (ds.hasdisease) {
-      hasdiseaselst.push(k);
-    }
-  }
-  if (ds2clst) {
-    const [butt3, folder3] = makefolder(cohort, cohort.show_genetable);
-    tp_gene_default(cohort, ds2clst, butt3, folder3, personcount > 0, hostURL);
-  }
-  let showheatmap = false;
-  if (hassamplelst.length || personcount > 0) {
-    cohort.patientset = {};
-    for (const patient in cohort.p2st) {
-      cohort.patientset[patient] = {
-        trlst: [],
-        samples: cohort.p2st[patient]
-      };
-    }
-    if (hassamplelst.length > 0 && !cohort.hardcodemap) {
-      showheatmap = true;
-    }
-  }
-  if (cohort.show_heatmap) {
-    showheatmap = true;
-  }
-  let hm_main;
-  if (showheatmap) {
-    const [hmbtn, hmdiv] = makefolder(cohort);
-    hmbtn.text("HEATMAP").style("font-size", ".8em");
-    const sjcharts = await getsjcharts();
-    const appname = (cohort.name ? cohort.name + "." : "") + "hm";
-    sjcharts.heatmap({
-      cohort,
-      hassamplelst,
-      blockinit: block_init_default,
-      debugmode,
-      // sjcharts has its own d3 instance so it has to
-      // re-select to bind the d3 'event' properly
-      dom: {
-        butt: hmbtn.node(),
-        holder: hmdiv.node()
-      },
-      tp_getgeneexpression,
-      show_heatmap: cohort.show_heatmap,
-      // use a subnested sjcharts object to namespace its instances
-      instanceTracker: app.instanceTracker && app.instanceTracker.sjcharts,
-      callbacks: app.callbacks && app.callbacks.sjcharts && (app.callbacks.sjcharts[appname] || app.callbacks.sjcharts.hm)
-    });
-  }
-  if (cohort.hardcodemap) {
-    const [hmbut, hmdiv] = makefolder(cohort, cohort.show_hardcodemap);
-    hmbut.text("HEATMAP").style("font-size", ".8em");
-    for (const hcmap of cohort.hardcodemap) {
-      const div = hmdiv.append("div").style("display", "inline-block").style("margin-bottom", "20px");
-      if (hcmap.name) {
-        div.append("h3").text(hcmap.name);
-      }
-      inithcmap(hcmap, div);
-    }
-  }
-  if (cohort.survivalJSON) {
-    const [srvbut, srvdiv] = makefolder(cohort, cohort.show_hardcodemap);
-    srvbut.text("SURVIVAL CURVE").style("font-size", ".8em").style("border-color", "transparent");
-    const sjcharts = await getsjcharts();
-    sjcharts.survival({
-      cohort,
-      dom: {
-        butt: srvbut.node(),
-        holder: srvdiv.node()
-      },
-      // use a subnested sjcharts object to namespace its instances
-      instanceTracker: app.instanceTracker && app.instanceTracker.sjcharts,
-      callbacks: app.callbacks && app.callbacks.sjcharts && app.callbacks.sjcharts.sv
-    });
-  }
-  if (cohort.browserview) {
-    const [butt, folder] = makefolder(cohort);
-    butt.style("font-size", ".8em").text("BROWSER");
-    let loaded = false;
-    butt.on("click", () => {
-      if (folder.style("display") == "none") {
-        butt.style("border-color", "black");
-        appear(folder);
-      } else {
-        butt.style("border-color", "transparent");
-        disappear(folder);
-      }
-      if (loaded) return;
-      loaded = true;
-      const arg = {
-        holder: folder,
-        genome: cohort.genome,
-        debugmode,
-        dogtag: cohort.genome.name,
-        hostURL,
-        jwt: cohort.jwt,
-        cohort,
-        nobox: cohort.browserview.nobox,
-        datasetqueries: cohort.browserview.datasetqueries,
-        tklst: []
-      };
-      if (cohort.browserview.position) {
-        arg.chr = cohort.browserview.position.chr;
-        arg.start = cohort.browserview.position.start;
-        arg.stop = cohort.browserview.position.stop;
-      }
-      if (cohort.browserview.nativetracks) {
-        arg.nativetracks = cohort.browserview.nativetracks;
-      }
-      if (cohort.browserview.tracks) {
-        for (const t of cohort.browserview.tracks) {
-          arg.tklst.push(t);
-        }
-      }
-      if (cohort.browserview.assays) {
-        if (!cohort.assaylst) {
-          console.error("assaylst not set!");
-          cohort.assaylst = [];
-        }
-        for (const assayname in cohort.browserview.assays) {
-          const assayview = cohort.browserview.assays[assayname];
-          if (!assayview.assayobj) {
-            continue;
-          }
-          if (assayview.combined) {
-            if (assayview.combinetk) {
-              arg.tklst.push(assayview.combinetk);
-            }
-          } else {
-            for (const pn in cohort.patientset) {
-              for (const st in cohort.patientset[pn].samples) {
-                for (const t of cohort.patientset[pn].samples[st].tktemplate) {
-                  if (t.id == assayview.assayobj.id) {
-                    arg.tklst.push(t);
-                  }
-                }
-              }
-            }
-          }
-        }
-      }
-      if (cohort.browserview.defaultassaytracks) {
-        const [err, lst] = cohort2assaytracks(cohort);
-        if (err) {
-          sayerror(holder, "error with .defaultassaytracks: " + err);
-        } else {
-          for (const t of lst) arg.tklst.push(t);
-        }
-      }
-      for (const t of arg.tklst) {
-        t.iscustom = true;
-      }
-      blocklazyload(arg);
-    });
-    if (cohort.show_browser) {
-      butt.node().click();
-    }
-  }
-  if (cohort.e2pca) {
-    const [butt, folder] = makefolder(cohort);
-    butt.text(cohort.e2pca.label).style("font-size", ".8em");
-    let loaded = false;
-    butt.on("click", () => {
-      if (folder.style("display") == "none") {
-        butt.style("border-color", "black");
-        appear(folder);
-      } else {
-        butt.style("border-color", "transparent");
-        disappear(folder);
-      }
-      if (loaded) return;
-      loaded = true;
-      tp_e2pca_default(cohort, folder);
-    });
-    if (cohort.show_e2pca) {
-      butt.node().click();
-    }
-  }
-}
-function makefolder(cohort, show) {
-  const butt = cohort.__tdleft.append("div").attr("class", "sja_menuoption").style("margin-top", "10px").style("white-space", "nowrap");
-  const folder = cohort.__tdright.append("div").style("padding-bottom", "20px");
-  butt.on("click", () => {
-    if (folder.style("display") == "block") {
-      disappear(folder);
-      butt.style("border", "solid 1px transparent");
-    } else {
-      butt.style("border", "solid 1px #545454");
-      appear(folder);
-    }
-  });
-  if (show) {
-    butt.style("border", "solid 1px #545454");
-    folder.style("display", "block");
-  } else {
-    butt.style("border", "solid 1px transparent");
-    folder.style("display", "none");
-  }
-  return [butt, folder];
-}
-function cohort2assaytracks(ct) {
-  if (!ct.browserview) return [null, []];
-  if (!ct.browserview.defaultassaytracks) return [null, []];
-  const tklst = [];
-  for (const t of ct.browserview.defaultassaytracks) {
-    const p = ct.p2st[t.level1];
-    if (!p) continue;
-    if (t.level2) {
-      const p2 = p[t.level2];
-      if (!p2) continue;
-      if (!p2.tktemplate) continue;
-      for (const tt of p2.tktemplate) {
-        if (tt.assayname == t.assay) {
-          tklst.push(tt);
-          if (t.justone) {
-            break;
-          }
-        }
-      }
-    } else {
-      for (const st in p) {
-        const p2 = p[st];
-        if (p2.tktemplate) {
-          for (const tt of p2.tktemplate) {
-            if (tt.assayname == t.assay) {
-              tklst.push(tt);
-            }
-          }
-        }
-      }
-    }
-  }
-  return [null, tklst];
-}
-export {
-  tpui as default
-};
-//# sourceMappingURL=tp.ui-EMWJCGRX.js.map