@sjcrh/proteinpaint-client 2.221.0 → 2.223.0

package/dist/tp.ui-X2BJWXKN.js

@@ -0,0 +1,1453 @@
+import {
+  blocklazyload
+} from "./chunk-55SYHMGG.js";
+import {
+  bulkin,
+  content2flag
+} from "./chunk-J3LWRVN3.js";
+import "./chunk-UHFO6LHS.js";
+import {
+  getsjcharts
+} from "./chunk-MKAF2BHB.js";
+import "./chunk-VLIOMJDR.js";
+import {
+  block_init_default
+} from "./chunk-2CDIFQPW.js";
+import {
+  appear2 as appear,
+  disappear2 as disappear,
+  export_data,
+  filetypeselect,
+  font,
+  newpane,
+  sayerror
+} from "./chunk-JP4IU7DO.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-IRAB3OI7.js";
+import {
+  Menu
+} from "./chunk-CNFTQSNE.js";
+import "./chunk-RIHO7ZD5.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import {
+  init_bulk_flag
+} from "./chunk-4TJO2DGU.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-MHWYRNGA.js";
+import "./chunk-JHLF2ZC2.js";
+import {
+  dtcloss,
+  dtdel,
+  dtitd,
+  dtnloss,
+  dtsnvindel,
+  json_default,
+  mclass,
+  mclasscnvgain,
+  mclasscnvloss,
+  mclassfusionrna,
+  mclasssv,
+  mclassutr3,
+  mclassutr5
+} from "./chunk-WJLRU5OF.js";
+import "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-PWYMHUXY.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",
+        headers: { "content-type": "application/json" },
+        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-BHYT5BNH.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-XZ5LEEUG.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-RRSEDWZ3.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-CU4SFUDO.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-X2BJWXKN.js.map