@sjcrh/proteinpaint-client 2.166.0 → 2.167.1

package/dist/samplematrix-L2HOSLUT.js

@@ -0,0 +1,2189 @@
+import {
+  appear2 as appear,
+  disappear2 as disappear,
+  export_data,
+  first_genetrack_tolist,
+  font,
+  make_table_2col,
+  newpane,
+  sayerror
+} from "./chunk-W5EG334J.js";
+import {
+  invalidcoord,
+  string2pos
+} from "./chunk-HJ6L54YS.js";
+import {
+  dofetch,
+  dofetch2,
+  dofetch3,
+  vcfparsemeta
+} from "./chunk-MK7RRJTX.js";
+import "./chunk-DKI7YOTJ.js";
+import {
+  bplen,
+  dt2label,
+  dtcnv,
+  dtfusionrna,
+  dtitd,
+  dtloh,
+  dtsnvindel,
+  dtsv,
+  getMax_byiqr,
+  mclass,
+  mclassitd,
+  tkt,
+  validtkt
+} from "./chunk-6VQ4C735.js";
+import {
+  Menu
+} from "./chunk-TGZA4ETW.js";
+import "./chunk-5MWX5HUZ.js";
+import "./chunk-IQIXGTQV.js";
+import "./chunk-ZFFHOEBE.js";
+import "./chunk-DDOM4XYV.js";
+import "./chunk-7NTZWOJV.js";
+import "./chunk-LD45BCVM.js";
+import "./chunk-RA5EXEHB.js";
+import {
+  category10_default
+} from "./chunk-2MN5JLZB.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import {
+  linear,
+  ordinal
+} from "./chunk-W2IWHXLL.js";
+import "./chunk-5OHXYXLD.js";
+import "./chunk-UJUXE42U.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-NDWTN4U5.js";
+import "./chunk-HFNDKYVF.js";
+
+// src/samplematrix.featuremenu.js
+function showMenu_isgenevalue(smat, f) {
+  smat.menu.d.append("div").attr("class", "sja_menuoption").text("Sort").on("click", () => {
+    smat.menu.hide();
+    if (f.sort) {
+      return;
+    }
+    for (const f2 of smat.features) {
+      if (f2.isgenevalue) delete f2.sort;
+    }
+    f.sort = 1;
+    smat.draw_matrix();
+  });
+}
+function showMenu_iscnv(smat, f, obj) {
+  {
+    const row = smat.menu.d.append("div").style("margin", "10px");
+    row.append("span").html("CNV log2(ratio) cutoff ");
+    row.append("input").property("value", obj.valuecutoff || 0).attr("type", "number").style("width", "50px").on("keyup", (event2) => {
+      if (event2.code != "Enter" && event2.code != "NumpadEnter") return;
+      let v = Number.parseFloat(event2.target.value);
+      if (!v || v < 0) {
+        v = 0;
+      }
+      if (v == 0) {
+        if (obj.valuecutoff) {
+          obj.valuecutoff = 0;
+          smat.update_singlefeature(f);
+        } else {
+        }
+        return;
+      }
+      if (obj.valuecutoff) {
+        if (obj.valuecutoff == v) {
+        } else {
+          obj.valuecutoff = v;
+          smat.update_singlefeature(f);
+        }
+      } else {
+        obj.valuecutoff = v;
+        smat.update_singlefeature(f);
+      }
+    });
+    row.append("div").style("font-size", ".7em").style("opacity", 0.5).html("Only show CNV with absolute log2(ratio) no less than cutoff.<br>Set to 0 to cancel.");
+  }
+  {
+    const row = smat.menu.d.append("div").style("margin", "10px");
+    row.append("span").html("CNV segment size limit&nbsp;");
+    row.append("input").property("value", obj.focalsizelimit || 0).attr("type", "number").style("width", "100px").on("keyup", (event2) => {
+      if (event2.code != "Enter" && event2.code != "NumpadEnter") return;
+      let v = Number.parseInt(event2.target.value);
+      if (!v || v < 0) {
+        v = 0;
+      }
+      if (v == 0) {
+        if (obj.focalsizelimit) {
+          obj.focalsizelimit = 0;
+          smat.update_singlefeature(f);
+        } else {
+        }
+        return;
+      }
+      if (obj.focalsizelimit) {
+        if (obj.focalsizelimit == v) {
+        } else {
+          obj.focalsizelimit = v;
+          smat.update_singlefeature(f);
+        }
+      } else {
+        obj.focalsizelimit = v;
+        smat.update_singlefeature(f);
+      }
+    });
+    row.append("span").text("bp");
+    row.append("div").style("font-size", ".7em").style("opacity", 0.5).html("Limit the CNV segment length to show only focal events.<br>Set to 0 to cancel.");
+  }
+}
+function showMenu_isloh(smat, f, obj) {
+  {
+    const row = smat.menu.d.append("div").style("margin", "10px");
+    row.append("span").html("LOH segmean cutoff&nbsp;");
+    row.append("input").property("value", obj.valuecutoff || 0).attr("type", "number").style("width", "50px").on("keyup", (event2) => {
+      if (event2.code != "Enter" && event2.code != "NumpadEnter") return;
+      let v = Number.parseFloat(event2.target.value);
+      if (!v || v < 0) {
+        v = 0;
+      }
+      if (v == 0) {
+        if (obj.valuecutoff) {
+          obj.valuecutoff = 0;
+          smat.update_singlefeature(f);
+        } else {
+        }
+        return;
+      }
+      if (obj.valuecutoff) {
+        if (obj.valuecutoff == v) {
+        } else {
+          obj.valuecutoff = v;
+          smat.update_singlefeature(f);
+        }
+      } else {
+        obj.valuecutoff = v;
+        smat.update_singlefeature(f);
+      }
+    });
+    row.append("div").style("font-size", ".7em").style("opacity", 0.5).html("Only show LOH with segmean no less than cutoff.<br>Set to 0 to cancel.");
+  }
+  {
+    const row = smat.menu.d.append("div").style("margin", "10px");
+    row.append("span").html("LOH segment size limit&nbsp;");
+    row.append("input").property("value", obj.focalsizelimit || 0).attr("type", "number").style("width", "100px").on("keyup", (event2) => {
+      if (event2.code != "Enter" && event2.code != "NumpadEnter") return;
+      let v = Number.parseInt(event2.target.value);
+      if (!v || v < 0) {
+        v = 0;
+      }
+      if (v == 0) {
+        if (obj.focalsizelimit) {
+          obj.focalsizelimit = 0;
+          smat.update_singlefeature(f);
+        } else {
+        }
+        return;
+      }
+      if (obj.focalsizelimit) {
+        if (obj.focalsizelimit == v) {
+        } else {
+          obj.focalsizelimit = v;
+          smat.update_singlefeature(f);
+        }
+      } else {
+        obj.focalsizelimit = v;
+        smat.update_singlefeature(f);
+      }
+    });
+    row.append("span").text("bp");
+    row.append("div").style("font-size", ".7em").style("opacity", 0.5).html("Limit the LOH segment length to show only focal events.<br>Set to 0 to cancel.");
+  }
+}
+function showMenu_ismutation(smat, f) {
+  {
+    const div = smat.menu.d.append("div").style("margin", "10px").style("border", "solid 1px #ededed");
+    const update = () => {
+      smat.update_singlefeature(f);
+      smat.menu.hide();
+    };
+    const table = div.append("table").style("margin", "10px").style("border-spacing", "1px");
+    const tbody = table.append("tbody");
+    {
+      const tr = tbody.append("tr");
+      tr.append("td").style("opacity", 0.5).text("CNV");
+      tr.append("td").attr("class", "sja_menuoption").text(f.cnv.hidden ? "Show" : "Hide").on("click", () => {
+        f.cnv.hidden = !f.cnv.hidden;
+        update();
+      });
+      tr.append("td").attr("class", "sja_menuoption").text("Show only").on("click", () => {
+        ismutation_hideallclass(f);
+        delete f.cnv.hidden;
+        update();
+      });
+      const td = tr.append("td");
+      if (!f.cnv.hidden) {
+        td.attr("class", "sja_menuoption").style("font-size", ".8em").text("CONFIG").on("click", () => {
+          smat.menu.clear();
+          showMenu_iscnv(smat, f, f.cnv);
+        });
+      }
+    }
+    {
+      const tr = tbody.append("tr");
+      tr.append("td").style("opacity", 0.5).text("LOH");
+      tr.append("td").attr("class", "sja_menuoption").text(f.loh.hidden ? "Show" : "Hide").on("click", () => {
+        f.loh.hidden = !f.loh.hidden;
+        update();
+      });
+      tr.append("td").attr("class", "sja_menuoption").text("Show only").on("click", () => {
+        ismutation_hideallclass(f);
+        delete f.loh.hidden;
+        update();
+      });
+      const td = tr.append("td");
+      if (!f.loh.hidden) {
+        td.attr("class", "sja_menuoption").style("font-size", ".8em").text("CONFIG").on("click", () => {
+          smat.menu.clear();
+          showMenu_isloh(smat, f, f.loh);
+        });
+      }
+    }
+    {
+      const tr = tbody.append("tr");
+      tr.append("td").style("opacity", 0.5).text("ITD");
+      tr.append("td").attr("class", "sja_menuoption").text(f.itd.hidden ? "Show" : "Hide").on("click", () => {
+        f.itd.hidden = !f.itd.hidden;
+        update();
+      });
+      tr.append("td").attr("class", "sja_menuoption").text("Show only").on("click", () => {
+        ismutation_hideallclass(f);
+        delete f.itd.hidden;
+        update();
+      });
+      const td = tr.append("td");
+      if (!f.itd.hidden) {
+      }
+    }
+    {
+      const tr = tbody.append("tr");
+      tr.append("td").style("opacity", 0.5).text("SV");
+      tr.append("td").attr("class", "sja_menuoption").text(f.sv.hidden ? "Show" : "Hide").on("click", () => {
+        f.sv.hidden = !f.sv.hidden;
+        update();
+      });
+      tr.append("td").attr("class", "sja_menuoption").text("Show only").on("click", () => {
+        ismutation_hideallclass(f);
+        delete f.sv.hidden;
+        update();
+      });
+      const td = tr.append("td");
+      if (!f.sv.hidden) {
+      }
+    }
+    {
+      const tr = tbody.append("tr");
+      tr.append("td").style("opacity", 0.5).text("Fusion");
+      tr.append("td").attr("class", "sja_menuoption").text(f.fusion.hidden ? "show" : "hide").on("click", () => {
+        f.fusion.hidden = !f.fusion.hidden;
+        update();
+      });
+      tr.append("td").attr("class", "sja_menuoption").text("show only").on("click", () => {
+        ismutation_hideallclass(f);
+        delete f.fusion.hidden;
+        update();
+      });
+      const td = tr.append("td");
+      if (!f.fusion.hidden) {
+      }
+    }
+    table.append("tbody").append("tr").append("td").attr("colspan", 4).style("padding-top", "10px").append("span").style("font-size", ".8em").text("List SNV/indel").attr("class", "sja_clbtext").on("click", () => {
+      if (tbody2.style("display") == "none") {
+        tbody2.style("display", "table-row-group");
+      } else {
+        tbody2.style("display", "none");
+      }
+    });
+    const tbody2 = table.append("tbody").style("display", "none");
+    for (const k in mclass) {
+      const c = mclass[k];
+      if (c.dt != dtsnvindel) {
+        continue;
+      }
+      const tr = tbody2.append("tr");
+      tr.append("td").style("opacity", 0.5).text(c.label);
+      tr.append("td").attr("class", "sja_menuoption").text(f.snvindel.excludeclasses[k] ? "Show" : "Hide").on("click", () => {
+        if (f.snvindel.excludeclasses[k]) {
+          delete f.snvindel.excludeclasses[k];
+        } else {
+          f.snvindel.excludeclasses[k] = 1;
+        }
+        update();
+      });
+      tr.append("td").attr("class", "sja_menuoption").text("Show only").on("click", () => {
+        ismutation_hideallclass(f);
+        delete f.snvindel.excludeclasses[k];
+        update();
+      });
+      const td = tr.append("td");
+    }
+    div.append("div").style("margin", "10px").append("span").style("font-size", ".8em").text("Show all classes").attr("class", "sja_clbtext").on("click", () => {
+      f.cnv.hidden = false;
+      f.loh.hidden = false;
+      f.itd.hidden = false;
+      f.sv.hidden = false;
+      f.fusion.hidden = false;
+      f.snvindel.excludeclasses = {};
+      update();
+    });
+  }
+}
+function ismutation_hideallclass(f) {
+  f.cnv.hidden = true;
+  f.loh.hidden = true;
+  f.itd.hidden = true;
+  f.sv.hidden = true;
+  f.fusion.hidden = true;
+  f.snvindel.excludeclasses = {};
+  for (const k in mclass) {
+    if (mclass[k].dt == dtsnvindel) f.snvindel.excludeclasses[k] = 1;
+  }
+}
+
+// src/samplematrix.kmplot.js
+function may_add_kmplotbutton(smat, buttonrow) {
+  if (!smat.mds || !smat.mds.survivalplot) return;
+  buttonrow.append("span").style("margin-right", "20px").style("font-size", ".8em").text("SURVIVAL PLOT").attr("class", "sja_clbtext").on("click", (event2) => {
+    smat.menu.clear().showunder(event2.target);
+    kmplot_menu(smat);
+  });
+}
+async function kmplot_menu(smat) {
+  const mutation_features = smat.features.filter((i) => i.ismutation);
+  try {
+    if (mutation_features.length != 2) throw "only works with two genomic features.";
+    await kmplot_do(smat, mutation_features[0], mutation_features[1]);
+  } catch (e) {
+    smat.menu.d.append("div").style("margin", "20px").text("Cannot make survival plot: " + (e.message || e));
+  }
+}
+async function kmplot_do(smat, f1, f2) {
+  const s1 = [], s2 = [], s12 = [];
+  for (const i of smat.samples) {
+    const in1 = f1.items.find((j) => j.sample == i.name);
+    const in2 = f2.items.find((j) => j.sample == i.name);
+    if (in1) {
+      if (in2) s12.push(i.name);
+      else s1.push(i.name);
+    } else {
+      s2.push(i.name);
+    }
+  }
+  const plot = {
+    renderplot: 1,
+    samplerule: {
+      full: {},
+      mutated_sets: [
+        { name: f1.label + " mutated (n=" + s1.length + ")", samplenames: s1 },
+        { name: f2.label + " mutated (n=" + s2.length + ")", samplenames: s2 },
+        { name: f1.label + " and " + f2.label + " mutated (n=" + s12.length + ")", samplenames: s12 }
+      ]
+    }
+  };
+  if (smat.limitsamplebyeitherannotation) {
+    plot.samplerule.full = {
+      byattr: 1,
+      key: smat.limitsamplebyeitherannotation[0].key,
+      value: smat.limitsamplebyeitherannotation[0].value,
+      immutable: 1
+    };
+  }
+  const pane = newpane({ x: 100, y: 100 });
+  pane.header.text(
+    (smat.limitsamplebyeitherannotation ? smat.limitsamplebyeitherannotation[0].value + " " : "") + "survival by " + f1.label + " and " + f2.label + " mutation status"
+  );
+  const _ = await import("./mds.survivalplot-GYK6VRQT.js");
+  _.init(
+    {
+      mds: smat.mds,
+      genome: smat.genome,
+      plotlist: [plot]
+    },
+    pane.body
+  );
+}
+
+// src/samplematrix.js
+var saynovalue = "na";
+var default_cnvgaincolor = "#D6683C";
+var default_cnvlosscolor = "#67a9cf";
+var default_genevaluecolor = "#095873";
+var default_lohcolor = "#858585";
+var default_svcolor = "#858585";
+var minheight2showname = 8;
+var Samplematrix = class {
+  /*
+  init ui
+  */
+  constructor(p) {
+    for (const k in p) {
+      this[k] = p[k];
+    }
+    if (this.debugmode) window.smat = this;
+    this.tip = new Menu({ padding: "0px", hideXmute: 1, hideYmute: 1 });
+    this.menu = new Menu({ padding: "0px" });
+    this.errdiv = this.holder.append("div");
+    if (!this.iscustom) {
+      try {
+        if (!this.dslabel) throw "not custom data but dslabel is missing";
+        this.mds = this.genome.datasets[this.dslabel];
+        if (!this.mds) throw "invalid dataset name: " + this.dslabel;
+        if (!this.mds.isMds) throw "improper dataset: " + this.dslabel;
+      } catch (e) {
+        this.error(e);
+      }
+    }
+    init_controlui(this);
+    if (this.header) {
+      this.holder.append("div").style("margin-bottom", "20px").html(this.header);
+    }
+    this.wait_div = this.holder.append("div");
+    this.wait_div.style("display", "block").text("Loading...");
+    this.svg = this.holder.append("svg");
+    this.validate_config().then(() => {
+      return this.get_features();
+    }).catch((err) => {
+      if (typeof err == "string") {
+        this.error(err);
+      } else {
+        this.error(err.message);
+        if (err.stack) console.log(err.stack);
+      }
+    });
+  }
+  error(m) {
+    sayerror(this.errdiv, m);
+  }
+  async validate_config() {
+    if (this.iscustom) {
+      if (!this.querykey2tracks) throw "querykey2tracks missing for custom dataset";
+      let novalidtk = true;
+      for (const key in this.querykey2tracks) {
+        const tk = this.querykey2tracks[key];
+        if (!tk.file && !tk.url) throw "no file or url for a custom track by key " + key;
+        if (!tk.type) throw "missing type for member track by key " + key;
+        if (!validtkt(tk.type)) throw "invalid type for a member track: " + tk.type;
+        novalidtk = false;
+      }
+      if (novalidtk) throw "no custom tracks from querykey2tracks";
+      let vcftk;
+      for (const key in this.querykey2tracks) {
+        const tk = this.querykey2tracks[key];
+        if (tk.type == tkt.mdsvcf) {
+          vcftk = tk;
+        }
+      }
+      if (vcftk) {
+        await this.may_init_customvcf(vcftk);
+      }
+    } else {
+      if (this.mds.mdsIsUninitiated) {
+        const d = await dofetch3(`getDataset?genome=${this.genome.name}&dsname=${this.mds.label}`);
+        if (d.error) throw d.error;
+        if (!d.ds) throw "ds missing";
+        Object.assign(this.mds, d.ds);
+        delete this.mds.mdsIsUninitiated;
+      }
+    }
+    if (this.limitsamplebyeitherannotation) {
+      if (!Array.isArray(this.limitsamplebyeitherannotation)) throw "limitsamplebyeitherannotation must be an array";
+      const tr = this.legendtable.append("tr");
+      for (const anno of this.limitsamplebyeitherannotation) {
+        if (!anno.key) throw ".key missing from an element of limitsamplebyeitherannotation";
+        if (!anno.value) throw ".value missing from an element of limitsamplebyeitherannotation";
+      }
+      this.showlegend_limitsample();
+    }
+    const cnv_tr = this.legendtable.append("tr");
+    cnv_tr.append("td").style("opacity", 0.5).style("text-align", "right").text("CNV cutoff");
+    this.legendtable.cnv_td = cnv_tr.append("td");
+    const loh_tr = this.legendtable.append("tr");
+    loh_tr.append("td").style("opacity", 0.5).style("text-align", "right").text("LOH cutoff");
+    this.legendtable.loh_td = loh_tr.append("td");
+    if (this.limitbysamplesetgroup) {
+      if (!Array.isArray(this.limitbysamplesetgroup.samples)) throw ".limitbysamplesetgroup.samples is not array";
+    }
+    if (!this.rowspace) this.rowspace = 1;
+    if (!this.colspace) this.colspace = 1;
+    if (!this.rowlabspace) this.rowlabspace = 5;
+    if (!this.collabspace) this.collabspace = 5;
+    if (!this.rowlabticksize) this.rowlabticksize = 5;
+    if (!this.collabticksize) this.collabticksize = 5;
+    if (!this.features) throw "missing features[]";
+    if (!Array.isArray(this.features)) throw "features must be an array";
+    if (this.features[0].height) this.ori_feature_height = this.features[0].height;
+    if (this.features[0].width) this.ori_feature_width = this.features[0].width;
+    for (const f of this.features) {
+      await this.validate_feature(f);
+    }
+  }
+  showlegend_limitsample() {
+    if (!this.limitsamplebyeitherannotation) return;
+  }
+  feature_parseposition_maygene(f) {
+    return Promise.resolve().then(() => {
+      if (f.position) {
+        const o = string2pos(f.position, this.genome);
+        if (o) {
+          f.chr = o.chr;
+          f.start = o.start;
+          f.stop = o.stop;
+        }
+      }
+      if (f.chr) {
+        const err = invalidcoord(this.genome, f.chr, f.start, f.stop);
+        if (err) {
+          throw 'feature "' + f.label + '" position error: ' + err;
+        } else {
+          return;
+        }
+      }
+      if (!f.genename) throw "position required for a feature: no position or genename given";
+      return dofetch("/genelookup", {
+        input: f.genename,
+        genome: this.genome.name,
+        deep: 1
+      }).then((data) => {
+        if (data.error) throw data.error;
+        if (!data.gmlst || data.gmlst.length == 0) throw "no gene can be found for " + f.genename;
+        const regions = [];
+        for (const gm of data.gmlst) {
+          let nooverlap = true;
+          for (const region of regions) {
+            if (gm.chr == region.chr && Math.max(gm.start, region.start) < Math.min(gm.stop, region.stop)) {
+              nooverlap = false;
+              region.start = Math.min(region.start, gm.start);
+              region.stop = Math.max(region.stop, gm.stop);
+              break;
+            }
+          }
+          if (nooverlap) {
+            regions.push({
+              chr: gm.chr,
+              start: gm.start,
+              stop: gm.stop
+            });
+          }
+        }
+        if (regions.length > 1) {
+          sayerror(
+            this.errdiv,
+            "multiple regions found for gene " + f.genename + " you'd better specify one in feature"
+          );
+        }
+        f.chr = regions[0].chr;
+        f.start = regions[0].start;
+        f.stop = regions[0].stop;
+      });
+    });
+  }
+  validate_feature(f) {
+    return Promise.resolve().then(() => {
+      f.id = Math.random().toString();
+      const tr = this.legendtable.append("tr");
+      f.legend_tr = tr;
+      if (f.isgenevalue) {
+        if (!f.genename) throw ".genename missing for isgenevalue feature";
+        f.label = f.genename + " expression";
+        if (this.dslabel) {
+          if (!f.querykey) throw ".querykey missing for isgenevalue feature while loading from official dataset";
+        } else {
+        }
+        if (!f.scale) f.scale = { auto: 1 };
+        if (f.missingvalue == void 0) f.missingvalue = 0;
+        tr.append("td").text(f.label).style("opacity", 0.5).style("text-align", "right");
+        f.legendholder = tr.append("td");
+        if (!f.width) f.width = 20;
+        if (!f.color) f.color = default_genevaluecolor;
+        return this.feature_parseposition_maygene(f);
+      }
+      if (f.iscnv) {
+        if (this.dslabel) {
+          if (!f.querykey) throw ".querykey missing for iscnv feature while loading from official dataset";
+        } else {
+        }
+        if (!f.label && f.genename) {
+          f.label = f.genename + " CNV";
+        }
+        tr.append("td").text(f.label).style("opacity", 0.5).style("text-align", "right");
+        f.legendholder = tr.append("td");
+        if (!f.width) f.width = 40;
+        if (!f.colorgain) f.colorgain = default_cnvgaincolor;
+        if (!f.colorloss) f.colorloss = default_cnvlosscolor;
+        return this.feature_parseposition_maygene(f).then(() => {
+          if (!f.label) f.label = f.chr + ":" + f.start + "-" + f.stop + " CNV";
+          f.coordscale = linear().domain([f.start, f.stop]).range([0, this.features_on_rows ? f.height : f.width]);
+        });
+      }
+      if (f.isloh) {
+        if (this.dslabel) {
+          if (!f.querykey) throw ".querykey missing for isloh feature while loading from official dataset";
+        } else {
+        }
+        if (!f.label && f.genename) {
+          f.label = f.genename + " LOH";
+        }
+        tr.append("td").text(f.label).style("opacity", 0.5).style("text-align", "right");
+        f.legendholder = tr.append("td");
+        if (!f.width) f.width = 40;
+        if (!f.color) f.color = default_lohcolor;
+        return this.feature_parseposition_maygene(f).then(() => {
+          if (!f.label) f.label = f.chr + ":" + f.start + "-" + f.stop + " LOH";
+          f.coordscale = linear().domain([f.start, f.stop]).range([0, this.features_on_rows ? f.height : f.width]);
+        });
+      }
+      if (f.isvcf) {
+        if (this.dslabel) {
+          if (!f.querykey) throw ".querykey missing for isvcf feature while loading from official dataset";
+        } else {
+        }
+        if (!f.label && f.genename) {
+          f.label = f.genename + " SNV/indel";
+        }
+        tr.append("td").text(f.label).style("opacity", 0.5).style("text-align", "right");
+        f.legendholder = tr.append("td");
+        if (!f.width) f.width = 20;
+        if (!f.snvindel) f.snvindel = {};
+        return this.feature_parseposition_maygene(f).then(() => {
+          if (!f.label) f.label = f.chr + ":" + f.start + "-" + f.stop + " SNV/indel";
+        });
+      }
+      if (f.isitd) {
+        if (this.dslabel) {
+          if (!f.querykey) throw ".querykey missing for isitd feature while loading from official dataset";
+        } else {
+        }
+        if (!f.label && f.genename) {
+          f.label = f.genename + " ITD";
+        }
+        if (!f.width) f.width = 20;
+        if (!f.color) f.color = mclass[mclassitd].color;
+        tr.append("td").text(f.label).style("opacity", 0.5).style("text-align", "right");
+        f.legendholder = tr.append("td");
+        f.legendholder.append("div").style("width", "20px").html("&nbsp;").style("background", f.color);
+        return this.feature_parseposition_maygene(f).then(() => {
+          if (!f.label) f.label = f.chr + ":" + f.start + "-" + f.stop + " ITD";
+        });
+      }
+      if (f.issvfusion) {
+        if (this.dslabel) {
+          if (!f.querykey) throw ".querykey missing for issvfusion feature while loading from official dataset";
+        } else {
+        }
+        if (!f.label && f.genename) {
+          f.label = f.genename + " SV/fusion";
+        }
+        if (!f.width) f.width = 20;
+        if (!f.color) f.color = default_svcolor;
+        tr.append("td").text(f.label).style("opacity", 0.5).style("text-align", "right");
+        f.legendholder = tr.append("td");
+        return this.feature_parseposition_maygene(f).then(() => {
+          if (!f.label) f.label = f.chr + ":" + f.start + "-" + f.stop + " SV/fusion";
+        });
+      }
+      if (f.issvcnv) {
+        if (this.dslabel) {
+          if (!f.querykey) throw ".querykey missing for issvcnv feature while loading from official dataset";
+        } else {
+        }
+        if (!f.label && f.genename) {
+          f.label = f.genename + " CNV/SV";
+        }
+        tr.append("td").text(f.label).style("color", "#858585").style("text-align", "right");
+        f.legendholder = tr.append("td");
+        initfeature_polymutation(f);
+        return this.feature_parseposition_maygene(f).then(() => {
+          if (!f.label) f.label = f.chr + ":" + f.start + "-" + f.stop + " CNV/SV";
+        });
+      }
+      if (f.ismutation) {
+        if (this.dslabel) {
+          if (!f.querykeylst) throw ".querykeylst missing for ismutation feature";
+          if (!Array.isArray(f.querykeylst)) throw ".querykeylst[] should be array for ismutation feature";
+          if (f.querykeylst.length == 0) throw "querykeylst[] empty array for ismutation feature";
+        } else {
+        }
+        if (!f.label && f.genename) {
+          f.label = f.genename + " mutation";
+        }
+        tr.append("td").text(f.label).style("opacity", 0.5).style("text-align", "right");
+        f.legendholder = tr.append("td");
+        initfeature_polymutation(f);
+        return this.feature_parseposition_maygene(f).then(() => {
+          if (!f.label) f.label = f.chr + ":" + f.start + "-" + f.stop + " mutation";
+          f.coordscale = linear().domain([f.start, f.stop]).range([0, this.features_on_rows ? f.height : f.width]);
+        });
+      }
+      if (f.issampleattribute) {
+        if (!this.dslabel) throw ".dslabel missing: sampleattribute only works for official dataset";
+        if (!f.key) throw ".key missing for issampleattribute feature";
+        if (!f.label) f.label = f.key;
+        if (this.mds && this.mds.sampleAttribute && this.mds.sampleAttribute.attributes) {
+          const registry = this.mds.sampleAttribute.attributes[f.key];
+          if (registry) {
+            f.values = registry.values;
+          }
+        }
+        if (!f.values) {
+          f.values = {};
+        }
+        f.assignmissingcolor = ordinal(category10_default);
+        if (!f.width && !this.features_on_rows) f.width = 20;
+        else if (!f.height && this.features_on_rows) f.height = 50;
+        tr.append("td").text(f.label).style("opacity", 0.5).style("text-align", "right");
+        f.legendholder = tr.append("td");
+        return Promise.resolve();
+      }
+      throw "unknown feature type in validating feature";
+    });
+  }
+  get_features(featureset) {
+    this.max_cnv = 0;
+    this.min_cnv = 0;
+    this.max_loh = 0;
+    this.min_loh = 0;
+    const arg = {
+      genome: this.genome.name,
+      limitsamplebyeitherannotation: this.limitsamplebyeitherannotation,
+      features: (featureset || this.features).map(feature2arg)
+    };
+    if (this.limitbysamplesetgroup) {
+      arg.sampleset = this.limitbysamplesetgroup.samples;
+    }
+    if (this.iscustom) {
+      arg.iscustom = 1;
+      arg.querykey2tracks = {};
+      for (const f of arg.features) {
+        if (f.querykey) {
+          arg.querykey2tracks[f.querykey] = this.querykey2tracks[f.querykey];
+        } else if (f.querykeylst) {
+          for (const k of f.querykeylst) arg.querykey2tracks[k] = this.querykey2tracks[k];
+        }
+      }
+    } else {
+      arg.dslabel = this.mds.label;
+    }
+    return dofetch("/samplematrix", arg).then((data) => {
+      if (data.error) {
+        for (const f0 of arg.features) {
+          const f = this.features.find((f2) => f2.id == f0.id);
+          if (f) f.items = [];
+        }
+        throw data.error;
+      }
+      for (const dat of data.results) {
+        const f = this.features.find((f2) => f2.id == dat.id);
+        if (!f) throw "feature not found: " + f.id;
+        f.items = dat.items;
+        this.prep_featuredata(f);
+      }
+      this.draw_matrix();
+      this.make_legend();
+      this.wait_div.style("display", "none");
+    });
+  }
+  update_singlefeature(f) {
+    this.get_features([f]).catch((err) => {
+      if (typeof err == "string") {
+        this.error(err);
+      } else {
+        this.error(err.message);
+        if (err.stack) console.log(err.stack);
+      }
+    });
+  }
+  addnewfeature_update(f) {
+    this.features.push(f);
+    this.validate_feature(f).then(() => {
+      return this.get_features([f]);
+    }).catch((err) => {
+      this.error(typeof err == "string" ? err : err.message);
+      if (err.stack) console.log(err.stack);
+    });
+  }
+  prep_featuredata(f) {
+    if (f.isgenevalue) {
+      f.scale.maxv = 0;
+      f.scale.minv = 0;
+      for (const i of f.items) {
+        f.scale.maxv = Math.max(f.scale.maxv, i.value);
+      }
+      return;
+    }
+    if (f.iscnv) {
+      const gain = [], loss = [];
+      for (const i of f.items) {
+        if (i.value > 0) {
+          gain.push(i.value);
+        } else {
+          loss.push(-i.value);
+        }
+      }
+      const gmax = getMax_byiqr(gain, 0);
+      const lmax = getMax_byiqr(loss, 0);
+      f.maxabslogratio = Math.max(gmax, lmax);
+      if (f.maxabslogratio > this.max_cnv) this.max_cnv = f.maxabslogratio;
+      return;
+    }
+    if (f.isloh) {
+      const values = f.items.map((i) => i.segmean);
+      f.minvalue = 0;
+      f.maxvalue = Math.max(...values);
+      if (f.maxvalue > this.max_loh) this.max_loh = f.maxvalue;
+      return;
+    }
+    if (f.isvcf) {
+      return;
+    }
+    if (f.isitd) {
+      return;
+    }
+    if (f.issvfusion) {
+      return;
+    }
+    if (f.issvcnv || f.ismutation) {
+      const cnvgain = [], cnvloss = [];
+      let lohmax = 0;
+      for (const i of f.items) {
+        if (i.dt == dtcnv) {
+          if (i.value > 0) {
+            cnvgain.push(i.value);
+          } else {
+            cnvloss.push(-i.value);
+          }
+        } else if (i.dt == dtloh) {
+          lohmax = Math.max(i.segmean, lohmax);
+        }
+      }
+      if (cnvgain.length + cnvloss.length > 0) {
+        const gmax = getMax_byiqr(cnvgain, 0);
+        const lmax = getMax_byiqr(cnvloss, 0);
+        f.cnv.maxabslogratio = Math.max(gmax, lmax);
+        if (f.cnv.maxabslogratio > this.max_cnv) {
+          this.max_cnv = f.cnv.maxabslogratio;
+          this.min_cnv = -f.cnv.maxabslogratio;
+          this.cnv_colorloss = f.cnv.colorloss;
+          this.cnv_colorgain = f.cnv.colorgain;
+        }
+      }
+      if (lohmax) {
+        f.loh.minvalue = 0;
+        f.loh.maxvalue = lohmax;
+        if (f.loh.maxvalue > this.max_loh) this.max_loh = f.loh.maxvalue;
+        this.loh_color = f.loh.color;
+      }
+      return;
+    }
+    if (f.issampleattribute) {
+      for (const i of f.items) {
+        if (!f.values[i.value]) {
+          f.values[i.value] = {
+            name: i.value,
+            color: f.assignmissingcolor(i.value)
+          };
+        }
+      }
+      return;
+    }
+    throw "unknown feature type in preparing feature data";
+  }
+  make_legend() {
+    for (const f of this.features) {
+      const h = f.legendholder;
+      h.selectAll("*").remove();
+      if (f.isgenevalue) {
+        h.append("span").text(f.scale.minv.toFixed(3));
+        h.append("div").style("margin", "2px 10px").style("display", "inline-block").style("width", "100px").style("height", "15px").style("background", "linear-gradient( to right, white, " + f.color + ")");
+        h.append("span").text(f.scale.maxv.toFixed(3));
+        continue;
+      }
+      if (f.iscnv) {
+        h.append("span").html(
+          'Gain <span style="background:' + f.colorgain + ';color:white;padding:1px 5px">' + f.maxabslogratio.toFixed(3) + '</span> &nbsp; Loss <span style="background:' + f.colorloss + ';color:white;padding:1px 5px">-' + f.maxabslogratio.toFixed(3) + "</span>"
+        );
+        continue;
+      }
+      if (f.isloh) {
+        h.append("span").text(f.minvalue.toFixed(3));
+        h.append("div").style("margin", "2px 10px").style("display", "inline-block").style("width", "100px").style("height", "15px").style("background", "linear-gradient( to right, white, " + f.color + ")");
+        h.append("span").text(f.maxvalue.toFixed(3));
+        continue;
+      }
+      if (f.isvcf) {
+        const classes = /* @__PURE__ */ new Set();
+        for (const m of f.items) {
+          if (m.class) {
+            classes.add(m.class);
+          } else {
+          }
+        }
+        for (const c of classes) {
+          const cell = h.append("div").style("display", "inline-block").style("margin-right", "10px");
+          cell.append("span").style("background", mclass[c].color).style("margin-right", "2px").html("&nbsp;&nbsp;&nbsp;");
+          cell.append("span").text(mclass[c].label).style("color", mclass[c].color);
+        }
+        continue;
+      }
+      if (f.isitd) {
+        continue;
+      }
+      if (f.issvfusion) {
+        continue;
+      }
+      if (f.issvcnv || f.ismutation) {
+        const vcfclass2count = /* @__PURE__ */ new Map();
+        let itdcount = 0;
+        let svcount = 0;
+        let fusioncount = 0;
+        for (const i of f.items) {
+          if (i.dt == dtsnvindel) {
+            if (i.class && i.sampledata) {
+              if (!vcfclass2count.has(i.class)) {
+                vcfclass2count.set(i.class, 0);
+              }
+              vcfclass2count.set(i.class, vcfclass2count.get(i.class) + i.sampledata.length);
+            } else {
+            }
+          } else if (i.dt == dtitd) {
+            itdcount++;
+          } else if (i.dt == dtsv) {
+            svcount++;
+          } else if (i.dt == dtfusionrna) {
+            fusioncount++;
+          }
+        }
+        if (vcfclass2count.size + itdcount + svcount + fusioncount > 0) {
+          const row = h.append("div").style("margin-bottom", "5px").style("white-space", "nowrap");
+          for (const [classname, count] of vcfclass2count) {
+            const c = mclass[classname];
+            const cell = row.append("div").style("display", "inline-block").style("margin-right", "20px");
+            cell.append("span").attr("class", "sja_mcdot").style("background", c.color).text(count);
+            cell.append("span").text(c.label).style("color", c.color);
+          }
+          if (itdcount) {
+            const cell = row.append("div").style("display", "inline-block").style("margin-right", "20px");
+            cell.append("span").attr("class", "sja_mcdot").style("background", f.itd.color).text(itdcount);
+            cell.append("span").text("ITD");
+          }
+          if (svcount) {
+            const cell = row.append("div").style("display", "inline-block").style("margin-right", "20px");
+            cell.append("span").attr("class", "sja_mcdot").style("background", f.sv.color).text(svcount);
+            cell.append("span").text("SV");
+          }
+          if (fusioncount) {
+            const cell = row.append("div").style("display", "inline-block").style("margin-right", "20px");
+            cell.append("span").attr("class", "sja_mcdot").style("background", f.fusion.color).text(fusioncount);
+            cell.append("span").text("Fusion");
+          }
+        }
+        continue;
+      }
+      if (f.issampleattribute) {
+        const value2count = /* @__PURE__ */ new Map();
+        for (const sample of this.samples) {
+          const anno = f.items.find((i) => i.sample == sample.name);
+          if (anno) {
+            value2count.set(anno.value, (value2count.get(anno.value) || 0) + 1);
+          }
+        }
+        for (const [value, count] of value2count) {
+          const cell = h.append("div").style("display", "inline-block").style("margin-right", "20px");
+          cell.append("span").attr("class", "sja_mcdot").style("background", f.values[value].color).text(count);
+          cell.append("span").text(f.values[value].name);
+        }
+        continue;
+      }
+      throw "unknown feature type in making legend";
+    }
+    this.makeGlobalCnvLohLegend();
+  }
+  makeGlobalCnvLohLegend() {
+    const legend_data = [
+      { type: "cnv", legend_label: "CNV log2(ratio): " },
+      { type: "loh", legend_label: "LOH seg.mean: " }
+    ];
+    const min_cnv_orig = parseFloat(this.min_cnv.toFixed(3));
+    const max_cnv_orig = parseFloat(this.max_cnv.toFixed(3));
+    const min_loh_orig = parseFloat(this.min_loh.toFixed(3));
+    const max_loh_orig = parseFloat(this.max_loh.toFixed(3));
+    let changed_flag = false;
+    legend_data.forEach((data) => {
+      let min_cutoff = data.type == "cnv" ? this.min_cnv : this.min_loh;
+      let max_cutoff = data.type == "cnv" ? this.max_cnv : this.max_loh;
+      const td = data.type == "cnv" ? this.legendtable.cnv_td : this.legendtable.loh_td;
+      const row = td.append("div").style("margin-bottom", "5px");
+      row.append("span").text(data.legend_label);
+      const lower_range_txt = row.append("span").text(min_cutoff.toFixed(3));
+      const lower_range_input = row.append("input").attr("type", "text").attr("size", 8).style("display", "none").property("value", min_cutoff.toFixed(3));
+      if (data.type == "cnv") {
+        row.append("div").style("margin", "4px 0 1px 10px").style("display", "inline-block").style("width", "50px").style("height", "15px").style("background", "linear-gradient( to right," + this.cnv_colorloss + ",white)");
+      }
+      row.append("div").style("margin", "4px 10px 1px 10px").style("margin-left", data.type == "cnv" ? "0" : "10px").style("display", "inline-block").style("width", data.type == "cnv" ? "50px" : "100px").style("height", "15px").style(
+        "background",
+        "linear-gradient( to right, white, " + (data.type == "cnv" ? this.cnv_colorgain : this.loh_color) + ")"
+      );
+      const upper_range_txt = row.append("span").text(max_cutoff.toFixed(3));
+      const upper_range_input = row.append("input").attr("type", "text").attr("size", 8).style("display", "none").property("value", max_cutoff.toFixed(3));
+      const edit_btn = row.append("button").style("margin", "2px 5px").style("padding", "3px 10px").text("Edit").on("click", () => {
+        lower_range_txt.style("display", "none");
+        upper_range_txt.style("display", "none");
+        lower_range_input.style("display", "inline-block");
+        upper_range_input.style("display", "inline-block");
+        edit_btn.style("display", "none");
+        submit_btn.style("display", "inline-block");
+      });
+      const submit_btn = row.append("button").style("display", "none").style("margin", "2px 5px").style("padding", "3px 10px").text("Submit").on("click", () => {
+        if (data.type == "cnv") {
+          this.min_cnv = min_cutoff = lower_range_input.property("value");
+          this.max_cnv = max_cutoff = upper_range_input.property("value");
+          if (this.min_cnv != min_cnv_orig || this.max_cnv != max_cnv_orig) changed_flag = true;
+        } else {
+          this.min_loh = min_cutoff = parseFloat(lower_range_input.property("value"));
+          this.max_loh = max_cutoff = parseFloat(upper_range_input.property("value"));
+          if (this.min_loh != min_loh_orig || this.max_loh != max_loh_orig) changed_flag = true;
+        }
+        lower_range_txt.style("display", "inline-block").text(parseFloat(min_cutoff).toFixed(3));
+        upper_range_txt.style("display", "inline-block").text(parseFloat(max_cutoff).toFixed(3));
+        lower_range_input.style("display", "none");
+        upper_range_input.style("display", "none");
+        edit_btn.style("display", "inline-block");
+        submit_btn.style("display", "none");
+        reset_btn.style("display", changed_flag ? "inline-block" : "none");
+        this.draw_matrix();
+      });
+      const reset_btn = row.append("button").style("display", "none").style("margin", "2px 5px").style("padding", "3px 10px").text("Reset").on("click", () => {
+        if (data.type == "cnv") {
+          this.min_cnv = min_cutoff = min_cnv_orig;
+          this.max_cnv = max_cutoff = max_cnv_orig;
+        } else {
+          this.min_loh = min_cutoff = min_loh_orig;
+          this.max_loh = max_cutoff = max_loh_orig;
+        }
+        lower_range_txt.text(parseFloat(min_cutoff).toFixed(3));
+        upper_range_txt.text(parseFloat(max_cutoff).toFixed(3));
+        lower_range_input.property("value", parseFloat(min_cutoff).toFixed(3));
+        upper_range_input.property("value", parseFloat(max_cutoff).toFixed(3));
+        reset_btn.style("display", "none");
+        changed_flag = false;
+        this.draw_matrix();
+      });
+      reset_btn.style("display", "none");
+    });
+  }
+  gatherSamplesFromFeatureData() {
+    const name2sample = /* @__PURE__ */ new Map();
+    for (const feature of this.features) {
+      if (feature.donotaddsample) {
+        continue;
+      }
+      if (feature.isgenevalue || feature.iscnv || feature.isloh || feature.isitd || feature.issvfusion || feature.issvcnv) {
+        for (const item of feature.items) {
+          if (!name2sample.has(item.sample)) {
+            name2sample.set(item.sample, {});
+          }
+        }
+      } else if (feature.isvcf) {
+        for (const m of feature.items) {
+          if (m.dt == dtsnvindel) {
+            if (!m.sampledata) continue;
+            for (const s of m.sampledata) {
+              if (!name2sample.has(s.sampleobj.name)) {
+                name2sample.set(s.sampleobj.name, {});
+              }
+            }
+          } else {
+            console.error("unsupported dt from isvcf: " + m.dt);
+          }
+        }
+      } else if (feature.ismutation) {
+        for (const m of feature.items) {
+          if (m.dt == dtsnvindel) {
+            if (!m.sampledata) continue;
+            for (const s of m.sampledata) {
+              if (!name2sample.has(s.sampleobj.name)) {
+                name2sample.set(s.sampleobj.name, {});
+              }
+            }
+          } else {
+            if (!m.sample) continue;
+            if (!name2sample.has(m.sample)) {
+              name2sample.set(m.sample, {});
+            }
+          }
+        }
+      } else if (feature.issampleattribute) {
+        for (const i of feature.items) {
+          if (!name2sample.has(i.sample)) {
+            name2sample.set(i.sample, {});
+          }
+        }
+      } else {
+        console.error("unknown feature type from this.data");
+      }
+    }
+    const uniformheight = Math.min(18, Math.max(1, Math.ceil(800 / name2sample.size)));
+    this.samples = [];
+    for (const [n, sample] of name2sample) {
+      if (!this.features_on_rows) sample.height = uniformheight;
+      else sample.width = uniformheight;
+      sample.name = n;
+      this.samples.push(sample);
+    }
+  }
+  /*********** __draw *****/
+  draw_matrix() {
+    this.svg.selectAll("*").remove();
+    const svgg = this.svg.append("g");
+    this.gatherSamplesFromFeatureData();
+    this.sortsamplesbyfeatures();
+    const rows_lst = this.features_on_rows ? this.features : this.samples;
+    const cols_lst = this.features_on_rows ? this.samples : this.features;
+    let y = 0, samplenamemaxwidth = 0;
+    for (const r of rows_lst) {
+      r.g = svgg.append("g").attr("transform", "translate(0," + y + ")");
+      y += r.height + this.rowspace;
+      if (r.height >= minheight2showname) {
+        r.g.append("text").attr("font-family", font).attr("font-size", Math.min(16, r.height)).attr("text-anchor", "end").attr("dominant-baseline", "central").attr("x", -this.rowlabspace - this.rowlabticksize).attr("y", r.height / 2).text(this.features_on_rows ? r.label + (r.count ? " (" + r.count + ")" : "") : r.name).each(function() {
+          samplenamemaxwidth = Math.max(samplenamemaxwidth, this.getBBox().width);
+        }).attr("class", "sja_clbtext").on("mouseover", () => {
+          this.features_on_rows ? this.showTip_feature(r) : this.showTip_sample(r);
+        }).on("mouseout", () => {
+          this.tip.hide();
+        }).on("click", () => {
+          if (this.features_on_rows) this.showMenu_feature(r);
+        });
+        r.g.append("line").attr("x1", -this.rowlabticksize).attr("y1", r.height / 2).attr("y2", r.height / 2).attr("stroke", "black").attr("shape-rendering", "crispEdges");
+      }
+    }
+    let x = 0, featurenamemaxwidth = 0;
+    for (const c of cols_lst) {
+      const g = svgg.append("g").attr("transform", "translate(" + (x + c.width / 2) + ",-" + (this.collabspace + this.collabticksize) + ")");
+      x += c.width + this.colspace;
+      const label = g.append("text").attr("font-family", font).attr("font-size", Math.min(16, c.width - 2)).attr("dominant-baseline", "central").attr("transform", "rotate(-90)").text(this.features_on_rows ? c.name : c.label + (c.count ? " (" + c.count + ")" : "")).each(function() {
+        featurenamemaxwidth = Math.max(featurenamemaxwidth, this.getBBox().width);
+      }).on("mouseover", () => {
+        this.features_on_rows ? this.showTip_sample(c) : this.showTip_feature(c);
+      }).on("mouseout", () => {
+        this.tip.hide();
+      }).on("click", () => {
+        if (!this.features_on_rows) this.showMenu_feature(c);
+      });
+      if (c.isgenevalue) {
+        label.attr("fill", c.color);
+      }
+      g.append("line").attr("y1", this.collabspace).attr("y2", this.collabspace + this.collabticksize).attr("stroke", "black").attr("shape-rendering", "crispEdges");
+    }
+    for (const r of rows_lst) {
+      let x2 = 0;
+      for (const c of cols_lst) {
+        const sample = this.features_on_rows ? c : r;
+        const feature = this.features_on_rows ? r : c;
+        const cell = r.g.append("g").attr("transform", "translate(" + x2 + ",0)");
+        x2 += c.width + this.colspace;
+        if (feature.isgenevalue) {
+          this.drawCell_isgenevalue(sample, feature, cell);
+        } else if (feature.iscnv) {
+          this.drawCell_iscnv(sample, feature, cell);
+        } else if (feature.isloh) {
+          this.drawCell_isloh(sample, feature, cell);
+        } else if (feature.isvcf) {
+          this.drawCell_isvcf(sample, feature, cell);
+        } else if (feature.isitd) {
+          this.drawCell_isitd(sample, feature, cell);
+        } else if (feature.issvfusion) {
+          this.drawCell_issvfusion(sample, feature, cell);
+        } else if (feature.issvcnv || feature.ismutation) {
+          this.drawCell_ismutation(sample, feature, cell);
+        } else if (feature.issampleattribute) {
+          this.drawCell_issampleattribute(sample, feature, cell);
+        } else {
+          console.error("unknown feature type when drawing cell");
+        }
+      }
+    }
+    svgg.attr(
+      "transform",
+      "translate(" + (samplenamemaxwidth + this.rowlabspace + this.rowlabticksize) + "," + (featurenamemaxwidth + this.collabspace + this.collabticksize) + ")"
+    );
+    this.svg.attr(
+      "width",
+      samplenamemaxwidth + this.rowlabspace + this.rowlabticksize + cols_lst.reduce((i, j) => i + j.width, 0) + cols_lst.length * this.colspace
+    ).attr(
+      "height",
+      featurenamemaxwidth + this.collabspace + this.collabticksize + rows_lst.reduce((i, j) => i + j.height, 0) + rows_lst.length * this.rowspace
+    );
+  }
+  drawCell_isgenevalue(sample, feature, g) {
+    const height = this.features_on_rows ? feature.height : sample.height;
+    const width = this.features_on_rows ? sample.width : feature.width;
+    const item = feature.items.find((i) => i.sample == sample.name);
+    if (!item) {
+      this.drawEmptycell(sample, feature, g);
+      return;
+    }
+    const rect = g.append("rect").attr("width", width).attr("height", height).attr("fill", feature.color).attr("stroke", "#ccc").attr("stroke-opacity", 0).attr("shape-rendering", "crispEdges").on("mouseover", (event2) => {
+      event2.target.setAttribute("stroke-opacity", 1);
+      this.showTip_cell(sample, feature);
+    }).on("mouseout", (event2) => {
+      event2.target.setAttribute("stroke-opacity", 0);
+      this.tip.hide();
+    }).on("click", () => {
+      this.click_cell(sample, feature);
+    });
+    if (item.value < feature.scale.maxv) {
+      rect.attr("fill-opacity", item.value / feature.scale.maxv);
+    }
+  }
+  drawCell_iscnv(sample, feature, g) {
+    const height = this.features_on_rows ? feature.height : sample.height;
+    const width = this.features_on_rows ? sample.width : feature.width;
+    const items = feature.items.filter((i) => i.sample == sample.name);
+    if (items.length == 0) {
+      this.drawEmptycell(sample, feature, g);
+      return;
+    }
+    for (const item of items) {
+      const x1 = feature.coordscale(Math.max(feature.start, item.start));
+      const x2 = feature.coordscale(Math.min(feature.stop, item.stop));
+      const maxabslogratio = this.max_cnv;
+      g.append("rect").attr("x", x1).attr("width", Math.max(1, x2 - x1)).attr("height", sample.height).attr("fill", item.value > 0 ? feature.colorgain : feature.colorloss).attr("fill-opacity", Math.abs(item.value / maxabslogratio)).attr("shape-rendering", "crispEdges");
+    }
+    g.append("rect").attr("fill", "white").attr("fill-opacity", 0).attr("width", width).attr("height", height).attr("stroke", "#ccc").attr("stroke-opacity", 0).attr("shape-rendering", "crispEdges").on("mouseover", (event2) => {
+      event2.target.setAttribute("stroke-opacity", 1);
+      this.showTip_cell(sample, feature);
+    }).on("mouseout", (event2) => {
+      event2.target.setAttribute("stroke-opacity", 0);
+      this.tip.hide();
+    }).on("click", () => {
+      this.click_cell(sample, feature);
+    });
+  }
+  drawCell_isloh(sample, feature, g) {
+    const height = this.features_on_rows ? feature.height : sample.height;
+    const width = this.features_on_rows ? sample.width : feature.width;
+    const items = feature.items.filter((i) => i.sample == sample.name);
+    if (items.length == 0) {
+      this.drawEmptycell(sample, feature, g);
+      return;
+    }
+    for (const item of items) {
+      const x1 = feature.coordscale(Math.max(feature.start, item.start));
+      const x2 = feature.coordscale(Math.min(feature.stop, item.stop));
+      const loh_range = this.max_loh - this.min_loh;
+      g.append("rect").attr("x", this.features_on_rows ? 0 : x1).attr("y", this.features_on_rows ? x1 : 0).attr("width", this.features_on_rows ? width : Math.max(1, x2 - x1)).attr("height", this.features_on_rows ? Math.max(1, x2 - x1) : height).attr("fill", feature.color).attr("fill-opacity", (item.segmean - this.min_loh) / loh_range).attr("shape-rendering", "crispEdges");
+    }
+    g.append("rect").attr("fill", "white").attr("fill-opacity", 0).attr("width", width).attr("height", height).attr("stroke", "#ccc").attr("stroke-opacity", 0).attr("shape-rendering", "crispEdges").on("mouseover", (event2) => {
+      event2.target.setAttribute("stroke-opacity", 1);
+      this.showTip_cell(sample, feature);
+    }).on("mouseout", (event2) => {
+      event2.target.setAttribute("stroke-opacity", 0);
+      this.tip.hide();
+    }).on("click", () => {
+      this.click_cell(sample, feature);
+    });
+  }
+  drawCell_isvcf(sample, feature, g) {
+    const height = this.features_on_rows ? feature.height : sample.height;
+    const width = this.features_on_rows ? sample.width : feature.width;
+    const mlst = getitemforsample_vcf(feature, sample);
+    if (mlst.length == 0) {
+      this.drawEmptycell(sample, feature, g);
+      return;
+    }
+    const class2count = /* @__PURE__ */ new Map();
+    for (const m of mlst) {
+      if (!class2count.has(m.class)) {
+        class2count.set(m.class, 0);
+      }
+      class2count.set(m.class, class2count.get(m.class) + 1);
+    }
+    let start = 0;
+    for (const [cname, count] of class2count) {
+      const span = count / mlst.length * this.features_on_rows ? height : width;
+      g.append("rect").attr("x", this.features_on_rows ? 0 : start).attr("y", this.features_on_rows ? start : 0).attr("width", this.features_on_rows ? width : span).attr("height", this.features_on_rows ? span : height).attr("fill", mclass[cname].color).attr("shape-rendering", "crispEdges");
+      start += span;
+    }
+    g.append("rect").attr("fill", "white").attr("fill-opacity", 0).attr("width", width).attr("height", height).attr("stroke", "#ccc").attr("stroke-opacity", 0).attr("shape-rendering", "crispEdges").on("mouseover", (event2) => {
+      event2.target.setAttribute("stroke-opacity", 1);
+      this.showTip_cell(sample, feature);
+    }).on("mouseout", (event2) => {
+      event2.target.setAttribute("stroke-opacity", 0);
+      this.tip.hide();
+    }).on("click", () => {
+      this.click_cell(sample, feature);
+    });
+  }
+  drawCell_isitd(sample, feature, g) {
+    const height = this.features_on_rows ? feature.height : sample.height;
+    const width = this.features_on_rows ? sample.width : feature.width;
+    const item = feature.items.find((i) => i.sample == sample.name);
+    if (!item) {
+      this.drawEmptycell(sample, feature, g);
+      return;
+    }
+    g.append("rect").attr("width", width).attr("height", height).attr("fill", feature.color).attr("stroke", "#ccc").attr("stroke-opacity", 0).attr("shape-rendering", "crispEdges").on("mouseover", (event2) => {
+      event2.target.setAttribute("stroke-opacity", 1);
+      this.showTip_cell(sample, feature);
+    }).on("mouseout", (event2) => {
+      event2.target.setAttribute("stroke-opacity", 0);
+      this.tip.hide();
+    }).on("click", () => {
+      this.click_cell(sample, feature);
+    });
+  }
+  drawCell_issampleattribute(sample, feature, g) {
+    const height = this.features_on_rows ? feature.height : sample.height;
+    const width = this.features_on_rows ? sample.width : feature.width;
+    const item = feature.items.find((i) => i.sample == sample.name);
+    if (!item) {
+      this.drawEmptycell(sample, feature, g);
+      return;
+    }
+    g.append("rect").attr("width", width).attr("height", height).attr("fill", feature.values[item.value].color).attr("stroke", "#ccc").attr("stroke-opacity", 0).attr("shape-rendering", "crispEdges").on("mouseover", (event2) => {
+      event2.target.setAttribute("stroke-opacity", 1);
+      this.showTip_cell(sample, feature);
+    }).on("mouseout", (event2) => {
+      event2.target.setAttribute("stroke-opacity", 0);
+      this.tip.hide();
+    }).on("click", () => {
+      this.click_cell(sample, feature);
+    });
+  }
+  drawCell_issvfusion(sample, feature, g) {
+    const height = this.features_on_rows ? feature.height : sample.height;
+    const width = this.features_on_rows ? sample.width : feature.width;
+    const item = feature.items.find((i) => i.sample == sample.name);
+    if (!item) {
+      this.drawEmptycell(sample, feature, g);
+      return;
+    }
+    g.append("rect").attr("width", width).attr("height", height).attr("fill", feature.color).attr("stroke", "#ccc").attr("stroke-opacity", 0).attr("shape-rendering", "crispEdges").on("mouseover", (event2) => {
+      event2.target.setAttribute("stroke-opacity", 1);
+      this.showTip_cell(sample, feature);
+    }).on("mouseout", (event2) => {
+      event2.target.setAttribute("stroke-opacity", 0);
+      this.tip.hide();
+    }).on("click", () => {
+      this.click_cell(sample, feature);
+    });
+  }
+  drawCell_ismutation(sample, feature, g) {
+    const [cnv, loh, itd, sv, fusion, snvindel] = getitemforsample_compound(feature, sample);
+    const height = this.features_on_rows ? feature.height : sample.height;
+    const width = this.features_on_rows ? sample.width : feature.width;
+    if (cnv.length + loh.length + itd.length + sv.length + fusion.length + snvindel.length == 0) {
+      this.drawEmptycell(sample, feature, g);
+      return;
+    }
+    let is_symbolic = false;
+    if (this.ismutation_allsymbolic) {
+      is_symbolic = true;
+    } else if (this.ismutation_allnotsymbolic) {
+    } else {
+      if (height <= 4) {
+        is_symbolic = true;
+      }
+    }
+    if (is_symbolic) {
+      this.drawCell_ismutation_symbolic(sample, feature, g, cnv, loh, itd, sv, fusion, snvindel);
+    } else {
+      if (loh.length) {
+        for (const item of loh) {
+          const x1 = feature.coordscale(Math.max(feature.start, item.start));
+          const x2 = feature.coordscale(Math.min(feature.stop, item.stop));
+          const loh_range = this.max_loh - this.min_loh;
+          g.append("rect").attr("x", this.features_on_rows ? 0 : x1).attr("y", this.features_on_rows ? x1 : 0).attr("width", this.features_on_rows ? width : Math.max(1, x2 - x1)).attr("height", this.features_on_rows ? Math.max(1, x2 - x1) : height).attr("fill", feature.loh.color).attr("fill-opacity", (item.segmean - this.min_loh) / loh_range).attr("shape-rendering", "crispEdges");
+        }
+      }
+      if (cnv.length) {
+        for (const item of cnv) {
+          const x1 = feature.coordscale(Math.max(feature.start, item.start));
+          const x2 = feature.coordscale(Math.min(feature.stop, item.stop));
+          const maxabslogratio = item.value > 0 ? this.max_cnv : this.min_cnv;
+          g.append("rect").attr("x", this.features_on_rows ? 0 : x1).attr("y", this.features_on_rows ? x1 : 0).attr("width", this.features_on_rows ? width : Math.max(1, x2 - x1)).attr("height", this.features_on_rows ? Math.max(1, x2 - x1) : height).attr("fill", item.value > 0 ? feature.cnv.colorgain : feature.cnv.colorloss).attr("fill-opacity", Math.abs(item.value / maxabslogratio)).attr("shape-rendering", "crispEdges");
+        }
+      }
+      if (itd.length) {
+        for (const item of itd) {
+          const x1 = feature.coordscale(Math.max(feature.start, item.start));
+          const x2 = feature.coordscale(Math.min(feature.stop, item.stop));
+          g.append("rect").attr("x", this.features_on_rows ? 0 : x1).attr("y", this.features_on_rows ? x1 : 0).attr("width", this.features_on_rows ? width : Math.max(1, x2 - x1)).attr("height", this.features_on_rows ? Math.max(1, x2 - x1) : height).attr("fill", feature.itd.color).attr("shape-rendering", "crispEdges");
+        }
+      }
+      if (sv.length) {
+        g.append("circle").attr("cx", width / 2).attr("cy", height / 2).attr("r", Math.min(width, height) / 2).attr("stroke", feature.sv.color).attr("fill", "none");
+      }
+      if (fusion.length) {
+        g.append("circle").attr("cx", width / 2).attr("cy", height / 2).attr("r", Math.min(width, height) / 2).attr("stroke", feature.fusion.color).attr("fill", "none");
+      }
+      if (snvindel.length) {
+        const m = snvindel[0];
+        const g2 = g.append("g").attr("transform", "translate(" + width / 2 + "," + height / 2 + ")");
+        const color = mclass[m.m.class].color;
+        const w = Math.min(width, height) / 2;
+        g2.append("line").attr("x1", -w).attr("x2", w).attr("y1", -w).attr("y2", w).attr("stroke", "white").attr("stroke-width", 3);
+        g2.append("line").attr("x1", -w).attr("x2", w).attr("y1", w).attr("y2", -w).attr("stroke", "white").attr("stroke-width", 3);
+        g2.append("line").attr("x1", -w).attr("x2", w).attr("y1", -w).attr("y2", w).attr("stroke", color);
+        g2.append("line").attr("x1", -w).attr("x2", w).attr("y1", w).attr("y2", -w).attr("stroke", color);
+      }
+    }
+    g.append("rect").attr("width", width).attr("height", height).attr("fill", "white").attr("fill-opacity", 0).attr("stroke", "#ccc").attr("stroke-opacity", 0).attr("shape-rendering", "crispEdges").on("mouseover", (event2) => {
+      event2.target.setAttribute("stroke-opacity", 1);
+      this.showTip_cell(sample, feature);
+    }).on("mouseout", (event2) => {
+      event2.target.setAttribute("stroke-opacity", 0);
+      this.tip.hide();
+    }).on("click", () => {
+      this.click_cell(sample, feature);
+    });
+  }
+  drawCell_ismutation_symbolic(sample, feature, g, cnv, loh, itd, sv, fusion, snvindel) {
+    const height = this.features_on_rows ? feature.height : sample.height;
+    const width = this.features_on_rows ? sample.width : feature.width;
+    const loh_range = this.max_loh - this.min_loh;
+    const lst = [];
+    if (cnv.length) {
+      for (const i of cnv) {
+        const maxabslogratio = i.value > 0 ? this.max_cnv : this.min_cnv;
+        let k;
+        if (i.value > 0) {
+          k = { color: feature.cnv.colorgain };
+        } else {
+          k = { color: feature.cnv.colorloss };
+        }
+        k.opacity = Math.abs(i.value / maxabslogratio);
+        lst.push(k);
+      }
+    }
+    if (loh.length) {
+      for (const i of loh) {
+        lst.push({
+          color: feature.loh.color,
+          opacity: (i.segmean - this.min_loh) / loh_range
+        });
+      }
+    }
+    if (itd.length) {
+      for (const i of itd) {
+        lst.push({ color: feature.itd.color });
+      }
+    }
+    if (sv.length) {
+      for (const i of sv) {
+        lst.push({ color: feature.sv.color });
+      }
+    }
+    if (fusion.length) {
+      for (const i of fusion) {
+        lst.push({ color: feature.fusion.color });
+      }
+    }
+    if (snvindel.length) {
+      for (const i of snvindel) {
+        lst.push({ color: mclass[i.m.class].color });
+      }
+    }
+    const f_len = this.features_on_rows ? height / lst.length : width / lst.length;
+    let f_start = 0;
+    for (const i of lst) {
+      const r = g.append("rect").attr("x", this.features_on_rows ? 0 : f_start).attr("y", this.features_on_rows ? f_start : 0).attr("width", this.features_on_rows ? width : f_len).attr("height", this.features_on_rows ? f_len : height).attr("fill", i.color).attr("shape-rendering", "crispEdges");
+      if (i.opacity) r.attr("opacity", i.opacity);
+      f_start += f_len;
+    }
+  }
+  // __newattr draw cell for new feature
+  /*********** __draw ends *****/
+  async click_cell(sample, feature) {
+    try {
+      let svcnvtk;
+      if (this.iscustom) {
+        svcnvtk = {
+          iscustom: true,
+          type: tkt.mdssvcnv,
+          singlesample: {
+            name: sample.name
+          }
+        };
+        for (const k in this.querykey2tracks) {
+          const t = this.querykey2tracks[k];
+          if (t.type == tkt.mdssvcnv) {
+            svcnvtk.name = t.name || "Custom tk";
+            svcnvtk.file = t.file;
+            svcnvtk.url = t.url;
+            svcnvtk.indexURL = t.indexURL;
+          } else if (t.type == tkt.mdsvcf) {
+            svcnvtk.checkvcf = {
+              file: t.file,
+              url: t.url,
+              indexURL: t.indexURL
+            };
+          } else if (t.type == tkt.mdsexpression) {
+            svcnvtk.checkexpressionrank = {
+              file: t.file,
+              url: t.url,
+              indexURL: t.indexURL
+            };
+          }
+        }
+      } else {
+        if (!this.mds) throw "not custom but .mds{} missing";
+        for (const querykey in this.mds.queries) {
+          const tk = this.mds.queries[querykey];
+          if (tk.type == tkt.mdssvcnv) {
+            svcnvtk = {
+              mds: this.mds,
+              querykey,
+              singlesample: {
+                name: sample.name
+              }
+            };
+            for (const k in tk) svcnvtk[k] = tk[k];
+            break;
+          }
+        }
+      }
+      if (!svcnvtk) throw "cannot find a svcnv tk";
+      svcnvtk.bplengthUpperLimit = 0;
+      const pane = newpane({ x: 100, y: 100 });
+      const blockarg = {
+        jwt: this.jwt,
+        hostURL: this.hostURL,
+        nobox: 1,
+        genome: this.genome,
+        holder: pane.body,
+        chr: feature.chr,
+        start: feature.start,
+        stop: feature.stop,
+        tklst: []
+      };
+      first_genetrack_tolist(this.genome, blockarg.tklst);
+      blockarg.tklst.push(svcnvtk);
+      if (!this.iscustom) {
+        if (!this.dslabel) throw "not custom but dslabel missing";
+        const par = {
+          genome: this.genome.name,
+          dslabel: this.dslabel,
+          querykey: svcnvtk.querykey,
+          gettrack4singlesample: sample.name
+        };
+        const data = await dofetch("/mdssvcnv", par);
+        if (data.error) throw "Error checking for assay track: " + data.error;
+        if (data.tracks) {
+          for (const t of data.tracks) blockarg.tklst.push(t);
+        }
+      }
+      const _ = await import("./block-QLSIELXK.js");
+      new _.Block(blockarg);
+    } catch (e) {
+      window.alert(e.message || e);
+      if (e.stack) console.log(e.stack);
+    }
+  }
+  /********** __menu and tooltip **********/
+  showTip_feature(f) {
+    this.tip.clear();
+    this.tipContent_feature(f, this.tip.d);
+    this.tip.showunder(event.target);
+  }
+  showMenu_feature(f) {
+    this.menu.showunder(event.target).clear();
+    this.tipContent_feature(f, this.menu.d);
+    this.menu.d.append("div").attr("class", "sja_menuoption").text("Remove this feature").on("click", () => {
+      this.menu.hide();
+      f.legend_tr.remove();
+      this.features.splice(
+        this.features.findIndex((i) => i.id == f.id),
+        1
+      );
+      this.draw_matrix();
+    });
+    if (f.isgenevalue) return showMenu_isgenevalue(this, f);
+    if (f.iscnv) return showMenu_iscnv(this, f, f);
+    if (f.isloh) return showMenu_isloh(this, f, f);
+    if (f.ismutation) return showMenu_ismutation(this, f);
+    if (f.isitd) {
+      return;
+    }
+    if (f.issvfusion) {
+      return;
+    }
+    if (f.issvcnv) {
+      return;
+    }
+    if (f.issampleattribute) {
+      return;
+    }
+  }
+  tipContent_feature(f, holder) {
+    holder.append("div").text(f.label).style("opacity", 0.5).style("font-size", ".7em").style("margin", "10px");
+    if (f.isgenevalue || f.iscnv || f.isloh || f.isitd || f.issvfusion) {
+      holder.append("div").html(f.chr + ":" + f.start + "-" + f.stop + " &nbsp; " + bplen(f.stop - f.start)).style("font-size", ".7em").style("opacity", 0.5).style("margin", "0px 10px 10px 10px");
+    } else if (f.issvcnv || f.ismutation) {
+      if (!f.genename) {
+        holder.append("div").html(f.chr + ":" + f.start + "-" + f.stop + " &nbsp; " + bplen(f.stop - f.start)).style("font-size", ".7em").style("opacity", 0.5).style("margin", "0px 10px 10px 10px");
+      }
+    } else if (f.issampleattribute) {
+      holder.append("div").text(f.label);
+    }
+    if (f.isgenevalue) {
+      holder.append("div").text("Min: " + f.scale.minv + ", max: " + f.scale.maxv).style("font-size", ".7em").style("opacity", 0.5).style("margin", "0px 10px 10px 10px");
+    }
+  }
+  showTip_sample(sample) {
+    this.tip.clear().d.append("div").text(sample.name).style("padding", "10px").style("font-size", ".7em");
+    const lst = [];
+    for (const f of this.features) {
+      if (lst.length > 10) {
+        lst.push({ k: "more", v: "..." });
+        break;
+      }
+      if (f.isgenevalue) {
+        const v = f.items.find((i) => i.sample == sample.name);
+        lst.push({ k: f.label, v: v ? v.value : saynovalue });
+        continue;
+      }
+      if (f.iscnv) {
+        const items = f.items.filter((i) => i.sample == sample.name);
+        let text;
+        if (items.length == 0) {
+          text = saynovalue;
+        } else {
+          const lst2 = items.map((i) => {
+            return "<div>" + i.chr + ":" + i.start + "-" + i.stop + ' <span style="font-size:.7em">' + bplen(i.stop - i.start) + '</span> <span style="font-size:.8em;background:' + (i.value > 0 ? f.colorgain : f.colorloss) + ';color:white;padding:1px 5px">' + i.value + "</span></div>";
+          });
+          text = lst2.join("");
+        }
+        lst.push({ k: f.label, v: text });
+        continue;
+      }
+      if (f.isloh) {
+        const items = f.items.filter((i) => i.sample == sample.name);
+        let text;
+        if (items.length == 0) {
+          text = saynovalue;
+        } else {
+          const lst2 = items.map((i) => {
+            return "<div>" + i.chr + ":" + i.start + "-" + i.stop + ' <span style="font-size:.7em">' + bplen(i.stop - i.start) + '</span> <span style="font-size:.8em;background:' + f.color + ';color:white;padding:1px 5px">' + i.segmean + "</span></div>";
+          });
+          text = lst2.join("");
+        }
+        lst.push({ k: f.label, v: text });
+        continue;
+      }
+      if (f.isvcf) {
+        const mlst = getitemforsample_vcf(f, sample);
+        let text;
+        if (mlst.length == 0) {
+          text = saynovalue;
+        } else {
+          text = mlst.map((m) => {
+            return '<div><span style="color:' + mclass[m.class].color + '">' + m.mname + '</span> <span style="font-size:.7em;opacity:.5">' + mclass[m.class].label + "</span></div>";
+          }).join("");
+        }
+        lst.push({ k: f.label, v: text });
+        continue;
+      }
+      if (f.isitd) {
+        const items = f.items.filter((i) => i.sample == sample.name);
+        let text;
+        if (items.length == 0) {
+          text = saynovalue;
+        } else {
+          text = '<div style="background:' + f.color + ';width:20px">&nbsp;</div>';
+        }
+        lst.push({ k: f.label, v: text });
+        continue;
+      }
+      if (f.issvfusion) {
+        const items = f.items.filter((i) => i.sample == sample.name);
+        let text;
+        if (items.length == 0) {
+          text = saynovalue;
+        } else {
+          text = '<div style="background:' + f.color + ';width:20px">&nbsp;</div>';
+        }
+        lst.push({ k: f.label, v: text });
+        continue;
+      }
+      if (f.issvcnv) {
+        continue;
+      }
+      if (f.ismutation) {
+        continue;
+      }
+      if (f.issampleattribute) {
+        const item = f.items.find((i) => i.sample == sample.name);
+        if (item) {
+          lst.push({ k: f.label, v: item.value });
+        }
+        continue;
+      }
+      console.error("sample tooltip: Unknown feature type");
+    }
+    make_table_2col(this.tip.d, lst);
+    this.tip.show(event.clientX, event.clientY);
+  }
+  showTip_cell(sample, f) {
+    const lst = [{ k: "sample", v: sample.name }];
+    if (f.isgenevalue) {
+      const v = f.items.find((i) => i.sample == sample.name);
+      lst.push({ k: f.label, v: v ? v.value : saynovalue });
+    } else if (f.iscnv) {
+      const items = f.items.filter((i) => i.sample == sample.name);
+      let text;
+      if (items.length == 0) {
+        text = saynovalue;
+      } else {
+        const lst2 = items.map((i) => {
+          return "<div>" + i.chr + ":" + i.start + "-" + i.stop + ' <span style="font-size:.7em">' + bplen(i.stop - i.start) + '</span> <span style="font-size:.8em;background:' + (i.value > 0 ? f.colorgain : f.colorloss) + ';color:white;padding:1px 5px">' + i.value + "</span></div>";
+        });
+        text = lst2.join("");
+      }
+      lst.push({ k: f.label, v: text });
+    } else if (f.isloh) {
+      const items = f.items.filter((i) => i.sample == sample.name);
+      let text;
+      if (items.length == 0) {
+        text = saynovalue;
+      } else {
+        const lst2 = items.map((i) => {
+          return "<div>" + i.chr + ":" + i.start + "-" + i.stop + ' <span style="font-size:.7em">' + bplen(i.stop - i.start) + '</span> <span style="font-size:.8em;background:' + f.color + ';color:white;padding:1px 5px">' + i.segmean + "</span></div>";
+        });
+        text = lst2.join("");
+      }
+      lst.push({ k: f.label, v: text });
+    } else if (f.isvcf) {
+      const mlst = getitemforsample_vcf(f, sample);
+      let text;
+      if (mlst.length == 0) {
+        text = saynovalue;
+      } else {
+        text = mlst.map((m) => {
+          return '<div><span style="color:' + mclass[m.class].color + '">' + m.mname + '</span> <span style="font-size:.7em;opacity:.5">' + mclass[m.class].label + "</span></div>";
+        }).join("");
+      }
+      lst.push({ k: f.label, v: text });
+    } else if (f.isitd) {
+      const items = f.items.filter((i) => i.sample == sample.name);
+      let text;
+      if (items.length == 0) {
+        text = saynovalue;
+      } else {
+        const lst2 = items.map((i) => {
+          return "<div>" + i.chr + ":" + i.start + "-" + i.stop + " </div>";
+        });
+        text = lst2.join("");
+      }
+      lst.push({ k: f.label, v: text });
+    } else if (f.issvfusion) {
+      const items = f.items.filter((i) => i.sample == sample.name);
+      let text;
+      if (items.length == 0) {
+        text = saynovalue;
+      } else {
+        const lst2 = items.map((i) => {
+          return "<div>" + i.chrA + ":" + i.posA + " - " + i.chrB + ":" + i.posB + " </div>";
+        });
+        text = lst2.join("");
+      }
+      lst.push({ k: f.label, v: text });
+    } else if (f.issvcnv || f.ismutation) {
+      const [cnv, loh, itd, sv, fusion, snvindel] = getitemforsample_compound(f, sample);
+      if (cnv.length) {
+        lst.push({
+          k: (f.genename || f.label) + " CNV",
+          v: cnv.map((i) => {
+            return '<div><span style="background:' + (i.value > 0 ? f.cnv.colorgain : f.cnv.colorloss) + ';color:white;padding:0px 3px">' + i.value + '</span> <span style="font-size:.8em">' + i.chr + ":" + i.start + "-" + i.stop + " &nbsp;&nbsp;" + bplen(i.stop - i.start) + "</span></div>";
+          }).join("")
+        });
+      }
+      if (loh.length) {
+        lst.push({
+          k: (f.genename || f.label) + " LOH",
+          v: loh.map((i) => {
+            return '<div><span style="background:' + f.loh.color + ';color:white;padding:0px 3px">' + i.segmean + '</span> <span style="font-size:.8em">' + i.chr + ":" + i.start + "-" + i.stop + " &nbsp;&nbsp;" + bplen(i.stop - i.start) + "</span></div>";
+          }).join("")
+        });
+      }
+      if (itd.length) {
+        lst.push({
+          k: (f.genename || f.label) + " ITD",
+          v: itd.map((i) => {
+            return '<div style="font-size:.8em">' + i.chr + ":" + i.start + "-" + i.stop + "</div>";
+          }).join("")
+        });
+      }
+      if (sv.length) {
+        lst.push({
+          k: (f.genename || f.label) + " SV",
+          v: sv.map((i) => {
+            return "<div>" + i.chrA + ":" + i.posA + "," + i.strandA + " &gt; " + i.chrB + ":" + i.posB + "," + i.strandB + "</div>";
+          }).join("")
+        });
+      }
+      if (fusion.length) {
+        lst.push({
+          k: (f.genename || f.label) + " fusion",
+          v: fusion.map((i) => {
+            return "<div>" + i.chrA + ":" + i.posA + "," + i.strandA + " &gt; " + i.chrB + ":" + i.posB + "," + i.strandB + "</div>";
+          }).join("")
+        });
+      }
+      if (snvindel.length) {
+        lst.push({
+          k: (f.genename || f.label) + " SNV/indel",
+          v: snvindel.map((m) => {
+            const c = mclass[m.m.class];
+            return '<div><span style="color:' + c.color + '">' + (m.m.mname || "") + '</span> <span style="font-size:.7em;opacity:.5">' + c.label + "</span></div>";
+          }).join("")
+        });
+      }
+    } else if (f.issampleattribute) {
+      const item = f.items.find((i) => i.sample == sample.name);
+      if (item) {
+        lst.push({
+          k: f.label,
+          v: item.value
+        });
+      }
+    } else {
+      console.error("cell tooltip: unknown feature type");
+    }
+    this.tip.clear();
+    make_table_2col(this.tip.d, lst);
+    this.tip.show(event.clientX, event.clientY);
+  }
+  /********** __menu ends **********/
+  sortsamplesbyfeatures() {
+    const sortbygenevalue = this.features.find((f) => f.isgenevalue && f.sort);
+    if (sortbygenevalue && sortbygenevalue.items) {
+      const sample2value = /* @__PURE__ */ new Map();
+      for (const i of sortbygenevalue.items) {
+        sample2value.set(i.sample, i.value);
+      }
+      this.samples.sort((i, j) => {
+        const vi = sample2value.has(i.name) ? sample2value.get(i.name) : sortbygenevalue.missingvalue;
+        const vj = sample2value.has(j.name) ? sample2value.get(j.name) : sortbygenevalue.missingvalue;
+        return vj - vi;
+      });
+    }
+  }
+  may_init_customvcf(tk) {
+    if (tk.info) return;
+    const arg = ["genome=" + this.genome.name];
+    if (tk.file) {
+      arg.push("file=" + tk.file);
+    } else {
+      arg.push("url=" + tk.url);
+      if (tk.indexURL) arg.push("indexURL=" + tk.indexURL);
+    }
+    return dofetch2("vcfheader?" + arg.join("&")).then((data) => {
+      const [info, format, samples, errs] = vcfparsemeta(data.metastr.split("\n"));
+      if (errs) throw "Error parsing VCF meta lines: " + errs.join("; ");
+      tk.info = info;
+      tk.format = format;
+      tk.samples = samples;
+      tk.nochr = data.nochr;
+    });
+  }
+  drawEmptycell(sample, feature, g) {
+    const height = this.features_on_rows ? feature.height : sample.height;
+    const width = this.features_on_rows ? sample.width : feature.width;
+    if (height < 5) return;
+    g.append("line").attr("x2", width).attr("y2", height).attr("stroke", "#ededed");
+  }
+  // end of class
+};
+function feature2arg(f) {
+  if (f.isgenevalue) {
+    return {
+      id: f.id,
+      isgenevalue: 1,
+      querykey: f.querykey,
+      genename: f.genename,
+      chr: f.chr,
+      start: f.start,
+      stop: f.stop
+    };
+  }
+  if (f.iscnv) {
+    return {
+      id: f.id,
+      iscnv: 1,
+      querykey: f.querykey,
+      chr: f.chr,
+      start: f.start,
+      stop: f.stop,
+      valuecutoff: f.valuecutoff,
+      focalsizelimit: f.focalsizelimit
+    };
+  }
+  if (f.isloh) {
+    return {
+      id: f.id,
+      isloh: 1,
+      querykey: f.querykey,
+      chr: f.chr,
+      start: f.start,
+      stop: f.stop,
+      valuecutoff: f.valuecutoff,
+      focalsizelimit: f.focalsizelimit
+    };
+  }
+  if (f.isvcf) {
+    return {
+      id: f.id,
+      isvcf: 1,
+      querykey: f.querykey,
+      chr: f.chr,
+      start: f.start,
+      stop: f.stop,
+      snvindel: {
+        excludeclasses: f.snvindel.excludeclasses
+      }
+    };
+  }
+  if (f.isitd) {
+    return {
+      id: f.id,
+      isitd: 1,
+      querykey: f.querykey,
+      chr: f.chr,
+      start: f.start,
+      stop: f.stop
+    };
+  }
+  if (f.issvfusion) {
+    return {
+      id: f.id,
+      issvfusion: 1,
+      querykey: f.querykey,
+      chr: f.chr,
+      start: f.start,
+      stop: f.stop
+    };
+  }
+  if (f.issvcnv || f.ismutation) {
+    const arg = {
+      id: f.id,
+      chr: f.chr,
+      start: f.start,
+      stop: f.stop,
+      cnv: {
+        hidden: f.cnv.hidden,
+        valuecutoff: f.cnv.valuecutoff,
+        focalsizelimit: f.cnv.focalsizelimit
+      },
+      loh: {
+        hidden: f.loh.hidden,
+        valuecutoff: f.loh.valuecutoff,
+        focalsizelimit: f.loh.focalsizelimit
+      },
+      itd: {
+        hidden: f.itd.hidden
+      },
+      sv: {
+        hidden: f.sv.hidden
+      },
+      fusion: {
+        hidden: f.fusion.hidden
+      },
+      snvindel: {
+        excludeclasses: f.snvindel.excludeclasses
+      }
+    };
+    if (f.issvcnv) {
+      arg.issvcnv = 1;
+      arg.querykey = f.querykey;
+    } else {
+      arg.ismutation = 1;
+      arg.querykeylst = f.querykeylst;
+    }
+    return arg;
+  }
+  if (f.issampleattribute) {
+    return {
+      id: f.id,
+      issampleattribute: 1,
+      key: f.key
+    };
+  }
+  throw "unknown feature type in making request parameter";
+}
+function getitemforsample_vcf(feature, sample) {
+  const mlst = [];
+  for (const m of feature.items) {
+    if (m.dt == dtsnvindel) {
+      if (m.sampledata.findIndex((i) => i.sampleobj.name == sample.name) != -1) {
+        mlst.push(m);
+      }
+    } else {
+      console.error("getitemforsample_vcf: unknown dt");
+    }
+  }
+  return mlst;
+}
+function getitemforsample_compound(feature, sample) {
+  const cnv = [], loh = [], itd = [], sv = [], fusion = [], snvindel = [];
+  for (const item of feature.items) {
+    if (item.dt == dtsnvindel) {
+      if (!item.sampledata) continue;
+      const m_sample = item.sampledata.find((s) => s.sampleobj.name == sample.name);
+      if (!m_sample) continue;
+      snvindel.push({
+        m: item,
+        m_sample
+      });
+      continue;
+    }
+    if (item.sample != sample.name) continue;
+    if (item.dt == dtcnv) {
+      cnv.push(item);
+    } else if (item.dt == dtloh) {
+      loh.push(item);
+    } else if (item.dt == dtitd) {
+      itd.push(item);
+    } else if (item.dt == dtsv) {
+      sv.push(item);
+    } else if (item.dt == dtfusionrna) {
+      fusion.push(item);
+    } else {
+      console.error("unknown dt: " + item.dt);
+    }
+  }
+  return [cnv, loh, itd, sv, fusion, snvindel];
+}
+function initfeature_polymutation(f) {
+  if (!f.width) f.width = 20;
+  if (!f.cnv) f.cnv = {};
+  if (!f.cnv.valuecutoff) f.cnv.valuecutoff = 0.2;
+  if (!Number.isInteger(f.cnv.focalsizelimit)) f.cnv.focalsizelimit = 2e6;
+  if (!f.cnv.colorgain) f.cnv.colorgain = default_cnvgaincolor;
+  if (!f.cnv.colorloss) f.cnv.colorloss = default_cnvlosscolor;
+  if (!f.loh) f.loh = {};
+  if (!f.loh.valuecutoff) f.loh.valuecutoff = 0.1;
+  if (!Number.isInteger(f.loh.focalsizelimit)) f.loh.focalsizelimit = 2e6;
+  if (!f.loh.color) f.loh.color = default_lohcolor;
+  if (!f.itd) f.itd = {};
+  if (!f.itd.color) f.itd.color = mclass[mclassitd].color;
+  if (!f.sv) f.sv = {};
+  if (!f.sv.color) f.sv.color = default_svcolor;
+  if (!f.fusion) f.fusion = {};
+  if (!f.fusion.color) f.fusion.color = default_svcolor;
+  if (!f.snvindel) f.snvindel = {};
+  if (!f.snvindel.excludeclasses) f.snvindel.excludeclasses = {};
+}
+function init_controlui(o) {
+  const buttonrow = o.holder.append("div").style("margin-bottom", "5px");
+  const folderdiv = o.holder.append("div").style("margin-bottom", "20px");
+  buttonrow.append("span").style("margin-right", "20px").style("font-size", ".8em").text("LEGEND").attr("class", "sja_clbtext").on("click", () => {
+    if (o.legendtable.style("display") == "none") {
+      appear(o.legendtable);
+    } else {
+      disappear(o.legendtable);
+    }
+  });
+  o.legendtable = folderdiv.append("table").style("border-top", "solid 1px #ededed").style("border-bottom", "solid 1px #ededed").style("border-spacing", "10px").style("display", "none");
+  buttonrow.append("span").style("margin-right", "20px").style("font-size", ".8em").text("CONFIG").attr("class", "sja_clbtext").on("click", () => {
+    if (generalconfig.style("display") == "none") {
+      appear(generalconfig);
+    } else {
+      disappear(generalconfig);
+    }
+  });
+  const generalconfig = folderdiv.append("div").style("border-top", "solid 1px #ededed").style("border-bottom", "solid 1px #ededed").style("display", "none");
+  const row = generalconfig.append("div").style("margin", "5px");
+  row.append("div").style("vertical-align", "top").style("display", "inline-block").html("Show features as &nbsp;&nbsp;");
+  const opts_div = row.append("div").style("display", "inline-block");
+  const mutation_opts = [
+    { value: "symbol", text: "CNV on genomic location, others as symbol" },
+    { value: "proportion", text: "All features as porportion" }
+  ];
+  mutation_opts.forEach((opt) => {
+    const opt_div = opts_div.append("div");
+    opt_div.append("input").attr("type", "radio").attr("id", opt.value).attr("name", "mutaion_display").attr("value", opt.value).property(
+      "checked",
+      opt.value == "symbol" && o.ismutation_allsymbolic === void 0 && o.ismutation_allnotsymbolic === void 0 ? 1 : opt.value == "symbol" && o.ismutation_allnotsymbolic ? 1 : opt.value == "proportion" && o.ismutation_allsymbolic ? 1 : 0
+    ).on("change", function() {
+      if (opt.value == "symbol" && o.ismutation_allnotsymbolic) return;
+      else if (opt.value == "proportion" && o.ismutation_allsymbolic) return;
+      else if (opt.value == "symbol") {
+        delete o.ismutation_allsymbolic;
+        o.ismutation_allnotsymbolic = true;
+      } else if (opt.value == "proportion") {
+        o.ismutation_allsymbolic = true;
+        delete o.ismutation_allnotsymbolic;
+      } else {
+        return;
+      }
+      o.draw_matrix();
+    });
+    opt_div.append("label").attr("for", opt.value).text(opt.text);
+  });
+  const row2 = generalconfig.append("div").style("margin", "5px");
+  row2.append("div").style("vertical-align", "top").style("display", "inline-block").html("Layout of Matrix &nbsp;&nbsp;");
+  const opts_div2 = row2.append("div").style("display", "inline-block");
+  const layout_opts = [
+    { value: "gene_on_row", text: "Genes as Rows" },
+    { value: "sam_on_row", text: "Samples as Rows" }
+  ];
+  layout_opts.forEach((opt) => {
+    const opt_div = opts_div2.append("div");
+    opt_div.append("input").attr("type", "radio").attr("id", opt.value).attr("name", "layout").attr("value", opt.value).property(
+      "checked",
+      opt.value == "gene_on_row" && o.features_on_rows ? 1 : opt.value == "sam_on_row" && !o.features_on_rows ? 1 : 0
+    ).on("change", function() {
+      if (opt.value == "gene_on_row" && o.features_on_rows) return;
+      else if (opt.value == "sam_on_row" && !o.features_on_rows) return;
+      else if (opt.value == "gene_on_row") {
+        o.features_on_rows = true;
+        if (o.ori_feature_width) o.features.forEach((f) => f.height = o.ori_feature_width);
+      } else {
+        o.features_on_rows = false;
+        if (o.ori_feature_height) o.features.forEach((f) => f.width = o.ori_feature_height);
+      }
+      o.draw_matrix();
+    });
+    opt_div.append("label").attr("for", opt.value).text(opt.text);
+  });
+  buttonrow.append("span").style("margin-right", "20px").style("font-size", ".8em").text("DATA").attr("class", "sja_clbtext").on("click", () => {
+    printData(o);
+  });
+  may_add_kmplotbutton(o, buttonrow);
+}
+function printData(o) {
+  const lst = ["sample	feature	varianttype	variant"];
+  for (const s of o.samples) {
+    for (const f of o.features) {
+      for (const i of f.items) {
+        if (i.sample && i.sample == s.name || i.sampledata && i.sampledata.findIndex((i2) => i2.sampleobj.name == s.name) != -1) {
+          lst.push(s.name + "	" + f.label + "	" + dt2label[i.dt] + "	" + item2string(i));
+        }
+      }
+    }
+  }
+  export_data("Matrix data", [{ text: lst.join("\n") }]);
+}
+function item2string(i) {
+  if (i.dt == dtsnvindel)
+    return i.mname + " " + mclass[i.class].label + " " + i.chr + "." + i.pos + "." + i.ref + "." + i.alt;
+  if (i.dt == dtfusionrna || i.dt == dtsv)
+    return i.chrA + "." + i.posA + "." + (i.strandA || "") + " > " + i.chrB + "." + i.posB + "." + (i.strandB || "");
+  if (i.dt == dtcnv) return i.chr + ":" + i.start + "-" + i.stop + ", log2(ratio): " + i.value;
+  if (i.dt == dtloh) return i.chr + ":" + i.start + "-" + i.stop + ", log2(ratio): " + i.segmean;
+  if (i.dt == dtitd) return i.chr + ":" + i.start + "-" + i.stop;
+  return "";
+}
+export {
+  Samplematrix
+};
+//# sourceMappingURL=samplematrix-L2HOSLUT.js.map