@sjcrh/proteinpaint-client 2.223.0 → 2.224.0

package/dist/block.mds.junction-2R4UBHO7.js

@@ -0,0 +1,1534 @@
+import {
+  spliceevent_exonskip_getdefault_default
+} from "./chunk-CAH6LJ5Z.js";
+import {
+  legend_newrow
+} from "./chunk-5WZ3ZWZC.js";
+import "./chunk-V2OJLJSK.js";
+import "./chunk-2GWAEK4R.js";
+import {
+  appear2 as appear,
+  axisstyle,
+  disappear2 as disappear,
+  font,
+  newpane,
+  sayerror,
+  tkt
+} from "./chunk-U45YALDI.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-KZXFNO75.js";
+import {
+  Menu
+} from "./chunk-CNFTQSNE.js";
+import "./chunk-RIHO7ZD5.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import {
+  dofetch2,
+  dofetch3
+} from "./chunk-KBTFT76L.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-MHWYRNGA.js";
+import "./chunk-JHLF2ZC2.js";
+import {
+  IN_frame,
+  axisRight,
+  bplen,
+  collide_default,
+  simulation_default,
+  x_default,
+  y_default
+} from "./chunk-WJLRU5OF.js";
+import "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import {
+  linear,
+  log
+} from "./chunk-4OLM3KSB.js";
+import "./chunk-PWYMHUXY.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-HS5PO5ZQ.js";
+
+// src/block.mds.js
+function makeLegend_cohort_hierarchy(arg) {
+  for (const hierarchyname in arg.hash) {
+    const tr = arg.tk.cohortFilter.holderTable.append("tr");
+    tr.append("td").style("vertical-align", "top").append("div").text(hierarchyname).style("color", "#858585").style("margin-top", "7px");
+    const treeholder = tr.append("td").append("div").style("display", "inline-block");
+    let folderstack = [];
+    const nodesofhierarchy = [];
+    for (const node of arg.hash[hierarchyname]) {
+      if (node.depth == 0) {
+        continue;
+      }
+      if (node.depth == 1) {
+        const [folder2, showhidebutton2] = make_one_node(arg, node, treeholder, hierarchyname);
+        if (folder2) {
+          folderstack = [folder2];
+        }
+        nodesofhierarchy.push({
+          nodeid: node.id,
+          showhidebutton: showhidebutton2
+        });
+        continue;
+      }
+      const itsholder = folderstack[node.depth - 2];
+      const [folder, showhidebutton] = make_one_node(arg, node, itsholder, hierarchyname);
+      if (folder) {
+        folderstack[node.depth - 1] = folder;
+      }
+      nodesofhierarchy.push({
+        nodeid: node.id,
+        showhidebutton
+      });
+    }
+    arg.tk.cohortFilter.hierarchies.keys[hierarchyname].allnodes = nodesofhierarchy;
+  }
+}
+function make_one_node(arg, node, holder, hierarchyname) {
+  const row = holder.append("div");
+  const labeldiv = row.append("div").style("display", "inline-block").style("margin-right", "10px");
+  arg.makenodelabel(node, labeldiv);
+  const showhidebutton = row.append("div").style("display", "inline-block").attr("class", "sja_handle_green").text("SHOW").style("font-size", ".8em").on("mousedown", (event) => {
+    event.stopPropagation();
+  }).on("click", (event) => {
+    event.stopPropagation();
+    arg.clicknode(node, hierarchyname);
+  });
+  if (arg.tk.subTracks.find((i) => i.permanentHierarchy.nodeid == node.id)) {
+    showhidebutton.text("HIDE").attr("class", "sja_handle_red");
+  }
+  let folder;
+  if (node.isleaf) {
+    row.style("padding", "5px 10px");
+  } else {
+    row.attr("class", "sja_clb").on("click", () => {
+      if (folder.style("display") == "none") {
+        arg.tk.cohortFilter.hierarchies.keys[hierarchyname].opennodeids.add(node.id);
+        appear(folder);
+        return;
+      }
+      disappear(folder);
+      arg.tk.cohortFilter.hierarchies.keys[hierarchyname].opennodeids.delete(node.id);
+    });
+    folder = holder.append("div").style("display", arg.tk.cohortFilter.hierarchies.keys[hierarchyname].opennodeids.has(node.id) ? "block" : "none").style("margin-left", "20px").style("border-left", "solid 1px " + arg.block.legend.legendcolor).style("padding-left", "5px").style("background", "white");
+  }
+  return [folder, showhidebutton];
+}
+function showHideSubtrack_byHierarchyLevel(parentTk, block, hierarchy) {
+  const arridx = parentTk.subTracks.findIndex((i) => i.permanentHierarchy.nodeid == hierarchy.nodeid);
+  if (arridx != -1) {
+    const subtkid = parentTk.subTracks[arridx].tkid;
+    parentTk.subTracks.splice(arridx, 1);
+    block.tk_remove(block.tklst.findIndex((i) => i.tkid == subtkid));
+    parentTk.cohortFilter.hierarchies.keys[hierarchy.hierarchyname].allnodes.find((i) => i.nodeid == hierarchy.nodeid).showhidebutton.text("SHOW").attr("class", "sja_handle_green");
+    return;
+  }
+  const tktemp = {};
+  {
+    const tk0 = parentTk.mds.queries[parentTk.querykey];
+    for (const k in tk0) {
+      tktemp[k] = tk0[k];
+    }
+    switch (tk0.type) {
+      case tkt.mdsjunction:
+        tktemp.readcountCutoff = parentTk.readcountCutoff;
+        tktemp.axisheight = parentTk.axisheight;
+        tktemp.legheight = parentTk.legheight;
+        tktemp.yscaleUseLog = parentTk.yscaleUseLog;
+        break;
+    }
+  }
+  const subtk = block.block_addtk_template(tktemp);
+  subtk.permanentHierarchy = hierarchy;
+  delete subtk.subTracks;
+  parentTk.subTracks.push(subtk);
+  subtk.querykey = parentTk.querykey;
+  subtk.mds = parentTk.mds;
+  subtk.parentTk = parentTk;
+  delete subtk.infoFilter;
+  delete subtk.cohortFilter;
+  block.tk_load(subtk);
+  parentTk.cohortFilter.hierarchies.keys[hierarchy.hierarchyname].allnodes.find((i) => i.nodeid == hierarchy.nodeid).showhidebutton.text("HIDE").attr("class", "sja_handle_red");
+}
+function subtrackclosehandle(tk, block, y) {
+  return block.maketklefthandle(tk, y || 0).text("Close").on("click", () => {
+    tk.parentTk.subTracks.splice(
+      tk.parentTk.subTracks.findIndex((i) => i.tkid == tk.tkid),
+      1
+    );
+    block.tk_remove(block.tklst.findIndex((i) => i.tkid == tk.tkid));
+    tk.parentTk.cohortFilter.hierarchies.keys[tk.permanentHierarchy.hierarchyname].allnodes.find((i) => i.nodeid == tk.permanentHierarchy.nodeid).showhidebutton.text("SHOW").attr("class", "sja_handle_green");
+  });
+}
+
+// src/block.mds.junction.js
+var minfontsize = 12;
+var lineopacity = 0.5;
+var discopacity = 0.5;
+var invalidCategoryColor = "#8EA399";
+var cohortLegendDotColor = "#858585";
+var notAnnotatedLabel = "Unannotated";
+var labyspace = 5;
+var hardcode_infoKey_type = "type";
+async function loadTk(tk, block, noViewRangeChange) {
+  if (noViewRangeChange) {
+    delete block.pannedpx;
+    if (tk.subTracks) {
+      for (const t of tk.subTracks) {
+        loadTk(t, block, true);
+      }
+    }
+  }
+  block.tkcloakon(tk);
+  block.block_setheight();
+  if (tk.uninitialized) {
+    makeTk(tk, block);
+  }
+  if (tk.mds.mdsIsUninitiated) {
+    const d = await dofetch3(`getDataset?genome=${block.genome.name}&dsname=${tk.mds.label}`);
+    if (d.error) throw d.error;
+    if (!d.ds) throw "ds missing";
+    Object.assign(tk.mds, d.ds);
+    delete tk.mds.mdsIsUninitiated;
+  }
+  const par = {
+    genome: block.genome.name,
+    rglst: block.tkarg_maygm(tk),
+    dslabel: tk.mds.label,
+    querykey: tk.querykey
+  };
+  if (block.subpanels.length == tk.subpanels.length) {
+    for (const r of block.subpanels) {
+      par.rglst.push({
+        chr: r.chr,
+        start: r.start,
+        stop: r.stop
+      });
+    }
+  }
+  addLoadParameter(par, tk);
+  if (tk.uninitialized) {
+    delete tk.uninitialized;
+  }
+  let data;
+  try {
+    data = await dofetch2("mdsjunction", {
+      method: "POST",
+      body: JSON.stringify(par)
+    });
+    if (data.error) throw data.error;
+    if (!data.lst) ".lst[] missing";
+    if (data.sample2client) tk.samples = data.sample2client;
+    if (data.lst.length == 0) throw "no data";
+    if (!data.maxreadcount) throw "got junctions but no maxreadcount";
+    const err = rawdata2track(data.lst, tk, block);
+    if (err) throw err;
+    tk.maxReadCount = data.maxreadcount;
+    renderTk(tk, block);
+    block.tkcloakoff(tk, {});
+  } catch (e) {
+    tk.data = [];
+    tk.leftaxis.selectAll("*").remove();
+    tk.glider.selectAll("*").remove();
+    block.tkcloakoff(tk, { error: tk.name + ": " + (e.message || e) });
+    if (e.stack) console.log(e.stack);
+  }
+  if (data.junctiontotalnumber) {
+    tk.junctionCountLabel.text(
+      (tk.data.length == data.junctiontotalnumber ? tk.data.length : tk.data.length + " of " + data.junctiontotalnumber) + " junction" + (data.junctiontotalnumber > 1 ? "s" : "")
+    );
+  } else {
+    tk.junctionCountLabel.text("");
+  }
+  if (data.samplecount) {
+    tk.sampleCountLabel.text(data.samplecount + " sample" + (data.samplecount > 1 ? "s" : ""));
+  } else {
+    tk.sampleCountLabel.text("");
+  }
+  if (tk.parentTk) {
+  } else {
+    makeLegend_cohort(data, tk, block);
+    for (const info of tk.infoFilter.lst) {
+      makeLegend_infoFilter(info, tk, block);
+    }
+  }
+  block.block_setheight();
+  updateLabel(tk, block);
+}
+function addLoadParameter(par, tk) {
+  if (tk.iscustom) {
+    if (tk.uninitialized) {
+      par.getsamples = 1;
+    }
+    par.iscustom = 1;
+    par.file = tk.file;
+    par.file2 = tk.file2;
+    par.url = tk.url;
+  }
+  if (tk.readcountCutoff) {
+    par.readcountCutoff = tk.readcountCutoff;
+  }
+  if (tk.permanentHierarchy) {
+    par.permanentHierarchy = tk.permanentHierarchy;
+  } else if (tk.cohortFilter && tk.cohortFilter.hiddenAttr) {
+    const a = {};
+    let hasfilter = false;
+    for (const key in tk.cohortFilter.hiddenAttr) {
+      let count = 0;
+      const b = {};
+      for (const value in tk.cohortFilter.hiddenAttr[key]) {
+        count++;
+        b[value] = 1;
+      }
+      if (count) {
+        hasfilter = true;
+        a[key] = b;
+      }
+    }
+    if (hasfilter) {
+      par.cohortHiddenAttr = a;
+    }
+  }
+  {
+    let infoFilter = (tk.parentTk || tk).infoFilter;
+    const a = {};
+    let hasfilter = false;
+    for (const info of infoFilter.lst) {
+      let count = 0;
+      const b2 = {};
+      for (const k in info.hiddenCategories) {
+        count++;
+        b2[k] = 1;
+      }
+      if (count) {
+        hasfilter = true;
+        a[info.key] = b2;
+      }
+    }
+    if (hasfilter) {
+      par.infoFilter = a;
+    }
+    const b = {};
+    hasfilter = false;
+    for (const info of infoFilter.lst) {
+      for (const eventcode in info.categories) {
+        const obj = info.categories[eventcode];
+        if (obj.valuePerSample && obj.valuePerSample.cutoffValueUseIdx != void 0) {
+          const cutoff = obj.valuePerSample.cutoffValueLst[obj.valuePerSample.cutoffValueUseIdx];
+          if (cutoff) {
+            hasfilter = true;
+            b[eventcode] = cutoff;
+          }
+        }
+      }
+    }
+    if (hasfilter) {
+      par.spliceEventPercentage = b;
+    }
+  }
+}
+function updateLabel(tk, block) {
+  const lst = [];
+  tk.tklabel.each(function() {
+    lst.push(this.getBBox().width);
+  });
+  if (tk.subhierarchylabel) {
+    tk.subhierarchylabel.each(function() {
+      lst.push(this.getBBox().width);
+    });
+  }
+  tk.junctionCountLabel.each(function() {
+    lst.push(this.getBBox().width);
+  });
+  tk.sampleCountLabel.each(function() {
+    lst.push(this.getBBox().width);
+  });
+  tk.leftLabelMaxwidth = Math.max(...lst);
+  block.setllabel();
+}
+function rawdata2track(raw, tk, block) {
+  const viewpxwidth = block.width + block.subpanels.reduce((i, j) => i + j.leftpad + j.width, 0);
+  const junctions = [];
+  for (const j of raw) {
+    if (j.sv && j.chr == j.sv.mate.chr) {
+      if (j.start > j.sv.mate.start) {
+        const p = j.start;
+        j.start = j.stop = j.sv.mate.start;
+        j.sv.mate.start = j.sv.mate.stop = p;
+        const q = j.strand;
+        j.strand = j.sv.mate.strand;
+        j.sv.mate.strand = q;
+      }
+    }
+    const e = j2block(j, block, viewpxwidth);
+    if (e) {
+      console.log(
+        "junction not in view range: " + j.chr + ":" + j.start + "-" + (j.sv ? j.sv.mate.chr + ":" + j.sv.mate.start : j.stop)
+      );
+      continue;
+    }
+    junctions.push(j);
+  }
+  if (tk.data) {
+    const map = /* @__PURE__ */ new Map();
+    tk.data.forEach((j) => map.set(j.chr + "." + j.start + "." + j.stop, j));
+    const pannedpx = Number.isInteger(block.pannedpx) ? block.pannedpx : 0;
+    for (const i of junctions) {
+      const j = map.get(i.chr + "." + i.start + "." + i.stop);
+      if (j) {
+        i.x = j.x + pannedpx;
+        i.axisy = j.axisy;
+      }
+    }
+  }
+  if (junctions.length == 0) {
+    return "no junctions in view range";
+  }
+  tk.data = junctions;
+}
+function j2block(j, block, viewpxwidth) {
+  let starthit;
+  let stophit;
+  {
+    const l = block.seekcoord(j.chr, j.start);
+    for (const hit of l) {
+      if (hit.ridx != void 0 && block.subpanels) {
+        if (hit.x < 0 || hit.x > block.width) {
+          continue;
+        }
+      }
+      starthit = hit;
+    }
+  }
+  {
+    const l = block.seekcoord(j.sv ? j.sv.mate.chr : j.chr, j.sv ? j.sv.mate.start : j.stop);
+    for (const hit of l) {
+      if (hit.ridx != void 0 && block.subpanels) {
+        if (hit.x < 0 || hit.x > block.width) {
+          continue;
+        }
+      }
+      stophit = hit;
+    }
+  }
+  if (starthit) {
+    if (!stophit) {
+      stophit = starthit;
+    }
+  } else {
+    if (stophit) {
+      starthit = stophit;
+    } else {
+      return true;
+    }
+  }
+  let startout = starthit.x < 0 || starthit.x > viewpxwidth;
+  let stopout = stophit.x < 0 || stophit.x > viewpxwidth;
+  if (startout && stopout) {
+    return true;
+  }
+  j.x0 = starthit.x;
+  j.x1 = stophit.x;
+  j.x = (j.x0 + j.x1) / 2;
+  j._x = j.x;
+  return false;
+}
+function infoFilter_inuse(tk) {
+  const a = (tk.parentTk || tk).infoFilter;
+  if (a.useFilterIndex == void 0) {
+    a.useFilterIndex = 0;
+  }
+  return a.lst[a.useFilterIndex];
+}
+function renderTk(tk, block) {
+  const viewpxwidth = block.width + block.subpanels.reduce((i, j) => i + j.leftpad + j.width, 0);
+  setColor(tk);
+  tk.glider.selectAll("*").remove();
+  const mg = tk.glider.append("g");
+  tk.data.sort((a, b) => {
+    return a._x - b._x;
+  });
+  const maxsamplecount = tk.data.reduce((max, j) => Math.max(max, j.sampleCount), 0);
+  {
+    const radius = 5;
+    let mrd = 0;
+    const w = Math.pow(radius, 2) * Math.PI;
+    if (maxsamplecount <= 10) {
+      mrd = w * maxsamplecount * 0.9;
+    } else if (maxsamplecount <= 100) {
+      mrd = w * 10;
+    } else if (maxsamplecount <= 1e3) {
+      mrd = w * 14;
+    } else {
+      mrd = w * 20;
+    }
+    const sf_discradius = linear().domain([
+      1,
+      maxsamplecount * 0.5 + 0.1,
+      maxsamplecount * 0.6 + 0.1,
+      maxsamplecount * 0.7 + 0.1,
+      maxsamplecount * 0.8 + 0.1,
+      maxsamplecount
+    ]).range([w, w + (mrd - w) * 0.8, w + (mrd - w) * 0.85, w + (mrd - w) * 0.9, w + (mrd - w) * 0.95, mrd]);
+    let maxradius = 0;
+    for (const j of tk.data) {
+      j.radius = Math.sqrt(sf_discradius(j.sampleCount) / Math.PI);
+      if (j.sampleCount > 1) {
+        mg.append("text").attr("font-family", font).attr("font-size", Math.max(minfontsize, j.radius)).text(j.sampleCount).each(function() {
+          const b = this.getBBox();
+          const newrad = Math.sqrt(Math.pow(b.width, 2) + Math.pow(b.height, 2)) / 2;
+          j.radius = Math.max(j.radius, newrad);
+        }).remove();
+      }
+      j.rimwidth = j.rimcount ? Math.max(2, j.radius / 6) : 0;
+      j.radius2 = j.radius + j.rimwidth + (j.rimwidth > 0 ? 1 : 0);
+      maxradius = Math.max(maxradius, j.radius2);
+    }
+    tk.maxradius = maxradius;
+  }
+  const maxmedian = tk.data.reduce((c, j) => Math.max(c, j.medianReadCount), 0);
+  tk.yscale = (tk.yscaleUseLog ? log() : linear()).domain([tk.readcountCutoff || 1, tk.maxReadCount]).range([tk.axisheight, 0]);
+  for (const j of tk.data) {
+    if (j.axisy == void 0) {
+      j.axisy = tk.axisheight - tk.yscale(j.medianReadCount);
+    }
+  }
+  tk.height_main = tk.toppad + tk.axisheight + tk.neckheight + tk.legheight + tk.bottompad;
+  tk.eventsg = tk.glider.append("g").attr("transform", "translate(0," + (tk.height_main - tk.toppad) + ")");
+  mg.attr("transform", "translate(0," + (tk.height_main - tk.toppad - tk.bottompad) + ")");
+  {
+    const topy = -tk.legheight - tk.neckheight - tk.axisheight;
+    mg.append("line").attr("x1", 0).attr("y1", topy).attr("y2", topy).attr("x2", viewpxwidth).attr("stroke", "#858585").attr("stroke-opacity", 0.2).attr("shape-rendering", "crispEdges");
+    mg.append("line").attr("x1", 0).attr("y1", topy + tk.axisheight).attr("y2", topy + tk.axisheight).attr("x2", viewpxwidth).attr("stroke", "#858585").attr("stroke-opacity", 0.2).attr("shape-rendering", "crispEdges");
+    let v = 10;
+    while (v <= tk.maxReadCount) {
+      mg.append("line").attr("x1", 0).attr("y1", topy + tk.yscale(v)).attr("y2", topy + tk.yscale(v)).attr("x2", viewpxwidth).attr("stroke", "#858585").attr("stroke-opacity", 0.2).attr("stroke-dasharray", "4,4").attr("shape-rendering", "crispEdges");
+      v *= 10;
+    }
+  }
+  const jug = mg.selectAll().data(tk.data).enter().append("g").attr("transform", (d) => set_jug(d)).each(function(j) {
+    j.jugg = this;
+  });
+  tk.jug = jug;
+  if (tk.hljunctions) {
+    jug.attr("class", (d) => {
+      for (const j of tk.hljunctions) {
+        if (d.chr == j.chr && d.start == j.start && d.stop == j.stop) {
+          return "sja_pulse";
+        }
+      }
+      return null;
+    });
+  }
+  jug.append("line").attr("stroke", (d) => d.color).attr("x1", (d) => set_leg_x1(d)).attr("y2", -tk.legheight).attr("stroke-opacity", lineopacity).attr("class", "sja_jug_leg1").each(function(d) {
+    d.leg1 = this;
+  });
+  jug.append("line").attr("stroke", (d) => d.color).attr("x2", (d) => set_leg_x2(d)).attr("y1", -tk.legheight).attr("stroke-opacity", lineopacity).attr("class", "sja_jug_leg2").each(function(d) {
+    d.leg2 = this;
+  });
+  const jug2 = jug.append("g").attr("class", "sja_jug_jug2").attr("transform", (d) => set_jug2(d, tk));
+  jug2.append("line").attr("stroke", (d) => d.color).attr("class", "sja_jug_stem").attr("stroke-dasharray", "2,2").attr("shape-rendering", "crispEdges").attr("y1", (d) => d.radius).attr("y2", (d) => {
+    return tk.neckheight + d.axisy;
+  }).attr("stroke-opacity", lineopacity).each(function(d) {
+    d.stem = this;
+  });
+  jug2.append("circle").each(function(d) {
+    d.disc = this;
+  }).attr("r", (d) => d.radius).attr("fill", (d) => d.color).attr("stroke", "white").attr("fill-opacity", discopacity);
+  jug2.filter((d) => d.sampleCount > 1).append("text").text((d) => d.sampleCount).attr("font-size", (d) => Math.max(minfontsize, d.radius)).attr("class", "sja_jug_discnum").attr("fill", "white").attr("font-family", font).attr("text-anchor", "middle").attr("dominant-baseline", "central");
+  jug2.append("circle").attr("r", (d) => d.radius).attr("stroke", (d) => d.color).attr("fill", "white").attr("fill-opacity", 0).attr("stroke-opacity", 0).on("mouseover", (event, d) => {
+    event.stopPropagation();
+    select_default(d.disc).attr("fill-opacity", 0.8);
+    select_default(d.stem).attr("stroke-opacity", 1);
+    select_default(d.leg1).attr("stroke-opacity", 1);
+    select_default(d.leg2).attr("stroke-opacity", 1);
+    mouseoverSpanBackground(d, tk, block, viewpxwidth);
+    mouseoverBoxplot(d, tk);
+    const p = event.target.getBoundingClientRect();
+    tk.tktip.clear().show(p.left + p.width, p.top - 50);
+    showOneJunction(d, tk, tk.tktip.d, block);
+  }).on("mouseout", (event, d) => {
+    tk.tktip.hide();
+    tk.pica.g.selectAll("*").remove();
+    block.cursorhlbar.attr("fill", block.cursorhlbarFillColor);
+    select_default(d.disc).attr("fill-opacity", discopacity);
+    select_default(d.stem).attr("stroke-opacity", lineopacity);
+    select_default(d.leg1).attr("stroke-opacity", lineopacity);
+    select_default(d.leg2).attr("stroke-opacity", lineopacity);
+  }).on("mousedown", (event) => {
+    event.stopPropagation();
+  }).on("mousemove", (event) => {
+    event.stopPropagation();
+  }).on("click", (event, j) => {
+    tk.tktip.hide();
+    const pane = newpane({ x: event.clientX, y: event.clientY });
+    if (!tk.iscustom) {
+      pane.header.append("span").style("color", "#858585").style("font-size", ".8em").text(tk.mds.queries[tk.querykey].name);
+    }
+    pane.header.append("text").text(j.chr + ":" + j.start + "-" + j.stop);
+    const div1 = pane.body.append("div").style("margin-top", "15px");
+    showOneJunction(j, tk, div1, block, true);
+    const div2 = pane.body.append("div");
+    queryOneJunction(j, tk, block, div2);
+  });
+  doForceLayout(tk, block, viewpxwidth).then(() => {
+    set_all(tk);
+    axisstyle({
+      axis: tk.leftaxis.transition().call(
+        axisRight().scale(tk.yscale).ticks(Math.floor(tk.axisheight / 20), ".0f")
+      ),
+      color: "black",
+      showline: true
+    });
+  });
+}
+function setColor(tk) {
+  const info = infoFilter_inuse(tk);
+  let datastructureerror = 0;
+  let invalidinfovalue = 0;
+  for (const j of tk.data) {
+    delete j.color;
+    if (!j.info) {
+      datastructureerror++;
+      continue;
+    }
+    const infovalue = j.info[info.key];
+    if (!infovalue) {
+      continue;
+    }
+    if (!infovalue.lst) {
+      datastructureerror++;
+      continue;
+    }
+    const value2count = /* @__PURE__ */ new Map();
+    for (const i of infovalue.lst) {
+      const v = i.attrValue;
+      if (v == void 0) {
+        datastructureerror++;
+        continue;
+      }
+      if (!info.categories[v]) {
+        invalidinfovalue++;
+        continue;
+      }
+      if (!value2count.has(v)) {
+        value2count.set(v, 0);
+      }
+      value2count.set(v, value2count.get(v));
+    }
+    if (value2count.size) {
+      const k = [...value2count].sort((a, b) => b[1] - a[1])[0][0];
+      j.color = info.categories[k].color;
+    }
+  }
+  for (const j of tk.data) {
+    if (!j.color) {
+      j.color = invalidCategoryColor;
+    }
+  }
+  const err = [];
+  if (datastructureerror) err.push("data structure error in " + datastructureerror + " junctions");
+  if (invalidinfovalue) err.push("invalid annotation value used in " + invalidinfovalue + " junctions");
+  if (err.length) {
+    console.log(err.join("\n"));
+  }
+}
+function set_jug(d) {
+  return "translate(" + d.x + ",0)";
+}
+function set_leg_x1(d) {
+  return d.x0 - d.x;
+}
+function set_leg_x2(d) {
+  return d.x1 - d.x;
+}
+function set_jug2(d, tk) {
+  return "translate(0,-" + (tk.legheight + tk.neckheight + d.axisy) + ")";
+}
+function set_all(tk) {
+  tk.data.forEach((j) => j.axisy = tk.axisheight - tk.yscale(j.medianReadCount));
+  const dur = 500;
+  tk.jug.selectAll(".sja_jug_leg1").transition().duration(dur).attr("y2", -tk.legheight).attr("x1", (d) => set_leg_x1(d));
+  tk.jug.selectAll(".sja_jug_leg2").transition().duration(dur).attr("y1", -tk.legheight).attr("x2", (d) => set_leg_x2(d));
+  tk.jug.selectAll(".sja_jug_jug2").transition().duration(dur).attr("transform", (d) => set_jug2(d, tk));
+  tk.jug.transition().duration(dur).attr("transform", (d) => set_jug(d));
+  tk.jug.selectAll(".sja_jug_stem").transition().duration(dur).attr("y2", (d) => tk.neckheight + d.axisy);
+}
+function doForceLayout(tk, block, viewpxwidth) {
+  const nodes = [];
+  let sumdiscwidth = 0;
+  tk.data.map((j) => {
+    let tox;
+    if (j.x0 < 0) {
+      tox = j.x1 - j.radius2 * 2;
+    } else if (j.x1 > viewpxwidth) {
+      tox = j.x0 + j.radius2 * 2;
+    } else {
+      tox = j._x;
+    }
+    nodes.push({
+      junction: j,
+      tox,
+      x: tox,
+      y: tk.axisheight - tk.yscale(j.medianReadCount)
+    });
+    sumdiscwidth += j.radius2 * 2;
+  });
+  nodes.sort((i, j) => i.tox - j.tox);
+  nodes.forEach((n, i) => n.index = i);
+  const collidestrength = sumdiscwidth <= viewpxwidth ? 1 : viewpxwidth / sumdiscwidth;
+  return new Promise((resolve, reject) => {
+    simulation_default(nodes).force(
+      "y",
+      y_default((d) => {
+        return tk.axisheight - tk.yscale(d.junction.medianReadCount);
+      }).strength(1)
+    ).force("x", x_default((d) => d.tox).strength(0.1)).force(
+      "collide",
+      collide_default((d) => {
+        return d.junction.radius2 + 2;
+      }).strength(collidestrength)
+    ).alphaMin(0.5).on("end", () => {
+      nodes.forEach((n) => {
+        n.junction.x = n.x;
+      });
+      resolve();
+    });
+  });
+}
+function mouseoverSpanBackground(j, tk, block, viewpxwidth) {
+  let xleft = Math.min(j.x0, j.x1);
+  let xright = Math.max(j.x0, j.x1);
+  if (block.usegm && block.usegm.strand == "-") {
+    xleft = j.x1;
+    xright = j.x0;
+  }
+  if (xleft >= 0 && xright <= viewpxwidth) {
+    block.cursorhlbar.attr("x", block.leftheadw + block.lpad + xleft).attr("y", 0).attr("width", xright - xleft).attr("height", block.totalheight()).attr("fill", "url(#" + tk.gradient4spanBackground.mid.id + ")");
+    return;
+  }
+  const boxwidth = 50;
+  if (xleft >= 0) {
+    block.cursorhlbar.attr("x", block.leftheadw + block.lpad + xleft).attr("fill", "url(#" + tk.gradient4spanBackground.left.id + ")");
+  } else {
+    block.cursorhlbar.attr("x", block.leftheadw + block.lpad + xright - boxwidth).attr("fill", "url(#" + tk.gradient4spanBackground.right.id + ")");
+  }
+  block.cursorhlbar.attr("y", 0).attr("width", boxwidth).attr("height", block.totalheight());
+}
+function mouseoverBoxplot(j, tk) {
+  if (!j.readcountBoxplot) return;
+  const color = "black";
+  const p5 = tk.yscale(j.readcountBoxplot.percentile[0]);
+  const p25 = tk.yscale(j.readcountBoxplot.percentile[1]);
+  const p50 = tk.yscale(j.readcountBoxplot.percentile[2]);
+  const p75 = tk.yscale(j.readcountBoxplot.percentile[3]);
+  const p95 = tk.yscale(j.readcountBoxplot.percentile[4]);
+  const w = 10;
+  tk.pica.g.selectAll("*").remove();
+  tk.pica.g.attr("transform", "translate(" + j.x + "," + p50 + ")");
+  const g = tk.pica.g.append("g").attr("transform", "translate(" + (-5 - w - j.radius2) + ",0)");
+  g.append("line").attr("x1", w / 2).attr("x2", w / 2).attr("y1", p95 - p50).attr("y2", p5 - p50).attr("stroke", color).attr("shape-rendering", "crispEdges");
+  g.append("line").attr("x1", 0).attr("x2", w).attr("y1", p5 - p50).attr("y2", p5 - p50).attr("stroke", color).attr("shape-rendering", "crispEdges");
+  g.append("line").attr("x1", 0).attr("x2", w).attr("y1", p95 - p50).attr("y2", p95 - p50).attr("stroke", color).attr("shape-rendering", "crispEdges");
+  g.append("rect").attr("y", p75 - p50).attr("width", w).attr("height", p25 - p75).attr("stroke", color).attr("fill", "white").attr("shape-rendering", "crispEdges");
+  if (p25 - p75 > 3) {
+    g.append("line").attr("x2", w).attr("stroke", color).attr("shape-rendering", "crispEdges");
+  }
+}
+function makeLegend_cohort(result, tk, block) {
+  tk.cohortFilter.holderTable.selectAll("*").remove();
+  if (result.attributeSummary) {
+    makeLegend_cohort_attribute(result.attributeSummary, tk, block);
+  }
+  if (result.hierarchySummary) {
+    if (!tk.cohortFilter.hierarchies) {
+      tk.cohortFilter.hierarchies = {
+        keys: {}
+        // to enable other attributes about hierarchies
+      };
+      for (const k in result.hierarchySummary) {
+        tk.cohortFilter.hierarchies.keys[k] = {
+          // allnodes[] will be added here, for collecting all nodes from view range, so existance of subtracks can be shown by different node style in parent tk
+          // refresh each time parent track loads
+          // in parent tk, nodes that are currently unfolded
+          opennodeids: /* @__PURE__ */ new Set()
+        };
+      }
+    }
+    makeLegend_cohort_hierarchy({
+      hash: result.hierarchySummary,
+      tk,
+      block,
+      makenodelabel: (node, row) => {
+        row.append("span").style("margin-right", "5px").attr("class", "sja_mcdot").style("background", "#858585").style("padding", "1px 6px").text(node.count);
+        const color = node.isleaf ? "#858585" : "inherit";
+        row.append("span").style("margin-right", "5px").style("color", color).text(node.label || node.name);
+        if (node.totalCount) {
+          row.append("span").style("font-size", ".7em").style("color", color).text(Math.ceil(100 * node.count / node.totalCount) + "%");
+        }
+      },
+      clicknode: (node, hierarchyname) => {
+        showHideSubtrack_byHierarchyLevel(tk, block, {
+          hierarchyname,
+          levelidx: node.depth - 1,
+          valuekey: node.name,
+          valuelabel: node.label,
+          nodeid: node.id
+        });
+      }
+    });
+  }
+}
+function makeLegend_cohort_attribute(lst, tk, block) {
+  for (const attr of lst) {
+    const tr = tk.cohortFilter.holderTable.append("tr").style("border-spacing", "5px").style("border-collapse", "separate");
+    tr.append("td").text(attr.label).style("color", "#858585");
+    const td = tr.append("td");
+    for (const item of attr.values) {
+      const div = td.append("div").style("display", "inline-block").style("padding", "10px").attr("class", "sja_clb").on("click", () => {
+        showMenu_cohortFilter(tk, block, attr, item, div);
+      });
+      if (item.label) {
+        div.property("title", item.label);
+      }
+      div.append("div").style("display", "inline-block").style("padding", "0px 5px").style("margin-right", "5px").attr("class", "sja_mcdot").style("background", cohortLegendDotColor).html(item.count > 1 ? item.count : "&nbsp;");
+      div.append("div").style("display", "inline-block").text(item.name);
+      if (item.totalCount) {
+        div.append("div").style("display", "inline-block").style("font-size", ".7em").style("color", "#858585").html("&nbsp;" + Math.ceil(100 * item.count / item.totalCount) + "%");
+      }
+    }
+    if (tk.cohortFilter.hiddenAttr[attr.key]) {
+      for (const value in tk.cohortFilter.hiddenAttr[attr.key]) {
+        const div = td.append("div").style("display", "inline-block").style("padding", "8px").style("color", "#858585").attr("class", "sja_clb").style("text-decoration", "line-through").text(value).on("click", () => {
+          showMenu_cohortFilter(tk, block, attr, { name: value }, div);
+        });
+      }
+    }
+  }
+  for (const key in tk.cohortFilter.hiddenAttr) {
+    if (lst.findIndex((i) => i.key == key) != -1) {
+      continue;
+    }
+    const tr = tk.cohortFilter.holderTable.append("tr").style("border-spacing", "5px").style("border-collapse", "separate");
+    tr.append("td").text(key).style("color", "#858585");
+    const td = tr.append("td");
+    for (const value in tk.cohortFilter.hiddenAttr[key]) {
+      const div = td.append("div").style("display", "inline-block").style("padding", "8px").style("color", "#858585").attr("class", "sja_clb").style("text-decoration", "line-through").text(value).on("click", () => {
+        showMenu_cohortFilter(tk, block, { key }, { name: value }, div);
+      });
+    }
+  }
+}
+function showMenu_cohortFilter(tk, block, attr, item, div) {
+  const tip = tk.legendMenu;
+  tip.clear().showunder(div.node());
+  if (item.count) {
+    tip.d.append("div").html(
+      item.totalCount ? '<span style="font-size:1.5em">' + item.count + "</span> / " + item.totalCount + " sample" + (item.count > 1 ? "s" : "") : item.count + " sample" + (item.count > 1 ? "s" : "")
+    ).style("margin", "10px").style("font-size", ".8em").style("color", "#858585");
+  }
+  if (item.label) {
+    tip.d.append("div").text(item.label).style("margin", "10px").style("font-size", ".8em").style("color", "#858585");
+  }
+  if (tk.cohortFilter.hiddenAttr[attr.key] && tk.cohortFilter.hiddenAttr[attr.key][item.name]) {
+    tip.d.append("div").attr("class", "sja_menuoption").text("Show").on("click", () => {
+      tip.hide();
+      div.text("Loading ...");
+      delete tk.cohortFilter.hiddenAttr[attr.key][item.name];
+      loadTk(tk, block, true);
+    });
+  } else {
+    tip.d.append("div").attr("class", "sja_menuoption").text("Hide").on("click", () => {
+      tip.hide();
+      div.text("Loading ...");
+      if (!tk.cohortFilter.hiddenAttr[attr.key]) {
+        tk.cohortFilter.hiddenAttr[attr.key] = {};
+      }
+      tk.cohortFilter.hiddenAttr[attr.key][item.name] = 1;
+      loadTk(tk, block, true);
+    });
+  }
+  tip.d.append("div").attr("class", "sja_menuoption").text("Show only").on("click", () => {
+    tip.hide();
+    div.text("Loading ...");
+    if (!tk.cohortFilter.hiddenAttr[attr.key]) {
+      tk.cohortFilter.hiddenAttr[attr.key] = {};
+    }
+    for (const v of attr.values) {
+      tk.cohortFilter.hiddenAttr[attr.key][v.name] = 1;
+    }
+    delete tk.cohortFilter.hiddenAttr[attr.key][item.name];
+    loadTk(tk, block, true);
+  });
+  if (tk.cohortFilter.hiddenAttr[attr.key]) {
+    let count = 0;
+    for (const k in tk.cohortFilter.hiddenAttr[attr.key]) {
+      count++;
+    }
+    if (count) {
+      tip.d.append("div").attr("class", "sja_menuoption").text("Show all").on("click", () => {
+        tip.hide();
+        div.text("Loading ...");
+        delete tk.cohortFilter.hiddenAttr[attr.key];
+        loadTk(tk, block, true);
+      });
+    }
+  }
+}
+function makeLegend_infoFilter(info, tk, block) {
+  info.holder.selectAll("*").remove();
+  info.value2junctioncount = /* @__PURE__ */ new Map();
+  info.value2junctioncount.set(notAnnotatedLabel, 0);
+  let err_missinginfo = 0;
+  for (const j of tk.data) {
+    if (!j.info) {
+      err_missinginfo++;
+      continue;
+    }
+    const infovalue = j.info[info.key];
+    if (!infovalue || !infovalue.lst) {
+      info.value2junctioncount.set(notAnnotatedLabel, info.value2junctioncount.get(notAnnotatedLabel) + 1);
+      continue;
+    }
+    const valueset = /* @__PURE__ */ new Set();
+    for (const i of infovalue.lst) {
+      const v = i.attrValue;
+      if (v == void 0) {
+        continue;
+      }
+      if (!info.categories[v]) {
+        continue;
+      }
+      valueset.add(v);
+    }
+    if (valueset.size == 0) {
+      info.value2junctioncount.set(notAnnotatedLabel, info.value2junctioncount.get(notAnnotatedLabel) + 1);
+    } else {
+      for (const v of valueset) {
+        if (!info.value2junctioncount.has(v)) {
+          info.value2junctioncount.set(v, 0);
+        }
+        info.value2junctioncount.set(v, info.value2junctioncount.get(v) + 1);
+      }
+    }
+  }
+  if (err_missinginfo) {
+    console.error(".info missing in " + err_missinginfo + " junctions");
+  }
+  if (info.value2junctioncount.get(notAnnotatedLabel) == 0) {
+    info.value2junctioncount.delete(notAnnotatedLabel);
+  }
+  const lst = [...info.value2junctioncount];
+  lst.sort((i, j) => j[1] - i[1]);
+  for (const [value, count] of lst) {
+    const category = value == notAnnotatedLabel ? { label: value, color: invalidCategoryColor } : info.categories[value];
+    const cell = info.holder.append("div").style("display", "inline-block").style("padding", "10px").attr("class", "sja_clb").on("click", () => {
+      tk.legendMenu.showunder(cell.node());
+      showMenu_infoFilter(info, value, tk, block);
+    });
+    cell.append("div").style("display", "inline-block").attr("class", "sja_mcdot").style("padding", "1px 5px").style("background-color", category.color).style("color", "white").html(count > 1 ? count : "&nbsp;").style("margin-right", "5px");
+    const lab = cell.append("span").style("color", category.color);
+    if (category.valuePerSample && category.valuePerSample.cutoffValueUseIdx != void 0) {
+      const cutoff = category.valuePerSample.cutoffValueLst[category.valuePerSample.cutoffValueUseIdx];
+      if (cutoff) {
+        lab.text(category.label + ", " + cutoff.label);
+      } else {
+        lab.text(category.label + " (invalid cutoff index)");
+      }
+    } else {
+      lab.text(category.label);
+    }
+  }
+  for (const value in info.hiddenCategories) {
+    const div = info.holder.append("div").style("display", "inline-block").style("padding", "8px").style("color", "#858585").attr("class", "sja_clb").style("text-decoration", "line-through").text(info.categories[value].label).on("click", () => {
+      tk.legendMenu.showunder(div.node());
+      showMenu_infoFilter(info, value, tk, block);
+    });
+  }
+  for (const value in info.categories) {
+    if (info.value2junctioncount.has(value) || info.hiddenCategories[value]) {
+      continue;
+    }
+    const category = info.categories[value];
+    const div = info.holder.append("div").style("display", "inline-block").style("padding", "8px").style("color", category.color).attr("class", "sja_clb").on("click", () => {
+      tk.legendMenu.showunder(div.node());
+      showMenu_infoFilter(info, value, tk, block);
+    });
+    if (category.valuePerSample && category.valuePerSample.cutoffValueUseIdx != void 0) {
+      const cutoff = category.valuePerSample.cutoffValueLst[category.valuePerSample.cutoffValueUseIdx];
+      if (cutoff) {
+        div.text(category.label + ", " + cutoff.label);
+      } else {
+        div.text(category.label + " (invalid cutoff index)");
+      }
+    } else {
+      div.text(category.label);
+    }
+  }
+}
+function showMenu_infoFilter(info, value, tk, block) {
+  const tip = tk.legendMenu;
+  tip.clear();
+  const jcount4thisvalue = info.value2junctioncount.get(value);
+  tip.d.append("div").text(jcount4thisvalue ? jcount4thisvalue + " junction" + (jcount4thisvalue > 1 ? "s" : "") : "no junction").style("font-size", ".8em").style("color", "#858585").style("margin", "10px");
+  const thisvalueishidden = info.hiddenCategories[value];
+  const category = info.categories[value];
+  if (category) {
+    if (category.description) {
+      tip.d.append("div").style("padding", "10px").html(info.categories[value].description);
+    }
+    if (!thisvalueishidden && category.valuePerSample) {
+      const row = tip.d.append("div").style("margin", "2px 10px 2px 10px");
+      for (const [i, cutoff] of category.valuePerSample.cutoffValueLst.entries()) {
+        const button = row.append("div").style("display", "inline-block").style("padding", "10px").text(cutoff.label);
+        if (i == category.valuePerSample.cutoffValueUseIdx) {
+          button.attr("class", "sja_clb_selected");
+        } else {
+          button.attr("class", "sja_clb");
+        }
+        button.on("click", () => {
+          tip.hide();
+          if (i == category.valuePerSample.cutoffValueUseIdx) {
+            delete category.valuePerSample.cutoffValueUseIdx;
+          } else {
+            category.valuePerSample.cutoffValueUseIdx = i;
+          }
+          loadTk(tk, block, true);
+        });
+      }
+      tip.d.append("div").text("Drop junctions with event percetage lower than selected cutoff.").style("margin", "2px 10px 10px 10px").style("font-size", ".7em").style("color", "#858585");
+    }
+  }
+  if (thisvalueishidden) {
+    tip.d.append("div").attr("class", "sja_menuoption").html("Show").on("click", () => {
+      tip.hide();
+      delete info.hiddenCategories[value];
+      loadTk(tk, block, true);
+    });
+  } else {
+    tip.d.append("div").attr("class", "sja_menuoption").html("Hide").on("click", () => {
+      tip.hide();
+      info.hiddenCategories[value] = 1;
+      loadTk(tk, block, true);
+    });
+  }
+  tip.d.append("div").attr("class", "sja_menuoption").html("Show only").on("click", () => {
+    tip.hide();
+    info.hiddenCategories = {};
+    for (const k in info.categories) {
+      if (k != value) {
+        info.hiddenCategories[k] = 1;
+      }
+    }
+    if (value != notAnnotatedLabel) {
+      info.hiddenCategories[notAnnotatedLabel] = 1;
+    }
+    loadTk(tk, block, true);
+  });
+  let hidenum = 0;
+  for (const k in info.hiddenCategories) {
+    hidenum++;
+  }
+  if (hidenum) {
+    tip.d.append("div").attr("class", "sja_menuoption").html("Show all").on("click", () => {
+      tip.hide();
+      info.hiddenCategories = {};
+      loadTk(tk, block, true);
+    });
+  }
+}
+function makeTk(tk, block) {
+  if (tk.dslabel) {
+    if (block.genome.datasets[tk.dslabel]) {
+      tk.mds = block.genome.datasets[tk.dslabel];
+      delete tk.iscustom;
+    }
+  }
+  {
+    const pale = "#FFFEAB";
+    const dark = "#F7F69E";
+    const id1 = Math.random().toString();
+    const id2 = Math.random().toString();
+    const id3 = Math.random().toString();
+    const defs = tk.gleft.append("defs");
+    const left = defs.append("linearGradient").attr("id", id1);
+    left.append("stop").attr("offset", 0).attr("stop-color", dark);
+    left.append("stop").attr("offset", 1).attr("stop-color", "white");
+    const mid = defs.append("linearGradient").attr("id", id2);
+    mid.append("stop").attr("offset", 0).attr("stop-color", pale);
+    mid.append("stop").attr("offset", 0.5).attr("stop-color", "white");
+    mid.append("stop").attr("offset", 1).attr("stop-color", pale);
+    const right = defs.append("linearGradient").attr("id", id3);
+    right.append("stop").attr("offset", 0).attr("stop-color", "white");
+    right.append("stop").attr("offset", 1).attr("stop-color", dark);
+    tk.gradient4spanBackground = {
+      left: { id: id1, gradient: left },
+      mid: { id: id2, gradient: mid },
+      right: { id: id3, gradient: right }
+    };
+  }
+  let laby = labyspace + block.labelfontsize;
+  if (tk.permanentHierarchy) {
+    tk.subhierarchylabel = block.maketklefthandle(tk, laby).text(tk.permanentHierarchy.hierarchyname + ": " + tk.permanentHierarchy.valuelabel).attr("class", null).attr("fill", "#858585");
+    laby += labyspace + block.labelfontsize;
+  }
+  {
+    const tip = new Menu({ padding: "none" });
+    tk.junctionCountLabel = block.maketklefthandle(tk, laby).on("click", () => {
+    });
+  }
+  laby += labyspace + block.labelfontsize;
+  {
+    const tip = new Menu({ padding: "none" });
+    tk.sampleCountLabel = block.maketklefthandle(tk, laby).on("click", () => {
+    });
+  }
+  laby += labyspace + block.labelfontsize;
+  if (tk.permanentHierarchy) {
+    subtrackclosehandle(tk, block, laby);
+  }
+  tk.config_handle = block.maketkconfighandle(tk).on("click", () => {
+    configPanel(tk, block);
+  });
+  if (tk.parentTk) {
+  } else {
+    tk.legendMenu = new Menu({ padding: "0px" });
+    const [tr, td] = legend_newrow(block, tk.name);
+    tk.tr_legend = tr;
+    tk.td_legend = td;
+    tk.infoFilter.holderTable = tk.td_legend.append("table");
+    tk.infoFilter.useFilterIndex = 0;
+    for (const [i, info] of tk.infoFilter.lst.entries()) {
+      const tr2 = tk.infoFilter.holderTable.append("tr");
+      info.labelButton = tr2.append("td").text(info.label).attr("class", i == tk.infoFilter.useFilterIndex ? "sja_clb_selected" : "sja_clb").on("click", () => {
+        if (tk.infoFilter.useFilterIndex == i) {
+          return;
+        }
+        tk.infoFilter.useFilterIndex = i;
+        tk.infoFilter.lst.forEach((j) => j.labelButton.attr("class", "sja_clb"));
+        info.labelButton.attr("class", "sja_clb_selected");
+        renderTk(tk, block);
+      });
+      info.holder = tr2.append("td");
+    }
+    tk.cohortFilter = {
+      holderTable: tk.td_legend.append("table"),
+      hiddenAttr: {}
+    };
+    if (tk.mds.cohortHiddenAttr) {
+      for (const k in tk.mds.cohortHiddenAttr) {
+        tk.cohortFilter.hiddenAttr[k] = {};
+        for (const v in tk.mds.cohortHiddenAttr[k]) {
+          tk.cohortFilter.hiddenAttr[k][v] = 1;
+        }
+      }
+    }
+  }
+}
+function configPanel(tk, block) {
+  tk.tkconfigtip.clear().showunder(tk.config_handle.node());
+  const holder = tk.tkconfigtip.d;
+  {
+    const row = holder.append("div").style("margin-bottom", "15px");
+    row.append("span").html("Read count cutoff&nbsp;");
+    row.append("input").property("value", tk.readcountCutoff || 0).attr("type", "number").style("width", "50px").on("keyup", (event) => {
+      if (event.code != "Enter" && event.code != "NumpadEnter") return;
+      let v = event.target.value;
+      if (!v || v < 0) {
+        v = 0;
+      }
+      if (v == 0) {
+        if (tk.readcountCutoff) {
+          tk.readcountCutoff = 0;
+          loadTk(tk, block, true);
+        } else {
+        }
+        return;
+      }
+      if (tk.readcountCutoff) {
+        if (tk.readcountCutoff == v) {
+        } else {
+          tk.readcountCutoff = v;
+          loadTk(tk, block, true);
+        }
+      } else {
+        tk.readcountCutoff = v;
+        loadTk(tk, block, true);
+      }
+    });
+    row.append("div").style("font-size", ".7em").style("color", "#858585").text("For a junction, samples with read count lower than cutoff will not be shown.");
+  }
+  {
+    const row = holder.append("div").style("margin-bottom", "15px");
+    row.append("span").text("Track height");
+    row.append("button").html("&nbsp;&nbsp;+&nbsp;&nbsp;").style("margin-left", "10px").on("click", () => {
+      tk.axisheight += 30;
+      tk.legheight = tk.axisheight / 4;
+      renderTk(tk, block);
+      block.block_setheight();
+    });
+    row.append("button").html("&nbsp;&nbsp;-&nbsp;&nbsp;").style("margin-left", "5px").on("click", () => {
+      if (tk.axisheight <= 90) return;
+      tk.axisheight -= 30;
+      tk.legheight = tk.axisheight / 4;
+      renderTk(tk, block);
+      block.block_setheight();
+    });
+  }
+  {
+    const row = holder.append("div").style("margin-bottom", "1px");
+    const id = Math.random();
+    const input = row.append("input").attr("type", "checkbox").style("margin-right", "10px").attr("id", id).on("change", () => {
+      tk.yscaleUseLog = !tk.yscaleUseLog;
+      renderTk(tk, block);
+    });
+    if (tk.yscaleUseLog) {
+      input.property("checked", 1);
+    }
+    row.append("label").text("Use log10 for Y scale read count").attr("for", id);
+  }
+}
+function showOneJunction(j, tk, holder, block, ifeventdetails) {
+  const row1 = holder.append("div").style("margin-bottom", "5px").style("white-space", "nowrap");
+  {
+    const info = infoFilter_inuse(tk);
+    const valueobj = j.info[info.key];
+    if (valueobj) {
+      const values = /* @__PURE__ */ new Set();
+      valueobj.lst.forEach((i) => values.add(i.attrValue));
+      for (const value of values) {
+        const anno = info.categories[value];
+        row1.append("span").attr("class", "sja_mcdot").style("padding", "1px 5px").style("background-color", anno ? anno.color : invalidCategoryColor).style("margin-right", "5px").text(anno ? anno.label : value);
+      }
+    }
+  }
+  {
+    const d = row1.append("div").style("display", "inline-block").style("margin-right", "10px");
+    if (!j.sv || j.chr == j.sv.mate.chr) {
+      d.html(
+        bplen(Math.abs(j.start - (j.sv ? j.sv.mate.start : j.stop))) + ' <span style="font-size:.8em;">' + j.chr + ":" + (j.start + 1) + "-" + ((j.sv ? j.sv.mate.start : j.stop) + 1) + "</span>"
+      );
+    } else {
+      d.html(
+        '<span style="font-size:.8em;">' + j.chr + ":" + (j.start + 1) + "-" + j.sv.mate.chr + ":" + (j.sv.mate.start + 1) + "</span>"
+      );
+    }
+  }
+  const row2 = holder.append("div").style("white-space", "nowrap");
+  if (j.sampleCount == 1) {
+    row2.append("div").html(j.medianReadCount + ' <span style="font-size:.8em;color:#858585">read count, single sample</span>');
+  } else {
+    row2.append("div").style("display", "inline-block").style("margin-right", "10px").html(j.medianReadCount + ' <span style="font-size:.8em;color:#858585">median read count</span>');
+    row2.append("div").style("display", "inline-block").style("margin-right", "10px").html(j.sampleCount + ' <span style="font-size:.8em;color:#858585">samples</span>');
+  }
+  const events_exonskipalt = [];
+  const events_a53ss = [];
+  if (j.info && j.info[hardcode_infoKey_type]) {
+    for (const e of j.info[hardcode_infoKey_type].lst) {
+      if (e.isskipexon || e.isaltexon) {
+        events_exonskipalt.push(e);
+      } else if (e.a5ss || e.a3ss) {
+        events_a53ss.push(e);
+      }
+    }
+  }
+  const div = holder.append("div");
+  if (events_exonskipalt.length + events_a53ss.length > 0) {
+    if (ifeventdetails) {
+      if (events_exonskipalt.length) {
+        listAllEvents(events_exonskipalt, div, j, tk, block);
+      }
+      if (events_a53ss.length) {
+        listAllEvents(events_a53ss, div, j, tk, block);
+      }
+      return;
+    }
+    if (events_exonskipalt.length) {
+      const showidx = spliceevent_exonskip_getdefault_default(events_exonskipalt);
+      const e = events_exonskipalt[showidx];
+      showEventdiagram_skipalt_fetchreadcount(j, e, tk, div, block);
+    }
+    if (events_a53ss.length) {
+      const e = events_a53ss[0];
+      showEventdiagram_a53ss(j, e, tk, div, block);
+    }
+  } else {
+    showJunctionDiagram(j, tk, div);
+  }
+}
+function showJunctionDiagram(j, tk, holder) {
+  if (!j.ongene) {
+    return;
+  }
+  const leftgenes = /* @__PURE__ */ new Map();
+  if (j.ongene.exonleft) j.ongene.exonleft.forEach((i) => leftgenes.set(i.isoform, { gene: i.gene, strand: i.strand }));
+  if (j.ongene.exonleftin)
+    j.ongene.exonleftin.forEach((i) => leftgenes.set(i.isoform, { gene: i.gene, strand: i.strand }));
+  if (j.ongene.intronleft)
+    j.ongene.intronleft.forEach((i) => leftgenes.set(i.isoform, { gene: i.gene, strand: i.strand }));
+  const rightgenes = /* @__PURE__ */ new Map();
+  if (j.ongene.exonright) j.ongene.exonright.forEach((i) => rightgenes.set(i.isoform, { gene: i.gene, strand: i.strand }));
+  if (j.ongene.exonrightin)
+    j.ongene.exonrightin.forEach((i) => rightgenes.set(i.isoform, { gene: i.gene, strand: i.strand }));
+  if (j.ongene.intronright)
+    j.ongene.intronright.forEach((i) => rightgenes.set(i.isoform, { gene: i.gene, strand: i.strand }));
+  let isoform;
+  let strand;
+  if (leftgenes.size) {
+    if (rightgenes.size) {
+      for (const [n, a] of leftgenes) {
+        if (rightgenes.has(n)) {
+          isoform = n;
+          strand = a.strand;
+          break;
+        }
+      }
+    } else {
+      const a = [...leftgenes][0];
+      isoform = a[0];
+      strand = a[1].strand;
+    }
+  } else if (rightgenes.size) {
+    const a = [...rightgenes][0];
+    isoform = a[0];
+    strand = a[1].strand;
+  }
+  if (isoform) {
+    if (strand != "+" && strand != "-") {
+      holder.text("unknown strand for " + isoform);
+      return;
+    }
+    import("./spliceevent.noeventdiagram-SUBU5BLZ.js").then((p) => {
+      p.samegene({
+        isoform,
+        reverse: strand == "-",
+        ongene: j.ongene,
+        holder
+      });
+    });
+    return;
+  }
+  import("./spliceevent.noeventdiagram-SUBU5BLZ.js").then((p) => {
+    p.differentgenes({
+      ongene: j.ongene,
+      holder
+    });
+  });
+}
+function showEventdiagram_a53ss(j, e, tk, holder, block) {
+  const e2 = {
+    junctionB: {
+      start: j.start,
+      stop: j.stop,
+      v: j.medianReadCount
+    },
+    a5ss: e.a5ss,
+    a3ss: e.a3ss,
+    altinintron: e.altinintron,
+    altinexon: e.altinexon,
+    frame: e.frame,
+    exon5idx: e.exon5idx,
+    strand: e.strand,
+    sitedist: e.sitedist
+  };
+  if (e.junctionA) {
+    e2.junctionA = { start: e.junctionA.start, stop: e.junctionA.stop, v: "..." };
+  }
+  import("./spliceevent.a53ss.diagram-WUHKYRWG.js").then((p) => {
+    const text = p.default({
+      event: e2,
+      holder
+    });
+    if (!text) return;
+    setTimeout(() => {
+      if (text.node().getBoundingClientRect().top == 0) return;
+      fetchReadcount4junctionAbyjunctionBsamples(
+        tk,
+        block,
+        j,
+        /* @__PURE__ */ new Map([[e.junctionA.start + "." + e.junctionA.stop, text]]),
+        [[e.junctionA.start, e.junctionA.stop]]
+      );
+    }, 1e3);
+  });
+}
+function showEventdiagram_skipalt_fetchreadcount(j, e, tk, holder, block) {
+  const e2 = {
+    gm: {
+      name: e.gene,
+      isoform: e.isoform
+    },
+    junctionB: {
+      data: [{ v: j.medianReadCount }]
+    },
+    skippedexon: e.skippedexon,
+    isskipexon: e.isskipexon,
+    isaltexon: e.isaltexon,
+    frame: e.frame,
+    junctionAlst: [],
+    color: "#99004d"
+  };
+  if (e.junctionAlst) {
+    for (const jA of e.junctionAlst) {
+      if (jA) {
+        jA.data = [{ v: "..." }];
+        e2.junctionAlst.push(jA);
+        continue;
+      }
+      e2.junctionAlst.push(null);
+    }
+  }
+  if (e.up1junction) {
+    e.up1junction.data = [{ v: "..." }];
+    e2.up1junction = e.up1junction;
+  }
+  if (e.down1junction) {
+    e.down1junction.data = [{ v: "..." }];
+    e2.down1junction = e.down1junction;
+  }
+  import("./spliceevent.exonskip.diagram-KAFGBL2I.js").then((p) => {
+    const [junction2readcounttext, junctionlst] = p.default({
+      event: e2,
+      holder,
+      nophrase: true
+    });
+    setTimeout(() => {
+      for (const [k, text] of junction2readcounttext) {
+        if (text.node().getBoundingClientRect().top == 0) {
+          return;
+        }
+      }
+      fetchReadcount4junctionAbyjunctionBsamples(tk, block, j, junction2readcounttext, junctionlst);
+    }, 1e3);
+  });
+}
+async function fetchReadcount4junctionAbyjunctionBsamples(tk, block, jB, junction2readcounttext, jAlst) {
+  const par = {
+    genome: block.genome.name,
+    dslabel: tk.mds.label,
+    querykey: tk.querykey,
+    readcountByjBsamples: true,
+    junctionB: { chr: jB.chr, start: jB.start, stop: jB.stop },
+    junctionAposlst: jAlst
+  };
+  addLoadParameter(par, tk);
+  try {
+    const data = await dofetch2("mdsjunction", {
+      method: "POST",
+      body: JSON.stringify(par)
+    });
+    if (data.error) throw data.error;
+    if (!data.lst) throw ".lst[] missing";
+    for (const j of data.lst) {
+      const key = j.start + "." + j.stop;
+      if (junction2readcounttext.has(key)) {
+        junction2readcounttext.get(key).text(j.v);
+      }
+    }
+  } catch (e) {
+    console.error(e.message || e);
+  }
+}
+function listAllEvents(lst, holder, j, tk, block) {
+  if (lst.length == 1) {
+    showEventdetail(lst[0], holder, j, tk, block);
+    return;
+  }
+  const div = holder.append("div").style("display", "inline-block").style("font-size", ".8em");
+  for (const e of lst) {
+    div.append("div").html(eventlabel(e)).attr("class", "sja_menuoption").on("click", (event) => {
+      tk.tktip.clear().show(event.clientX + 20, event.clientY - 40);
+      showEventdetail(e, tk.tktip.d, j, tk, block);
+    });
+  }
+}
+function showEventdetail(e, holder, j, tk, block) {
+  const tr = holder.append("table").append("tr");
+  const td1 = tr.append("td");
+  const p = td1.append("p");
+  if (e.isskipexon || e.isaltexon) {
+    p.html(eventlabel(e));
+    showEventdiagram_skipalt_fetchreadcount(j, e, tk, td1, block);
+  } else {
+    p.html(eventlabel(e));
+    showEventdiagram_a53ss(j, e, tk, td1, block);
+  }
+  const td2 = tr.append("td");
+}
+function eventlabel(e) {
+  if (e.isskipexon || e.isaltexon) {
+    return (e.isskipexon ? "Exon skip" : "Exon alt") + " " + e.gene + " " + e.isoform + " " + (e.frame == void 0 ? "" : e.frame == IN_frame ? "IN frame" : "OUT of frame");
+  }
+  return (e.a5ss ? "A5SS" : "A3SS") + " " + e.gene + " " + e.isoform + " " + (e.frame == void 0 ? "" : e.frame == IN_frame ? "IN frame" : "OUT of frame");
+}
+async function queryOneJunction(j, tk, block, holder) {
+  const par = {
+    genome: block.genome.name,
+    dslabel: tk.mds.label,
+    querykey: tk.querykey,
+    junction: {
+      chr: j.chr,
+      start: j.start,
+      stop: j.stop
+    }
+  };
+  addLoadParameter(par, tk);
+  const wait = holder.append("div").text("Loading ...");
+  try {
+    const data = await dofetch2("mdsjunction", {
+      method: "POST",
+      body: JSON.stringify(par)
+    });
+    if (data.error) throw data.error;
+    wait.remove();
+    if (data.readcountboxplotpercohort) {
+      const row = holder.append("div");
+      for (const group of data.readcountboxplotpercohort) {
+        const div = row.append("div").style("margin", "10px").style("display", "inline-block").style("vertical-align", "top");
+        div.append("h3").text(group.label).style("text-align", "center");
+        const p = await import("./plot.boxplot-FOXP2N7H.js");
+        const err = p.default({
+          holder: div,
+          list: group.boxplots,
+          axislabel: "Read count"
+        });
+        if (err) {
+          sayerror(div, "Boxplot error: " + err);
+        }
+      }
+    } else if (data.samples) {
+      if (data.sampletotalnumber) {
+        holder.append("p").text("Displaying top " + data.samples.length + " samples").style("opacity", 0.5);
+      }
+      const div = holder.append("div").style("margin-top", "20px").style("display", "grid").style("grid-template-columns", "auto auto").style("gap-row-gap", "1px").style("align-items", "center").style("justify-items", "left");
+      const [c1, c2] = get_list_cells(div);
+      c1.text("Sample").style("opacity", 0.5).style("font-size", ".7em");
+      c2.text("Read count").style("opacity", 0.5).style("font-size", ".7em");
+      for (const s of data.samples) {
+        const [c12, c22] = get_list_cells(div);
+        c12.text(s.sample_name ? s.sample_name : tk.samples[s.i]);
+        c22.text(s.readcount);
+      }
+    }
+  } catch (e) {
+    if (e.stack) console.log(e.stack);
+    wait.text("Error: " + (e.message || e));
+  }
+}
+function get_list_cells(table) {
+  return [
+    table.append("div").style("width", "100%").style("padding", "5px 20px 5px 0px").style("border-bottom", "solid 1px #ededed"),
+    table.append("div").style("width", "100%").style("border-bottom", "solid 1px #ededed").style("padding", "5px 20px 5px 0px")
+  ];
+}
+export {
+  loadTk
+};
+//# sourceMappingURL=block.mds.junction-2R4UBHO7.js.map