@sjcrh/proteinpaint-client 2.222.0 → 2.223.0

package/dist/block.tk.menu-BIORXN3G.js

@@ -0,0 +1,1050 @@
+import {
+  appear2 as appear,
+  disappear2 as disappear,
+  gmmode,
+  newpane,
+  tkexists,
+  tkt
+} from "./chunk-JP4IU7DO.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-IRAB3OI7.js";
+import {
+  Menu
+} from "./chunk-CNFTQSNE.js";
+import "./chunk-RIHO7ZD5.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-4TJO2DGU.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-MHWYRNGA.js";
+import "./chunk-JHLF2ZC2.js";
+import {
+  category10_default
+} from "./chunk-WJLRU5OF.js";
+import "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import {
+  ordinal
+} from "./chunk-4OLM3KSB.js";
+import "./chunk-PWYMHUXY.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-HS5PO5ZQ.js";
+
+// src/block.tk.menu.js
+var colorfunc = ordinal(category10_default);
+function block_tk_menu_default(block, tip, x, y, button) {
+  tip.clear();
+  const div = tip.d;
+  onesearchui(block, div);
+  facettrigger(block, div, tip);
+  for (const s of block.genome.tkset) {
+    if (s.facetlst) {
+      for (const f of s.facetlst) {
+        if (f.facetpane) {
+          disappear(f.facetpane.pane);
+        }
+      }
+    }
+    if (s.facetpane) {
+      disappear(s.facetpane.pane);
+    }
+  }
+  hardlist4block(block, div);
+  if (!JSON.parse(sessionStorage.getItem("optionalFeatures")).disableCustomTrackUI) {
+    div.append("div").html("Add custom track »").style("padding", "15px").style("text-align", "center").attr("class", "sja_menuoption").on("click", () => {
+      customtracktypeui(block, div);
+    });
+  }
+  tip.show2(x, y, { elem: button });
+}
+function onesearchui(block, div) {
+  let count = 0;
+  for (const s of block.genome.tkset) {
+    count += s.tklst.length;
+  }
+  if (count == 0) {
+    return;
+  }
+  const searchrow = div.append("div").style("margin", count == 0 ? "0px" : "15px 15px 5px 15px");
+  const input = searchrow.append("input").attr("size", 15).attr("placeholder", "Search " + count + " tracks");
+  const searchsays = searchrow.append("span").style("font-size", ".8em").style("padding-left", "10px");
+  input.on("keyup", (event) => {
+    founddiv.selectAll("*").remove();
+    searchsays.text("");
+    const v = event.target.value;
+    if (v.length < 2) {
+      return;
+    }
+    const vv = v.toLowerCase();
+    let foundnum = 0;
+    for (const set of block.genome.tkset) {
+      const hits = [];
+      for (const t of set.tklst) {
+        if (t.name && t.name.toLowerCase().indexOf(vv) != -1) {
+          hits.push(t);
+          continue;
+        }
+        if (t.patient && t.patient.toLowerCase().indexOf(vv) != -1) {
+          hits.push(t);
+          continue;
+        }
+        if (t.sampletype && t.sampletype.toLowerCase().indexOf(vv) != -1) {
+          hits.push(t);
+          continue;
+        }
+        if (t.assayname && t.assayname.toLowerCase().indexOf(vv) != -1) {
+          hits.push(t);
+          continue;
+        }
+      }
+      foundnum += hits.length;
+      if (hits.length == 0) continue;
+      const color = colorfunc(set.name);
+      const tr = founddiv.append("table").style("border-spacing", "0px").append("tr");
+      const thisscroll = tr.append("td").style("padding", "0px 10px 0px 20px").append("div").style("border", "solid 1px " + color);
+      if (hits.length > 13) {
+        thisscroll.style("padding", "10px 10px 10px 0px").style("height", "300px").style("overflow-y", "scroll").style("resize", "vertical");
+      }
+      const tktable = thisscroll.append("table").style("border-spacing", "1px");
+      tr.append("td").style("color", color).style("font-size", ".8em").style("font-weight", "bold").text(set.name);
+      for (const cold of hits) {
+        let hot = null;
+        for (const t of block.tklst) {
+          if (t.id == cold.id && t.file == cold.file && t.url == cold.url) {
+            hot = t;
+            break;
+          }
+        }
+        const tr2 = tktable.append("tr");
+        const td1 = tr2.append("td").style("color", "#555").style("font-size", ".7em");
+        if (hot) {
+          td1.text("SHOWN");
+        }
+        const handle = tr2.append("td").classed("sja_menuoption", true).text(tkhtmllabel(cold, block));
+        if (hot) {
+          handle.on("click", () => tkhandleclick(block, hot, td1));
+        } else {
+          handle.on("click", () => tkhandleclick(block, cold, td1));
+        }
+      }
+    }
+    searchsays.text(foundnum == 0 ? "No tracks found" : "Found " + foundnum + " track" + (foundnum > 1 ? "s" : ""));
+  });
+  const founddiv = div.append("div").style("margin-top", "3px");
+}
+function hardlist4block(block, div) {
+  const harddiv = div.append("div").style("margin", "20px");
+  {
+    const set = /* @__PURE__ */ new Set();
+    for (const t of block.tklst) {
+      set.add(t.name);
+    }
+    for (const t of block.genome.tracks) {
+      set.add(t.name);
+    }
+    if (set.size > 13) {
+      harddiv.style("border-top", "solid 1px #eee").style("border-bottom", "solid 1px #eee").style("padding", "10px 10px 10px 0px").style("height", "300px").style("overflow-y", "scroll").style("resize", "vertical");
+    }
+  }
+  const hardtable = harddiv.append("table");
+  for (const tk of block.tklst) {
+    const tr = hardtable.append("tr");
+    const td1 = tr.append("td");
+    td1.text("SHOWN").style("color", "#555").style("font-size", ".7em");
+    const handle = tr.append("td").text(tkhtmllabel(tk, block));
+    if (notAllowedToHideThisTrack(tk)) {
+      handle.style("padding", "5px 10px");
+    } else {
+      handle.attr("class", "sja_menuoption").on("click", () => {
+        tkhandleclick(block, tk, td1);
+      });
+    }
+  }
+  for (const tk of block.genome.tracks) {
+    let ishot = false;
+    for (const t of block.tklst) {
+      if (t.tkid == tk.tkid) {
+        ishot = true;
+        break;
+      }
+    }
+    if (ishot) {
+      continue;
+    }
+    const tr = hardtable.append("tr");
+    const td1 = tr.append("td").style("color", "#555").style("font-size", ".7em");
+    const handle = tr.append("td").attr("class", "sja_menuoption").text(tkhtmllabel(tk, block));
+    handle.on("click", () => {
+      tkhandleclick(block, tk, td1);
+    });
+  }
+}
+function customtracktypeui(block, div) {
+  div.selectAll("*").remove();
+  div.append("div").style("margin", "30px").style("text-align", "center").style("color", "#858585").text("Add track for " + block.genome.name + " genome");
+  const d1 = div.append("div").style("margin", "20px");
+  d1.append("div").attr("class", "sja_menuoption").html('bigWig <span style="opacity:.5;font-size:.8em">numerical data</span>').on("click", () => newtk_bw(block, div));
+  d1.append("div").attr("class", "sja_menuoption").html('JSON-BED <span style="opacity:.5;font-size:.8em">positional annotations</span>').on("click", () => newtk_bedj(block, div));
+  d1.append("div").attr("class", "sja_menuoption").text("Splice junction").on("click", () => newtk_junction(block, div));
+  d1.append("div").attr("class", "sja_menuoption").html('VCF <span style="opacity:.5;font-size:.8em">SNV/indel</span>').on("click", () => newtk_vcf(block, div));
+  d1.append("div").attr("class", "sja_menuoption").html('Interaction <span style="opacity:.5;font-size:.8em">pairs of genomic regions</span>').on("click", () => newtk_interaction(block, div));
+  const d2 = div.append("div").style("margin", "20px");
+  d2.append("p").style("color", "#858585").text("Declare tracks as JSON text:");
+  const ta = d2.append("textarea").attr("rows", 5).attr("cols", "30").attr("placeholder", "Enter JSON text");
+  const row = d2.append("div").style("margin-top", "3px");
+  row.append("button").text("Submit").on("click", () => {
+    const v = ta.property("value");
+    if (v == "") return;
+    let j;
+    try {
+      j = JSON.parse(v);
+    } catch (e) {
+      alert("Invalid JSON: " + e);
+      return;
+    }
+    if (!Array.isArray(j)) {
+      j = [j];
+    }
+    for (const t of j) {
+      if (t.hidden) {
+        delete t.hidden;
+        block.genome.tracks.push(t);
+      } else {
+        const tt = block.block_addtk_template(t);
+        if (tt) {
+          block.tk_load(tt);
+        }
+      }
+    }
+  });
+  row.append("button").text("Clear").on("click", () => ta.property("value", ""));
+  row.append("span").style("padding-left", "10px").html("<a href=https://github.com/stjude/proteinpaint/wiki/Tracks target=_blank>Track format</a>");
+  row.append("span").style("padding-left", "10px").html("<a href=https://jsonlint.com/ target=_blank>debug</a>");
+}
+function may_add_customtk(tk, block, div) {
+  const tk_reg = tkexists(tk, block.genome.tracks);
+  if (tk_reg) {
+    if (tkexists(tk, block.tklst)) {
+      window.alert("The track is already shown");
+    } else {
+      const tk2 = block.block_addtk_template(tk_reg);
+      block.tk_load(tk2);
+      customtracktypeui(block, div);
+    }
+  } else {
+    tk.tkid = Math.random().toString();
+    block.genome.tracks.push(tk);
+    const tk2 = block.block_addtk_template(tk);
+    block.tk_load(tk2);
+    customtracktypeui(block, div);
+  }
+}
+function newtk_bw(block, div) {
+  div.selectAll("*").remove();
+  div.append("div").style("margin", "20px").style("display", "inline-block").html("\u226A Go back").attr("class", "sja_menuoption").on("click", () => customtracktypeui(block, div));
+  {
+    const box = div.append("div").style("margin", "0px 20px 20px 20px");
+    box.append("p").text("Add a single track").style("color", "#858585").style("font-size", ".7em");
+    const iname = box.append("p").append("input").attr("type", "text").attr("placeholder", "bigWig track name").attr("size", 20);
+    const iurl = box.append("p").append("input").attr("type", "text").attr("placeholder", remoteFileAllowed() ? "URL or server-side file path" : "Server-side file path").attr("size", 40);
+    mayShowRemoteFileNote(box);
+    const p2 = box.append("p");
+    p2.append("button").text("Add bigWig track").on("click", () => {
+      const text = iurl.property("value").trim();
+      if (text == "") return;
+      if (urlNotAllowed(text)) return;
+      let file, url;
+      if (stringisurl(text)) {
+        url = text;
+      } else {
+        file = text;
+      }
+      const tk = {
+        type: tkt.bigwig,
+        name: iname.property("value").trim() || "bigwig track",
+        scale: {
+          auto: 1
+        },
+        file,
+        url,
+        iscustom: true
+      };
+      may_add_customtk(tk, block, div);
+    });
+    p2.append("button").text("Clear").on("click", () => iurl.node().value = iname.node().value = "");
+  }
+  {
+    const box = div.append("div").style("margin", "0px 20px 20px 20px");
+    box.append("p").text("Add multiple tracks").style("color", "#858585").style("font-size", ".7em");
+    const input = box.append("p").append("textarea").attr(
+      "placeholder",
+      "one track per line: [track name]," + (remoteFileAllowed() ? "[path/to/file.bw or URL]" : "[path/to/file.bw]")
+    ).attr("rows", 2).attr("cols", 50);
+    mayShowRemoteFileNote(box);
+    const p2 = box.append("p");
+    p2.append("button").text("Add tracks").on("click", () => {
+      const text = input.property("value").trim();
+      if (text == "") return;
+      if (text.split(/[\r\n]/).some((s) => urlNotAllowed((s.split(",")[1] || "").trim()))) return;
+      for (const s of text.split(/[\r\n]/)) {
+        const l = s.split(",");
+        if (l[0] && l[1]) {
+          const t = {
+            type: tkt.bigwig,
+            name: l[0].trim(),
+            scale: { auto: 1 },
+            iscustom: true
+          };
+          const tmp = l[1].trim();
+          if (stringisurl(tmp)) t.url = tmp;
+          else t.file = tmp;
+          const t2 = block.block_addtk_template(t);
+          block.tk_load(t2);
+        }
+      }
+    });
+    p2.append("button").text("Clear").on("click", () => input.node().value = "");
+  }
+  div.append("div").style("margin", "20px").html("<a href=https://genome.ucsc.edu/goldenpath/help/bigWig.html target=_blank>bigWig file format</a>");
+}
+function newtk_bedj(block, div) {
+  div.selectAll("*").remove();
+  div.append("div").style("margin", "20px").style("display", "inline-block").html("&lt; go back").attr("class", "sja_menuoption").on("click", () => customtracktypeui(block, div));
+  const box = div.append("div").style("margin", "20px");
+  const nta = box.append("p").append("input").attr("type", "text").attr("placeholder", "JSON-BED track name").attr("size", 20);
+  const ta = box.append("p").append("input").attr("type", "text").attr("placeholder", remoteFileAllowed() ? "URL or server-side file path" : "Server-side file path").attr("size", 40);
+  mayShowRemoteFileNote(box);
+  const p = box.append("p");
+  p.append("button").text("Add JSON-BED track").on("click", () => {
+    const text = ta.property("value").trim();
+    if (text == "") return;
+    if (urlNotAllowed(text)) return;
+    let file, url;
+    if (stringisurl(text)) {
+      url = text;
+    } else {
+      file = text;
+    }
+    const tk = {
+      type: tkt.bedj,
+      name: nta.property("value").trim() || "JSON-BED",
+      file,
+      url,
+      iscustom: true
+    };
+    may_add_customtk(tk, block, div);
+  });
+  p.append("button").text("Clear").on("click", () => ta.node().value = nta.node().value = "");
+  box.append("p").html(
+    "<a href=https://github.com/stjude/proteinpaint/wiki/Tracks#Track-JSON-BED-track-format target=_blank>JSON-BED format</a>"
+  );
+}
+function newtk_junction(block, div) {
+  div.selectAll("*").remove();
+  div.append("div").style("margin", "20px").style("display", "inline-block").html("&lt; go back").attr("class", "sja_menuoption").on("click", () => customtracktypeui(block, div));
+  const box = div.append("div").style("margin", "20px");
+  const nta = box.append("p").append("input").attr("type", "text").attr("placeholder", "Junction track name").attr("size", 20);
+  const ta = box.append("p").append("input").attr("type", "text").attr("placeholder", remoteFileAllowed() ? "URL or server-side file path" : "Server-side file path").attr("size", 40);
+  mayShowRemoteFileNote(box);
+  const p = box.append("p");
+  p.append("button").text("Add junction track").on("click", () => {
+    const text = ta.property("value").trim();
+    if (text == "") return;
+    if (urlNotAllowed(text)) return;
+    let file, url;
+    if (stringisurl(text)) {
+      url = text;
+    } else {
+      file = text;
+    }
+    const tk = {
+      type: tkt.junction,
+      name: nta.property("value").trim() || "junction",
+      tracks: [
+        {
+          file,
+          url
+        }
+      ],
+      iscustom: true
+    };
+    may_add_customtk(tk, block, div);
+  });
+  p.append("button").text("Clear").on("click", () => ta.node().value = nta.node().value = "");
+  box.append("p").html(
+    "<a href=https://github.com/stjude/proteinpaint/wiki/Tracks#Track-splice-junction target=_blank>Junction track format</a>"
+  );
+}
+function newtk_vcf(block, div) {
+  div.selectAll("*").remove();
+  div.append("div").style("margin", "20px").style("display", "inline-block").html("&lt; go back").attr("class", "sja_menuoption").on("click", () => customtracktypeui(block, div));
+  const box = div.append("div").style("margin", "20px");
+  const nta = box.append("p").append("input").attr("type", "text").attr("placeholder", "VCF track name").attr("size", 20);
+  const ta = box.append("p").append("input").attr("type", "text").attr("placeholder", remoteFileAllowed() ? "URL or server-side file path" : "Server-side file path").attr("size", 40);
+  mayShowRemoteFileNote(box);
+  const p = box.append("p");
+  p.append("button").text("Add VCF track").on("click", () => {
+    const text = ta.property("value").trim();
+    if (text == "") return;
+    if (urlNotAllowed(text)) return;
+    let file, url;
+    if (stringisurl(text)) {
+      url = text;
+    } else {
+      file = text;
+    }
+    const vcfid = Math.random().toString();
+    const ds = {
+      label: nta.property("value").trim() || "VCF",
+      id2vcf: {}
+    };
+    ds.id2vcf[vcfid] = {
+      vcfid,
+      file,
+      url,
+      headernotloaded: true
+    };
+    const tk = {
+      type: tkt.ds,
+      ds,
+      isvcf: true,
+      // trigger
+      iscustom: true
+    };
+    may_add_customtk(tk, block, div);
+  });
+  p.append("button").text("Clear").on("click", () => ta.node().value = nta.node().value = "");
+  box.append("p").html("<a href=https://en.wikipedia.org/wiki/Variant_Call_Format target=_blank>VCF format</a>");
+  box.append("p").style("color", "#858585").style("font-size", ".8em").text("SNV/indel data only");
+}
+function newtk_interaction(block, div) {
+  div.selectAll("*").remove();
+  div.append("div").style("margin", "20px").style("display", "inline-block").html("&lt; go back").attr("class", "sja_menuoption").on("click", () => customtracktypeui(block, div));
+  const box = div.append("div").style("margin", "20px");
+  const tknameinput = box.append("p").append("input").attr("type", "text").attr("placeholder", "Interaction track name").attr("size", 20);
+  const tr = box.append("table").append("tr");
+  tr.append("td").text("Data source").style("opacity", 0.5).style("vertical-align", "top").style("padding-right", "10px");
+  const td = tr.append("td");
+  const id = Math.random().toString();
+  {
+    const row = td.append("div");
+    row.append("input").attr("type", "radio").attr("name", id).attr("id", id + 1).property("checked", 1).on("change", () => change(1));
+    row.append("label").attr("class", "sja_clbtext").html("&nbsp;Hi-C, juicebox format").attr("for", id + 1);
+  }
+  {
+    const row = td.append("div");
+    row.append("input").attr("type", "radio").attr("name", id).attr("id", id + 2).on("change", () => change(2));
+    row.append("label").attr("class", "sja_clbtext").html("&nbsp;BED file, compressed and indexed").attr("for", id + 2);
+  }
+  {
+    const row = td.append("div");
+    row.append("input").attr("type", "radio").attr("name", id).attr("id", id + 3).on("change", () => change(3));
+    row.append("label").attr("class", "sja_clbtext").html("&nbsp;Text input").attr("for", id + 3);
+  }
+  const div1 = box.append("div");
+  {
+    div1.append("p").html(
+      "Juicebox: <a href=https://github.com/theaidenlab/Juicebox target=_blank>github.com/theaidenlab/Juicebox</a>"
+    );
+    const urlinput = div1.append("p").append("input").attr("type", "text").attr("placeholder", remoteFileAllowed() ? "*.hic file URL or server-side path" : "*.hic file server-side path").attr("size", 40);
+    mayShowRemoteFileNote(div1);
+    let enzymeselect;
+    if (block.genome.hicenzymefragment) {
+      const p = div1.append("p");
+      p.append("span").html("Restriction enzyme:&nbsp;");
+      enzymeselect = p.append("select");
+      enzymeselect.append("option").text("none");
+      for (const e of block.genome.hicenzymefragment) {
+        enzymeselect.append("option").text(e.enzyme).property("value", e.enzyme);
+      }
+    }
+    div1.append("p").append("button").text("Add track").on("click", () => {
+      const str = urlinput.property("value");
+      if (!str) return;
+      if (urlNotAllowed(str)) return;
+      const tk = {
+        type: tkt.hicstraw,
+        name: tknameinput.property("value") || "Custom interaction",
+        mode_hm: true,
+        mode_arc: false,
+        iscustom: 1
+      };
+      if (stringisurl(str)) tk.url = str;
+      else tk.file = str;
+      if (enzymeselect) {
+        const s = enzymeselect.node();
+        tk.enzyme = s.options[s.selectedIndex].value;
+        if (tk.enzyme == "none") delete tk.enzyme;
+      }
+      may_add_customtk(tk, block, div);
+    });
+  }
+  const div2 = box.append("div").style("display", "none");
+  {
+    div2.append("p").html(
+      "<a href=https://github.com/stjude/proteinpaint/wiki/Tracks#track-json-bed-track-format target=_blank>BED file format</a>"
+    );
+    const urlinput = div2.append("p").append("input").attr("type", "text").attr("placeholder", remoteFileAllowed() ? "*.gz file URL or server-side path" : "*.gz file server-side path").attr("size", 40);
+    mayShowRemoteFileNote(div2);
+    div2.append("p").append("button").text("Add track").on("click", () => {
+      const str = urlinput.property("value");
+      if (!str) return;
+      if (urlNotAllowed(str)) return;
+      const tk = {
+        type: tkt.hicstraw,
+        name: tknameinput.property("value") || "Custom interaction",
+        mode_hm: false,
+        mode_arc: true,
+        iscustom: 1
+      };
+      if (stringisurl(str)) tk.bedurl = str;
+      else tk.bedfile = str;
+      may_add_customtk(tk, block, div);
+    });
+  }
+  const div3 = box.append("div").style("display", "none");
+  {
+    div3.append("p").html(
+      "Enter interaction data as <a href=https://github.com/stjude/proteinpaint/wiki/Tracks#Track-splice-junction target=_blank>tab-delimited text</a>."
+    );
+    const textinput = div3.append("textarea").attr("placeholder", "One line per interaction").attr("cols", 45).attr("rows", 5);
+    div3.append("p").append("button").text("Add track").on("click", () => {
+      const str = textinput.property("value");
+      if (!str) return;
+      const tk = {
+        type: tkt.hicstraw,
+        name: tknameinput.property("value") || "Custom interaction",
+        mode_hm: false,
+        mode_arc: true,
+        iscustom: 1,
+        textdata: { raw: str }
+      };
+      may_add_customtk(tk, block, div);
+    });
+  }
+  const change = (i) => {
+    div1.style("display", i == 1 ? "block" : "none");
+    div2.style("display", i == 2 ? "block" : "none");
+    div3.style("display", i == 3 ? "block" : "none");
+  };
+}
+function facettrigger(block, holder, menutip) {
+  const toshow = [];
+  for (const tkset of block.genome.tkset) {
+    if (tkset.facetlst) {
+      toshow.push(tkset);
+      continue;
+    }
+    if (tkset.isfacet) {
+      toshow.push(tkset);
+      continue;
+    }
+    console.log("the .isfacet flag is missing on this tkset and may need to be supported");
+  }
+  if (toshow.length == 0) {
+    return;
+  }
+  const div = holder.append("div").style("margin", "15px");
+  div.append("div").text("FACET").style("color", "#858585").style("font-size", ".7em");
+  for (const tkset of toshow) {
+    if (tkset.facetlst) {
+      for (const flet of tkset.facetlst) {
+        div.append("div").style("display", "inline-block").attr("class", "sja_menuoption").text((flet.name ? flet.name + ": " : "") + tkset.name).on("click", (event) => {
+          menutip.hide();
+          if (flet.facetpane) {
+            document.body.appendChild(flet.facetpane.pane.node());
+            appear(flet.facetpane.pane);
+          } else {
+            const pane = newpane({
+              x: event.clientX - 100,
+              y: event.clientY - 20,
+              closekeep: true
+            });
+            flet.facetpane = pane;
+          }
+          facetmake(block, tkset, flet);
+        });
+      }
+      continue;
+    }
+    div.append("div").style("display", "inline-block").attr("class", "sja_menuoption").text(tkset.tklst.length + " tracks from " + tkset.name).on("click", (event) => {
+      menutip.hide();
+      if (tkset.facetpane) {
+        document.body.appendChild(tkset.facetpane.pane.node());
+        appear(tkset.facetpane.pane);
+      } else {
+        const pane = newpane({
+          x: event.clientX - 100,
+          y: event.clientY - 20,
+          closekeep: true
+        });
+        tkset.facetpane = pane;
+      }
+      facetmake(block, tkset);
+    });
+  }
+}
+function facetmake(block, tkset, flet) {
+  const tip = new Menu();
+  const facetpane = (flet || tkset).facetpane;
+  facetpane.header.html('<span style="color:#858585;font-size:.8em">Tracks from</span> ' + tkset.name);
+  facetpane.body.selectAll("*").remove();
+  backward_compatible(tkset.tklst);
+  const [assays, sample2assay2tracks, level2sample, L1_2_L2, samplewithlevel] = get_dimensions(tkset, flet);
+  const [assaynamelst] = sort_dimensions(assays, flet);
+  const scrollholder = facetpane.body.append("div");
+  if (sample2assay2tracks.size > 50) {
+    scrollholder.style("height", "500px").style("overflow-y", "scroll").style("resize", "vertical");
+  }
+  const table = scrollholder.append("table").style("margin", "10px").style("border-spacing", "3px").style("border-collapse", "separate").attr("class", "sja_simpletable");
+  const tr = table.append("tr");
+  if (L1_2_L2) {
+    tr.append("td");
+    tr.append("td");
+  } else if (level2sample) {
+    tr.append("td");
+  }
+  tr.append("td");
+  for (const assay of assaynamelst) {
+    tr.append("td").text(assay).attr("class", "sja_clbtext").on("click", () => {
+      batchselect_assay(assay);
+    });
+  }
+  if (L1_2_L2) {
+    for (const [L1, o] of L1_2_L2) {
+      let samplecount = 0;
+      for (const s of o.values()) {
+        samplecount += s.size;
+      }
+      let tr2 = table.append("tr");
+      let createnewrow_at_L2 = false;
+      tr2.append("td").text(L1).attr("class", "sja_clbtext").attr("rowspan", samplecount).on("click", () => {
+        batchselect_sample({ L1 });
+      });
+      for (const [L2, sampleset] of o) {
+        if (createnewrow_at_L2) tr2 = table.append("tr");
+        let createnewrow_at_sample = false;
+        tr2.append("td").text(L2).attr("rowspan", sampleset.size).attr("class", "sja_clbtext").on("click", () => {
+          batchselect_sample({ L1, L2 });
+        });
+        for (const sample of sampleset) {
+          if (createnewrow_at_sample) tr2 = table.append("tr");
+          tr2.append("td").text(sample).attr("class", "sja_clbtext").on("click", () => {
+            batchselect_sample({ L1, L2, sample });
+          });
+          for (const assay of assaynamelst) {
+            makecell(sample, assay, tr2);
+          }
+          createnewrow_at_sample = true;
+        }
+        createnewrow_at_L2 = true;
+      }
+    }
+  }
+  if (level2sample) {
+    for (const [level, sampleset] of level2sample) {
+      let tr2 = table.append("tr");
+      let createnewrow = false;
+      const td = tr2.append("td").text(level).attr("rowspan", sampleset.size).attr("class", "sja_clbtext").on("click", () => {
+        batchselect_sample({ level });
+      });
+      if (L1_2_L2) {
+        td.attr("colspan", 2);
+      }
+      for (const sample of sampleset) {
+        if (createnewrow) tr2 = table.append("tr");
+        tr2.append("td").text(sample).attr("class", "sja_clbtext").on("click", () => {
+          batchselect_sample({ level, sample });
+        });
+        for (const assay of assaynamelst) {
+          makecell(sample, assay, tr2);
+        }
+        createnewrow = true;
+      }
+      createnewrow = true;
+    }
+  }
+  for (const [sample, o] of sample2assay2tracks) {
+    if (samplewithlevel.has(sample)) continue;
+    const tr2 = table.append("tr");
+    const td = tr2.append("td").text(sample).attr("class", "sja_clbtext").on("click", () => {
+      batchselect_sample({ sample });
+    });
+    if (L1_2_L2) {
+      td.attr("colspan", 3);
+    } else if (level2sample) {
+      td.attr("colspan", 2);
+    }
+    for (const assay of assaynamelst) {
+      makecell(sample, assay, tr2);
+    }
+  }
+  function makecell(sample, assay, tr2) {
+    const td = tr2.append("td");
+    const s = sample2assay2tracks.get(sample);
+    if (!s) return;
+    const tklst = s.get(assay);
+    if (!tklst) return;
+    td.attr("class", "sja_menuoption").style("font-size", ".7em").style("text-align", "center");
+    let numdisplayed = 0;
+    for (const t of tklst) {
+      if (findtkbytkid(block, t.tkid)) {
+        numdisplayed++;
+      }
+    }
+    if (tklst.length > 1) {
+      td.text(tklst.length).on("click", (event) => {
+        tip.clear().show(event.clientX, event.clientY);
+        const table2 = tip.d.append("table");
+        for (const t of tklst) {
+          const tr3 = table2.append("tr");
+          const td1 = tr3.append("td").style("color", "#555").style("font-size", ".7em");
+          if (findtkbytkid(block, t.tkid)) {
+            td1.text("SHOWN");
+          }
+          tr3.append("td").text(t.partname || t.name).attr("class", "sja_menuoption").on("click", () => {
+            tkhandleclick(block, t, td1);
+          });
+        }
+      });
+    } else {
+      if (findtkbytkid(block, tklst[0].tkid)) {
+        td.text("SHOWN");
+      }
+      td.on("click", () => {
+        tkhandleclick(block, tklst[0], td);
+      });
+    }
+  }
+  function batchselect_assay(assay) {
+    const tklst = [];
+    for (const t of tkset.tklst) {
+      if (flet) {
+        if (!assays.has(t.assay)) continue;
+      }
+      if (t.assay == assay) {
+        tklst.push(t);
+      }
+    }
+    toggle_tracks(tklst);
+    facetmake(block, tkset, flet);
+  }
+  function batchselect_sample({ L1, L2, level, sample }) {
+    const tklst = [];
+    for (const t of tkset.tklst) {
+      if (flet) {
+        if (!assays.has(t.assay)) continue;
+      }
+      const l1 = t.level1;
+      const l2 = t.level2;
+      if (L1) {
+        if (l1 != L1) continue;
+        if (L2) {
+          if (l2 != L2) continue;
+          if (sample) {
+            if (t.sample == sample) tklst.push(t);
+          } else {
+            tklst.push(t);
+          }
+        } else {
+          tklst.push(t);
+        }
+      } else if (level) {
+        if (l1 && l2 || !l1 && !l2) continue;
+        const l = l1 || l2;
+        if (l != level) continue;
+        if (sample) {
+          if (t.sample == sample) tklst.push(t);
+        } else {
+          tklst.push(t);
+        }
+      } else if (sample) {
+        if (l1 || l2) continue;
+        if (t.sample == sample) tklst.push(t);
+      }
+    }
+    toggle_tracks(tklst);
+    facetmake(block, tkset, flet);
+  }
+  function toggle_tracks(lst) {
+    if (lst.length == 0) return;
+    const notshown = [];
+    for (const t of lst) {
+      if (!findtkbytkid(block, t.tkid)) {
+        notshown.push(t);
+      }
+    }
+    if (notshown.length) {
+      for (const t of notshown) {
+        const t2 = block.block_addtk_template(t);
+        if (t2) {
+          block.tk_load(t2);
+        } else {
+        }
+      }
+    } else {
+      for (const t of lst) {
+        for (let i = 0; i < block.tklst.length; i++) {
+          if (block.tklst[i].tkid == t.tkid) {
+            block.tk_remove(i);
+            break;
+          }
+        }
+      }
+    }
+  }
+}
+function get_dimensions(tkset, flet) {
+  const assays = /* @__PURE__ */ new Map();
+  const sample2assay2tracks = /* @__PURE__ */ new Map();
+  let level2sample;
+  let L1_2_L2;
+  const samplewithlevel = /* @__PURE__ */ new Set();
+  if (flet) {
+    for (const n of flet.assays) {
+      assays.set(n, 0);
+    }
+    for (const n of flet.samples) {
+      sample2assay2tracks.set(n, /* @__PURE__ */ new Map());
+    }
+    for (const t of tkset.tklst) {
+      if (!assays.has(t.assay)) continue;
+      const sample = t.patient || t.sample;
+      if (!sample2assay2tracks.has(sample)) continue;
+      assays.set(t.assay, assays.get(t.assay) + 1);
+      if (!sample2assay2tracks.get(sample).has(t.assay)) sample2assay2tracks.get(sample).set(t.assay, []);
+      sample2assay2tracks.get(sample).get(t.assay).push(t);
+    }
+    return [assays, sample2assay2tracks, null, null, samplewithlevel];
+  }
+  for (const t of tkset.tklst) {
+    if (!assays.has(t.assay)) assays.set(t.assay, 0);
+    assays.set(t.assay, assays.get(t.assay) + 1);
+  }
+  let hasl1 = false, hasl2 = false;
+  for (const t of tkset.tklst) {
+    if (t.level1) hasl1 = true;
+    if (t.level2) hasl2 = true;
+  }
+  if (hasl1 || hasl2) {
+    level2sample = /* @__PURE__ */ new Map();
+    if (hasl1 && hasl2) {
+      L1_2_L2 = /* @__PURE__ */ new Map();
+    }
+  }
+  for (const t of tkset.tklst) {
+    const sample = t.sample;
+    const assay = t.assay;
+    if (!assay || !sample) {
+      continue;
+    }
+    if (!sample2assay2tracks.has(sample)) sample2assay2tracks.set(sample, /* @__PURE__ */ new Map());
+    if (!sample2assay2tracks.get(sample).has(assay)) sample2assay2tracks.get(sample).set(assay, []);
+    sample2assay2tracks.get(sample).get(assay).push(t);
+    const L1 = t.level1, L2 = t.level2;
+    if (L1 || L2) {
+      samplewithlevel.add(sample);
+      if (L1 && L2) {
+        if (!L1_2_L2.has(L1)) L1_2_L2.set(L1, /* @__PURE__ */ new Map());
+        if (!L1_2_L2.get(L1).has(L2)) L1_2_L2.get(L1).set(L2, /* @__PURE__ */ new Set());
+        L1_2_L2.get(L1).get(L2).add(sample);
+      } else {
+        const L = L1 || L2;
+        if (!level2sample.has(L)) level2sample.set(L, /* @__PURE__ */ new Set());
+        level2sample.get(L).add(sample);
+      }
+    }
+  }
+  return [assays, sample2assay2tracks, level2sample, L1_2_L2, samplewithlevel];
+}
+function sort_dimensions(assays, flet) {
+  let assaynamelst;
+  if (flet && flet.nosortassay) {
+    assaynamelst = [...assays].map((a) => a[0]);
+  } else {
+    assaynamelst = [...assays].sort((a, b) => {
+      const [aname, atknum] = a;
+      const [bname, btknum] = b;
+      if (atknum == btknum) {
+        if (aname < bname) return -1;
+        return 1;
+      } else {
+        return btknum - atknum;
+      }
+    }).map((a) => a[0]);
+  }
+  return [assaynamelst];
+}
+function backward_compatible(lst) {
+  for (const t of lst) {
+    if (t.assayname) {
+      t.assay = t.assayname;
+      delete t.assayname;
+    }
+    if (!t.assay) continue;
+    if (t.patient) {
+      if (t.sampletype && t.patient == t.sampletype) {
+        delete t.sampletype;
+      }
+      if (!t.sample) {
+        t.sample = t.patient;
+        delete t.patient;
+      }
+    }
+    if (!t.sample) continue;
+    if (t.patient) {
+      t.level1 = t.patient;
+      delete t.patient;
+      if (t.sampletype) {
+        t.level2 = t.sampletype;
+        delete t.sampletype;
+      }
+    }
+  }
+}
+function findtkbytkid(block, tkid) {
+  for (const t of block.tklst) {
+    if (t.tkid == tkid) return true;
+  }
+  return false;
+}
+function tkhandleclick(block, tk, td1) {
+  for (let i = 0; i < block.tklst.length; i++) {
+    const t = block.tklst[i];
+    let equal = false;
+    if (tk.ds && tk.ds.iscustom) {
+      if (t.ds && t.ds.label == tk.ds.label) {
+        equal = true;
+      }
+    } else if (tk.tkid) {
+      if (t.tkid == tk.tkid) equal = true;
+    } else if (tk.id) {
+      if (t.id == tk.id && t.file == tk.file && t.url == tk.url) {
+        equal = true;
+      }
+    }
+    if (equal) {
+      block.tk_remove(i);
+      block.tkchangeaffectlegend(tk);
+      if (td1) {
+        td1.text("");
+      }
+      return;
+    }
+  }
+  let newt;
+  if (tk.type == tkt.ds) {
+    const newtemplate = {
+      type: tk.type,
+      tkid: tk.tkid,
+      // must retain tkid
+      ds: tk.ds,
+      isvcf: tk.isvcf,
+      itemlabelname: tk.itemlabelname,
+      iscustom: tk.iscustom,
+      vcfinfofilter: tk.vcfinfofilter,
+      populationfrequencyfilter: tk.populationfrequencyfilter,
+      url4variant: tk.url4variant,
+      button4variant: tk.button4variant,
+      viewrangeupperlimit: tk.viewrangeupperlimit
+    };
+    if (tk.ds.iscustom) {
+      block.addchilddsnoload(tk.ds);
+    }
+    newt = block.block_addtk_template(newtemplate);
+  } else {
+    newt = block.block_addtk_template(tk);
+  }
+  block.tk_load(newt);
+  if (td1) {
+    td1.text("SHOWN");
+  }
+}
+function tkhtmllabel(tk, block) {
+  let basename;
+  if (tk.type == tkt.usegm) {
+    if (block) {
+      switch (block.gmmode) {
+        case gmmode.gmsum:
+          const usecount = block.allgm.reduce((i, j) => i + (j.hidden ? 0 : 1), 0);
+          basename = tk.name + ", sum of " + (usecount < block.allgm.length ? usecount + " of " + block.allgm.length : usecount) + " isoforms";
+          break;
+        case gmmode.splicingrna:
+          basename = tk.name + " exons";
+          break;
+        case gmmode.exononly:
+          basename = tk.name + " RNA";
+          break;
+        case gmmode.genomic:
+          basename = tk.name + " genomic view";
+          break;
+        case gmmode.protein:
+          basename = tk.name + " protein";
+          break;
+      }
+    } else {
+      basename = tk.name;
+    }
+  } else if (tk.type == tkt.ds) {
+    basename = tk.ds.label;
+  } else if (tk.name) {
+    basename = tk.name;
+  } else {
+    if (tk.dslabel) {
+      basename = tk.dslabel;
+    } else {
+      const lst = [];
+      if (tk.patient) lst.push(tk.patient);
+      if (tk.sampletype) lst.push(tk.sampletype);
+      if (tk.assayname) lst.push(tk.assayname);
+      basename = lst.join(" ");
+    }
+  }
+  if (tk.type == tkt.junction) {
+    if (tk.totalsamplecount == void 0) {
+      return basename;
+    }
+    if (tk.totalsamplecount == 1) {
+      return basename;
+    }
+    return `${basename} (${tk.totalsamplecount})`;
+  }
+  if (!tk.tracks || tk.tracks.length == 1) {
+    return basename;
+  }
+  return `${basename} (${tk.tracks.length})`;
+}
+var remoteFileNotSupported = "Remote file not supported on this server.";
+function remoteFileAllowed() {
+  return JSON.parse(sessionStorage.getItem("optionalFeatures") || "{}").ALLOW_remotefilefromurl;
+}
+function mayShowRemoteFileNote(holder) {
+  if (remoteFileAllowed()) return;
+  holder.append("p").style("color", "#858585").style("font-size", ".8em").text(remoteFileNotSupported);
+}
+function urlNotAllowed(s) {
+  if (remoteFileAllowed() || !stringisurl(s)) return false;
+  window.alert(remoteFileNotSupported);
+  return true;
+}
+function stringisurl(s) {
+  const ss = s.toLowerCase();
+  if (ss.startsWith("http://")) return true;
+  if (ss.startsWith("https://")) return true;
+  if (ss.startsWith("ftp://")) return true;
+  return false;
+}
+function notAllowedToHideThisTrack(tk) {
+  if (tk.type == tkt.usegm) return true;
+  if (tk.type == "mds3" && tk.dslabel) return true;
+  if (tk.type == "bam" && tk.gdcFile) return true;
+  return false;
+}
+export {
+  block_tk_menu_default as default
+};
+//# sourceMappingURL=block.tk.menu-BIORXN3G.js.map