@sjcrh/proteinpaint-client 2.217.0 → 2.218.0

package/dist/block.tk.menu-7JBJOY2O.js

@@ -1,1050 +0,0 @@
-import {
-  appear2 as appear,
-  disappear2 as disappear,
-  gmmode,
-  newpane,
-  tkexists,
-  tkt
-} from "./chunk-NNDKYTUV.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-HWNQOADC.js";
-import {
-  Menu
-} from "./chunk-CNFTQSNE.js";
-import "./chunk-PLFPXOGX.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import "./chunk-BIJOXCLN.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-L2WOLNZK.js";
-import "./chunk-AMW5LCUB.js";
-import {
-  category10_default
-} from "./chunk-ZPWBYHNE.js";
-import "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import {
-  ordinal
-} from "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// src/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-7JBJOY2O.js.map