@sjcrh/proteinpaint-client 2.221.0 → 2.222.0

package/dist/leftlabel.sample-QKXIODCS.js

@@ -1,253 +0,0 @@
-import {
-  displaySampleTable,
-  getFilterName,
-  makelabel
-} from "./chunk-ENPMWVWG.js";
-import "./chunk-FE5TCBIT.js";
-import "./chunk-YPBY37KD.js";
-import "./chunk-VBTBUXXX.js";
-import "./chunk-V2OJLJSK.js";
-import "./chunk-4FTH4L3A.js";
-import "./chunk-VLIOMJDR.js";
-import {
-  Tabs,
-  fillbar,
-  filterInit,
-  getNormalRoot,
-  renderTable,
-  violinRenderer
-} from "./chunk-WD7FZ5EE.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-WXSMUSU7.js";
-import "./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 "./chunk-WJLRU5OF.js";
-import "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-PWYMHUXY.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// mds3/leftlabel.sample.js
-function makeSampleLabel(data, tk, block, laby) {
-  if (!tk.leftlabels.doms.samples) {
-    tk.leftlabels.doms.samples = makelabel(tk, block, laby);
-  }
-  if (data.sampleTotalNumber) {
-    tk.leftlabels.doms.samples.attr("class", "sja_clbtext2").style("opacity", 1).text(`${data.sampleTotalNumber} sample${data.sampleTotalNumber > 1 ? "s" : ""}`).attr("data-testid", "sjpp_mds3tk_samples_label").on("click", async (event) => {
-      tk.menutip.clear().showunder(event.target);
-      await mayShowSummary(tk, block);
-      const buttonrow = tk.menutip.d.append("div").style("margin", "10px");
-      menu_listSamples(buttonrow, data, tk, block);
-    });
-  } else {
-    tk.leftlabels.doms.samples.text("No samples").attr("class", "").style("opacity", 0.5).on("click", null);
-  }
-}
-function makeSampleFilterLabel(data, tk, block, laby) {
-  if (!tk.leftlabels.doms.filterObj) {
-    tk.leftlabels.doms.filterObj = makelabel(tk, block, laby);
-    tk.leftlabels.doms.filterObj.attr("data-testid", "sjpp_mds3tk_leftlabel_samplefilter");
-  }
-  tk.leftlabels.doms.filterObj.text(getFilterName(tk.filterObj)).on("click", async (event) => {
-    tk.menutip.clear().showunder(event.target);
-    const arg = {
-      holder: tk.menutip.d.append("div").style("margin", "10px"),
-      vocabApi: tk.mds.termdb.vocabApi,
-      callback: (f) => {
-        tk.filterObj = f;
-        tk.load();
-      }
-    };
-    mayAddGetCategoryArgs(arg, block);
-    filterInit(arg).main(tk.filterObj);
-  });
-}
-function mayAddGetCategoryArgs(arg, block) {
-  if (block.usegm) {
-    arg.getCategoriesArguments = { currentGeneNames: [block.usegm.name] };
-  } else {
-    arg.getCategoriesArguments = { rglst: structuredClone(block.rglst) };
-  }
-}
-async function mayShowSummary(tk, block) {
-  if (!tk.mds.variant2samples.twLst) {
-    return;
-  }
-  const div = tk.menutip.d.append("div").style("margin", "10px");
-  const wait = div.append("div").text("Loading...");
-  try {
-    const { summary } = await tk.mds.getSamples({ isSummary: true });
-    tk.leftlabels.__samples_data = summary;
-    wait.remove();
-    await showSummary4terms(summary, div.append("div").attr("data-testid", "sja_mds3samplesummarydiv"), tk, block);
-  } catch (e) {
-    wait.text(`Error: ${e.message || e}`);
-    if (e.stack) console.log(e.stack);
-  }
-}
-async function showSummary4terms(data, div, tk, block) {
-  const tabs = [];
-  for (const { termid, numbycategory } of data) {
-    tabs.push({
-      label: tk.mds.variant2samples.twLst.find((i) => i.term.id == termid).term.name + (numbycategory ? `<span style="font-size:.8em;float:right;margin-left: 5px;">n=${numbycategory.length}</span>` : ""),
-      keydownCallback: function(event) {
-        setTimeout(() => {
-          const tr = this.contentHolder.select("tbody").select("tr").node();
-          if (!tr) return;
-          tr.focus();
-        }, 100);
-      }
-    });
-  }
-  new Tabs({
-    holder: div,
-    tabsPosition: "vertical",
-    linePosition: "right",
-    tabs
-  }).main();
-  for (const [i, d] of data.entries()) {
-    const holder = tabs[i].contentHolder.style("padding-left", "20px");
-    if (d.numbycategory) {
-      holder.append("div").text("Click a category to create new track.").style("margin-bottom", "10px").style("font-size", ".8em").style("opacity", 0.5);
-      showSummary4oneTerm(d.termid, holder, d.numbycategory, tk, block);
-      continue;
-    }
-    if (d.density_data) {
-      if (!Number.isFinite(d.density_data.min) || !Number.isFinite(d.density_data.max)) {
-        holder.append("div").text("No data");
-        continue;
-      }
-      holder.append("div").text("Select a range to create new track.").style("margin-bottom", "10px").style("font-size", ".8em").style("opacity", 0.5);
-      showDensity4oneTerm(d.termid, holder, d, tk, block);
-      continue;
-    }
-    throw "unknown summary data";
-  }
-}
-function showSummary4oneTerm(termid, div, numbycategory, tk, block) {
-  const tw = tk.mds.variant2samples.twLst.find((i) => i.term.id == termid);
-  if (!tw) throw "showSummary4oneTerm(): tw not found from variant2samples.twLst";
-  const rows = [];
-  for (const [category_key, count, total] of numbycategory) {
-    const sk = category_key.replace(/\s/g, "-");
-    const row = [
-      { value: tw.term.values?.[category_key]?.label || category_key },
-      { html: total == void 0 ? "" : fillbar(null, { f: count / total, v1: count, v2: total }) },
-      {
-        html: `<span data-testid=sjpp-mds3tk-samsumcatmutcount-${sk}>${count}</span>
-			${total ? ` <span style="font-size:.8em">/ <span data-testid=sjpp-mds3tk-samsumcattotalcount-${sk}>` + total + "</span></span>" : ""}`
-      }
-    ];
-    rows.push(row);
-  }
-  renderTable({
-    div,
-    rows,
-    columns: [
-      {
-        nowrap: true
-        // to force all category values to show in one line without wrap. otherwise they wrap and column width appears fixed
-      },
-      {},
-      {}
-    ],
-    showHeader: false,
-    singleMode: true,
-    noRadioBtn: true,
-    noButtonCallback: (i) => {
-      clickCategory(numbycategory[i][0]);
-    }
-  });
-  async function clickCategory(category) {
-    tk.menutip.clear();
-    const term = await tk.mds.termdb.vocabApi.getterm(termid);
-    if (!term.values || Object.keys(term.values).length == 0) {
-      term.values = {};
-      for (const c of numbycategory) {
-        term.values[c[0]] = { label: c[0], samplecount: c[1] };
-      }
-    }
-    const tvs = {
-      type: "tvs",
-      tvs: { term, values: [{ key: category }] }
-    };
-    createSubTk(tk, block, tvs);
-  }
-}
-function getNewFilter(tk, tvs) {
-  if (tk.filterObj) {
-    return getNormalRoot({
-      type: "tvslst",
-      join: "and",
-      in: true,
-      lst: [tk.filterObj, tvs]
-    });
-  }
-  return {
-    type: "tvslst",
-    in: true,
-    join: "",
-    lst: [tvs]
-  };
-}
-async function showDensity4oneTerm(termid, div, data, tk, block) {
-  const term = await tk.mds.termdb.vocabApi.getterm(termid);
-  const callback = async (range) => {
-    tk.menutip.clear();
-    const tvs = {
-      type: "tvs",
-      tvs: { term, ranges: [{ start: range.range_start, stop: range.range_end }] }
-    };
-    createSubTk(tk, block, tvs);
-  };
-  const vr = new violinRenderer({
-    holder: div,
-    rd: data.density_data,
-    width: 400,
-    height: 100,
-    radius: 8,
-    callback,
-    scaleFactor: term.valueConversion ? term.valueConversion.scaleFactor : 1
-  });
-  vr.render();
-}
-function createSubTk(tk, block, tvs) {
-  const tk2 = block.block_addtk_template(tk.duplicateTk(getNewFilter(tk, tvs)));
-  tk2.subtk = true;
-  block.tk_load(tk2);
-}
-function menu_listSamples(buttonrow, data, tk, block) {
-  buttonrow.append("div").text(`List ${data.sampleTotalNumber} sample${data.sampleTotalNumber > 1 ? "s" : ""}`).attr("class", "sja_menuoption sja_mds3_slb_sampletablebtn").attr("data-testid", "sjpp-mds3-list-samples-option").on("click", async () => {
-    tk.menutip.clear();
-    const wait = tk.menutip.d.append("div").text("Loading...").style("margin", "15px");
-    try {
-      const { samples } = await tk.mds.getSamples();
-      await displaySampleTable(samples, {
-        div: tk.menutip.d,
-        tk,
-        block
-      });
-      wait.remove();
-    } catch (e) {
-      wait.text(e.message || e);
-      console.log(e);
-    }
-  });
-}
-export {
-  makeSampleFilterLabel,
-  makeSampleLabel
-};
-//# sourceMappingURL=leftlabel.sample-QKXIODCS.js.map

package/dist/lollipop-TSZ62PBH.js

@@ -1,162 +0,0 @@
-import {
-  block_init_default
-} from "./chunk-K3G56J5R.js";
-import {
-  addGeneSearchbox,
-  first_genetrack_tolist
-} from "./chunk-WD7FZ5EE.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-WXSMUSU7.js";
-import {
-  Menu
-} from "./chunk-CNFTQSNE.js";
-import "./chunk-RIHO7ZD5.js";
-import "./chunk-TVJOSRCH.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import {
-  dofetch3
-} from "./chunk-4TJO2DGU.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-MHWYRNGA.js";
-import "./chunk-JHLF2ZC2.js";
-import "./chunk-WJLRU5OF.js";
-import "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-PWYMHUXY.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// gdc/lollipop.js
-var tip = new Menu({ padding: "" });
-async function init(arg, holder, genomes) {
-  const useGenome = arg.genome || "hg38";
-  const useDslabel = arg.dslabel || "GDC";
-  const genome = genomes[useGenome];
-  if (!genome) throw useGenome + " missing";
-  if (arg.geneSearch4GDCmds3.onloadalltk_always && typeof arg.geneSearch4GDCmds3.onloadalltk_always != "function")
-    throw "arg.geneSearch4GDCmds3.onloadalltk_always not function";
-  if (arg.geneSearch4GDCmds3.postRender && typeof arg.geneSearch4GDCmds3.postRender != "function")
-    throw "arg.geneSearch4GDCmds3.postRender not function";
-  holder.selectAll(".sja_lollipop_holder").remove();
-  const mainDiv = holder.append("div").attr("class", "sja_lollipop_holder");
-  const geneInputDiv = mainDiv.append("div").style("margin-left", "20px");
-  geneInputDiv.append("div").text(
-    arg.geneSearch4GDCmds3.hardcodeCnvOnly ? `To view ${useDslabel} CNV segments over a gene or region, enter genomic position (chr11:108195437-108267444), dbSNP accesion, or gene name (MYC).` : `To view ${useDslabel} mutations on a gene, enter one of gene symbol (MYC), alias (c-Myc), GENCODE accession (ENSG00000136997, ENST00000621592), or RefSeq accession (NM_002467).`
-  );
-  const graphDiv = mainDiv.append("div").attr("class", "sja_geneSearch4GDCmds3_blockdiv");
-  const searchOpt = {
-    genome,
-    tip,
-    row: geneInputDiv,
-    callback: launchView,
-    geneSymbol: arg.geneSymbol,
-    triggerSearch: arg.geneSymbol && arg.geneSearch4GDCmds3?.hardcodeCnvOnly == true,
-    hideInputBeforeCallback: arg.geneSearch4GDCmds3?.hardcodeCnvOnly == true
-  };
-  if (!arg.geneSearch4GDCmds3.hardcodeCnvOnly) {
-    searchOpt.searchOnly = "gene";
-  }
-  const coordInput = addGeneSearchbox(searchOpt);
-  let userSelection;
-  await arg.geneSearch4GDCmds3.postRender?.({ tip });
-  if (arg.state) {
-    if (arg.state.userSelection) launchView(false, arg.state.userSelection);
-    delete arg.state;
-  }
-  async function launchView(triggeredByInput = true, userSelection2) {
-    const pa = {
-      // param for instantiating block
-      genome,
-      holder: graphDiv,
-      gmmode: "exon only",
-      nobox: 1,
-      hide_dsHandles: arg.hide_dsHandles,
-      onloadalltk_always: arg.geneSearch4GDCmds3.onloadalltk_always
-    };
-    if (arg.tracks) {
-      pa.tklst = arg.tracks;
-    } else {
-      const tk = {
-        type: "mds3",
-        dslabel: useDslabel,
-        allow2selectSamples: arg.allow2selectSamples,
-        filter0: arg.filter0
-      };
-      pa.tklst = [tk];
-      if (arg.geneSearch4GDCmds3.hardcodeCnvOnly) {
-        tk.hardcodeCnvOnly = 1;
-        delete pa.gmmode;
-        first_genetrack_tolist(pa.genome, pa.tklst);
-      }
-      if (arg.geneSearch4GDCmds3.snvIndelOnly) {
-        tk.snvIndelOnly = 1;
-      }
-    }
-    if (userSelection2) {
-      if (arg.geneSearch4GDCmds3.hardcodeCnvOnly) {
-        if (typeof userSelection2 != "object") throw "userSelection not object when pa.block is true";
-        pa.chr = userSelection2.chr;
-        pa.start = userSelection2.start;
-        pa.stop = userSelection2.stop;
-        if (!pa.chr || !Number.isInteger(pa.start) || !Number.isInteger(pa.stop))
-          throw "userSelection not {chr,start,stop}";
-      } else {
-        if (typeof userSelection2 != "string") throw "userSelection should be string when pa.block is not true";
-        pa.query = userSelection2;
-      }
-    } else {
-      if (arg.geneSearch4GDCmds3.hardcodeCnvOnly) {
-        if (!coordInput.chr || !Number.isInteger(coordInput.start) || !Number.isInteger(coordInput.stop)) {
-          if (triggeredByInput) throw "coordInput.chr/start/stop missing";
-        }
-        pa.chr = coordInput.chr;
-        pa.start = coordInput.start;
-        pa.stop = coordInput.stop;
-      } else {
-        if (!coordInput.geneSymbol) {
-          if (triggeredByInput) throw "coordInput.geneSymbol missing";
-        }
-        const gmlst = (await dofetch3(`genelookup?deep=1&input=${coordInput.geneSymbol}&genome=${useGenome}`)).gmlst;
-        if (!Array.isArray(gmlst) || gmlst.length == 0) throw "gmlst is not non-empty array";
-        pa.query = getSelectedIsoform(coordInput, gmlst);
-        if (gmlst.some((i) => i.coding)) pa.gmmode = "protein";
-      }
-    }
-    graphDiv.selectAll("*").remove();
-    if (!arg.geneSearch4GDCmds3.hardcodeCnvOnly) return await block_init_default(pa);
-    const _ = await import("./block-GLF6QNKY.js");
-    return new _.Block(pa);
-  }
-  const api = {
-    update: (_arg) => {
-      Object.assign(arg, _arg);
-      launchView(false);
-    },
-    getState: () => ({ userSelection })
-  };
-  return api;
-}
-function getSelectedIsoform(coordInput, gmlst) {
-  if (coordInput.fromWhat) {
-    if (gmlst.some((i) => i.isoform.toUpperCase() == coordInput.fromWhat.toUpperCase())) {
-      return coordInput.fromWhat;
-    }
-    if (coordInput.fromWhat.toUpperCase().startsWith("ENSG")) {
-      for (const i of gmlst) {
-        if (i.isdefault && i.isoform.startsWith("ENST")) return i.isoform;
-      }
-    }
-  }
-  const defaultIsoform = gmlst.find((i) => i.isdefault);
-  if (defaultIsoform) return defaultIsoform.isoform;
-  return gmlst[0].isoform;
-}
-export {
-  init
-};
-//# sourceMappingURL=lollipop-TSZ62PBH.js.map