@sjcrh/proteinpaint-client 2.204.0 → 2.205.0

package/dist/chunk-IS4VLUEX.js

@@ -0,0 +1,382 @@
+import {
+  Menu
+} from "./chunk-ELJX3QIQ.js";
+import {
+  mclass
+} from "./chunk-IK2BO37K.js";
+import {
+  copyMerge
+} from "./chunk-WINIL2KN.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+
+// plots/matrix/matrix.sorterUi.js
+var alphabet = `ABCDEFGHIJKLMNOPQRSTUVWXYZ`.split("");
+function getSorterUi(opts) {
+  const { controls, holder } = opts;
+  const parent = controls.parent;
+  const s = structuredClone(parent.config.settings.matrix);
+  const l = s.controlLabels;
+  const tip = new Menu({ padding: "", parent_menu: parent.app.tip?.d.node() });
+  let input, theads = [], sectionData, dragged = {};
+  const self = {
+    dom: { tip },
+    opts,
+    highlightColor: "none",
+    label: `Sort ${l.Samples}`,
+    title: `Set how to sort ${l.samples}`,
+    type: "custom",
+    expanded: opts.expanded || false,
+    expandedSection: opts.expandedSection || "",
+    init(overrides = {}, _opts = {}) {
+      tip.clear().hide();
+      if (parent.config.settings.matrix != s) copyMerge(s, parent.config.settings.matrix);
+      if (s !== overrides) copyMerge(s, overrides);
+      self.settings = s;
+      self.activeOption = structuredClone(s.sortOptions[s.sortSamplesBy]);
+      sectionData = [
+        // TODO: add an advanced menu section here for sortBySampleAncestry = 'first'
+        {
+          label: `For each selected row, sort ${l.samples} by matching data`,
+          notDraggable: true,
+          tiebreakers: [],
+          handler: handleSelectedTerms
+        },
+        ...self.activeOption.sortPriority,
+        {
+          label: `Sort ${l.samples} by name, alphabetically`,
+          notDraggable: true,
+          tiebreakers: []
+        }
+      ];
+      Object.assign(opts, _opts);
+      opts.holder.selectAll("*").remove();
+      const topDiv = opts.holder.append("div").style("text-align", "right");
+      topDiv.append("button").html("Apply").on("click", apply);
+      topDiv.append("button").html("Reset").on("click", (event, d) => self.init());
+      const table = opts.holder.append("table");
+      const tr = table.append("thead");
+      tr.append("th").html("Priority").style("text-align", "left").style("max-width", "0px");
+      tr.append("th").html("Description");
+      tr.append("th").html("Action");
+      let i = 0, j = 0;
+      for (const sd of sectionData) {
+        const hasTbOrder = sd.tiebreakers?.[0]?.order || sd.handler;
+        const thead = table.append("thead").datum(sd).property("draggable", !sd.notDraggable).attr("droppable", true).on("dragstart", trackDraggedSection).on("dragover", highlightSection).on("dragleave", unhighlightSection).on("drop", adjustSortPriority);
+        theads.push(select_default(thead));
+        const tr2 = thead.append("tr").style("background-color", "#eee").on("mouseover", undoMouseoverHighlights);
+        tr2.append("th").style("padding", "5px").style("vertical-align", "top").style("font-weight", 400).html(alphabet[j++]).on("click", hasTbOrder ? toggleSection : null);
+        const td2 = tr2.append("th").style("padding", "5px").style("vertical-align", "top").style("text-align", "left").style("cursor", hasTbOrder ? "pointer" : "").on("click", hasTbOrder ? toggleSection : null);
+        td2.append("span").style("margin-right", "12px").style("font-weight", 400).html(sd.label);
+        tr2.append("th").style("padding", "5px").style("vertical-align", "top").style("text-align", "center").style("font-weight", 400).style("cursor", hasTbOrder ? "pointer" : "").append("span").html(hasTbOrder ? "Details" : " ").on("click", hasTbOrder ? toggleSection : null);
+        const tbody = table.append("tbody").datum(sd).style("display", self.expandedSection == "all" || self.expandedSection == sd.label ? "" : "none");
+        for (const tb of sd.tiebreakers) {
+          if (tb.skip) continue;
+          if (!sd.types?.includes("geneVariant")) {
+            continue;
+          }
+          const tr3 = tbody.append("tr").on("mouseover", undoMouseoverHighlights).datum(tb).attr("draggable", !tb.disabled && sd.types?.length !== 0).attr("droppable", !tb.disabled && sd.types?.length !== 0).on("dragstart", trackDraggedTieBreaker).on("dragover", highlightTieBreaker).on("dragleave", unhighlightTieBreaker).on("drop", adjustTieBreakers);
+          if (!tb.disabled) i++;
+          const td1 = tr3.append("td").attr(
+            "title",
+            tb.disabled ? `This tiebreaker is currently not being used to sort ${l.cases}. Check the box to use.` : `The number indicates the order in which this tiebreaker is used. Unched the box to skip.`
+          ).datum(tb);
+          td1.style("padding", "5px").style("vertical-align", "top").style("text-align", "center");
+          td1.append("span").html(!tb.disabled ? i : "");
+          const td22 = tr3.append("td").style("opacity", tb.disabled ? 0.5 : 1).style("padding", "5px").style("vertical-align", "top").style("max-width", "500px");
+          td22.append("span").html(tb.label || "");
+          if (!tb.disabled) {
+            const label = td22.append("label");
+            label.append("span").html("<br>(use data list order ");
+            if (!tb.isOrdered) tb.isOrdered = false;
+            const checkbox = label.append("input").datum(tb).attr("type", "checkbox").property("checked", tb.isOrdered).style("vertical-align", "bottom").on("change", toggleTieBreakerIsOrdered);
+            label.append("span").html(")");
+            const order = tb.order;
+            td22.append("div").attr("class", "sjpp-matrix-sorter-ui-value").selectAll("div").data(
+              order.map((key, index) => ({
+                lstName: "order",
+                key,
+                cls: mclass[key],
+                tb,
+                dragstart: trackDraggedValue,
+                dragover: highlightValue,
+                dragleave: unhighlightValue,
+                drop: adjustValueOrder,
+                filterByClass: s.filterByClass,
+                index
+              }))
+            ).enter().append("div").style("display", tb.isOrdered ? "block" : "inline-block").each(setValueDiv);
+            if (tb.notUsed?.length) {
+              const notUsed = td22.append("div");
+              notUsed.append("div").attr("data-testid", "sjpp-matrix-sorter-ui-hidden-add").style("display", "inline-block").style("padding", "5x").style("vertical-align", "top").style("padding", "3px 5px").style("cursor", "pointer").html(`+Add`).on("click", showNotUsedValues);
+            }
+          }
+          const td3 = tr3.append("td").style("text-align", "center").style("vertical-align", "top");
+          if (tb.mayToggle) {
+            td3.append("button").datum(tb).html(tb.disabled ? "Enable" : "Disable").on("click", toggleTieBreakerDisabled);
+          }
+        }
+        const lastTr = tbody.append("tr").attr("draggable", true).on("mouseover", undoMouseoverHighlights);
+        lastTr.append("td").html("&nbsp;");
+        const tdNew = lastTr.append("td").style("text-align", "left").html(sd.details && !sd.order?.length ? sd.details : "&nbsp;");
+        if (sd.handler) sd.handler(tdNew, lastTr, tbody);
+        lastTr.append("td").html("&nbsp;");
+      }
+    },
+    toggleSection,
+    trackDraggedSection,
+    highlightSection,
+    unhighlightSection,
+    adjustSortPriority,
+    trackDraggedTieBreaker,
+    highlightTieBreaker,
+    unhighlightTieBreaker,
+    adjustTieBreakers,
+    trackDraggedValue,
+    highlightValue,
+    unhighlightValue,
+    adjustValueOrder,
+    apply
+  };
+  function toggleSection(event, d = { label: "all" }) {
+    self.expandedSection = self.expandedSection === d.label ? "" : d.label;
+    self.expanded = !!self.expandedSection;
+    self.init();
+  }
+  function trackDraggedSection(event, d) {
+    dragged.type = "sortPriority";
+    dragged.data = d;
+    dragged.index = self.activeOption.sortPriority.indexOf(d);
+  }
+  function highlightSection(event, d) {
+    if (dragged.type != "sortPriority" || d == dragged.data) return;
+    event.preventDefault();
+    const i = self.activeOption.sortPriority.indexOf(d);
+    const borderSide = i < dragged.index ? "border-top" : i > dragged.index ? "border-bottom" : "";
+    if (!borderSide) return;
+    select_default(this).selectAll("th").style(borderSide, "2px solid blue");
+  }
+  function unhighlightSection(event, d) {
+    if (dragged.type != "sortPriority") return;
+    event.preventDefault();
+    select_default(this).selectAll("th").style("border", "none");
+  }
+  function adjustSortPriority(event, d) {
+    if (d == dragged.data) return;
+    const i = self.activeOption.sortPriority.indexOf(d);
+    const s2 = parent.config.settings.matrix;
+    self.activeOption.sortPriority.splice(dragged.index, 1);
+    self.activeOption.sortPriority.splice(i, 0, dragged.data);
+    self.init({
+      sortOptions: {
+        [s2.sortSamplesBy]: self.activeOption
+      }
+    });
+  }
+  function trackDraggedTieBreaker(event, d) {
+    dragged.type = "tiebreaker";
+    dragged.data = d;
+    dragged.sectionData = event.target.closest("tbody").__data__;
+    dragged.priorityIndex = self.activeOption.sortPriority.indexOf(dragged.sectionData);
+    dragged.index = dragged.sectionData.tiebreakers.indexOf(d);
+  }
+  function highlightTieBreaker(event, d) {
+    if (dragged.type != "tiebreaker" || d == dragged.data) return;
+    event.preventDefault();
+    const i = dragged.sectionData.tiebreakers.indexOf(d);
+    const borderSide = i < dragged.index ? "border-top" : i > dragged.index ? "border-bottom" : "";
+    if (!borderSide) return;
+    select_default(this).selectAll("td:nth-child(2)").style(borderSide, "2px solid blue");
+  }
+  function unhighlightTieBreaker(event, d) {
+    if (dragged.type != "tiebreaker") return;
+    event.preventDefault();
+    select_default(this).selectAll("td:nth-child(2)").style("border", "none");
+  }
+  function toggleTieBreakerIsOrdered(event, tb) {
+    event.stopPropagation();
+    tb.isOrdered = !tb.isOrdered;
+    self.init({
+      sortOptions: {
+        [s.sortSamplesBy]: self.activeOption
+      }
+    });
+  }
+  function toggleTieBreakerDisabled(event, tb) {
+    event.stopPropagation();
+    tb.disabled = !tb.disabled;
+    self.init({
+      sortOptions: {
+        [s.sortSamplesBy]: self.activeOption
+      }
+    });
+  }
+  function adjustTieBreakers(event, d) {
+    if (dragged.type != "tiebreaker" || d == dragged.data) return;
+    event.preventDefault();
+    const i = dragged.sectionData.tiebreakers.indexOf(d);
+    const s2 = parent.config.settings.matrix;
+    dragged.sectionData.tiebreakers.splice(dragged.index, 1);
+    dragged.sectionData.tiebreakers.splice(i, 0, dragged.data);
+    self.init({
+      sortOptions: {
+        [s2.sortSamplesBy]: self.activeOption
+      }
+    });
+  }
+  function setValueDiv(d) {
+    const title = [];
+    if (d.tb.notUsed?.includes(d.key)) title.push(`- Click on this label to include in used data values.`);
+    if (d.filterByClass[d.key])
+      title.unshift("- Click on the corresponding entry in the matrix legend or Mutation/CNV menus to unhide");
+    if (title.length) title.unshift(`To use this data value for sorting ${l.samples}:`);
+    const skipped = d.tb.notUsed?.includes(d.key);
+    const opacity = d.filterByClass[d.key] == "value" ? 0.5 : 1;
+    const div = select_default(this).attr("aria-label", title.length ? title.join("\n") : `Click to not use this data value to sort ${l.samples}`).attr("draggable", d.tb.isOrdered ? true : false).attr("droppable", d.tb.isOrdered ? true : false).style("width", "fit-content").style("margin-right", "10px").style("overflow", "hidden").style("white-space", "nowrap").style("opacity", opacity).style("cursor", "pointer").on("dragstart", d.dragstart).on("dragover", d.dragover).on("dragleave", d.dragleave).on("drop", d.drop).on("mouseenter", () => toggle.style("opacity", 1)).on("mouseleave", () => toggle.style("opacity", 0)).on("click", () => {
+      if (title.length) {
+        const cls = "sjpp-matrix-sorter-value-note";
+        div.selectAll(`.${cls}`).remove();
+        const note = div.append("div").attr("class", cls).style("max-width", "200px").style("padding", "5px");
+        note.html(title.join("<br>"));
+        if (d.filterByClass[d.key]) return;
+      }
+      const targetLstName = d.lstName == "order" ? "notUsed" : "order";
+      if (!d.tb[targetLstName]) d.tb[targetLstName] = [];
+      const targetLst = d.tb[targetLstName];
+      d.tb[d.lstName].splice(d.index, 1);
+      if (d.lstName == "order") targetLst.unshift(d.key);
+      else targetLst.push(d.key);
+      self.init({
+        sortOptions: {
+          [s.sortSamplesBy]: self.activeOption
+        }
+      });
+    });
+    div.append("div").style("display", "inline-block").style("cursor", "pointer").style("width", "12px").style("height", "12px").style("margin-right", "3px").style("background-color", d.cls.color);
+    div.append("span").style("cursor", "pointer").style("text-decoration", d.filterByClass[d.key] == "case" ? "line-through" : "").html(d.cls.label + (d.filterByClass[d.key] ? " (<i>not used since this value is hidden</i>)" : ""));
+    const toggle = div.append("div").style("display", "inline-block").style("width", "12px").style("cursor", "pointer").style("opacity", 0).style("color", d.lstName == "order" ? "red" : "green").html(d.lstName == "order" ? "&cross;" : "&check;");
+  }
+  function trackDraggedValue(event, d) {
+    event.stopPropagation?.();
+    dragged.type = "value";
+    dragged.data = d;
+    dragged.sectionData = event.target.closest("tbody").__data__;
+    dragged.priorityIndex = self.activeOption.sortPriority.indexOf(dragged.sectionData);
+    dragged.tiebreaker = event.target.closest("tr").__data__;
+    dragged.tbIndex = dragged.sectionData.tiebreakers.indexOf(dragged.priorityIndex);
+    dragged.order = dragged.tiebreaker.order;
+  }
+  function highlightValue(event, d) {
+    event.stopPropagation?.();
+    if (dragged.type != "value" || d == dragged.data) return;
+    if (d.tb != dragged.data.tb) return;
+    event.preventDefault();
+    const i = dragged.order.indexOf(d);
+    select_default(this).style("border", "2px solid blue");
+  }
+  function unhighlightValue(event, d) {
+    event.stopPropagation?.();
+    if (dragged.type != "value") return;
+    event.preventDefault();
+    select_default(this).style("border", "none");
+  }
+  function adjustValueOrder(event, d) {
+    event.stopPropagation?.();
+    if (dragged.type != "value" || d == dragged.data) return;
+    event.preventDefault();
+    const s2 = self.settings;
+    dragged.data.tb[dragged.data.lstName].splice(dragged.data.index, 1);
+    d.tb[d.lstName].splice(d.index, 0, dragged.data.key);
+    const j = s2.hiddenVariants.indexOf(dragged.data.key);
+    const hiddenVariants = structuredClone(s2.hiddenVariants);
+    const filterByClass = structuredClone(s2.filterByClass);
+    if (j != -1) {
+      hiddenVariants.splice(j, 1);
+      filterByClass[dragged.data.key] = false;
+    }
+    self.init({
+      hiddenVariants,
+      filterByClass,
+      sortOptions: {
+        [s2.sortSamplesBy]: self.activeOption
+      }
+    });
+  }
+  function showNotUsedValues(event, tb) {
+    event?.stopPropagation();
+    const availDiv = tip.clear().d.append("div").attr("data-testid", "sjpp-matrix-sorter-ui-hidden-vals").style("margin-top", "3px").style("vertical-align", "top").style("padding-left", "12px");
+    availDiv.selectAll("div").data(
+      tb.notUsed.map((key, index) => ({
+        lstName: "notUsed",
+        key,
+        cls: mclass[key],
+        tb,
+        dragstart: trackDraggedValue,
+        dragover: highlightValue,
+        dragleave: unhighlightValue,
+        drop: adjustValueOrder,
+        filterByClass: s.filterByClass,
+        index
+      }))
+    ).enter().append("div").style("display", "block").each(setValueDiv);
+    tip.showunder(event.target);
+  }
+  function apply() {
+    parent.app.tip?.hide();
+    parent.app.dispatch({
+      type: "plot_edit",
+      id: parent.id,
+      config: {
+        settings: {
+          matrix: {
+            sortOptions: {
+              [s.sortSamplesBy]: self.activeOption
+            }
+          }
+        }
+      }
+    });
+  }
+  function undoMouseoverHighlights() {
+  }
+  function handleSelectedTerms(td, tr) {
+    if (!parent.selectedTermsToSortAgainst?.length) {
+      td.html(`Click on a matrix row label and the left triangle to add an entry here`);
+      return;
+    }
+    const selectedTerms = parent.selectedTermsToSortAgainst.map((t) => {
+      return {
+        t,
+        label: t.tw.term.name + (t.tw.term.type == "geneVariant" ? " alterations" : " values")
+      };
+    });
+    const tbody = select_default(tr.node().parentNode);
+    tbody.selectAll("tr").remove();
+    tbody.selectAll("tr").data(selectedTerms).enter().append("tr").selectAll("td").data((d, i) => [
+      { label: i + 1, textAlign: "center", cursor: "", t: d.t },
+      { label: d.label, textAlign: "left", cursor: "" },
+      {
+        label: "Delete",
+        textAlign: "center",
+        cursor: "pointer",
+        click: parent.unsortSamplesAgainstTerm,
+        data: d
+      }
+    ]).enter().append("td").style("text-align", (d) => d.textAlign).style("cursor", (d) => d.cursor).html((d) => d.label).on("click", (event, d) => d.click?.(event, d));
+  }
+  self.init();
+  self.api = {
+    main: self.init,
+    destroy: () => {
+      opts.holder.selectAll("*").remove();
+    }
+  };
+  if (opts.debug) self.api.Inner = self;
+  return self.api;
+}
+
+export {
+  getSorterUi
+};
+//# sourceMappingURL=chunk-IS4VLUEX.js.map

package/dist/chunk-J2DICGKC.js

@@ -0,0 +1,194 @@
+import {
+  sample_match_termvaluesetting
+} from "./chunk-T46FA72N.js";
+import {
+  isDictionaryType
+} from "./chunk-RN4BOWRH.js";
+import {
+  __export
+} from "./chunk-HS5PO5ZQ.js";
+
+// plots/matrix/matrix.data.js
+var matrix_data_exports = {};
+__export(matrix_data_exports, {
+  applyLegendValueFilter: () => applyLegendValueFilter,
+  getMatrixRequestOpts: () => getMatrixRequestOpts,
+  mayRequireToken: () => mayRequireToken,
+  setData: () => setData
+});
+function mayRequireToken(tokenMessage = "") {
+  const message = tokenMessage || this.state.tokenVerificationMessage;
+  if (!message && this.state.hasVerifiedToken) {
+    this.dom.errdiv.style("display", "none").html();
+    this.dom.controls.style("display", this.opts.controls ? "inline-block" : "");
+    this.dom.svg.style("display", "");
+    return false;
+  } else {
+    this.dom.errdiv.style("display", "").html(message || "Requires login");
+    this.dom.controls.style("display", "none");
+    this.dom.svg.style("display", "none");
+    return true;
+  }
+}
+function getMatrixRequestOpts(state, config) {
+  const terms = [];
+  const termgroups = this.chartType == "hierCluster" ? config.termgroups.filter((grp) => grp.type != "hierCluster") : config.termgroups;
+  for (const grp of termgroups) {
+    terms.push(...getNormalizedTwLstCopy(grp.lst));
+  }
+  if (config.divideBy) terms.push(normalizeTwForRequest(structuredClone(config.divideBy)));
+  const opts = {
+    terms,
+    filter: state.filter,
+    filter0: state.filter0,
+    maxGenes: state.config.settings.matrix.maxGenes,
+    /*********** quick fix
+    when the flag is true, set artificially large number to ensure all genes are sent in one query
+    this avoids changing getAnnotatedSampleData()
+    additional non-matrix app that calls getAnnotatedSampleData will NEED THE SAME FIX
+    */
+    termsPerRequest: this.app.vocabApi.termdbConfig.queries?.snvindel?.byisoform?.processTwsInOneQuery ? 1e3 : 1
+  };
+  if (this.chartType == "hierCluster") {
+    opts.isHierCluster = 1;
+  }
+  return opts;
+}
+function getNormalizedTwLstCopy(twlst) {
+  const lst = [];
+  for (const tw of twlst) {
+    if (tw.type && tw.constructor.name != "Object") lst.push(tw);
+    else lst.push(normalizeTwForRequest(tw));
+  }
+  lst.forEach(normalizeTwForRequest);
+  lst.sort(sortTwLst);
+  return lst;
+}
+function normalizeTwForRequest(_tw) {
+  const tw = structuredClone(_tw);
+  if (!tw?.term) return;
+  delete tw.term.category2samplecount;
+  if (isDictionaryType(tw.term.type) && tw.term.type !== "samplelst") delete tw.term.values;
+  return tw;
+}
+function sortTwLst(twa, twb) {
+  const a = twa?.$id || twa.term?.id || twa?.term?.name;
+  const b = twb?.$id || twb.term?.id || twb?.term?.name;
+  return a < b ? -1 : 1;
+}
+async function setData(_data) {
+  const opts = this.currRequestOpts?.matrix || this.getMatrixRequestOpts(this.state, this.config);
+  this.numTerms = opts.terms.length;
+  opts.loadingDiv = this.chartType != "hierCluster" && this.dom.loadingDiv;
+  opts.signal = this.api.getAbortSignal();
+  const data = await this.app.vocabApi.getAnnotatedSampleData(opts, _data);
+  this.data = data;
+  this.origData = structuredClone(this.data);
+  this.sampleIdMap = {};
+  for (const d of this.data.lst) {
+    this.sampleIdMap[d.sample] = d._ref_.label;
+  }
+}
+function applyLegendValueFilter() {
+  const self = this;
+  if (!self.config.legendValueFilter.lst.length && !self.config.legendGrpFilter.lst.length) return;
+  for (const grpFilter of self.config.legendGrpFilter.lst) {
+    if (grpFilter.dt) {
+      const filteredOutCats = /* @__PURE__ */ new Set();
+      for (const oneSampleData of self.origData.lst) {
+        for (const annoForOneTerm of Object.values(oneSampleData)) {
+          if (annoForOneTerm.values) {
+            const newValues = [];
+            for (const v of annoForOneTerm.values) {
+              if (!(grpFilter.dt.includes(v.dt) && (!grpFilter.origin || v.origin == grpFilter.origin))) {
+                newValues.push(v);
+              } else {
+                filteredOutCats.add(v.class);
+              }
+            }
+            annoForOneTerm.values = newValues;
+          }
+        }
+      }
+      grpFilter.filteredOutCats = [...filteredOutCats];
+      for (const oneSampleData of Object.values(self.origData.samples)) {
+        for (const annoForOneTerm of Object.values(oneSampleData)) {
+          if (annoForOneTerm.values)
+            annoForOneTerm.values = annoForOneTerm.values.filter(
+              (v) => !(grpFilter.dt.includes(v.dt) && (!grpFilter.origin || v.origin == grpFilter.origin))
+            );
+        }
+      }
+    }
+  }
+  const geneVariant$ids = Object.values(self.data.refs.byTermId).filter((v) => v.term?.type == "geneVariant").map((v) => v.$id);
+  const data = { samples: {}, lst: [], refs: self.data.refs };
+  const onlyHardFilter = structuredClone(self.config.legendValueFilter);
+  onlyHardFilter.lst = onlyHardFilter.lst.filter(
+    (l) => !l.tvs.legendFilterType || l.tvs.legendFilterType !== "geneVariant_soft"
+  );
+  for (const row of self.origData.lst) {
+    const include = sample_match_termvaluesetting(row, onlyHardFilter, geneVariant$ids);
+    if (include || self.chartType == "hierCluster") {
+      data.samples[row.sample] = row;
+      data.lst.push(row);
+    }
+  }
+  for (const valFilter of self.config.legendValueFilter.lst) {
+    if (valFilter.tvs.legendFilterType !== "geneVariant_soft") continue;
+    const tvsV = valFilter.tvs.values[0];
+    const filteredOutCats = /* @__PURE__ */ new Set();
+    for (const oneSampleData of data.lst) {
+      for (const annoForOneTerm of Object.values(oneSampleData)) {
+        if (annoForOneTerm.values) {
+          const newValues = [];
+          for (const v of annoForOneTerm.values) {
+            if (!(v.dt == tvsV.dt && (!tvsV.origin || v.origin == tvsV.origin) && tvsV.mclasslst.includes(v.class))) {
+              newValues.push(v);
+            } else {
+              filteredOutCats.add(v.class);
+            }
+          }
+          annoForOneTerm.values = newValues;
+        }
+      }
+    }
+    valFilter.filteredOutCats = [...filteredOutCats];
+    for (const oneSampleData of Object.values(data.samples)) {
+      for (const annoForOneTerm of Object.values(oneSampleData)) {
+        if (annoForOneTerm.values)
+          annoForOneTerm.values = annoForOneTerm.values.filter(
+            (v) => !(v.dt == tvsV.dt && (!tvsV.origin || v.origin == tvsV.origin) && tvsV.mclasslst.includes(v.class))
+          );
+      }
+    }
+  }
+  if (self.chartType !== "hierCluster" && geneVariant$ids.length && self.app.vocabApi.termdbConfig?.matrix?.removeEmptySamples)
+    remove_empty_sample(data, geneVariant$ids);
+  self.data = data;
+}
+function remove_empty_sample(data) {
+  for (const oneSampleData of data.lst) {
+    let removeSample = true;
+    for (const [key, annoForOneTerm] of Object.entries(oneSampleData)) {
+      if (!annoForOneTerm.values) continue;
+      const annoType = data.refs.byTermId[key].term.type;
+      if (annoType != "geneVariant") continue;
+      if (annoForOneTerm.values.length) removeSample = false;
+    }
+    if (removeSample) {
+      data.lst = data.lst.filter((dl) => dl.sample !== oneSampleData.sample);
+      delete data.samples[parseInt(oneSampleData.sample)];
+    }
+  }
+  return data;
+}
+
+export {
+  mayRequireToken,
+  getMatrixRequestOpts,
+  setData,
+  applyLegendValueFilter,
+  matrix_data_exports
+};
+//# sourceMappingURL=chunk-J2DICGKC.js.map