@sjcrh/proteinpaint-client 2.205.0 → 2.206.1

package/dist/chunk-IS4VLUEX.js

@@ -1,382 +0,0 @@
-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

@@ -1,194 +0,0 @@
-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