@sjcrh/proteinpaint-client 2.198.0 → 2.200.0

package/dist/chunk-BOZJHPJP.js

@@ -1,216 +0,0 @@
-import {
-  make_radios
-} from "./chunk-5VOPABBA.js";
-import {
-  initBinConfig
-} from "./chunk-M6EF3WVV.js";
-import {
-  format
-} from "./chunk-NSTL4MY2.js";
-
-// termsetting/handlers/NumRegularBinEditor.ts
-var NumRegularBinEditor = class {
-  constructor(editHandler) {
-    this.dom = {};
-    this.editHandler = editHandler;
-    this.opts = editHandler.opts;
-    this.tw = editHandler.tw;
-    this.termsetting = editHandler.termsetting;
-  }
-  render(div) {
-    this.tw = this.editHandler.tw;
-    this.q = this.getDefaultQ();
-    this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
-    if (this.dom.binsTable) {
-      if (this.editHandler.dom.binsDiv?.node().contains(this.dom.binsTable.node())) return;
-      else {
-        this.dom.binsTable.remove();
-        delete this.dom.binsTable;
-      }
-    }
-    const binsTable = div.append("table");
-    this.dom.binsTable = binsTable;
-    this.renderBinSizeInput(binsTable.append("tr"));
-    this.renderFirstBinInput(binsTable.append("tr"));
-    this.renderLastBinInputs(binsTable.append("tr"));
-  }
-  getDefaultQ() {
-    if (this.tw.q.type == "regular-bin") return JSON.parse(JSON.stringify(this.tw.q));
-    const t = this.tw.term;
-    const defaultQ = this.termsetting.opts.use_bins_less && t.bins?.less || t.bins?.default;
-    if (defaultQ) return JSON.parse(JSON.stringify(defaultQ));
-    const binConfig = initBinConfig(this.editHandler.handler.density_data);
-    return typeof binConfig == "string" ? JSON.parse(binConfig) : binConfig;
-  }
-  renderBinSizeInput(tr) {
-    const handler = this.editHandler.handler;
-    tr.append("td").style("margin", "5px").style("opacity", 0.5).text("Bin Size");
-    const { min, max } = handler.density_data;
-    const q = this.q;
-    const origBinSize = q.bin_size;
-    this.dom.bin_size_input = tr.append("td").append("input").attr("type", "number").attr("value", "rounding" in q ? format(q.rounding || ".0f")(q.bin_size) : q.bin_size).attr("data-testid", "sjpp-num-reg-bin-editor-size").style("margin-left", "15px").style("width", "100px").style("color", () => q.bin_size > Math.abs(max - min) ? "red" : "").on("change", (event) => {
-      const newValue = Number(event.target.value);
-      if (newValue <= 0) {
-        window.alert("Please enter non-negative bin size.");
-        event.target.value = origBinSize;
-        return;
-      }
-      if ((max - min) / newValue > 100) {
-        window.alert("Bin size too small. Try setting a bigger value.");
-        event.target.value = origBinSize;
-        return;
-      }
-      q.bin_size = newValue;
-      this.dom.bin_size_input.style("color", q.bin_size > max - min ? "red" : newValue != origBinSize ? "green" : "");
-      handler.density.setBinLines(this.getBoundaryOpts());
-    });
-  }
-  renderFirstBinInput(tr) {
-    const handler = this.editHandler.handler;
-    const q = this.q;
-    if (!q.first_bin) throw "missing q.first_bin";
-    tr.append("td").style("margin", "5px").style("opacity", 0.5).text("First Bin Stop");
-    const { min, max } = handler.density_data;
-    const origValue = q.first_bin.stop;
-    this.dom.first_stop_input = tr.append("td").append("input").attr("type", "number").property("value", origValue).style("width", "100px").style("margin-left", "15px").on("change", (event) => {
-      const newValue = Number(event.target.value);
-      if (newValue < min || newValue > max) {
-        window.alert("First bin stop value out of bound.");
-        event.target.value = origValue;
-        return;
-      }
-      this.q.first_bin.stop = newValue;
-      handler.density.setBinLines(this.getBoundaryOpts());
-    });
-    tr.append("td").append("div").style("font-size", ".6em").style("opacity", 0.5).style("display", handler.density.no_density_data ? "none" : "block").text("Indicated by left-most red line. Drag to change.");
-  }
-  renderLastBinInputs(tr) {
-    const handler = this.editHandler.handler;
-    const q = this.q;
-    const isAuto = !q.last_bin || !Number.isFinite(q.last_bin.start);
-    tr.append("td").style("padding-top", "4px").style("opacity", 0.5).style("vertical-align", "top").text("Last Bin Start");
-    const td1 = tr.append("td").style("padding-left", "15px").style("vertical-align", "top");
-    const radio_div = td1.append("div");
-    const radios = make_radios({
-      holder: radio_div,
-      options: [
-        { label: "Automatic", value: "auto", checked: isAuto },
-        { label: "Fixed", value: "fixed", checked: !isAuto }
-      ],
-      callback: (v) => {
-        if (v == "auto") {
-          delete q.last_bin;
-          edit_div.style("display", "none");
-          handler.density.setBinLines(this.getBoundaryOpts());
-          return;
-        }
-        edit_div.style("display", "inline-block");
-        if (this.dom.last_start_input.property("value") == "") {
-          this.dom.last_start_input.property("value", this.tw.q.last_bin?.start || handler.density_data.max);
-        }
-        this.setLastBinStart();
-      }
-    });
-    this.dom.fixed_radio = radios.inputs.filter((_, i) => i === 1);
-    const edit_div = tr.append("td").append("div").style("display", isAuto ? "none" : "inline-block");
-    this.dom.last_start_input = edit_div.append("input").attr("type", "number").property("value", q.last_bin?.start || "").style("width", "100px").on("change", () => this.setLastBinStart());
-    edit_div.append("div").style("font-size", ".6em").style("opacity", 0.5).style("display", handler.density.no_density_data ? "none" : "block").text("Indicated by right-most red line. Drag to change.");
-  }
-  setLastBinStart() {
-    const q = this.q;
-    const { max } = this.editHandler.handler.density_data;
-    const strInput = this.dom.last_start_input.property("value");
-    if (strInput === "") return;
-    const inputValue = Number(strInput);
-    if (q.first_bin && inputValue <= q.first_bin.stop) {
-      window.alert("Last bin start cannot be smaller than first bin stop.");
-      this.dom.last_start_input.property("value", max);
-      return;
-    }
-    if (inputValue > max) {
-      window.alert("Last bin start value out of bound.");
-      this.dom.last_start_input.property("value", max);
-      return;
-    }
-    if (q.last_bin) q.last_bin.start = inputValue;
-    else
-      q.last_bin = {
-        start: inputValue,
-        stopunbounded: true,
-        stopinclusive: false
-      };
-    this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
-  }
-  getBoundaryOpts() {
-    const { min, max } = this.editHandler.handler.density_data;
-    const binLinesStop = this.q.last_bin?.start ?? max + Math.abs(this.q.first_bin.stop) - Math.min(min, 0);
-    const boundaryValues = [];
-    for (let i = this.q.first_bin.stop; i <= binLinesStop; i = i + this.q.bin_size) {
-      if (this.q.last_bin?.start === i) break;
-      if (i > binLinesStop) boundaryValues[boundaryValues.length - 1].isLastVisibleLine = true;
-      const isDraggable = i === this.q.first_bin.stop || i === this.q.bin_size - 1;
-      boundaryValues.push({ x: i, isDraggable, movesWithLineIndex: !isDraggable ? 0 : -1 });
-    }
-    if (this.q.last_bin) {
-      boundaryValues.push({
-        x: this.q.last_bin.start,
-        isDraggable: true,
-        isLastVisibleLine: true,
-        movesWithLineIndex: -1
-      });
-    }
-    return {
-      values: boundaryValues,
-      callback: (d, value) => {
-        if (d.index === 0) {
-          this.dom.first_stop_input.property("value", value);
-          this.q.first_bin.stop = value;
-        } else {
-          this.editHandler.handler.dom.last_start_input.property("value", value);
-          if (this.q.last_bin) this.q.last_bin.start = value;
-        }
-      }
-    };
-  }
-  getEditedQ(destroyDom = true) {
-    const bin_size = this.dom.bin_size_input.property("value");
-    const config = {
-      mode: "discrete",
-      type: "regular-bin",
-      startinclusive: this.editHandler.boundaryInclusion == "startinclusive",
-      stopinclusive: this.editHandler.boundaryInclusion == "stopinclusive",
-      bin_size: Number(bin_size),
-      first_bin: {
-        startunbounded: true,
-        stop: Number(this.dom.first_stop_input.property("value"))
-      },
-      rounding: bin_size.includes(".") && !bin_size.endsWith(".") ? `.${bin_size.split(".")[1].length}f` : ".0f"
-    };
-    if (this.dom.fixed_radio.property("checked")) {
-      config.last_bin = {
-        start: Number(this.dom.last_start_input.property("value")),
-        stopunbounded: true
-      };
-    }
-    if (destroyDom) {
-      for (const name of Object.keys(this.dom)) {
-        this.dom[name].remove();
-        delete this.dom[name];
-      }
-    }
-    return config;
-  }
-  undoEdits() {
-    this.q = this.getDefaultQ();
-    this.dom.binsTable.selectAll("*").remove();
-    this.renderBinSizeInput(this.dom.binsTable.append("tr"));
-    this.renderFirstBinInput(this.dom.binsTable.append("tr"));
-    this.renderLastBinInputs(this.dom.binsTable.append("tr"));
-    this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
-  }
-};
-
-export {
-  NumRegularBinEditor
-};
-//# sourceMappingURL=chunk-BOZJHPJP.js.map

package/dist/chunk-CDD7LYJM.js

@@ -1,194 +0,0 @@
-import {
-  sample_match_termvaluesetting
-} from "./chunk-NELOT3NJ.js";
-import {
-  isDictionaryType
-} from "./chunk-I6WR4CG7.js";
-import {
-  __export
-} from "./chunk-HFNDKYVF.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.vocab?.dslabel == "GDC")
-    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-CDD7LYJM.js.map

package/dist/chunk-CDD7LYJM.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/matrix/matrix.data.js"],
-  "sourcesContent": ["import { getCompInit, copyMerge, deepEqual } from '#rx'\nimport { sample_match_termvaluesetting } from '#common/termutils'\nimport { isDictionaryType } from '#shared/terms.js'\n\nexport function mayRequireToken(tokenMessage = '') {\n\tconst message = tokenMessage || this.state.tokenVerificationMessage\n\tif (!message && this.state.hasVerifiedToken) {\n\t\tthis.dom.errdiv.style('display', 'none').html()\n\t\tthis.dom.controls.style('display', this.opts.controls ? 'inline-block' : '')\n\t\tthis.dom.svg.style('display', '')\n\t\treturn false\n\t} else {\n\t\tthis.dom.errdiv.style('display', '').html(message || 'Requires login')\n\t\tthis.dom.controls.style('display', 'none')\n\t\tthis.dom.svg.style('display', 'none')\n\t\treturn true\n\t}\n}\n\nexport function getMatrixRequestOpts(state, config) {\n\t/* requests data for all terms shown in matrix,\n\t\tby creating request argument for getAnnotatedSampleData and run it\n\t\tNOTE this excludes the term group used for hierCluster, as its data request is done separately\n\t\t*/\n\tconst terms = []\n\n\tconst termgroups =\n\t\tthis.chartType == 'hierCluster' ? config.termgroups.filter(grp => grp.type != 'hierCluster') : config.termgroups\n\tfor (const grp of termgroups) {\n\t\tterms.push(...getNormalizedTwLstCopy(grp.lst))\n\t}\n\tif (config.divideBy) terms.push(normalizeTwForRequest(structuredClone(config.divideBy)))\n\n\t// !!! NOTE !!!\n\t// all parameters here must remove payload properties that are\n\t// not relevant to the data request, so that the dofetch and/or\n\t// browser caching would work\n\tconst opts = {\n\t\tterms,\n\t\tfilter: state.filter,\n\t\tfilter0: state.filter0,\n\t\tmaxGenes: state.config.settings.matrix.maxGenes,\n\t\t/*********** quick fix\n\t\twhen the flag is true, set artificially large number to ensure all genes are sent in one query\n\t\tthis avoids changing getAnnotatedSampleData()\n\t\tadditional non-matrix app that calls getAnnotatedSampleData will NEED THE SAME FIX\n\t\t*/\n\t\ttermsPerRequest: this.app.vocabApi.termdbConfig.queries?.snvindel?.byisoform?.processTwsInOneQuery ? 1000 : 1\n\t}\n\n\tif (this.chartType == 'hierCluster') {\n\t\t/* quick fix, only needed for gdc\n\t\t\tso backend case query will know this context and pull cases with gene exp data\n\t\t\tis ignored by non-gdc datasets\n\t\t\t*/\n\t\topts.isHierCluster = 1\n\t}\n\n\treturn opts\n}\n\nfunction getNormalizedTwLstCopy(twlst) {\n\tconst lst = []\n\tfor (const tw of twlst) {\n\t\tif (tw.type && tw.constructor.name != 'Object') lst.push(tw)\n\t\telse lst.push(normalizeTwForRequest(tw))\n\t}\n\tlst.forEach(normalizeTwForRequest)\n\tlst.sort(sortTwLst)\n\treturn lst\n}\n\nfunction normalizeTwForRequest(_tw) {\n\tconst tw = structuredClone(_tw)\n\tif (!tw?.term) return\n\t// These props are cohort-dependent and should be ignored like termfilter.filter0.\n\t// Note that state filter, filter0 are always sent to the server for dataset-related requests,\n\t// which indirectly covers the computed properties below that are being deleted.\n\tdelete tw.term.category2samplecount\n\t// for GDC, the term.values may not be known ahead of time\n\t// and only filled in as data comes in, should ignore this\n\t// computed value as to avoid affecting tracked state\n\n\t// for dictionary term, term.values is queryed from terms table\n\tif (isDictionaryType(tw.term.type) && tw.term.type !== 'samplelst') delete tw.term.values\n\treturn tw\n}\n\nfunction sortTwLst(twa, twb) {\n\tconst a = twa?.$id || twa.term?.id || twa?.term?.name\n\tconst b = twb?.$id || twb.term?.id || twb?.term?.name\n\treturn a < b ? -1 : 1\n}\n\nexport async function setData(_data) {\n\tconst opts = this.currRequestOpts?.matrix || this.getMatrixRequestOpts(this.state, this.config)\n\tthis.numTerms = opts.terms.length\n\topts.loadingDiv = this.chartType != 'hierCluster' && this.dom.loadingDiv\n\topts.signal = this.api.getAbortSignal()\n\tconst data = await this.app.vocabApi.getAnnotatedSampleData(opts, _data)\n\tthis.data = data\n\tthis.origData = structuredClone(this.data)\n\tthis.sampleIdMap = {}\n\tfor (const d of this.data.lst) {\n\t\t// mapping of sample string name to integer id\n\t\t// TODO: not able to find matching sample names between ASH and termdb?\n\t\tthis.sampleIdMap[d.sample] = d._ref_.label\n\t}\n}\n\nexport function applyLegendValueFilter() {\n\tconst self = this\n\tif (!self.config.legendValueFilter.lst.length && !self.config.legendGrpFilter.lst.length) return\n\n\tfor (const grpFilter of self.config.legendGrpFilter.lst) {\n\t\tif (grpFilter.dt) {\n\t\t\tconst filteredOutCats = new Set() // the classes removed by the grpFilter\n\t\t\tfor (const oneSampleData of self.origData.lst) {\n\t\t\t\tfor (const annoForOneTerm of Object.values(oneSampleData)) {\n\t\t\t\t\tif (annoForOneTerm.values) {\n\t\t\t\t\t\tconst newValues = []\n\t\t\t\t\t\tfor (const v of annoForOneTerm.values) {\n\t\t\t\t\t\t\tif (!(grpFilter.dt.includes(v.dt) && (!grpFilter.origin || v.origin == grpFilter.origin))) {\n\t\t\t\t\t\t\t\tnewValues.push(v)\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tfilteredOutCats.add(v.class)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tannoForOneTerm.values = newValues\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t\tgrpFilter.filteredOutCats = [...filteredOutCats]\n\t\t\tfor (const oneSampleData of Object.values(self.origData.samples)) {\n\t\t\t\tfor (const annoForOneTerm of Object.values(oneSampleData)) {\n\t\t\t\t\tif (annoForOneTerm.values)\n\t\t\t\t\t\tannoForOneTerm.values = annoForOneTerm.values.filter(\n\t\t\t\t\t\t\tv => !(grpFilter.dt.includes(v.dt) && (!grpFilter.origin || v.origin == grpFilter.origin))\n\t\t\t\t\t\t)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\tconst geneVariant$ids = Object.values(self.data.refs.byTermId)\n\t\t.filter(v => v.term?.type == 'geneVariant')\n\t\t.map(v => v.$id)\n\tconst data = { samples: {}, lst: [], refs: self.data.refs }\n\n\tconst onlyHardFilter = structuredClone(self.config.legendValueFilter)\n\tonlyHardFilter.lst = onlyHardFilter.lst.filter(\n\t\tl => !l.tvs.legendFilterType || l.tvs.legendFilterType !== 'geneVariant_soft'\n\t)\n\tfor (const row of self.origData.lst) {\n\t\tconst include = sample_match_termvaluesetting(row, onlyHardFilter, geneVariant$ids)\n\t\tif (include || self.chartType == 'hierCluster') {\n\t\t\t// for hierCluster, should not filter out any samples by sample_match_termvaluesetting\n\t\t\t// samples are filtered out by joining legendValueFilter with filter in setHierClusterData\n\t\t\tdata.samples[row.sample] = row\n\t\t\tdata.lst.push(row)\n\t\t}\n\t}\n\n\tfor (const valFilter of self.config.legendValueFilter.lst) {\n\t\tif (valFilter.tvs.legendFilterType !== 'geneVariant_soft') continue\n\t\t// applying each soft filter\n\t\tconst tvsV = valFilter.tvs.values[0]\n\t\tconst filteredOutCats = new Set() // the classes removed by the grpFilter\n\t\tfor (const oneSampleData of data.lst) {\n\t\t\tfor (const annoForOneTerm of Object.values(oneSampleData)) {\n\t\t\t\tif (annoForOneTerm.values) {\n\t\t\t\t\tconst newValues = []\n\t\t\t\t\tfor (const v of annoForOneTerm.values) {\n\t\t\t\t\t\tif (!(v.dt == tvsV.dt && (!tvsV.origin || v.origin == tvsV.origin) && tvsV.mclasslst.includes(v.class))) {\n\t\t\t\t\t\t\tnewValues.push(v)\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tfilteredOutCats.add(v.class)\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tannoForOneTerm.values = newValues\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tvalFilter.filteredOutCats = [...filteredOutCats]\n\t\tfor (const oneSampleData of Object.values(data.samples)) {\n\t\t\tfor (const annoForOneTerm of Object.values(oneSampleData)) {\n\t\t\t\tif (annoForOneTerm.values)\n\t\t\t\t\tannoForOneTerm.values = annoForOneTerm.values.filter(\n\t\t\t\t\t\tv => !(v.dt == tvsV.dt && (!tvsV.origin || v.origin == tvsV.origin) && tvsV.mclasslst.includes(v.class))\n\t\t\t\t\t)\n\t\t\t}\n\t\t}\n\t}\n\tif (self.chartType !== 'hierCluster' && geneVariant$ids.length && self.app.vocabApi.vocab?.dslabel == 'GDC')\n\t\tremove_empty_sample(data, geneVariant$ids)\n\tself.data = data\n}\n\n// each time gene legend soft filter or gene legend group filter is applied (when cell gene values updated), remove\n// the samples that have empty cells (not even WT or BLANK)\nfunction remove_empty_sample(data) {\n\tfor (const oneSampleData of data.lst) {\n\t\tlet removeSample = true\n\t\tfor (const [key, annoForOneTerm] of Object.entries(oneSampleData)) {\n\t\t\tif (!annoForOneTerm.values) continue\n\t\t\tconst annoType = data.refs.byTermId[key].term.type\n\t\t\tif (annoType != 'geneVariant') continue\n\t\t\tif (annoForOneTerm.values.length) removeSample = false\n\t\t}\n\t\tif (removeSample) {\n\t\t\tdata.lst = data.lst.filter(dl => dl.sample !== oneSampleData.sample)\n\t\t\tdelete data.samples[parseInt(oneSampleData.sample)]\n\t\t}\n\t}\n\treturn data\n}\n"],
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