@sjcrh/proteinpaint-client 2.203.0 → 2.203.1

package/dist/chunk-DAGONMWK.js

@@ -0,0 +1,261 @@
+import {
+  getMclassSorter,
+  getSampleGroupSorter,
+  getSampleSorter,
+  getTermSorter
+} from "./chunk-SNCZRDS5.js";
+import {
+  filterVariantValues,
+  sample_match_termvaluesetting
+} from "./chunk-EO6M3LY3.js";
+import {
+  dtcnv,
+  dtfusionrna,
+  dtgeneexpression,
+  dtsnvindel
+} from "./chunk-4QBRVM4V.js";
+import {
+  __export
+} from "./chunk-HFNDKYVF.js";
+
+// plots/matrix/matrix.groups.js
+var matrix_groups_exports = {};
+__export(matrix_groups_exports, {
+  classifyValues: () => classifyValues,
+  getSampleGroups: () => getSampleGroups,
+  getSampleOrder: () => getSampleOrder,
+  getTermOrder: () => getTermOrder,
+  stackSiblingCellsByClass: () => stackSiblingCellsByClass
+});
+function getTermOrder(data) {
+  const s = this.settings.matrix;
+  this.termSorter = getTermSorter(this, s);
+  const termOrder = [];
+  let totalIndex = 0, visibleGrpIndex = 0, numClusterTerms = 0;
+  this.mclassSorter = getMclassSorter(this);
+  for (const [grpIndex, grp] of this.termGroups.entries()) {
+    const lst = [];
+    for (const [index, tw] of grp.lst.entries()) {
+      const counts = { samples: 0, hits: 0 };
+      const countedSamples = /* @__PURE__ */ new Set();
+      for (const sd of data.lst) {
+        if (countedSamples.has(sd.sample)) continue;
+        countedSamples.add(sd.sample);
+        const anno = sd[tw.$id];
+        if (anno) {
+          const { filteredValues, countedValues, renderedValues } = this.classifyValues(anno, tw, grp, s, sd);
+          anno.filteredValues = filteredValues;
+          anno.countedValues = countedValues;
+          anno.renderedValues = renderedValues;
+          if (anno.countedValues?.length) {
+            const v = tw.term.values?.[anno.value];
+            if (v?.uncountable) continue;
+            counts.samples += 1;
+            counts.hits += anno.countedValues.length;
+            if (tw.q?.mode == "continuous") {
+              const v2 = anno.value;
+              if (!("minval" in counts) || counts.minval > v2) counts.minval = v2;
+              if (!("maxval" in counts) || counts.maxval < v2) counts.maxval = v2;
+            }
+          }
+        }
+      }
+      if (grp.type != "hierCluster" || counts.samples) lst.push({ tw, counts, index });
+      if (grp.type == "hierCluster") numClusterTerms++;
+    }
+    const termSorter = grp.sortTermsBy || grp.type == "hierCluster" ? getTermSorter(this, s, grp) : this.termSorter;
+    const processedLst = lst.filter((t) => {
+      if ("minNumSamples" in t.tw) return t.tw.minNumSamples <= t.counts.samples;
+      if (!grp.settings) return true;
+      return !("minNumSamples" in grp.settings) || t.counts.samples >= grp.settings.minNumSamples;
+    }).sort(termSorter);
+    if (!processedLst.length) continue;
+    for (const [index, t] of processedLst.entries()) {
+      const { tw, counts } = t;
+      const ref = data.refs.byTermId[t.tw.$id] || {};
+      termOrder.push({
+        grp,
+        grpIndex,
+        visibleGrpIndex,
+        tw,
+        index,
+        // rendered index
+        lstIndex: t.index,
+        // as-listed index, before applying term filters
+        processedLst,
+        prevGrpTotalIndex: totalIndex,
+        totalIndex: totalIndex + index,
+        ref,
+        allCounts: counts
+        // note: term label will be assigned after sample counts are known
+        // label: t.tw.label || t.tw.term.name,
+      });
+    }
+    totalIndex += processedLst.length;
+    visibleGrpIndex += 1;
+  }
+  this.numTerms = termOrder.length;
+  this.numClusterTerms = numClusterTerms;
+  return termOrder;
+}
+function getSampleGroups(data) {
+  const s = this.settings.matrix;
+  const defaultSampleGrp = {
+    id: this.config.divideBy?.$id,
+    name: this.config.divideBy ? "Not annotated" : "",
+    lst: []
+  };
+  const sampleGroups = /* @__PURE__ */ new Map();
+  const term = this.config.divideBy?.term || {};
+  const $id = this.config.divideBy?.$id || "-";
+  const exclude = this.config.divideBy?.exclude || [];
+  const values = term.values || {};
+  const ref = data.refs.byTermId[$id] || {};
+  for (const row of data.lst) {
+    if ($id in row) {
+      const cell = row[$id];
+      const keys = term.type == "multivalue" && Array.isArray(cell.values) ? cell.values.map((v) => v.key) : [cell.key];
+      for (const key of keys) {
+        const name = key in values && values[key].label ? values[key].label : key;
+        if (!sampleGroups.has(key)) {
+          const grp = {
+            name: `${name}`,
+            // convert to a string
+            id: key,
+            lst: [],
+            tw: this.config.divideBy,
+            legendGroups: {},
+            isExcluded: exclude.includes(key)
+          };
+          if (ref.bins && s.sortSampleGrpsBy == "name") grp.order = ref.bins.findIndex((bin) => bin.name == key);
+          else delete grp.order;
+          sampleGroups.set(key, grp);
+        }
+        sampleGroups.get(key).lst.push(row);
+      }
+    } else {
+      defaultSampleGrp.lst.push(row);
+    }
+  }
+  const sampleGrpsArr = [...sampleGroups.values()];
+  const n = sampleGroups.size;
+  if (n > 100 && sampleGrpsArr.filter((sg) => sg.lst.length < 3).length > 0.8 * n) {
+    const l = s.controlLabels;
+    throw `Did not group ${l.samples} by "${term.name}": too many ${l.sample} groups (${n}), with the majority of groups having <= 2 ${l.samples} per group.`;
+  }
+  if (defaultSampleGrp.lst.length && !sampleGroups.size) {
+    sampleGroups.set(void 0, defaultSampleGrp);
+    sampleGrpsArr.push(...sampleGroups.values());
+  }
+  this.asListedSampleOrder = [];
+  for (const grp of sampleGrpsArr) {
+    this.asListedSampleOrder.push(...grp.lst.map((s2) => s2.sample));
+  }
+  const selectedDictTerms = this.termOrder.filter((t) => t.tw.sortSamples && t.tw.term.type != "geneVariant");
+  const noGrpSampleSorter = getSampleSorter(this, s, data.lst, {
+    skipSorter: (p, tw) => !p.types?.includes("geneVariant") && selectedDictTerms.find((t) => t.tw.$id === tw.$id)
+  });
+  const noGrpSampleOrder = data.lst.sort(noGrpSampleSorter);
+  const allowedSamples = noGrpSampleOrder.slice(0, s.maxSample);
+  const dataFilter = (d) => allowedSamples.includes(d);
+  const hitsPerSample = (t, c) => t + (typeof c == "object" && c.countedValues?.length ? 1 : 0);
+  const countHits = (total, d) => total + (Object.values(d).reduce(hitsPerSample, 0) ? 1 : 0);
+  const grpLstSampleSorter = getSampleSorter(this, s, data.lst);
+  for (const grp of sampleGrpsArr) {
+    grp.lst = grp.lst.filter(dataFilter);
+    grp.totalCountedValues = grp.lst.reduce(countHits, 0);
+    grp.lst.sort(grpLstSampleSorter);
+  }
+  const sampleGrpSorter = getSampleGroupSorter(this);
+  return sampleGrpsArr.sort(sampleGrpSorter);
+}
+function getSampleOrder(data) {
+  const s = this.settings.matrix;
+  this.visibleSampleGrps = /* @__PURE__ */ new Set();
+  const sampleOrder = [];
+  let total = 0, numHiddenGrps = 0;
+  for (const [grpIndex, grp] of this.sampleGroups.entries()) {
+    if (!grp.lst.length) continue;
+    if (grp.isExcluded) numHiddenGrps++;
+    let processedLst = grp.lst;
+    for (const [index, row] of processedLst.entries()) {
+      sampleOrder.push({
+        grp,
+        grpIndex: grpIndex - numHiddenGrps,
+        // : this.sampleGroups.length,
+        row,
+        index,
+        prevGrpTotalIndex: total,
+        totalIndex: total + index,
+        totalHtAdjustments: 0,
+        // may be required when transposed???
+        grpTotals: { htAdjustment: 0 },
+        // may be required when transposed???
+        processedLst
+      });
+    }
+    if (!grp.isExcluded) total += processedLst.length;
+    this.visibleSampleGrps.add(grp);
+  }
+  this.unfilteredSampleOrder = sampleOrder;
+  return sampleOrder.filter((so) => !so.grp.isExcluded);
+}
+function classifyValues(anno, tw, grp, s, sample) {
+  let values = "value" in anno ? [anno.value] : anno.values;
+  if (!values) return { filteredValues: null, countedValues: null, renderedValues: null };
+  if (tw.term.type == "geneVariant" && tw.q?.type == "values" && tw.q.variantFilter) {
+    values = filterVariantValues(values, tw.q.variantFilter);
+  }
+  const isSpecific = [tw.valueFilter || grp.valueFilter].filter((v) => v && true);
+  if (isSpecific.length && isSpecific[0].type !== "tvs" && isSpecific[0].type !== "tvslst")
+    throw `unknown matrix value filter type='${isSpecific.type}'`;
+  let filteredValues = !isSpecific.length ? values : values.filter((v) => sample_match_termvaluesetting(v, isSpecific[0], tw.term, sample));
+  const renderedValues = [];
+  if (tw.term.type == "geneVariant" && tw.q?.type == "values") {
+    filteredValues.sort(this.mclassSorter);
+    if (s.cellEncoding == "") renderedValues.push(...filteredValues);
+    else {
+      const sortedFilteredValues = [];
+      for (const dt of [dtcnv, dtsnvindel, dtfusionrna, dtgeneexpression]) {
+        const v = dt == dtgeneexpression ? filteredValues.find((v2) => v2.dt === dt) : filteredValues.find((v2) => v2.dt === dt && v2.class !== "WT" && v2.class !== "Blank");
+        if (v) renderedValues.push(v);
+        const oneDtV = filteredValues.filter((v2) => v2.dt === dt);
+        sortedFilteredValues.push(...oneDtV);
+      }
+      filteredValues = sortedFilteredValues;
+    }
+  } else {
+    renderedValues.push(...filteredValues);
+  }
+  return {
+    filteredValues,
+    countedValues: filteredValues.filter((v) => {
+      if (tw.term.type == "geneVariant") {
+        if (tw.q?.type == "predefined-groupset" || tw.q?.type == "custom-groupset") {
+          const groupset = tw.q.type == "predefined-groupset" ? tw.term.groupsetting.lst[tw.q.predefined_groupset_idx] : tw.q.customset;
+          if (!groupset) throw "groupset not found";
+          const group = groupset.groups[0];
+          if (v != group.name) return false;
+        } else {
+          if (v.class == "WT" || v.class == "Blank" || s.geneVariantCountSamplesSkipMclass.includes(v.class))
+            return false;
+        }
+      }
+      return true;
+    }),
+    renderedValues
+  };
+}
+function stackSiblingCellsByClass(a, b) {
+  return a.class === b.class ? 0 : a.class === "Blank" ? 1 : b.class == "Blank" ? -1 : a.class < b.class ? -1 : 1;
+}
+
+export {
+  getTermOrder,
+  getSampleGroups,
+  getSampleOrder,
+  classifyValues,
+  stackSiblingCellsByClass,
+  matrix_groups_exports
+};
+//# sourceMappingURL=chunk-DAGONMWK.js.map

package/dist/chunk-DAGONMWK.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/matrix/matrix.groups.js"],
+  "sourcesContent": ["import { sample_match_termvaluesetting } from '#shared/filter.js'\nimport { filterVariantValues } from '#shared/geneVariantFilter.js'\nimport { getSampleSorter, getTermSorter, getSampleGroupSorter, getMclassSorter } from './matrix.sort'\nimport { dtsnvindel, dtcnv, dtfusionrna, dtgeneexpression, dtsv } from '#shared/common.js'\n\nexport function getTermOrder(data) {\n\tconst s = this.settings.matrix\n\tthis.termSorter = getTermSorter(this, s)\n\t//this.termGroups = JSON.parse(JSON.stringify(this.config.termgroups))\n\tconst termOrder = []\n\tlet totalIndex = 0,\n\t\tvisibleGrpIndex = 0,\n\t\tnumClusterTerms = 0\n\n\tthis.mclassSorter = getMclassSorter(this)\n\tfor (const [grpIndex, grp] of this.termGroups.entries()) {\n\t\tconst lst = [] // will derive a mutable copy of grp.lst\n\t\tfor (const [index, tw] of grp.lst.entries()) {\n\t\t\tconst counts = { samples: 0, hits: 0 }\n\t\t\tconst countedSamples = new Set()\n\t\t\t// sd = sample data, s = this.settings.matrix\n\t\t\tfor (const sd of data.lst) {\n\t\t\t\tif (countedSamples.has(sd.sample)) continue\n\t\t\t\tcountedSamples.add(sd.sample)\n\t\t\t\tconst anno = sd[tw.$id]\n\t\t\t\tif (anno) {\n\t\t\t\t\t// This is the first time classifyValues(), to help sort\n\t\t\t\t\t// terms by sample counts (to the top) and samples by hits\n\t\t\t\t\t// (if applicable, to the left)\n\t\t\t\t\t//\n\t\t\t\t\t// This call will determine what is considered \"visible\",\n\t\t\t\t\t// even when columns are out-of-view when zoomed-in.\n\t\t\t\t\t//\n\t\t\t\t\t// NOTE: the displayed case counts or variant hits are determined\n\t\t\t\t\t// not in this call, but in the second call to\n\t\t\t\t\t// classifyValues(), + in getSerieses() and getLegendData()\n\t\t\t\t\tconst { filteredValues, countedValues, renderedValues } = this.classifyValues(anno, tw, grp, s, sd)\n\t\t\t\t\tanno.filteredValues = filteredValues\n\t\t\t\t\tanno.countedValues = countedValues\n\t\t\t\t\tanno.renderedValues = renderedValues\n\t\t\t\t\tif (anno.countedValues?.length) {\n\t\t\t\t\t\tconst v = tw.term.values?.[anno.value]\n\t\t\t\t\t\tif (v?.uncountable) continue\n\t\t\t\t\t\tcounts.samples += 1\n\t\t\t\t\t\tcounts.hits += anno.countedValues.length\n\t\t\t\t\t\tif (tw.q?.mode == 'continuous') {\n\t\t\t\t\t\t\tconst v = anno.value\n\t\t\t\t\t\t\tif (!('minval' in counts) || counts.minval > v) counts.minval = v\n\t\t\t\t\t\t\tif (!('maxval' in counts) || counts.maxval < v) counts.maxval = v\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (grp.type != 'hierCluster' || counts.samples) lst.push({ tw, counts, index })\n\t\t\tif (grp.type == 'hierCluster') numClusterTerms++\n\t\t}\n\n\t\t// may override the settings.sortTermsBy with a sorter that is specific to a term group\n\t\tconst termSorter = grp.sortTermsBy || grp.type == 'hierCluster' ? getTermSorter(this, s, grp) : this.termSorter\n\t\tconst processedLst = lst\n\t\t\t.filter(t => {\n\t\t\t\tif ('minNumSamples' in t.tw) return t.tw.minNumSamples <= t.counts.samples\n\t\t\t\tif (!grp.settings) return true\n\t\t\t\treturn !('minNumSamples' in grp.settings) || t.counts.samples >= grp.settings.minNumSamples\n\t\t\t})\n\t\t\t/*\n                NOTE: When sorting terms by sample counts, those counts would have been computed before applying the s.maxSample truncation.\n                The sample counts are then re-computed, if applicable, in setSampleCountByTerm() after sample list truncation.\n                If the left-most sample group does not have much less hits relative to sample groups to its right, then this\n                may look like a term with less sample count got mistakenly sorted to the top.\n\n                TODO: \n                (a) Option for s.sortSampleGroupBy = hits-by-term-order, and force this option so that the left-most sample group would\n                    make visually sense with s.maxSample is not empty and s.sortTermsBy = 'sampleCount'\n                (b) OR, re-sort the term lst based on sample counts without rearranging sample groups\n            */\n\t\t\t.sort(termSorter)\n\n\t\tif (!processedLst.length) continue\n\t\tfor (const [index, t] of processedLst.entries()) {\n\t\t\tconst { tw, counts } = t\n\t\t\tconst ref = data.refs.byTermId[t.tw.$id] || {}\n\t\t\ttermOrder.push({\n\t\t\t\tgrp,\n\t\t\t\tgrpIndex,\n\t\t\t\tvisibleGrpIndex,\n\t\t\t\ttw,\n\t\t\t\tindex, // rendered index\n\t\t\t\tlstIndex: t.index, // as-listed index, before applying term filters\n\t\t\t\tprocessedLst,\n\t\t\t\tprevGrpTotalIndex: totalIndex,\n\t\t\t\ttotalIndex: totalIndex + index,\n\t\t\t\tref,\n\t\t\t\tallCounts: counts\n\t\t\t\t// note: term label will be assigned after sample counts are known\n\t\t\t\t// label: t.tw.label || t.tw.term.name,\n\t\t\t})\n\t\t}\n\n\t\ttotalIndex += processedLst.length\n\t\tvisibleGrpIndex += 1\n\t}\n\tthis.numTerms = termOrder.length\n\tthis.numClusterTerms = numClusterTerms\n\treturn termOrder\n}\n\nexport function getSampleGroups(data) {\n\tconst s = this.settings.matrix\n\tconst defaultSampleGrp = {\n\t\tid: this.config.divideBy?.$id,\n\t\tname: this.config.divideBy ? 'Not annotated' : '',\n\t\tlst: []\n\t}\n\tconst sampleGroups = new Map()\n\tconst term = this.config.divideBy?.term || {}\n\tconst $id = this.config.divideBy?.$id || '-'\n\tconst exclude = this.config.divideBy?.exclude || []\n\tconst values = term.values || {}\n\tconst ref = data.refs.byTermId[$id] || {}\n\n\tfor (const row of data.lst) {\n\t\tif ($id in row) {\n\t\t\t// a membership multivalue divideBy cell may carry multiple {key} entries;\n\t\t\t// the sample then appears in the group of each category it belongs to,\n\t\t\t// same as the barchart/violin divide-by behavior\n\t\t\tconst cell = row[$id]\n\t\t\tconst keys = term.type == 'multivalue' && Array.isArray(cell.values) ? cell.values.map(v => v.key) : [cell.key]\n\t\t\tfor (const key of keys) {\n\t\t\t\tconst name = key in values && values[key].label ? values[key].label : key\n\t\t\t\tif (!sampleGroups.has(key)) {\n\t\t\t\t\tconst grp = {\n\t\t\t\t\t\tname: `${name}`, // convert to a string\n\t\t\t\t\t\tid: key,\n\t\t\t\t\t\tlst: [],\n\t\t\t\t\t\ttw: this.config.divideBy,\n\t\t\t\t\t\tlegendGroups: {},\n\t\t\t\t\t\tisExcluded: exclude.includes(key)\n\t\t\t\t\t}\n\t\t\t\t\tif (ref.bins && s.sortSampleGrpsBy == 'name') grp.order = ref.bins.findIndex(bin => bin.name == key)\n\t\t\t\t\telse delete grp.order\n\t\t\t\t\tsampleGroups.set(key, grp)\n\t\t\t\t}\n\t\t\t\tsampleGroups.get(key).lst.push(row)\n\t\t\t}\n\t\t} else {\n\t\t\tdefaultSampleGrp.lst.push(row)\n\t\t}\n\t}\n\n\tconst sampleGrpsArr = [...sampleGroups.values()]\n\tconst n = sampleGroups.size\n\tif (n > 100 && sampleGrpsArr.filter(sg => sg.lst.length < 3).length > 0.8 * n) {\n\t\tconst l = s.controlLabels\n\t\tthrow `Did not group ${l.samples} by \"${term.name}\": too many ${l.sample} groups (${n}), with the majority of groups having <= 2 ${l.samples} per group.`\n\t}\n\n\tif (defaultSampleGrp.lst.length && !sampleGroups.size) {\n\t\tsampleGroups.set(undefined, defaultSampleGrp)\n\t\tsampleGrpsArr.push(...sampleGroups.values())\n\t}\n\tthis.asListedSampleOrder = []\n\tfor (const grp of sampleGrpsArr) {\n\t\tthis.asListedSampleOrder.push(...grp.lst.map(s => s.sample))\n\t}\n\tconst selectedDictTerms = this.termOrder.filter(t => t.tw.sortSamples && t.tw.term.type != 'geneVariant')\n\t// initial sorting for ungrouped samples, prioritizes grouping by gene variant, skippin other sorters at this step\n\tconst noGrpSampleSorter = getSampleSorter(this, s, data.lst, {\n\t\tskipSorter: (p, tw) => !p.types?.includes('geneVariant') && selectedDictTerms.find(t => t.tw.$id === tw.$id)\n\t})\n\tconst noGrpSampleOrder = data.lst.sort(noGrpSampleSorter)\n\t// truncate the samples based on the initial sorting\n\tconst allowedSamples = noGrpSampleOrder.slice(0, s.maxSample)\n\t// do not include samples that are not in the truncated allowedSamples\n\tconst dataFilter = d => allowedSamples.includes(d)\n\t// these hits counter functions may be used for sortSampleGrpsBy = 'hits'\n\tconst hitsPerSample = (t, c) => t + (typeof c == 'object' && c.countedValues?.length ? 1 : 0)\n\tconst countHits = (total, d) => total + (Object.values(d).reduce(hitsPerSample, 0) ? 1 : 0)\n\t// this second sorter will be applied within each group of samples\n\tconst grpLstSampleSorter = getSampleSorter(this, s, data.lst)\n\tfor (const grp of sampleGrpsArr) {\n\t\tgrp.lst = grp.lst.filter(dataFilter)\n\t\tgrp.totalCountedValues = grp.lst.reduce(countHits, 0)\n\t\tgrp.lst.sort(grpLstSampleSorter)\n\t}\n\tconst sampleGrpSorter = getSampleGroupSorter(this)\n\treturn sampleGrpsArr.sort(sampleGrpSorter)\n}\n\nexport function getSampleOrder(data) {\n\tconst s = this.settings.matrix\n\tthis.visibleSampleGrps = new Set()\n\tconst sampleOrder = []\n\tlet total = 0,\n\t\tnumHiddenGrps = 0\n\tfor (const [grpIndex, grp] of this.sampleGroups.entries()) {\n\t\tif (!grp.lst.length) continue\n\t\tif (grp.isExcluded) numHiddenGrps++\n\t\tlet processedLst = grp.lst\n\t\tfor (const [index, row] of processedLst.entries()) {\n\t\t\tsampleOrder.push({\n\t\t\t\tgrp,\n\t\t\t\tgrpIndex: grpIndex - numHiddenGrps, // : this.sampleGroups.length,\n\t\t\t\trow,\n\t\t\t\tindex,\n\t\t\t\tprevGrpTotalIndex: total,\n\t\t\t\ttotalIndex: total + index,\n\t\t\t\ttotalHtAdjustments: 0, // may be required when transposed???\n\t\t\t\tgrpTotals: { htAdjustment: 0 }, // may be required when transposed???\n\t\t\t\tprocessedLst\n\t\t\t})\n\t\t}\n\t\tif (!grp.isExcluded) total += processedLst.length\n\t\tthis.visibleSampleGrps.add(grp)\n\t\t//if (s.maxSample && total >= s.maxSample) break // *** Apply group sorting before column truncation ????? ****\n\t}\n\tthis.unfilteredSampleOrder = sampleOrder\n\treturn sampleOrder.filter(so => !so.grp.isExcluded)\n}\n\n/*\nGiven the anno of a term for a sample, generate the \n    filteredValues (values matched the filter)\n    countedValues (values counted, Class = Blank or WT are not counted)\n    renderedValues (values rendered on matrix)\n*/\nexport function classifyValues(anno, tw, grp, s, sample) {\n\tlet values = 'value' in anno ? [anno.value] : anno.values\n\tif (!values) return { filteredValues: null, countedValues: null, renderedValues: null }\n\n\tif (tw.term.type == 'geneVariant' && tw.q?.type == 'values' && tw.q.variantFilter) {\n\t\t/* a per-row variant filter, e.g. to show only KRAS G12D in this row while\n\t\tanother row of the same gene shows G12V. applied here, at the head of the\n\t\tone function that classifies an annotation, so that the rendered cells, the\n\t\trow sample counts, the sample sorting and the legend counts all see the same\n\t\tvalues. see shared/utils/src/geneVariantFilter.ts */\n\t\tvalues = filterVariantValues(values, tw.q.variantFilter)\n\t}\n\n\t// isSpecific is the filter that is specific to the term\n\tconst isSpecific = [tw.valueFilter || grp.valueFilter].filter(v => v && true)\n\tif (isSpecific.length && isSpecific[0].type !== 'tvs' && isSpecific[0].type !== 'tvslst')\n\t\tthrow `unknown matrix value filter type='${isSpecific.type}'`\n\n\t// filteredValues are the values passed the isSpecific filter\n\tlet filteredValues = !isSpecific.length\n\t\t? values\n\t\t: values.filter(v => sample_match_termvaluesetting(v, isSpecific[0], tw.term, sample))\n\n\tconst renderedValues = []\n\tif (tw.term.type == 'geneVariant' && tw.q?.type == 'values') {\n\t\t// filteredValues.sort((a, b) => getMclassOrder(a) - getMclassOrder(b))\n\t\tfilteredValues.sort(this.mclassSorter)\n\n\t\tif (s.cellEncoding == '') renderedValues.push(...filteredValues)\n\t\telse {\n\t\t\tconst sortedFilteredValues = []\n\t\t\t// dt=1 are SNVindels, dt=4 CNV, dt=3 Gene Expression\n\t\t\t// will render only one matching value per dt\n\t\t\tfor (const dt of [dtcnv, dtsnvindel, dtfusionrna, dtgeneexpression]) {\n\t\t\t\tconst v =\n\t\t\t\t\tdt == dtgeneexpression\n\t\t\t\t\t\t? filteredValues.find(v => v.dt === dt)\n\t\t\t\t\t\t: filteredValues.find(v => v.dt === dt && v.class !== 'WT' && v.class !== 'Blank')\n\t\t\t\tif (v) renderedValues.push(v)\n\n\t\t\t\tconst oneDtV = filteredValues.filter(v => v.dt === dt)\n\t\t\t\tsortedFilteredValues.push(...oneDtV)\n\t\t\t}\n\t\t\tfilteredValues = sortedFilteredValues\n\t\t}\n\t} else {\n\t\trenderedValues.push(...filteredValues)\n\t}\n\n\t// group stacked cell values to avoid striped pattern\n\t// if (tw.term.type == 'geneVariant') {\n\t// renderedValues.sort(this.stackSiblingCellsByClass)\n\t// filteredValues.sort(this.stackSiblingCellsByClass)\n\t// }\n\n\treturn {\n\t\tfilteredValues,\n\t\tcountedValues: filteredValues.filter(v => {\n\t\t\tif (tw.term.type == 'geneVariant') {\n\t\t\t\tif (tw.q?.type == 'predefined-groupset' || tw.q?.type == 'custom-groupset') {\n\t\t\t\t\t// groupsetting in use\n\t\t\t\t\t// values are group assignments\n\t\t\t\t\t// only count assignments to group with highest\n\t\t\t\t\t// priority in groupset\n\t\t\t\t\tconst groupset =\n\t\t\t\t\t\ttw.q.type == 'predefined-groupset' ? tw.term.groupsetting.lst[tw.q.predefined_groupset_idx] : tw.q.customset\n\t\t\t\t\tif (!groupset) throw 'groupset not found'\n\t\t\t\t\tconst group = groupset.groups[0]\n\t\t\t\t\tif (v != group.name) return false\n\t\t\t\t} else {\n\t\t\t\t\t// groupsetting not in use\n\t\t\t\t\t// values are mutation classes\n\t\t\t\t\t// do not count WT, blank, or skipped classes\n\t\t\t\t\tif (v.class == 'WT' || v.class == 'Blank' || s.geneVariantCountSamplesSkipMclass.includes(v.class))\n\t\t\t\t\t\treturn false\n\t\t\t\t}\n\t\t\t}\n\t\t\treturn true\n\t\t}),\n\t\trenderedValues\n\t}\n}\n\nexport function stackSiblingCellsByClass(a, b) {\n\treturn a.class === b.class ? 0 : a.class === 'Blank' ? 1 : b.class == 'Blank' ? -1 : a.class < b.class ? -1 : 1\n}\n"],
+  "mappings": ";;;;;;;;;;;;;;;;;;;;;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAKO,SAAS,aAAa,MAAM;AAClC,QAAM,IAAI,KAAK,SAAS;AACxB,OAAK,aAAa,cAAc,MAAM,CAAC;AAEvC,QAAM,YAAY,CAAC;AACnB,MAAI,aAAa,GAChB,kBAAkB,GAClB,kBAAkB;AAEnB,OAAK,eAAe,gBAAgB,IAAI;AACxC,aAAW,CAAC,UAAU,GAAG,KAAK,KAAK,WAAW,QAAQ,GAAG;AACxD,UAAM,MAAM,CAAC;AACb,eAAW,CAAC,OAAO,EAAE,KAAK,IAAI,IAAI,QAAQ,GAAG;AAC5C,YAAM,SAAS,EAAE,SAAS,GAAG,MAAM,EAAE;AACrC,YAAM,iBAAiB,oBAAI,IAAI;AAE/B,iBAAW,MAAM,KAAK,KAAK;AAC1B,YAAI,eAAe,IAAI,GAAG,MAAM,EAAG;AACnC,uBAAe,IAAI,GAAG,MAAM;AAC5B,cAAM,OAAO,GAAG,GAAG,GAAG;AACtB,YAAI,MAAM;AAWT,gBAAM,EAAE,gBAAgB,eAAe,eAAe,IAAI,KAAK,eAAe,MAAM,IAAI,KAAK,GAAG,EAAE;AAClG,eAAK,iBAAiB;AACtB,eAAK,gBAAgB;AACrB,eAAK,iBAAiB;AACtB,cAAI,KAAK,eAAe,QAAQ;AAC/B,kBAAM,IAAI,GAAG,KAAK,SAAS,KAAK,KAAK;AACrC,gBAAI,GAAG,YAAa;AACpB,mBAAO,WAAW;AAClB,mBAAO,QAAQ,KAAK,cAAc;AAClC,gBAAI,GAAG,GAAG,QAAQ,cAAc;AAC/B,oBAAMA,KAAI,KAAK;AACf,kBAAI,EAAE,YAAY,WAAW,OAAO,SAASA,GAAG,QAAO,SAASA;AAChE,kBAAI,EAAE,YAAY,WAAW,OAAO,SAASA,GAAG,QAAO,SAASA;AAAA,YACjE;AAAA,UACD;AAAA,QACD;AAAA,MACD;AACA,UAAI,IAAI,QAAQ,iBAAiB,OAAO,QAAS,KAAI,KAAK,EAAE,IAAI,QAAQ,MAAM,CAAC;AAC/E,UAAI,IAAI,QAAQ,cAAe;AAAA,IAChC;AAGA,UAAM,aAAa,IAAI,eAAe,IAAI,QAAQ,gBAAgB,cAAc,MAAM,GAAG,GAAG,IAAI,KAAK;AACrG,UAAM,eAAe,IACnB,OAAO,OAAK;AACZ,UAAI,mBAAmB,EAAE,GAAI,QAAO,EAAE,GAAG,iBAAiB,EAAE,OAAO;AACnE,UAAI,CAAC,IAAI,SAAU,QAAO;AAC1B,aAAO,EAAE,mBAAmB,IAAI,aAAa,EAAE,OAAO,WAAW,IAAI,SAAS;AAAA,IAC/E,CAAC,EAYA,KAAK,UAAU;AAEjB,QAAI,CAAC,aAAa,OAAQ;AAC1B,eAAW,CAAC,OAAO,CAAC,KAAK,aAAa,QAAQ,GAAG;AAChD,YAAM,EAAE,IAAI,OAAO,IAAI;AACvB,YAAM,MAAM,KAAK,KAAK,SAAS,EAAE,GAAG,GAAG,KAAK,CAAC;AAC7C,gBAAU,KAAK;AAAA,QACd;AAAA,QACA;AAAA,QACA;AAAA,QACA;AAAA,QACA;AAAA;AAAA,QACA,UAAU,EAAE;AAAA;AAAA,QACZ;AAAA,QACA,mBAAmB;AAAA,QACnB,YAAY,aAAa;AAAA,QACzB;AAAA,QACA,WAAW;AAAA;AAAA;AAAA,MAGZ,CAAC;AAAA,IACF;AAEA,kBAAc,aAAa;AAC3B,uBAAmB;AAAA,EACpB;AACA,OAAK,WAAW,UAAU;AAC1B,OAAK,kBAAkB;AACvB,SAAO;AACR;AAEO,SAAS,gBAAgB,MAAM;AACrC,QAAM,IAAI,KAAK,SAAS;AACxB,QAAM,mBAAmB;AAAA,IACxB,IAAI,KAAK,OAAO,UAAU;AAAA,IAC1B,MAAM,KAAK,OAAO,WAAW,kBAAkB;AAAA,IAC/C,KAAK,CAAC;AAAA,EACP;AACA,QAAM,eAAe,oBAAI,IAAI;AAC7B,QAAM,OAAO,KAAK,OAAO,UAAU,QAAQ,CAAC;AAC5C,QAAM,MAAM,KAAK,OAAO,UAAU,OAAO;AACzC,QAAM,UAAU,KAAK,OAAO,UAAU,WAAW,CAAC;AAClD,QAAM,SAAS,KAAK,UAAU,CAAC;AAC/B,QAAM,MAAM,KAAK,KAAK,SAAS,GAAG,KAAK,CAAC;AAExC,aAAW,OAAO,KAAK,KAAK;AAC3B,QAAI,OAAO,KAAK;AAIf,YAAM,OAAO,IAAI,GAAG;AACpB,YAAM,OAAO,KAAK,QAAQ,gBAAgB,MAAM,QAAQ,KAAK,MAAM,IAAI,KAAK,OAAO,IAAI,OAAK,EAAE,GAAG,IAAI,CAAC,KAAK,GAAG;AAC9G,iBAAW,OAAO,MAAM;AACvB,cAAM,OAAO,OAAO,UAAU,OAAO,GAAG,EAAE,QAAQ,OAAO,GAAG,EAAE,QAAQ;AACtE,YAAI,CAAC,aAAa,IAAI,GAAG,GAAG;AAC3B,gBAAM,MAAM;AAAA,YACX,MAAM,GAAG,IAAI;AAAA;AAAA,YACb,IAAI;AAAA,YACJ,KAAK,CAAC;AAAA,YACN,IAAI,KAAK,OAAO;AAAA,YAChB,cAAc,CAAC;AAAA,YACf,YAAY,QAAQ,SAAS,GAAG;AAAA,UACjC;AACA,cAAI,IAAI,QAAQ,EAAE,oBAAoB,OAAQ,KAAI,QAAQ,IAAI,KAAK,UAAU,SAAO,IAAI,QAAQ,GAAG;AAAA,cAC9F,QAAO,IAAI;AAChB,uBAAa,IAAI,KAAK,GAAG;AAAA,QAC1B;AACA,qBAAa,IAAI,GAAG,EAAE,IAAI,KAAK,GAAG;AAAA,MACnC;AAAA,IACD,OAAO;AACN,uBAAiB,IAAI,KAAK,GAAG;AAAA,IAC9B;AAAA,EACD;AAEA,QAAM,gBAAgB,CAAC,GAAG,aAAa,OAAO,CAAC;AAC/C,QAAM,IAAI,aAAa;AACvB,MAAI,IAAI,OAAO,cAAc,OAAO,QAAM,GAAG,IAAI,SAAS,CAAC,EAAE,SAAS,MAAM,GAAG;AAC9E,UAAM,IAAI,EAAE;AACZ,UAAM,iBAAiB,EAAE,OAAO,QAAQ,KAAK,IAAI,eAAe,EAAE,MAAM,YAAY,CAAC,8CAA8C,EAAE,OAAO;AAAA,EAC7I;AAEA,MAAI,iBAAiB,IAAI,UAAU,CAAC,aAAa,MAAM;AACtD,iBAAa,IAAI,QAAW,gBAAgB;AAC5C,kBAAc,KAAK,GAAG,aAAa,OAAO,CAAC;AAAA,EAC5C;AACA,OAAK,sBAAsB,CAAC;AAC5B,aAAW,OAAO,eAAe;AAChC,SAAK,oBAAoB,KAAK,GAAG,IAAI,IAAI,IAAI,CAAAC,OAAKA,GAAE,MAAM,CAAC;AAAA,EAC5D;AACA,QAAM,oBAAoB,KAAK,UAAU,OAAO,OAAK,EAAE,GAAG,eAAe,EAAE,GAAG,KAAK,QAAQ,aAAa;AAExG,QAAM,oBAAoB,gBAAgB,MAAM,GAAG,KAAK,KAAK;AAAA,IAC5D,YAAY,CAAC,GAAG,OAAO,CAAC,EAAE,OAAO,SAAS,aAAa,KAAK,kBAAkB,KAAK,OAAK,EAAE,GAAG,QAAQ,GAAG,GAAG;AAAA,EAC5G,CAAC;AACD,QAAM,mBAAmB,KAAK,IAAI,KAAK,iBAAiB;AAExD,QAAM,iBAAiB,iBAAiB,MAAM,GAAG,EAAE,SAAS;AAE5D,QAAM,aAAa,OAAK,eAAe,SAAS,CAAC;AAEjD,QAAM,gBAAgB,CAAC,GAAG,MAAM,KAAK,OAAO,KAAK,YAAY,EAAE,eAAe,SAAS,IAAI;AAC3F,QAAM,YAAY,CAAC,OAAO,MAAM,SAAS,OAAO,OAAO,CAAC,EAAE,OAAO,eAAe,CAAC,IAAI,IAAI;AAEzF,QAAM,qBAAqB,gBAAgB,MAAM,GAAG,KAAK,GAAG;AAC5D,aAAW,OAAO,eAAe;AAChC,QAAI,MAAM,IAAI,IAAI,OAAO,UAAU;AACnC,QAAI,qBAAqB,IAAI,IAAI,OAAO,WAAW,CAAC;AACpD,QAAI,IAAI,KAAK,kBAAkB;AAAA,EAChC;AACA,QAAM,kBAAkB,qBAAqB,IAAI;AACjD,SAAO,cAAc,KAAK,eAAe;AAC1C;AAEO,SAAS,eAAe,MAAM;AACpC,QAAM,IAAI,KAAK,SAAS;AACxB,OAAK,oBAAoB,oBAAI,IAAI;AACjC,QAAM,cAAc,CAAC;AACrB,MAAI,QAAQ,GACX,gBAAgB;AACjB,aAAW,CAAC,UAAU,GAAG,KAAK,KAAK,aAAa,QAAQ,GAAG;AAC1D,QAAI,CAAC,IAAI,IAAI,OAAQ;AACrB,QAAI,IAAI,WAAY;AACpB,QAAI,eAAe,IAAI;AACvB,eAAW,CAAC,OAAO,GAAG,KAAK,aAAa,QAAQ,GAAG;AAClD,kBAAY,KAAK;AAAA,QAChB;AAAA,QACA,UAAU,WAAW;AAAA;AAAA,QACrB;AAAA,QACA;AAAA,QACA,mBAAmB;AAAA,QACnB,YAAY,QAAQ;AAAA,QACpB,oBAAoB;AAAA;AAAA,QACpB,WAAW,EAAE,cAAc,EAAE;AAAA;AAAA,QAC7B;AAAA,MACD,CAAC;AAAA,IACF;AACA,QAAI,CAAC,IAAI,WAAY,UAAS,aAAa;AAC3C,SAAK,kBAAkB,IAAI,GAAG;AAAA,EAE/B;AACA,OAAK,wBAAwB;AAC7B,SAAO,YAAY,OAAO,QAAM,CAAC,GAAG,IAAI,UAAU;AACnD;AAQO,SAAS,eAAe,MAAM,IAAI,KAAK,GAAG,QAAQ;AACxD,MAAI,SAAS,WAAW,OAAO,CAAC,KAAK,KAAK,IAAI,KAAK;AACnD,MAAI,CAAC,OAAQ,QAAO,EAAE,gBAAgB,MAAM,eAAe,MAAM,gBAAgB,KAAK;AAEtF,MAAI,GAAG,KAAK,QAAQ,iBAAiB,GAAG,GAAG,QAAQ,YAAY,GAAG,EAAE,eAAe;AAMlF,aAAS,oBAAoB,QAAQ,GAAG,EAAE,aAAa;AAAA,EACxD;AAGA,QAAM,aAAa,CAAC,GAAG,eAAe,IAAI,WAAW,EAAE,OAAO,OAAK,KAAK,IAAI;AAC5E,MAAI,WAAW,UAAU,WAAW,CAAC,EAAE,SAAS,SAAS,WAAW,CAAC,EAAE,SAAS;AAC/E,UAAM,qCAAqC,WAAW,IAAI;AAG3D,MAAI,iBAAiB,CAAC,WAAW,SAC9B,SACA,OAAO,OAAO,OAAK,8BAA8B,GAAG,WAAW,CAAC,GAAG,GAAG,MAAM,MAAM,CAAC;AAEtF,QAAM,iBAAiB,CAAC;AACxB,MAAI,GAAG,KAAK,QAAQ,iBAAiB,GAAG,GAAG,QAAQ,UAAU;AAE5D,mBAAe,KAAK,KAAK,YAAY;AAErC,QAAI,EAAE,gBAAgB,GAAI,gBAAe,KAAK,GAAG,cAAc;AAAA,SAC1D;AACJ,YAAM,uBAAuB,CAAC;AAG9B,iBAAW,MAAM,CAAC,OAAO,YAAY,aAAa,gBAAgB,GAAG;AACpE,cAAM,IACL,MAAM,mBACH,eAAe,KAAK,CAAAD,OAAKA,GAAE,OAAO,EAAE,IACpC,eAAe,KAAK,CAAAA,OAAKA,GAAE,OAAO,MAAMA,GAAE,UAAU,QAAQA,GAAE,UAAU,OAAO;AACnF,YAAI,EAAG,gBAAe,KAAK,CAAC;AAE5B,cAAM,SAAS,eAAe,OAAO,CAAAA,OAAKA,GAAE,OAAO,EAAE;AACrD,6BAAqB,KAAK,GAAG,MAAM;AAAA,MACpC;AACA,uBAAiB;AAAA,IAClB;AAAA,EACD,OAAO;AACN,mBAAe,KAAK,GAAG,cAAc;AAAA,EACtC;AAQA,SAAO;AAAA,IACN;AAAA,IACA,eAAe,eAAe,OAAO,OAAK;AACzC,UAAI,GAAG,KAAK,QAAQ,eAAe;AAClC,YAAI,GAAG,GAAG,QAAQ,yBAAyB,GAAG,GAAG,QAAQ,mBAAmB;AAK3E,gBAAM,WACL,GAAG,EAAE,QAAQ,wBAAwB,GAAG,KAAK,aAAa,IAAI,GAAG,EAAE,uBAAuB,IAAI,GAAG,EAAE;AACpG,cAAI,CAAC,SAAU,OAAM;AACrB,gBAAM,QAAQ,SAAS,OAAO,CAAC;AAC/B,cAAI,KAAK,MAAM,KAAM,QAAO;AAAA,QAC7B,OAAO;AAIN,cAAI,EAAE,SAAS,QAAQ,EAAE,SAAS,WAAW,EAAE,kCAAkC,SAAS,EAAE,KAAK;AAChG,mBAAO;AAAA,QACT;AAAA,MACD;AACA,aAAO;AAAA,IACR,CAAC;AAAA,IACD;AAAA,EACD;AACD;AAEO,SAAS,yBAAyB,GAAG,GAAG;AAC9C,SAAO,EAAE,UAAU,EAAE,QAAQ,IAAI,EAAE,UAAU,UAAU,IAAI,EAAE,SAAS,UAAU,KAAK,EAAE,QAAQ,EAAE,QAAQ,KAAK;AAC/G;",
+  "names": ["v", "s"]
+}

package/dist/chunk-DXLO4OAB.js

@@ -0,0 +1,357 @@
+import {
+  CATEGORICAL,
+  COHORT,
+  CONDITION,
+  DATE,
+  DNA_METHYLATION,
+  FLOAT,
+  GENE_EXPRESSION,
+  GENE_VARIANT,
+  INTEGER,
+  ISOFORM_EXPRESSION,
+  JUNCTION,
+  METABOLITE_INTENSITY,
+  MULTIVALUE,
+  PROTEOME_ABUNDANCE,
+  PSEUDOBULK,
+  SAMPLELST,
+  SINGLECELL_CELLTYPE,
+  SINGLECELL_GENE_EXPRESSION,
+  SNP,
+  SNP_LIST,
+  SNP_LOCUS,
+  SSGSEA,
+  SURVIVAL,
+  TERM_COLLECTION,
+  TermTypeGroups,
+  dtTerms,
+  dtdnamethylation,
+  dtgeneexpression,
+  dtmetaboliteintensity,
+  dtproteomeabundance,
+  dtssgsea
+} from "./chunk-4QBRVM4V.js";
+
+// ../shared/utils/dist/src/terms.js
+var ROOT_SAMPLE_TYPE = 1;
+var DEFAULT_SAMPLE_TYPE = 2;
+var NumericModes = {
+  continuous: "continuous",
+  discrete: "discrete"
+};
+var dtTermTypes = new Set(dtTerms.map((t) => t.type));
+var TermTypes2Dt = {
+  [GENE_EXPRESSION]: dtgeneexpression,
+  [SSGSEA]: dtssgsea,
+  [DNA_METHYLATION]: dtdnamethylation,
+  [METABOLITE_INTENSITY]: dtmetaboliteintensity,
+  [PROTEOME_ABUNDANCE]: dtproteomeabundance
+};
+var typeGroup = {
+  [CATEGORICAL]: TermTypeGroups.DICTIONARY_VARIABLES,
+  [CONDITION]: TermTypeGroups.DICTIONARY_VARIABLES,
+  [FLOAT]: TermTypeGroups.DICTIONARY_VARIABLES,
+  [INTEGER]: TermTypeGroups.DICTIONARY_VARIABLES,
+  [SAMPLELST]: TermTypeGroups.DICTIONARY_VARIABLES,
+  [SURVIVAL]: TermTypeGroups.DICTIONARY_VARIABLES,
+  [DATE]: TermTypeGroups.DICTIONARY_VARIABLES,
+  [MULTIVALUE]: TermTypeGroups.DICTIONARY_VARIABLES,
+  [GENE_VARIANT]: TermTypeGroups.MUTATION_CNV_FUSION,
+  [SNP]: TermTypeGroups.SNP,
+  [SNP_LIST]: TermTypeGroups.SNP_LIST,
+  [SNP_LOCUS]: TermTypeGroups.SNP_LOCUS,
+  [GENE_EXPRESSION]: TermTypeGroups.GENE_EXPRESSION,
+  [ISOFORM_EXPRESSION]: TermTypeGroups.ISOFORM_EXPRESSION,
+  [JUNCTION]: TermTypeGroups.SPLICE_JUNCTION,
+  [SSGSEA]: TermTypeGroups.SSGSEA,
+  [DNA_METHYLATION]: TermTypeGroups.DNA_METHYLATION,
+  [METABOLITE_INTENSITY]: TermTypeGroups.METABOLITE_INTENSITY,
+  [PROTEOME_ABUNDANCE]: TermTypeGroups.PROTEOME_ABUNDANCE,
+  [PSEUDOBULK]: TermTypeGroups.PSEUDOBULK,
+  [TERM_COLLECTION]: TermTypeGroups.TERM_COLLECTION,
+  [SINGLECELL_CELLTYPE]: TermTypeGroups.SINGLECELL_CELLTYPE,
+  [SINGLECELL_GENE_EXPRESSION]: TermTypeGroups.SINGLECELL_GENE_EXPRESSION,
+  [COHORT]: TermTypeGroups.COHORT
+};
+var nonDictTypes = /* @__PURE__ */ new Set([
+  SNP,
+  SNP_LIST,
+  SNP_LOCUS,
+  GENE_EXPRESSION,
+  ISOFORM_EXPRESSION,
+  JUNCTION,
+  SSGSEA,
+  DNA_METHYLATION,
+  GENE_VARIANT,
+  METABOLITE_INTENSITY,
+  PROTEOME_ABUNDANCE,
+  PSEUDOBULK,
+  SINGLECELL_CELLTYPE,
+  SINGLECELL_GENE_EXPRESSION,
+  COHORT
+]);
+for (const dtTermType of dtTermTypes) {
+  nonDictTypes.add(dtTermType);
+}
+var numericTypes = /* @__PURE__ */ new Set([
+  INTEGER,
+  FLOAT,
+  GENE_EXPRESSION,
+  ISOFORM_EXPRESSION,
+  JUNCTION,
+  SSGSEA,
+  DNA_METHYLATION,
+  METABOLITE_INTENSITY,
+  PROTEOME_ABUNDANCE,
+  SINGLECELL_GENE_EXPRESSION,
+  DATE,
+  PSEUDOBULK
+]);
+var dictionaryNumericTypes = /* @__PURE__ */ new Set([INTEGER, FLOAT, DATE]);
+var categoricalTypes = /* @__PURE__ */ new Set([CATEGORICAL, SNP]);
+var singleCellTerms = /* @__PURE__ */ new Set([
+  SINGLECELL_CELLTYPE,
+  SINGLECELL_GENE_EXPRESSION
+  /*PSEUDOBULK*/
+]);
+function isSingleCellTerm(term) {
+  if (!term) return false;
+  return singleCellTerms.has(term.type);
+}
+function isNumericTerm(term) {
+  if (!term) return false;
+  return numericTypes.has(term.type);
+}
+function isNumericTw(tw) {
+  if (!tw?.term) return false;
+  return isNumericTerm(tw.term) || tw.term.type === TERM_COLLECTION && tw.term.memberType === "numeric" && tw.type === "TermCollectionTWFraction";
+}
+function isCategoricalTerm(term) {
+  if (!term) return false;
+  return categoricalTypes.has(term.type);
+}
+function isDictionaryType(type) {
+  return !isNonDictionaryType(type);
+}
+function isNonDictionaryType(type) {
+  if (!type) throw new Error("Type is not defined");
+  return nonDictTypes.has(type);
+}
+function isNumTermCollection(term) {
+  if (!term || !term.type) throw new Error("Term or term type is not defined");
+  return term.type === TERM_COLLECTION;
+}
+function equals(t1, t2) {
+  if (!t1) throw new Error("First term is not defined ");
+  if (!t2) throw new Error("Second term is not defined ");
+  if (t1.type !== t2.type) return false;
+  if (isDictionaryType(t1.type) && isDictionaryType(t2.type) && t1.type != SAMPLELST) return t1.id === t2.id;
+  switch (t1.type) {
+    case GENE_EXPRESSION:
+      return t1.gene == t2.gene;
+    case ISOFORM_EXPRESSION:
+      return t1.isoform == t2.isoform;
+    case JUNCTION:
+      return t1.chr == t2.chr && t1.start == t2.start && t1.stop == t2.stop && t1.strand == t2.strand;
+    case SSGSEA:
+      return t1.id == t2.id;
+    case DNA_METHYLATION:
+      return t1.chr == t2.chr && t1.start == t2.start && t1.stop == t2.stop;
+    case METABOLITE_INTENSITY:
+    case PROTEOME_ABUNDANCE:
+      return t1.name == t2.name;
+    case GENE_VARIANT:
+      return t1.gene == t2.gene || t1.chr == t2.chr && t1.start == t2.start && t1.stop == t2.stop;
+    // TO DO: Add more cases
+    // case SNP_LIST:
+    // case SNP_LOCUS:
+    // case SAMPLELST:
+    default:
+      return false;
+  }
+}
+function trimGvTermCopy(term, q) {
+  if (term?.type != GENE_VARIANT) return term;
+  delete term.childTerms;
+  if (q?.customset) clearGroupsetParentTerms(q.customset);
+  const lst = term.groupsetting?.lst;
+  if (!lst?.length) return term;
+  if (q?.type == "predefined-groupset") {
+    const idx = q.predefined_groupset_idx;
+    term.groupsetting.lst = lst.map((groupset, i) => i === idx ? groupset : null);
+    clearDtTermMnames(term.groupsetting.lst[idx]);
+    clearGroupsetParentTerms(term.groupsetting.lst[idx]);
+  } else {
+    delete term.groupsetting.lst;
+  }
+  return term;
+}
+function trimGvTermsForSave(obj) {
+  if (!obj || typeof obj != "object") return obj;
+  if (obj.q && obj.term?.type == GENE_VARIANT) {
+    delete obj.term.childTerms;
+    delete obj.term.groupsetting;
+    if (obj.q.customset) clearGroupsetParentTerms(obj.q.customset);
+  }
+  for (const k in obj) trimGvTermsForSave(obj[k]);
+  return obj;
+}
+function restoreGvQueryEntry(v, queries) {
+  if (!queries || v?.$q === void 0) return false;
+  Object.assign(v, queries[v.$q]);
+  delete v.$q;
+  return true;
+}
+function matchesGvQueryEntry(entry, v) {
+  if (entry.gene) return entry.gene == v.gene;
+  const r = entry.region;
+  if (r) return !!v.region && r.chr == v.region.chr && r.start == v.region.start && r.stop == v.region.stop;
+  return true;
+}
+function setGroupsetParentTerms(groupset, term) {
+  if (term?.type != GENE_VARIANT) throw "parent of a groupset tvs must be a geneVariant term";
+  const parentTerm = structuredClone(term);
+  delete parentTerm.childTerms;
+  delete parentTerm.groupsetting;
+  walkTvs(groupset, (tvs) => {
+    if (!dtTermTypes.has(tvs.term?.type)) throw `groupset tvs term is not a dt term`;
+    tvs.term.parentTerm = parentTerm;
+  });
+  return groupset;
+}
+function clearGroupsetParentTerms(groupset) {
+  walkTvs(groupset, (tvs) => {
+    if (tvs.term) delete tvs.term.parentTerm;
+  });
+  return groupset;
+}
+function walkTvs(obj, fn) {
+  if (!obj || typeof obj != "object") return;
+  if (obj.type == "tvs" && obj.tvs) {
+    fn(obj.tvs);
+    return;
+  }
+  for (const k in obj) walkTvs(obj[k], fn);
+}
+function getDtsFromGroups(groups) {
+  const dts = /* @__PURE__ */ new Set();
+  for (const group of groups) {
+    for (const dt of getDtsFromFilter(group.filter)) dts.add(dt);
+  }
+  return [...dts];
+}
+function getDtsFromFilter(filter) {
+  const dts = /* @__PURE__ */ new Set();
+  for (const item of filter.lst) {
+    if (item.type == "tvslst") {
+      for (const dt of getDtsFromFilter(item)) dts.add(dt);
+    } else {
+      dts.add(item.tvs.term.dt);
+    }
+  }
+  return dts;
+}
+function clearDtTermMnames(obj) {
+  walkTvs(obj, (tvs) => {
+    if (tvs.term) delete tvs.term.mnames;
+  });
+  return obj;
+}
+var typeMap = {
+  categorical: "Categorical",
+  condition: "Condition",
+  float: "Numerical",
+  integer: "Numerical",
+  date: "Date",
+  geneExpression: "Gene Expression",
+  isoformExpression: "Isoform Expression",
+  [JUNCTION]: "Splice junction",
+  ssGSEA: "Geneset Expression",
+  dnaMethylation: "DNA Methylation",
+  geneVariant: "Gene Variant",
+  metaboliteIntensity: "Metabolite Intensity",
+  proteomeAbundance: "Proteome Abundance",
+  proteomeDAP: "Proteome DAP",
+  multivalue: "Multi Value",
+  singleCellGeneExpression: "Single Cell, Gene Expression",
+  singleCellCellType: "Single Cell, Cell Type",
+  snplocus: "SNP Locus",
+  snp: "SNP",
+  snplst: "SNP List",
+  termCollection: "Term Collection"
+};
+function termItemType(t) {
+  switch (t.type) {
+    case JUNCTION:
+      return "Splice junction";
+    case GENE_EXPRESSION:
+    case SINGLECELL_GENE_EXPRESSION:
+      return "Gene";
+    case ISOFORM_EXPRESSION:
+      return "Isoform";
+    case SSGSEA:
+      return "Gene set";
+    case METABOLITE_INTENSITY:
+      return "Metabolite";
+    // keep adding here
+    default:
+      return "Variable";
+  }
+}
+function termType2label(type) {
+  const s = typeMap[type];
+  if (s) return s;
+  throw new Error("termType2label(): unknown value");
+}
+function getDateFromNumber(value) {
+  const year = Math.floor(value);
+  const january1st = new Date(year, 0, 1);
+  const totalDays = getDaysInYear(year);
+  const time = Math.round((value - year) * totalDays) * oneDayTime;
+  const date = new Date(january1st.getTime() + time);
+  return date;
+}
+var oneDayTime = 24 * 60 * 60 * 1e3;
+function getDateStrFromNumber(value) {
+  const date = getDateFromNumber(value);
+  return date.toLocaleDateString("en-US", {
+    year: "numeric",
+    month: "long"
+  });
+}
+function getDaysInYear(year) {
+  const isLeap = new Date(year, 1, 29).getMonth() === 1;
+  const days = isLeap ? 366 : 365;
+  return days;
+}
+
+export {
+  ROOT_SAMPLE_TYPE,
+  DEFAULT_SAMPLE_TYPE,
+  NumericModes,
+  dtTermTypes,
+  TermTypes2Dt,
+  typeGroup,
+  numericTypes,
+  dictionaryNumericTypes,
+  isSingleCellTerm,
+  isNumericTerm,
+  isNumericTw,
+  isCategoricalTerm,
+  isDictionaryType,
+  isNonDictionaryType,
+  isNumTermCollection,
+  equals,
+  trimGvTermCopy,
+  trimGvTermsForSave,
+  restoreGvQueryEntry,
+  matchesGvQueryEntry,
+  setGroupsetParentTerms,
+  getDtsFromGroups,
+  clearDtTermMnames,
+  termItemType,
+  termType2label,
+  getDateFromNumber,
+  getDateStrFromNumber
+};
+//# sourceMappingURL=chunk-DXLO4OAB.js.map