@sjcrh/proteinpaint-client 2.224.2 → 2.225.0

package/dist/chunk-HGC4EON3.js

@@ -0,0 +1,348 @@
+import {
+  matchesGvQueryEntry
+} from "./chunk-QFQJO7LD.js";
+import {
+  mclass
+} from "./chunk-2N345NXD.js";
+
+// ../shared/utils/dist/src/termCollection.js
+function validateTermCollectionTerm(term) {
+  if (!Array.isArray(term?.termlst) || !term.termlst.length)
+    throw new Error("termCollection requires nonempty term.termlst[]");
+  const memberIds = /* @__PURE__ */ new Set();
+  const types = /* @__PURE__ */ new Set();
+  for (const t of term.termlst) {
+    if (typeof t.id != "string" || !t.id) throw new Error("member term id not non-empty string");
+    if (typeof t.type != "string" || !t.type) throw new Error("member term type not non-empty string");
+    if (memberIds.has(t.id)) throw new Error(`duplicate member term id '${t.id}'`);
+    memberIds.add(t.id);
+    types.add(t.type == "integer" || t.type == "float" ? "numDict" : t.type);
+  }
+  if (types.size > 1) throw new Error("termCollection.termlst[] not allowed to mix multiple term types");
+  return memberIds;
+}
+function validateFractionMembers(numerators, denominators, memberIds) {
+  if (!Array.isArray(denominators) || !denominators.length) throw new Error("fraction requires nonempty denominators[]");
+  if (!Array.isArray(numerators) || !numerators.length) throw new Error("fraction requires nonempty numerators[]");
+  if (new Set(denominators).size !== denominators.length) throw new Error("fraction denominators[] contains duplicates");
+  if (new Set(numerators).size !== numerators.length) throw new Error("fraction numerators[] contains duplicates");
+  for (const id of denominators) {
+    if (typeof id != "string" || !id) throw new Error("fraction denominator id not non-empty string");
+    if (!memberIds.has(id)) throw new Error(`fraction denominator '${id}' is not a collection member`);
+  }
+  for (const id of numerators) {
+    if (typeof id != "string" || !id) throw new Error("fraction numerator id not non-empty string");
+    if (!denominators.includes(id)) throw new Error(`fraction numerator '${id}' is not included in denominators[]`);
+  }
+}
+var FRACTION_TW_TYPE = "TermCollectionTWFraction";
+function isFractionTw(tw) {
+  return tw?.type === FRACTION_TW_TYPE && tw?.term?.type === "termCollection";
+}
+function getFractionTvsTerm(tw) {
+  if (!isFractionTw(tw)) throw new Error("not a fraction termCollection tw");
+  const term = structuredClone(tw.term);
+  const memberIds = term.termlst?.length ? validateTermCollectionTerm(term) : new Set(term.termIds || []);
+  const denominators = tw.q?.denominators?.length ? [...tw.q.denominators] : [...memberIds];
+  const numerators = tw.q?.numerators?.length ? [...tw.q.numerators] : [...denominators];
+  validateFractionMembers(numerators, denominators, memberIds);
+  term.numerators = numerators;
+  term.denominators = denominators;
+  return term;
+}
+function validateTermCollectionFraction(q, term) {
+  const memberIds = validateTermCollectionTerm(term);
+  validateFractionMembers(q?.numerators, q?.denominators, memberIds);
+  if (q.mode === "discrete" && q.type !== "regular-bin" && q.type !== "custom-bin")
+    throw new Error("discrete fraction termCollection requires regular-bin or custom-bin q.type");
+}
+
+// ../shared/utils/dist/src/filter.js
+function getFilteredSamples(sampleAnno, filter) {
+  setDatasetAnnotations(filter);
+  const samples = /* @__PURE__ */ new Set();
+  for (const anno of sampleAnno) {
+    if (samples.has(anno.sample)) continue;
+    const data = anno.s || anno.data;
+    if (data && sample_match_termvaluesetting(data, filter)) {
+      samples.add(anno.sample);
+    }
+  }
+  return samples;
+}
+function sample_match_termvaluesetting(row, filter, _term = null, sample = null) {
+  const lst = filter.type == "tvslst" ? filter.lst : [filter];
+  let numberofmatchedterms = 0;
+  for (const item of lst) {
+    if ("type" in item && item.type == "tvslst") {
+      if (sample_match_termvaluesetting(row, item, _term, sample)) {
+        numberofmatchedterms++;
+      }
+    } else {
+      const itemCopy = JSON.parse(JSON.stringify(item));
+      const t = itemCopy.tvs;
+      if (_term && t.term) {
+        if (!(_term.name == t.term.name && _term.type == t.term.type)) {
+          numberofmatchedterms++;
+          continue;
+        }
+      }
+      let samplevalue;
+      if (_term && !t.term) {
+        if (t.term$type && t.term$type !== _term.type) {
+          numberofmatchedterms++;
+          continue;
+        }
+        t.term = _term;
+        samplevalue = typeof row === "object" && t.term.id in row ? row[t.term.id] : row;
+      } else if (sample && t.term.$id) {
+        samplevalue = sample[t.term.$id].value;
+      } else {
+        samplevalue = t.term.id in row ? row[t.term.id] : row;
+      }
+      setDatasetAnnotations(itemCopy);
+      let thistermmatch;
+      if (t.term.type == "categorical") {
+        if (samplevalue === void 0) continue;
+        thistermmatch = t.valueset.has(samplevalue);
+      } else if (t.term.type == "integer" || t.term.type == "float") {
+        if (samplevalue === void 0) continue;
+        for (const range of t.ranges) {
+          if ("value" in range) {
+            thistermmatch = samplevalue === range.value;
+            if (thistermmatch) break;
+          } else if (samplevalue == range.name) {
+            thistermmatch = true;
+            break;
+          } else {
+            if (t.term.values) {
+              const v = t.term.values[samplevalue.toString()];
+              if (v && v.uncomputable) {
+                continue;
+              }
+            }
+            let left, right;
+            if (range.startunbounded) {
+              left = true;
+            } else if ("start" in range) {
+              if (range.startinclusive) {
+                left = samplevalue >= range.start;
+              } else {
+                left = samplevalue > range.start;
+              }
+            }
+            if (range.stopunbounded) {
+              right = true;
+            } else if ("stop" in range) {
+              if (range.stopinclusive) {
+                right = samplevalue <= range.stop;
+              } else {
+                right = samplevalue < range.stop;
+              }
+            }
+            thistermmatch = left && right;
+          }
+          if (thistermmatch) break;
+        }
+      } else if (t.term.type == "condition") {
+        const key = getPrecomputedKey(t);
+        const anno = samplevalue && samplevalue[key];
+        if (anno) {
+          thistermmatch = Array.isArray(anno) ? t.values.find((d) => anno.includes(d.key)) : t.values.find((d) => d.key == anno);
+        }
+      } else if (t.term.type == "geneVariant") {
+        const svalues = samplevalue.values || [samplevalue];
+        for (const sv of svalues) {
+          thistermmatch = t.values.find(
+            (v) => v.dt == sv.dt && (!v.origin || sv.origin == v.origin) && (!v.mclasslst || v.mclasslst.includes(sv.class))
+          ) && true;
+          if (thistermmatch) break;
+        }
+      } else {
+        throw "unknown term type [sample_match_termvaluesetting() shared/utils/src/filter.ts]";
+      }
+      if (t.isnot) {
+        thistermmatch = !thistermmatch;
+      }
+      if (thistermmatch) numberofmatchedterms++;
+    }
+    if (filter.join == "or") {
+      if (numberofmatchedterms && filter.in) return true;
+      if (!numberofmatchedterms && !filter.in) return true;
+    }
+  }
+  if (!("in" in filter)) filter.in = true;
+  return filter.in == (numberofmatchedterms == lst.length);
+}
+function setDatasetAnnotations(item, ds = null) {
+  if (item.type == "tvslst") {
+    for (const subitem of item.lst) {
+      setDatasetAnnotations(subitem, ds);
+    }
+  } else {
+    if (ds && typeof ds.setAnnoByTermId == "function") {
+      ds.setAnnoByTermId(item.tvs.term.id);
+    }
+    if (item.tvs.term.type == "categorical") {
+      const tvsAny = item.tvs;
+      tvsAny.valueset = new Set(tvsAny.values.map((i) => i.key));
+    }
+  }
+}
+function getPrecomputedKey(q) {
+  const precomputedKey = q.bar_by_children && q.value_by_max_grade ? "childrenAtMaxGrade" : q.bar_by_children && q.value_by_most_recent ? "childrenAtMostRecent" : q.bar_by_children && q.value_by_computable_grade ? "children" : q.bar_by_grade && q.value_by_max_grade ? "maxGrade" : q.bar_by_grade && q.value_by_most_recent ? "mostRecentGrades" : q.bar_by_grade && q.value_by_computable_grade ? "computableGrades" : "";
+  if (!precomputedKey) throw `unknown condition term bar_by_* and/or value_by_*`;
+  return precomputedKey;
+}
+function getWrappedTvslst(lst = [], join = "", $id = null) {
+  const filter = {
+    type: "tvslst",
+    in: true,
+    join,
+    lst
+  };
+  if ($id !== null) filter.$id = $id;
+  return filter;
+}
+function getTvsDenominators(term) {
+  if (Array.isArray(term?.denominators) && term.denominators.length) return term.denominators;
+  return (term?.termlst || []).map((t) => t.id);
+}
+function validateTermCollectionTvs(term) {
+  const memberIds = validateTermCollectionTerm(term);
+  if (!term.numerators) return;
+  validateFractionMembers(term.numerators, getTvsDenominators(term), memberIds);
+}
+
+// ../shared/utils/dist/src/geneVariantFilter.js
+var statusClasses = /* @__PURE__ */ new Set(["WT", "Blank"]);
+function unsupported(what) {
+  return `tw.q.variantFilter does not support ${what}, which qualifies a sample rather than an individual variant. Use a groupset (q.type='custom-groupset') for a sample-level filter.`;
+}
+function validateVariantFilter(filter, term) {
+  if (!filter) return;
+  if (filter.type != "tvslst") throw `tw.q.variantFilter.type must be 'tvslst'`;
+  if (!Array.isArray(filter.lst) || !filter.lst.length) throw "tw.q.variantFilter.lst[] is empty";
+  if (filter.lst.length > 1 && filter.join != "and" && filter.join != "or")
+    throw `tw.q.variantFilter.join must be 'and' or 'or' when lst[] has more than one item`;
+  const dts = term?.childTerms?.length ? new Set(term.childTerms.map((t) => t.dt)) : null;
+  for (const item of filter.lst) {
+    if (item.type == "tvslst") {
+      validateVariantFilter(item, term);
+      continue;
+    }
+    if (item.type != "tvs") throw `unexpected tw.q.variantFilter item.type='${item.type}'`;
+    const tvs = item.tvs;
+    if (!tvs) throw "missing tvs of a tw.q.variantFilter item";
+    if (!Number.isInteger(tvs.term?.dt)) throw "tw.q.variantFilter tvs.term must be a dt term, with an integer .dt";
+    if (dts && !dts.has(tvs.term.dt))
+      throw `tw.q.variantFilter tvs.term.dt=${tvs.term.dt} is not a dt of term '${term.name}'`;
+    if (!Array.isArray(tvs.values) || !tvs.values.length) throw "tw.q.variantFilter tvs.values[] is empty";
+    for (const v of tvs.values) {
+      if (!v.key) throw "a tw.q.variantFilter tvs.values[] entry is missing .key";
+      if (statusClasses.has(v.key))
+        throw `tw.q.variantFilter cannot select the '${v.key}' class, which is a testing status and not a variant`;
+      if (v.partnerBreakpointRange) throw unsupported("partnerBreakpointRange");
+    }
+    if (tvs.genotype && tvs.genotype != "variant") throw unsupported(`genotype='${tvs.genotype}'`);
+    if (tvs.mcount && tvs.mcount != "any") throw unsupported(`mcount='${tvs.mcount}'`);
+    if (tvs.mafFilter) throw unsupported("mafFilter");
+    if (tvs.continuousCnv) throw unsupported("continuousCnv");
+    if (tvs.selfBreakpointRange) throw unsupported("selfBreakpointRange");
+  }
+}
+function getTvsOrigins(tvs) {
+  return tvs.origins?.length ? tvs.origins : void 0;
+}
+function getFilterScope(filter, scope = /* @__PURE__ */ new Set()) {
+  for (const item of filter.lst) {
+    if (item.type == "tvslst") {
+      getFilterScope(item, scope);
+      continue;
+    }
+    const origins = getTvsOrigins(item.tvs);
+    if (origins) for (const origin of origins) scope.add(`${item.tvs.term.dt}:${origin}`);
+    else scope.add(`${item.tvs.term.dt}:*`);
+  }
+  return scope;
+}
+function isInScope(v, scope) {
+  return scope.has(`${v.dt}:*`) || scope.has(`${v.dt}:${v.origin || ""}`);
+}
+function matchTvs(v, tvs) {
+  let match = false;
+  const origins = getTvsOrigins(tvs);
+  if (v.dt == tvs.term.dt && (!origins || origins.includes(v.origin))) {
+    match = tvs.values.some((e) => e.key == v.class && (!e.mname || e.mname == v.mname && matchesGvQueryEntry(e, v)));
+  }
+  return tvs.isnot ? !match : match;
+}
+function matchFilter(v, filter) {
+  const lst = filter.type == "tvslst" ? filter.lst : [filter];
+  let numMatched = 0;
+  for (const item of lst) {
+    const matched = item.type == "tvslst" ? matchFilter(v, item) : matchTvs(v, item.tvs);
+    if (matched) numMatched++;
+    if (filter.join == "or" && numMatched) break;
+  }
+  const pass = filter.join == "or" ? numMatched > 0 : numMatched == lst.length;
+  return filter.in === false ? !pass : pass;
+}
+function filterVariantValues(values, filter) {
+  if (!filter || !values) return values;
+  const scope = getFilterScope(filter);
+  const kept = [];
+  const annotated = /* @__PURE__ */ new Set();
+  const dropped = /* @__PURE__ */ new Map();
+  for (const v of values) {
+    if (!isInScope(v, scope)) continue;
+    const key = `${v.dt}:${v.origin || ""}`;
+    if (statusClasses.has(v.class) || matchFilter(v, filter)) {
+      kept.push(v);
+      annotated.add(key);
+    } else if (!dropped.has(key)) {
+      dropped.set(key, v);
+    }
+  }
+  for (const [key, v] of dropped) {
+    if (annotated.has(key)) continue;
+    const wt = { dt: v.dt, class: "WT", label: mclass.WT.label };
+    if (v.gene) wt.gene = v.gene;
+    if (v.origin) wt.origin = v.origin;
+    kept.push(wt);
+  }
+  return kept;
+}
+function variantFilterLabel(filter, mclassOverride, maxItems = 3) {
+  if (!filter) return "";
+  const entries = [];
+  collect(filter, false);
+  function collect(f, negated) {
+    const flipped = f.in === false ? !negated : negated;
+    for (const item of f.lst) {
+      if (item.type == "tvslst") collect(item, flipped);
+      else if (flipped === !!item.tvs.isnot) entries.push(...item.tvs.values);
+    }
+  }
+  if (!entries.length) return "";
+  const classes = mclass;
+  const names = [
+    ...new Set(entries.map((e) => e.mname || mclassOverride?.[e.key]?.label || classes[e.key]?.label || e.key))
+  ];
+  return names.length > maxItems ? `${names.slice(0, maxItems).join("/")}\u2026` : names.join("/");
+}
+
+export {
+  isFractionTw,
+  getFractionTvsTerm,
+  validateTermCollectionFraction,
+  getFilteredSamples,
+  sample_match_termvaluesetting,
+  getWrappedTvslst,
+  getTvsDenominators,
+  validateTermCollectionTvs,
+  validateVariantFilter,
+  filterVariantValues,
+  variantFilterLabel
+};
+//# sourceMappingURL=chunk-HGC4EON3.js.map

package/dist/chunk-HM23KADV.js

@@ -0,0 +1,281 @@
+import {
+  getMclassSorter,
+  getSampleGroupSorter,
+  getSampleSorter,
+  getTermSorter
+} from "./chunk-UXLT7W2N.js";
+import {
+  setRelatedSamples
+} from "./chunk-C2MCQZWH.js";
+import {
+  filterVariantValues,
+  sample_match_termvaluesetting
+} from "./chunk-HGC4EON3.js";
+import {
+  dtcnv,
+  dtfusionrna,
+  dtgeneexpression,
+  dtsnvindel
+} from "./chunk-2N345NXD.js";
+import {
+  __export
+} from "./chunk-HS5PO5ZQ.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);
+  this.samplesByAncestorId = /* @__PURE__ */ new Map();
+  const seenAncestorSamples = /* @__PURE__ */ new Set();
+  for (const sd of data.lst) {
+    if (seenAncestorSamples.has(sd.sample)) continue;
+    seenAncestorSamples.add(sd.sample);
+    if (!sd._ref_?.ancestors) continue;
+    for (const a of sd._ref_.ancestors) {
+      const id = a.ancestor_id;
+      if (id === void 0) continue;
+      if (!this.samplesByAncestorId.has(id)) this.samplesByAncestorId.set(id, /* @__PURE__ */ new Set());
+      this.samplesByAncestorId.get(id).add(sd);
+    }
+  }
+  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;
+  }
+  for (const [ancestor_id, samples] of this.samplesByAncestorId.entries()) {
+    if (samples.size < 2) this.samplesByAncestorId.delete(ancestor_id);
+  }
+  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);
+    if (this.config.chartType == "matrix" && s.sortBySampleAncestry) setRelatedSamples(grp);
+  }
+  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-HM23KADV.js.map