@sjcrh/proteinpaint-client 2.224.2 → 2.225.0

package/dist/chunk-ZLQ6PAI6.js

@@ -1,299 +0,0 @@
-import {
-  first_genetrack_tolist,
-  gmmode,
-  sayerror
-} from "./chunk-ZIMAIUZD.js";
-import {
-  dofetch3
-} from "./chunk-ZUXXBQ7D.js";
-import {
-  codon_stop,
-  nt2aa,
-  proteinDomainColorScale
-} from "./chunk-R2H22S4J.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-
-// common/snp.js
-async function string2snp(genome, str) {
-  const data = await dofetch3("snp", {
-    method: "POST",
-    body: JSON.stringify({ byName: true, genome: genome.name, lst: [str] })
-  });
-  if (data.error) throw data.error;
-  if (!data.results || data.results.length == 0) throw str + ": not a SNP";
-  for (const i of data.results) {
-    const chr = genome.chrlookup[i.chrom.toUpperCase()];
-    if (chr && chr.major) {
-      return {
-        chr: i.chrom,
-        start: i.chromStart,
-        stop: i.chromEnd
-      };
-    }
-  }
-  const r = data.results[0];
-  return {
-    chr: r.chrom,
-    start: r.chromStart,
-    stop: r.chromEnd
-  };
-}
-
-// src/block.init.js
-async function block_init_default(arg) {
-  if (!arg.holder) throw "No holder for block.init";
-  if (!arg.genome) throw "no genome";
-  if (arg.holder instanceof Element) arg.holder = select_default(arg.holder);
-  if (!arg.tklst) arg.tklst = [];
-  if (arg.query) {
-    await step1_findgm(arg);
-    return;
-  }
-  if (arg.model && arg.allmodels) {
-    await step2_getseq(arg);
-    return;
-  }
-}
-async function step1_findgm(arg) {
-  const wait = arg.holder.append("p").style("font-size", "2em").style("color", "#858585").text("Searching for " + arg.query + " ...");
-  const data = await dofetch3("genelookup", {
-    body: { deep: 1, input: arg.query, genome: arg.genome.name }
-  });
-  if (!data) throw "querying genes: server error";
-  if (data.error) throw "error querying genes: " + data.error;
-  if (!data.gmlst || data.gmlst.length == 0) {
-    if (arg.genome.hasSNP) {
-      try {
-        const r = await string2snp(arg.genome, arg.query);
-        wait.remove();
-        const par = {
-          genome: arg.genome,
-          holder: arg.holder,
-          chr: r.chr,
-          start: Math.max(0, r.start - 300),
-          stop: r.start + 300,
-          nobox: true,
-          tklst: arg.tklst,
-          debugmode: arg.debugmode
-        };
-        first_genetrack_tolist(arg.genome, par.tklst);
-        const b = await import("./block-DXRSU62C.js");
-        const block = new b.Block(par);
-        block.addhlregion(r.chr, r.start, r.stop - 1);
-      } catch (e) {
-        wait.text("Not a gene or SNP: " + arg.query);
-      }
-    } else {
-      wait.text("No match to gene: " + arg.query);
-    }
-    return;
-  }
-  wait.remove();
-  arg.allmodels = data.gmlst;
-  for (const m of arg.allmodels) {
-    if (m.isoform.toUpperCase() == (data.found_isoform ? data.found_isoform.toUpperCase() : arg.query.toUpperCase())) {
-      arg.model = m;
-      await step2_getseq(arg);
-      return;
-    }
-  }
-  const defaultisoforms = [];
-  for (const m of arg.allmodels) {
-    if (!m.isoform) throw "isoform missing from one gene model: " + JSON.stringify(m);
-    const n = m.isoform.toUpperCase();
-    if (arg.genome.isoformcache.has(n)) {
-      let nothas = true;
-      for (const m2 of arg.genome.isoformcache.get(n)) {
-        if (m2.chr == m.chr && m2.start == m.start && m2.stop == m.stop && m2.strand == m.strand) {
-          nothas = false;
-          break;
-        }
-      }
-      if (nothas) {
-        arg.genome.isoformcache.get(n).push(m);
-      }
-    } else {
-      arg.genome.isoformcache.set(n, [m]);
-    }
-    if (m.isoform.toUpperCase() == arg.query.toUpperCase()) {
-      defaultisoforms.push(m);
-      break;
-    }
-    if (m.isdefault) {
-      defaultisoforms.push(m);
-    }
-  }
-  if (defaultisoforms.length == 1) {
-    arg.model = defaultisoforms[0];
-  } else if (defaultisoforms.length > 1) {
-    for (const m of defaultisoforms) {
-      if (m.chr == "chrY") {
-        continue;
-      }
-      const chr = arg.genome.chrlookup[m.chr.toUpperCase()];
-      if (!chr) {
-        continue;
-      }
-      if (!chr.major) {
-        continue;
-      }
-      arg.model = m;
-      break;
-    }
-    if (!arg.model) {
-      arg.model = defaultisoforms[0];
-    }
-  }
-  if (!arg.model) {
-    arg.model = arg.allmodels[0];
-  }
-  await step2_getseq(arg);
-}
-async function step2_getseq(arg) {
-  if (arg.model.genomicseq) {
-    checker();
-    step2_getpdomain(arg);
-    return;
-  }
-  const par = {
-    genome: arg.genome.name,
-    coord: arg.model.chr + ":" + (arg.model.start + 1) + "-" + arg.model.stop
-  };
-  const data = await dofetch3("ntseq", { method: "POST", body: JSON.stringify(par) });
-  if (!data) throw "getting sequence: server error";
-  if (data.error) throw "getting sequence: " + data.error;
-  if (!data.seq) throw "no nt seq???";
-  arg.model.genomicseq = data.seq.toUpperCase();
-  arg.model.aaseq = nt2aa(arg.model);
-  checker();
-  await step2_getpdomain(arg);
-  function checker() {
-    if (arg.model.aaseq) {
-      const stop = arg.model.aaseq.indexOf(codon_stop);
-      const cdslen = arg.model.cdslen - (arg.model.startCodonFrame ? 3 - arg.model.startCodonFrame : 0);
-      if (stop != -1 && stop < cdslen / 3 - 1) {
-        sayerror(arg.holder, "Translating " + arg.model.isoform + " ends at " + stop + " AA, expecting " + cdslen / 3);
-      }
-    }
-  }
-}
-async function step2_getpdomain(arg) {
-  const isoform2gm = /* @__PURE__ */ new Map();
-  for (const m of arg.allmodels) {
-    if (!m.pdomains) {
-      m.pdomains = [];
-      m.domain_hidden = {};
-      if (!isoform2gm.has(m.isoform)) isoform2gm.set(m.isoform, []);
-      isoform2gm.get(m.isoform).push(m);
-    }
-  }
-  if (isoform2gm.size == 0) {
-    await step3(arg);
-    return;
-  }
-  const data = await dofetch3("pdomain", {
-    method: "POST",
-    body: JSON.stringify({ genome: arg.genome.name, isoforms: [...isoform2gm.keys()] })
-  });
-  if (data.error) throw "error getting protein domain: " + data.error;
-  if (!Array.isArray(data.lst)) throw ".lst[] not array";
-  for (const a of data.lst) {
-    for (const m of isoform2gm.get(a.name)) {
-      m.pdomains = a.pdomains;
-      if (arg.hidePdomain) {
-        for (const i of a.pdomains) {
-          m.domain_hidden[i.name + i.description] = 1;
-        }
-      }
-    }
-  }
-  if (arg.geneDomains) {
-    if (typeof arg.geneDomains != "object") throw "geneDomains not object";
-    for (const isoform in arg.geneDomains) {
-      const lst = isoform2gm.get(isoform);
-      if (!lst) throw `unknown isoform ${isoform} from geneDomains{}`;
-      for (const g of lst) {
-        if (!g.pdomains) g.pdomains = [];
-        if (!Array.isArray(arg.geneDomains[isoform])) throw `geneDomains[${isoform}] not array`;
-        for (const b of arg.geneDomains[isoform]) {
-          if (typeof b != "object") throw "element from geneDomains[] not object";
-          if (!Number.isInteger(b.start)) throw "start not integer from geneDomains[]";
-          if (!Number.isInteger(b.stop)) throw "stop not integer from geneDomains[]";
-          if (b.start > b.stop) throw "start>stop from geneDomains[]";
-          if (!b.name) b.name = "Custom domain";
-          if (!g.pdomains.find((a) => a.start == b.start && a.stop == b.stop && a.name == b.name)) g.pdomains.push(b);
-        }
-      }
-    }
-  }
-  const s = proteinDomainColorScale();
-  for (const lst of isoform2gm.values()) {
-    for (const g of lst) {
-      for (const d of g.pdomains || []) {
-        if (!d.color) d.color = s(d.name + d.description);
-      }
-    }
-  }
-  await step3(arg);
-}
-async function step3(arg) {
-  let mode = arg.gmmode;
-  if (!mode) {
-    if (arg.model.cdslen) {
-      mode = gmmode.protein;
-    } else {
-      mode = gmmode.exononly;
-    }
-  }
-  if (arg.dataset) {
-    if (!Array.isArray(arg.dataset)) throw "dataset is not array";
-    for (const dsname of arg.dataset) {
-      if (arg.genome.datasets[dsname] && !arg.genome.datasets[dsname].legacyDsIsUninitiated) continue;
-      const d = await dofetch3(`getDataset?genome=${arg.genome.name}&dsname=${dsname}`);
-      if (d.error) throw `invalid name from dataset[]: ${d.error}`;
-      if (!d.ds) throw ".ds missing";
-      const ds = arg.genome.datasets[d.ds.label];
-      Object.assign(ds, d.ds);
-      const _ = await import("./legacyDataset-IEFWFVS6.js");
-      _.validate_oldds(ds);
-      delete ds.legacyDsIsUninitiated;
-    }
-  }
-  const b = await import("./block-DXRSU62C.js");
-  arg.__blockInstance = new b.Block({
-    genome: arg.genome,
-    holder: arg.holder,
-    nobox: true,
-    usegm: arg.model,
-    gmstackheight: 37,
-    allgm: arg.allmodels,
-    datasetlst: arg.dataset,
-    legacyDsFilter: arg.legacyDsFilter,
-    mset: arg.mset,
-    hlaachange: arg.hlaachange,
-    hlvariants: arg.hlvariants,
-    hlregions: arg.hlregions,
-    aarange: arg.aarange,
-    gmmode: mode,
-    hidedatasetexpression: arg.hidedatasetexpression,
-    hidegenecontrol: arg.hidegenecontrol,
-    hidegenelegend: arg.hidegenelegend,
-    variantPageCall_snv: arg.variantPageCall_snv,
-    datasetqueries: arg.datasetqueries,
-    samplecart: arg.samplecart,
-    debugmode: arg.debugmode,
-    tklst: arg.tklst,
-    mclassOverride: arg.mclassOverride,
-    hide_dsHandles: arg.hide_dsHandles,
-    onloadalltk_always: arg.onloadalltk_always,
-    onAddRemoveTk: arg.onAddRemoveTk
-  });
-}
-
-export {
-  string2snp,
-  block_init_default
-};
-//# sourceMappingURL=chunk-ZLQ6PAI6.js.map

package/dist/chunk-ZUG4EY4T.js

@@ -1,348 +0,0 @@
-import {
-  matchesGvQueryEntry
-} from "./chunk-5FD6NRGE.js";
-import {
-  mclass
-} from "./chunk-R2H22S4J.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-ZUG4EY4T.js.map