@sjcrh/proteinpaint-client 2.209.0 → 2.210.0

package/dist/chunk-AUZ63NKJ.js

@@ -0,0 +1,70 @@
+import {
+  junctionCustomTermSource
+} from "./chunk-JTANDSTD.js";
+import {
+  mayRenderFractionSelection
+} from "./chunk-55FABQU2.js";
+
+// termdb/handlers/junction.ts
+var SearchHandler = class {
+  async init(opts) {
+    if (!opts?.holder) throw new Error("opts.holder is required");
+    if (typeof opts.callback != "function") throw new Error("opts.callback is required");
+    const entries = getJunctionCustomTerms(opts.app.vocabApi.state?.customTerms);
+    render(opts, entries);
+  }
+};
+function getJunctionCustomTerms(customTerms) {
+  if (!Array.isArray(customTerms)) return [];
+  return customTerms.filter((term) => term?.source === junctionCustomTermSource && term.tw?.term);
+}
+function render(opts, entries) {
+  const holder = opts.holder;
+  holder.selectAll("*").remove();
+  const div = holder.append("div").style("padding", "10px 0px");
+  if (!entries.length) {
+    div.append("div").text("Junctions selected from genome browser will be shown here.");
+    return;
+  }
+  const listDiv = div.append("div");
+  const fractionDiv = div.append("div");
+  for (const entry of entries) {
+    if (entry.eventlabel) renderJunctionEvent(listDiv, fractionDiv, entry, opts);
+    else renderJunction(listDiv, entry, opts);
+  }
+  listDiv.append("div").style("font-size", ".7em").style("margin-top", "10px").style("opacity", 0.7).text("Select additional junctions from genome browser.");
+}
+function renderJunction(holder, entry, opts) {
+  const choice = holder.append("div");
+  choice.append("div").attr("class", "ts_pill sja_filter_tag_btn sja_tree_click_term").style("display", "inline-block").style("border-radius", "6px").style("margin", "1px 0").text(entry.tw.term.name).on("click", () => opts.callback(entry.tw.term));
+  addDeleteButton(choice, entry, opts);
+}
+function renderJunctionEvent(holder, fractionDiv, entry, opts) {
+  const eventHolder = holder.append("div");
+  const pillRow = eventHolder.append("div");
+  pillRow.append("div").attr("class", "ts_pill sja_filter_tag_btn sja_tree_click_term").style("display", "inline-block").style("border-radius", "6px").style("margin", "1px 0").text(entry.eventlabel).on("click", () => selectJunctionEvent(holder, fractionDiv, entry, opts));
+  addDeleteButton(pillRow, entry, opts);
+  eventHolder.append("div").style("margin-left", "10px").style("font-size", ".7em").selectAll("div").data(entry.tw.term.termlst, (term) => term.id).enter().append("div").text((term) => term.name);
+}
+function selectJunctionEvent(listDiv, fractionDiv, entry, opts) {
+  const isStaged = mayRenderFractionSelection({
+    term: entry.tw.term,
+    selectionMode: opts.termCollectionSelectionMode,
+    listDiv,
+    fractionDiv,
+    callback: (tw) => opts.callback(tw)
+  });
+  if (!isStaged) opts.callback(entry.tw.term);
+}
+function addDeleteButton(holder, entry, opts) {
+  holder.append("button").attr("data-testid", "sjpp-junction-delete").style("margin-left", "4px").attr("aria-label", `Delete ${entry.name}`).text("\xD7").on("click", async () => {
+    await opts.app.vocabApi.deleteCustomTermById(entry.id);
+    render(opts, getJunctionCustomTerms(opts.app.vocabApi.state?.customTerms));
+  });
+}
+
+export {
+  SearchHandler,
+  getJunctionCustomTerms
+};
+//# sourceMappingURL=chunk-AUZ63NKJ.js.map

package/dist/chunk-B563DUNQ.js

@@ -0,0 +1,217 @@
+import {
+  DATermTypes,
+  DMRCATE_DEFAULTS
+} from "./chunk-55FABQU2.js";
+import {
+  dofetch3
+} from "./chunk-VA57CUC7.js";
+import {
+  DMR_SCAN_ELEMENT_TYPE
+} from "./chunk-SB36AUG7.js";
+import {
+  rgb
+} from "./chunk-Q5RDQNIT.js";
+
+// plots/volcano/colors.ts
+function getGroupColors(config) {
+  const groups = config?.samplelst?.groups;
+  const termValues = config?.tw?.term?.values;
+  const rawDown = termValues?.[groups?.[0]?.name]?.color || "red";
+  const rawUp = termValues?.[groups?.[1]?.name]?.color || "blue";
+  return {
+    controlColor: toHex(rawDown, "red"),
+    caseColor: toHex(rawUp, "blue")
+  };
+}
+function toHex(color, fallback) {
+  const c = rgb(color || fallback);
+  return c.displayable() ? c.formatHex() : rgb(fallback).formatHex();
+}
+
+// plots/volcano/model/VolcanoModel.ts
+var VolcanoModel = class {
+  /** TODO: This model is used in both the volcano and gsea.
+   * In the future, create base model in DA and use specific
+   * classes for the volcano and gsea. */
+  constructor(plot, termType) {
+    this.plot = plot;
+    this.app = plot.app;
+    this.termType = termType;
+  }
+  /** May use mapper instead as more termTypes are added */
+  async getData(config, settings) {
+    this.config = config;
+    this.settings = settings;
+    if (this.termType === DATermTypes.GENE_EXPRESSION) {
+      const body = await this.getGERequestBody();
+      const response = await dofetch3("termdb/DE", { body, signal: this.plot.api?.getAbortSignal() });
+      if (response && !response.error) response.daRequest = body;
+      return response;
+    }
+    if (this.termType === DATermTypes.DNA_METHYLATION) {
+      const body = await this.getDMRequestBody();
+      const response = await dofetch3("termdb/diffMeth", { body, signal: this.plot.api?.getAbortSignal() });
+      if (response && !response.error) response.daRequest = body;
+      return response;
+    }
+    if (this.termType === DATermTypes.SINGLECELL_CELLTYPE) {
+      const body = await this.getSCCTRequestBody();
+      return await dofetch3("termdb/singlecellDEgenes", { body, signal: this.plot.api?.getAbortSignal() });
+    }
+    if (this.termType === DATermTypes.PROTEOME_DAP) {
+      const body = this.getDapRequestBody();
+      return await dofetch3("termdb/dapVolcano", { body, signal: this.plot.api?.getAbortSignal() });
+    }
+    if (this.termType === DATermTypes.SINGLECELL_GENE_EXPRESSION) {
+    }
+    throw new Error(`Volcano plot does not support route for termType='${this.termType}'`);
+  }
+  //Gene expression
+  async getGERequestBody() {
+    await this.getOtherSamples(this.config.samplelst);
+    const state = this.app.getState();
+    const body = {
+      kind: "DE",
+      genome: this.app.vocabApi.vocab.genome,
+      dslabel: this.app.vocabApi.vocab.dslabel,
+      method: this.settings.method,
+      min_count: this.settings.minCount,
+      min_total_count: this.settings.minTotalCount,
+      samplelst: this.config.samplelst,
+      filter: state.termfilter.filter,
+      filter0: state.termfilter.filter0,
+      cpm_cutoff: this.settings.cpmCutoff,
+      volcanoRender: this.getVolcanoRender()
+    };
+    const pseudobulk = this.config.tw?.pseudobulk;
+    if (pseudobulk) body.pseudobulk = pseudobulk;
+    this.addConfounderTw(body);
+    return body;
+  }
+  //DNA methylation
+  async getDMRequestBody() {
+    await this.getOtherSamples(this.config.samplelst);
+    const state = this.app.getState();
+    const body = {
+      kind: "DM",
+      genome: this.app.vocabApi.vocab.genome,
+      dslabel: this.app.vocabApi.vocab.dslabel,
+      samplelst: this.config.samplelst,
+      filter: state.termfilter.filter,
+      filter0: state.termfilter.filter0,
+      min_samples_per_group: this.settings.minSamplesPerGroup,
+      exclude_sex_chr: this.settings.excludeSexChr,
+      /* Omitted rather than sent as 'promoter' when it is the default, so a request
+      from a promoter-only dataset is byte-identical to what this client sent before
+      the element picker existed. The server resolves an absent element_type to
+      'promoter'. This does NOT preserve cache keys -- the key object gained the
+      field server-side, so every pre-existing dm/ entry is orphaned on deploy
+      regardless of what the client sends. */
+      ...this.settings.elementType && this.settings.elementType != "promoter" ? { element_type: this.settings.elementType } : {},
+      // the scan's own knobs; the server ignores them for any other element type
+      ...this.settings.elementType == DMR_SCAN_ELEMENT_TYPE ? {
+        scan: {
+          ...this.settings.scanChromosome ? { chromosome: this.settings.scanChromosome } : {},
+          backgroundCorrection: !!this.settings.backgroundCorrection,
+          minCpgs: this.settings.minCpgs,
+          profileBinBp: this.settings.profileBinBp,
+          // only when changed: an explicit default would orphan every cached scan
+          ...this.settings.lambda != DMRCATE_DEFAULTS.lambda ? { lambda: this.settings.lambda } : {},
+          ...this.settings.C != DMRCATE_DEFAULTS.C ? { C: this.settings.C } : {},
+          ...this.settings.fdrCutoff != DMRCATE_DEFAULTS.fdrCutoff ? { fdrCutoff: this.settings.fdrCutoff } : {}
+        }
+      } : {},
+      volcanoRender: this.getVolcanoRender()
+    };
+    if (this.settings.elementType != DMR_SCAN_ELEMENT_TYPE) this.addConfounderTw(body);
+    return body;
+  }
+  /** Parameters telling the server to run the `volcano` Rust renderer and return a
+   * volcano PNG + top-significant rows instead of the full dot list. */
+  getVolcanoRender() {
+    const dotRadius = Math.max(this.settings.width, this.settings.height) / 80;
+    const { caseColor, controlColor } = getGroupColors(this.config);
+    const useDeltaBeta = this.termType === DATermTypes.DNA_METHYLATION && this.settings.xAxis == "delta_beta";
+    return {
+      significanceThresholds: {
+        pValueCutoff: this.settings.pValue,
+        pValueType: this.settings.pValueType,
+        foldChangeCutoff: useDeltaBeta ? this.settings.deltaBetaCutoff : this.settings.foldChangeCutoff
+      },
+      ...useDeltaBeta ? { xField: "delta_beta" } : {},
+      // Tied to the delta-beta axis: the control that sets it is only offered for
+      // methylation, and centering a log2 fold-change axis is a different conversation.
+      ...useDeltaBeta && this.settings.centerDeltaBeta ? { centerX: true } : {},
+      pixelWidth: this.settings.width,
+      pixelHeight: this.settings.height,
+      colorSignificant: toHex(this.settings.defaultSignColor, "red"),
+      colorSignificantUp: caseColor,
+      colorSignificantDown: controlColor,
+      colorNonsignificant: toHex(this.settings.defaultNonSignColor, "black"),
+      dotRadius,
+      maxInteractiveDots: this.settings.maxInteractiveDots,
+      // Render the PNG at device-pixel resolution so it stays sharp on
+      // retina screens. The server reports the plot extent in CSS-space,
+      // so SVG overlay coords are unaffected.
+      //
+      // Oversample by 2× so the PNG also stays sharp when the user
+      // *zooms in after* the initial render (the captured DPR is frozen
+      // at fetch time — bigger headroom = more tolerable post-render
+      // zoom before pixelation appears). The server clamp keeps the
+      // bitmap memory bounded.
+      devicePixelRatio: (typeof window !== "undefined" ? window.devicePixelRatio : 1) * 2
+    };
+  }
+  //This is a workaround until the server can accept an arr of confounder tws
+  addConfounderTw(body) {
+    const confounders = this.config?.confounderTws;
+    if (confounders?.length) {
+      body.tw = this.config.confounderTws[0];
+      if (confounders.length > 1) body.tw2 = this.config.confounderTws[1];
+    }
+  }
+  //Single cell cell type
+  getSCCTRequestBody() {
+    const body = {
+      genome: this.app.vocabApi.vocab.genome,
+      dslabel: this.app.vocabApi.vocab.dslabel,
+      sample: this.config.sample,
+      termId: this.config.termId,
+      categoryName: this.config.categoryName,
+      volcanoRender: this.getVolcanoRender()
+    };
+    return body;
+  }
+  getDapRequestBody() {
+    const { organism, assay, cohort } = this.config.proteomeDetails;
+    return {
+      genome: this.app.vocabApi.vocab.genome,
+      dslabel: this.app.vocabApi.vocab.dslabel,
+      organism,
+      assay,
+      cohort,
+      volcanoRender: this.getVolcanoRender()
+    };
+  }
+  /** retrieve the sampleId/sampleName for samples in
+   * the "others" group instead of using {in: false} */
+  async getOtherSamples(samplelst) {
+    const othersSamplesGroup = samplelst.groups.find((g) => !g.in);
+    if (!othersSamplesGroup) return;
+    const state = this.app.getState();
+    const samplesGroup = samplelst.groups.find((g) => g.in);
+    othersSamplesGroup.values = [];
+    for (const s of await this.plot.vocabApi.getFilteredSampleList(state.termfilter.filter)) {
+      if (!samplesGroup.values.some((i) => i.sampleId == s.id)) {
+        othersSamplesGroup.values.push({ sampleId: s.id, sample: s.name });
+      }
+    }
+    othersSamplesGroup.in = true;
+  }
+};
+
+export {
+  getGroupColors,
+  VolcanoModel
+};
+//# sourceMappingURL=chunk-B563DUNQ.js.map

package/dist/chunk-BK6UDL7F.js

@@ -0,0 +1,339 @@
+import {
+  matchesGvQueryEntry
+} from "./chunk-KIAMLQ7S.js";
+import {
+  mclass
+} from "./chunk-SB36AUG7.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='${tvs.mcount}'`);
+    if (tvs.mafFilter) throw unsupported("mafFilter");
+    if (tvs.continuousCnv) throw unsupported("continuousCnv");
+    if (tvs.selfBreakpointRange) throw unsupported("selfBreakpointRange");
+  }
+}
+function getFilterScope(filter, scope = /* @__PURE__ */ new Set()) {
+  for (const item of filter.lst) {
+    if (item.type == "tvslst") getFilterScope(item, scope);
+    else scope.add(`${item.tvs.term.dt}:${item.tvs.term.origin || "*"}`);
+  }
+  return scope;
+}
+function isInScope(v, scope) {
+  return scope.has(`${v.dt}:*`) || scope.has(`${v.dt}:${v.origin || ""}`);
+}
+function matchTvs(v, tvs) {
+  let match = false;
+  if (v.dt == tvs.term.dt && (!tvs.term.origin || v.origin == tvs.term.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-BK6UDL7F.js.map