@sjcrh/proteinpaint-client 2.210.0 → 2.210.1

package/dist/chunk-AUZ63NKJ.js

@@ -1,70 +0,0 @@
-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

@@ -1,217 +0,0 @@
-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

@@ -1,339 +0,0 @@
-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