@sjcrh/proteinpaint-client 2.206.1 → 2.207.0

package/dist/chunk-M4XXKTH2.js

@@ -1,339 +0,0 @@
-import {
-  matchesGvQueryEntry
-} from "./chunk-5ILEFNXJ.js";
-import {
-  mclass
-} from "./chunk-IZUYLFOX.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-M4XXKTH2.js.map

package/dist/chunk-NJ7N2VFX.js

@@ -1,263 +0,0 @@
-import {
-  Matrix
-} from "./chunk-EF4QV5YH.js";
-import {
-  hierCluster_renderers_exports
-} from "./chunk-OXWLQQXL.js";
-import {
-  hierCluster_interactivity_exports
-} from "./chunk-GUH5IG5N.js";
-import {
-  filterJoin,
-  getNormalRoot
-} from "./chunk-XDLCPJCK.js";
-import {
-  clusterMethodLst,
-  distanceMethodLst,
-  dofetch3
-} from "./chunk-RPDVFM7E.js";
-import {
-  TermTypes2Dt,
-  dictionaryNumericTypes
-} from "./chunk-5ILEFNXJ.js";
-import {
-  colorScaleMap
-} from "./chunk-IZUYLFOX.js";
-import {
-  deepEqual,
-  getCompInit
-} from "./chunk-WINIL2KN.js";
-import {
-  extent,
-  linear
-} from "./chunk-4OLM3KSB.js";
-
-// plots/matrix/hierCluster.js
-var HierCluster = class _HierCluster extends Matrix {
-  static type = "hierCluster";
-  constructor(opts) {
-    super(opts);
-    this.type = _HierCluster.type;
-    this.chartType = _HierCluster.type;
-  }
-  async init(appState) {
-    await super.init(appState);
-    this.maySetSandboxHeader(appState);
-    this.hcClipId = this.seriesClipId + "-hc";
-    this.dom.hcClipRect = this.dom.svg.select("defs").append("clipPath").attr("id", this.hcClipId).attr("clipPathUnits", "userSpaceOnUse").append("rect").attr("display", "block");
-    this.dom.topDendrogram = this.dom.svg.insert("g", "g").attr("clip-path", `url(#${this.hcClipId})`).append("g").attr("class", "sjpp-matrix-dendrogram").attr("data-testid", "hierCluster_top_dendrogram").on("click", (event) => {
-      const clickedClusterId = this.getClusterFromTopDendrogram(event);
-      if (clickedClusterId) {
-        this.clickedClusterIds = this.getAllChildrenClusterIds(clickedClusterId);
-        this.clickedClusterIds.push(clickedClusterId);
-        const clickedCluster = this.hierClusterData.clustering.col.mergedClusters.get(clickedClusterId);
-        const clickedClusterSampleNames = clickedCluster.children.map((c) => c.name);
-        this.addSelectedSamplesOptions(clickedClusterSampleNames, event);
-      } else {
-        delete this.clickedClusterIds;
-      }
-      if (this.clickedLeftClusterIds) {
-        delete this.clickedLeftClusterIds;
-        this.plotDendrogramHclust();
-      } else this.plotDendrogramHclust("top");
-    });
-    this.dom.leftDendrogram = this.dom.svg.insert("g", "g").attr("class", "sjpp-matrix-dendrogram").attr("data-testid", "hierCluster_left_dendrogram").on("click", (event) => {
-      const clickedLeftClusterId = this.getClusterFromLeftDendrogram(event);
-      if (clickedLeftClusterId) {
-        this.clickedLeftClusterIds = this.getAllChildrenClusterIds(clickedLeftClusterId, true);
-        this.clickedLeftClusterIds.push(clickedLeftClusterId);
-        const clickedLeftCluster = this.hierClusterData.clustering.row.mergedClusters.get(clickedLeftClusterId);
-        const clickedLeftClusterRowsNames = clickedLeftCluster.children.map((c) => c.name);
-        this.addSelectedRowsOptions(clickedLeftClusterRowsNames, event);
-      } else {
-        delete this.clickedLeftClusterIds;
-      }
-      if (this.clickedClusterIds) {
-        delete this.clickedClusterIds;
-        this.plotDendrogramHclust();
-      } else this.plotDendrogramHclust("left");
-    });
-  }
-  async setHierClusterData(_data = {}) {
-    this.prevServerData = this.currServerData;
-    const [d, twlst] = await this.requestData({});
-    if (d.error) throw d.error;
-    this.currServerData = structuredClone(d);
-    if (!deepEqual(this.prevServerData, this.currServerData)) {
-      delete this.clickedClusterIds;
-      delete this.clickedLeftClusterIds;
-    }
-    const s = this.settings.hierCluster;
-    if (!d.clustering) {
-      if (d.gene) {
-        throw `Cannot do clustering: data is only available for 1 gene (${d.gene}). Try again by adding more genes.`;
-      }
-    }
-    this.hierClusterData = d;
-    const c = this.hierClusterData.clustering;
-    this.setHierColorScale(c);
-    const samples = {};
-    for (const [i, column] of c.col.order.entries()) {
-      samples[column.name] = { sample: column.name };
-      for (const [j, row] of c.row.order.entries()) {
-        const tw = twlst.find((tw2) => tw2.$id === row.name || tw2.id === row.name);
-        const value = c.matrix[j][i];
-        samples[column.name][tw.$id] = {
-          key: tw.term.name,
-          values: [
-            {
-              sample: column.name,
-              dt: TermTypes2Dt[this.state.config.dataType],
-              label: s.termGroupName,
-              // gene: tw.term.name,
-              // chr: tw.term.chr,
-              // pos: `${tw.term.start}-${tw.term.stop}`,
-              value
-              // the color will be computed in matrix.cells, so that
-              // it can get updated even when there are no nonsetting state diff
-            }
-          ]
-        };
-      }
-    }
-    this.hcTermNameOrder = this.settings.hierCluster.sortClusterRows == "asListed" ? twlst.map((t) => t.term.name) : this.settings.hierCluster.sortClusterRows == "byName" ? twlst.map((t) => t.term.name).sort() : dictionaryNumericTypes.has(this.config.dataType) ? c.row.order.map((row) => twlst.find((t) => t.$id == row.name || t.term.id == row.name)?.term.name) : c.row.order.map((row) => twlst.find((t) => t.$id == row.name)?.term.name);
-    if (this.hcTermNameOrder.includes(void 0)) throw `unable to map row.name to term.name`;
-    this.hcTermSorter = (a, b) => {
-      const i = this.hcTermNameOrder.indexOf(a.tw.term.name);
-      const j = this.hcTermNameOrder.indexOf(b.tw.term.name);
-      if (i == -1 && j == -1) return 0;
-      if (i == -1) return 1;
-      if (j == -1) return -1;
-      return i - j;
-    };
-    this.hcSampleNameOrder = c.col.order.map((col) => col.name);
-    this.hcSampleSorter = (a, b) => {
-      const i = this.hcSampleNameOrder.indexOf(a.sample);
-      const j = this.hcSampleNameOrder.indexOf(b.sample);
-      if (i == -1 && j == -1) return 0;
-      if (i == -1) return 1;
-      if (j == -1) return -1;
-      return i - j;
-    };
-    const byTermId = {};
-    for (const tw of twlst) {
-      if (d.byTermId?.[tw.term.name]) byTermId[tw.$id] = d.byTermId[tw.term.name];
-    }
-    this.hierClusterSamples = {
-      refs: { byTermId, bySampleId: d.bySampleId },
-      lst: c.col.order.map((c2) => samples[c2.name]),
-      samples,
-      removedHierClusterTerms: d.removedHierClusterTerms
-    };
-  }
-  async requestData() {
-    const body = this.currRequestOpts?.hierCluster || this.getHCRequestBody(this.state);
-    const twlst = this.hcTermGroup.lst;
-    const data = await dofetch3("termdb/cluster", { body, signal: this.api.getAbortSignal?.() });
-    return [data, twlst];
-  }
-  getHCRequestBody(state) {
-    this.hcTermGroup = this.config.termgroups.find((grp) => grp.type == "hierCluster") || this.termOrder?.find((t) => t.grp.type == "hierCluster")?.grp;
-    const s = state.config.settings.hierCluster;
-    const dictionaryLegendFilter = {
-      type: "tvslst",
-      in: true,
-      join: "and",
-      lst: state.config.legendValueFilter.lst.filter((f) => !f.tvs.legendFilterType)
-    };
-    const terms = this.getClusterRowTermsAsParameter();
-    if (!terms.length) throw "no data";
-    if (!clusterMethodLst.find((i) => i.value == s.clusterMethod)) throw "Invalid cluster method";
-    if (!distanceMethodLst.find((i) => i.value == s.distanceMethod)) throw "Invalid distance method";
-    const body = {
-      genome: state.vocab.genome,
-      dslabel: state.vocab.dslabel,
-      dataType: state.config.dataType,
-      clusterMethod: s.clusterMethod,
-      distanceMethod: s.distanceMethod,
-      zScoreTransformation: s.zScoreTransformation,
-      terms,
-      filter: getNormalRoot(filterJoin([state.filter, dictionaryLegendFilter])),
-      filter0: state.filter0
-    };
-    if (state.config.dataType == "proteomeAbundance") {
-      body.proteomeDetails = {
-        organism: state.config.proteomeDetails?.organism,
-        assay: state.config.proteomeDetails?.assay,
-        cohort: state.config.proteomeDetails?.cohort
-      };
-    }
-    return body;
-  }
-  combineData() {
-    if (!this.hierClusterSamples) return;
-    const d = this.data;
-    const removedHierClusterTerms = this.hierClusterSamples.removedHierClusterTerms;
-    const samples = {};
-    const lst = [];
-    for (const sampleId in this.hierClusterSamples.samples) {
-      const s = this.hierClusterSamples.samples[sampleId];
-      samples[sampleId] = s;
-      lst.push(s);
-      if (sampleId in d.samples) Object.assign(s, d.samples[sampleId]);
-      const _ref_ = this.hierClusterSamples.refs.bySampleId[sampleId] || {};
-      if (!s._ref_) s._ref_ = _ref_;
-      else Object.assign(s._ref_, _ref_);
-    }
-    const t = this.hierClusterSamples.refs.byTermId;
-    for (const $id of Object.keys(t)) {
-      d.refs.byTermId[$id] = Object.assign({}, d.refs.byTermId[$id] || {}, t[$id]);
-    }
-    this.data = { samples, lst, refs: d.refs, removedHierClusterTerms };
-  }
-  setHierColorScale(c) {
-    const hc = this.settings.hierCluster;
-    const scale = linear(colorScaleMap[hc.colorScale].domain, colorScaleMap[hc.colorScale].range).clamp(true);
-    const globalMinMaxes = [];
-    for (const row of c.matrix) {
-      globalMinMaxes.push(...extent(row));
-    }
-    const absMax = Math.min(hc.zScoreCap, Math.max(...extent(globalMinMaxes).map(Math.abs)));
-    const [min, max] = hc.zScoreTransformation ? [-absMax, absMax] : [Math.min(...globalMinMaxes), Math.max(...globalMinMaxes)];
-    this.hierClusterValues = { scale, min, max };
-  }
-  getValueColor(value) {
-    const hc = this.settings.hierCluster;
-    if (hc.zScoreTransformation) {
-      const zScoreCap = this.settings.hierCluster.zScoreCap;
-      return this.hierClusterValues.scale((value - -zScoreCap) / (zScoreCap * 2));
-    } else {
-      return this.hierClusterValues.scale(value / this.hierClusterValues.max);
-    }
-  }
-  /* returns list of gene terms as request parameter, e.g. {gene,chr,start,stop}
-  	request parameter only need term but not tw, as it will simply fetch continuous sample values on terms without transform
-  
-  	use of this function is unfortunate because:
-  		the incomplete migration of {name} to {gene} for gene-based term
-  		geneset edit ui is hardcoded to return {name}
-  		existing plot states contain {name}
-  
-  	!!! migration instruction !!!
-  	- term.name is for display only, if a term is gene-based, it has term.gene=str
-  	- a geneVariant term can be based on a genomic range (and not a gene), in that case it won't have term.gene and cannot be used where gene is expected, e.g. gene-based clustering analysis
-  
-  	*/
-  getClusterRowTermsAsParameter() {
-    const lst = this.hcTermGroup.lst.map(this.opts.app.vocabApi.getTwMinCopy);
-    lst.sort((a, b) => a.term.name < b.term.name ? -1 : 1);
-    return lst;
-  }
-};
-for (const methods of [hierCluster_renderers_exports, hierCluster_interactivity_exports]) {
-  for (const methodName in methods) HierCluster.prototype[methodName] = methods[methodName];
-}
-var hierClusterInit = getCompInit(HierCluster);
-var componentInit = hierClusterInit;
-
-export {
-  HierCluster,
-  hierClusterInit,
-  componentInit
-};
-//# sourceMappingURL=chunk-NJ7N2VFX.js.map