@sjcrh/proteinpaint-client 2.187.0 → 2.188.0

package/dist/chunk-IABWKPRK.js

@@ -1,534 +0,0 @@
-import {
-  isDictionaryType
-} from "./chunk-EGWVYY7K.js";
-import {
-  dtcnv,
-  dtfusionrna,
-  dtsnvindel,
-  mclasscnvAmp,
-  mclasscnvHomozygousDel,
-  mclasscnvgain,
-  mclasscnvloh,
-  mclasscnvloss
-} from "./chunk-AMYSEKPF.js";
-
-// plots/matrix/matrix.sort.js
-function getSampleSorter(self, settings, rows, opts = {}) {
-  const s = settings;
-  validateSettings(s);
-  if (self.config.chartType == "hierCluster" && self.config.settings.hierCluster.clusterSamples) {
-    return self.hcSampleSorter;
-  }
-  if (s.sortSamplesBy == "asListed") {
-    return (a, b) => {
-      return self.asListedSampleOrder.indexOf(a.sample) - self.asListedSampleOrder.indexOf(b.sample);
-    };
-  }
-  if (s.sortSamplesBy == "name") {
-    return sortSamplesByName;
-  }
-  const activeOption = s.sortOptions[s.sortSamplesBy];
-  if (!activeOption) throw `unsupported s.sortSamplesBy='${s.sortSamplesBy}'`;
-  self.selectedTermsToSortAgainst = self.termOrder.filter((t) => t.tw.sortSamples);
-  const selectedTerms = self.selectedTermsToSortAgainst.map((t) => t.tw).sort((a, b) => a.sortSamples.priority - b.sortSamples.priority);
-  const sorterTerms = [];
-  const sortPriority = activeOption.sortPriority;
-  if (sortPriority) {
-    for (const _tw of selectedTerms) {
-      const tw = structuredClone(_tw);
-      if (tw.sortSamples?.by) {
-        sorterTerms.push(Object.assign({}, tw));
-        continue;
-      }
-      for (const p of sortPriority) {
-        if (opts.skipSorter?.(p, tw)) continue;
-        const type = tw.term.type == "geneVariant" && tw.q.type != "values" ? "categorical" : tw.term.type;
-        if (!p.types.includes(type)) continue;
-        for (const tb of p.tiebreakers) {
-          const sortSamples = Object.assign(structuredClone(tw.sortSamples || {}), tb);
-          const sorter = Object.assign(structuredClone(tw), { sortSamples });
-          sorterTerms.push(sorter);
-        }
-      }
-    }
-  }
-  if (sortPriority) {
-    for (const p of sortPriority) {
-      for (const t of self.termOrder) {
-        if (selectedTerms.find((tw) => tw.$id === t.tw.$id)) continue;
-        if (opts.skipSorter?.(p, t.tw)) continue;
-        if (!p.types.includes(t.tw.term.type)) continue;
-        for (const tb of p.tiebreakers) {
-          sorterTerms.push(Object.assign({}, t.tw, { sortSamples: tb }));
-        }
-      }
-    }
-  } else {
-    const unSelectedDictTerms = self.app.vocabApi.vocab?.dslabel == "PNET" ? [] : self.termOrder.filter(
-      (t) => !t.tw.sortSamples && isDictionaryType(t.tw.term.type) && !selectedTerms.find((tw) => tw.$id === t.tw.$id)
-    ).map((t) => Object.assign({ sortSamples: { by: "values" } }, t.tw));
-    const unSelectedNonDictTerms = self.app.vocabApi.vocab?.dslabel == "PNET" ? [] : self.termOrder.filter(
-      (t) => !t.tw.sortSamples && !isDictionaryType(t.tw.term.type) && !selectedTerms.find((tw) => tw.$id === t.tw.$id)
-    ).map((t) => Object.assign({ sortSamples: { by: "hits" } }, t.tw));
-    sorterTerms.push(...unSelectedNonDictTerms, ...unSelectedDictTerms);
-  }
-  if (opts.tiebreaker) sorterTerms.push(opts.tiebreaker);
-  sorterTerms.push(...s.sortSamplesTieBreakers.map((st) => st));
-  const sampleSorters = [];
-  self.maxSampleSet = /* @__PURE__ */ new Set();
-  for (const st of sorterTerms) {
-    if (typeof st === "function") sampleSorters.push(st);
-    else if (st.$id == "sample") sampleSorters.push(sortSamplesByName);
-    else if (st.sortSamples.by == "hits") sampleSorters.push(getSortSamplesByHits(st, self, rows, s));
-    else if (st.term.type != "geneVariant") sampleSorters.push(getSortSamplesByValues(st, self, rows, s));
-    else if (st.sortSamples.by == "values") sampleSorters.push(getSortSamplesByValues(st, self, rows, s));
-    else if (st.sortSamples.by == "dt") sampleSorters.push(getSortSamplesByDt(st, self, rows, s));
-    else if (st.sortSamples.by == "class") sampleSorters.push(getSortSamplesByClass(st, self, rows, s));
-    else throw `unsupported sortSamplesBy entry by='${st.sortSamples.by}'`;
-  }
-  if (!sampleSorters.find((f) => f.$id === "sample")) {
-    sampleSorters.push(sortSamplesByName);
-  }
-  return (a, b) => {
-    for (const sorter of sampleSorters) {
-      const i = sorter(a, b);
-      if (i !== 0) return i;
-    }
-  };
-}
-function validateSettings(s) {
-  if (!s.sortOptions) s.sortOptions = "custom";
-  if (["selectedTerms", "class", "dt", "hits"].includes(s.sortSamplesBy)) s.sortSamplesBy = "custom";
-}
-function sortSamplesByName(a, b) {
-  if (a._ref_.label && b._ref_.label) {
-    return a._ref_.label < b._ref_.label ? -1 : a._ref_.label > b._ref_.label ? 1 : 0;
-  }
-  if (!a.sample && !b.sample && a.row.sample) {
-    return a.row.sample < b.row.sample ? -1 : a.row.sample > b.row.sample ? 1 : 0;
-  }
-  return a.sample < b.sample ? -1 : a.sample > b.sample ? 1 : 0;
-}
-function getSortSamplesByHits(st, self, rows, s) {
-  const { $id, sortSamples } = st;
-  const hits = {};
-  for (const row of rows) {
-    if (!hits[row.sample]) hits[row.sample] = 0;
-    if ($id in row) {
-      hits[row.sample] += row[$id].countedValues?.length || 0;
-    }
-  }
-  return (a, b) => hits[a.sample] == hits[b.sample] ? 0 : hits[a.sample] > hits[b.sample] ? -1 : 1;
-}
-function getSortSamplesByValues(st, self, rows, s) {
-  const { $id, sortSamples } = st;
-  const t = self.termOrder.find((t2) => t2.tw.$id === $id);
-  if (t.grp.type == "hierCluster") {
-    return (a, b) => {
-      if ($id in a && $id in b) {
-        return a[$id]?.values[0].value - b[$id]?.values[0].value;
-      }
-      if ($id in a) return -1;
-      if ($id in b) return 1;
-      return 0;
-    };
-  }
-  if (t.tw.term.type == "termCollection") {
-    return (a, b) => {
-      if ($id in a && $id in b) {
-        return a[$id]?.numerators_sum - b[$id]?.numerators_sum;
-      }
-      if ($id in a) return -1;
-      if ($id in b) return 1;
-      return 0;
-    };
-  }
-  if (t.tw.q?.mode == "continuous") {
-    return (a, b) => {
-      if ($id in a && $id in b) {
-        return a[$id]?.value - b[$id]?.value;
-      }
-      if ($id in a) return -1;
-      if ($id in b) return 1;
-      return 0;
-    };
-  }
-  const values = [];
-  if (t?.term?.values) {
-    for (const v of term.values) {
-      values.push(v.key);
-    }
-    values.sort((a, b) => term.values[a].order < term.values[a].order ? -1 : 1);
-  } else if (t?.ref?.bins) {
-    values.push(...t.ref.bins.map((b) => b.name));
-  } else if (t.tw.q?.type == "predefined-groupset" || t.tw.q?.type == "custom-groupset") {
-    const groupset = t.tw.q.type == "predefined-groupset" ? t.tw.term.groupsetting.lst[t.tw.q.predefined_groupset_idx] : t.tw.q.customset;
-    if (!groupset) throw "groupset missing";
-    const grpNames = groupset.groups.filter((group) => !group.uncomputable).map((group) => group.name);
-    values.push(...grpNames);
-  } else {
-    for (const row of rows) {
-      if (!($id in row)) continue;
-      const v = row[$id].override?.key || row[$id].key;
-      if (values.indexOf(v) == -1) values.push(v);
-    }
-  }
-  return (a, b) => {
-    if (!a[$id] && !b[$id]) return 0;
-    if (!a[$id]) return b[$id].override ? -1 : 1;
-    if (!b[$id]) return a[$id].override ? 1 : -1;
-    if (a[$id].override && b[$id].override) {
-      const ak = "order" in a[$id].override ? a[$id].override.order : values.indexOf(a[$id].override.key);
-      const bk = "order" in b[$id].override ? b[$id].override.order : values.indexOf(b[$id].override.key);
-      return ak - bk;
-    }
-    if (!a[$id].override && !b[$id].override) {
-      return values.indexOf(a[$id].key) - values.indexOf(b[$id].key);
-    }
-    if (!a[$id].override) return -1;
-    if (!b[$id].override) return 1;
-    return 0;
-  };
-}
-function getSortSamplesByDt(st, self, rows, s) {
-  const { $id, sortSamples, term: term2 } = st;
-  const order = sortSamples.order;
-  const nextRound = order.length + 1;
-  const dt = /* @__PURE__ */ new Map();
-  function setSortIndex(row) {
-    if (!($id in row)) {
-      dt.set(row.sample, nextRound);
-      return;
-    }
-    if (sortSamples.filter && !findMatchingValue(row[$id].values, sortSamples.filter.values)) {
-      dt.set(row.sample, nextRound);
-      return;
-    }
-    const indices = row[$id].values.map((v) => order.indexOf(v.dt)).filter((i) => i !== -1);
-    dt.set(row.sample, indices.length ? Math.min(...indices) : nextRound);
-  }
-  return (a, b) => {
-    if (!dt.has(a.sample)) setSortIndex(a);
-    if (!dt.has(b.sample)) setSortIndex(b);
-    return dt.get(a.sample) - dt.get(b.sample);
-  };
-}
-function getSortSamplesByClass(st, self, rows, s) {
-  const { $id, sortSamples } = st;
-  if (sortSamples.disabled) return () => 0;
-  const m = self.config.settings.matrix;
-  const includeSSM = m.showMatrixMutation != "none" && !m.allMatrixMutationHidden;
-  const includeCNV = m.showMatrixCNV != "none" && !m.allMatrixCNVHidden;
-  const order = sortSamples.order.filter(
-    includeSSM && includeCNV ? (v) => !m.hiddenVariants.includes(v) : !includeSSM && !includeCNV ? () => false : includeSSM ? (v) => m.mutationClasses.includes(v) && !m.hiddenVariants.includes(v) : includeCNV ? (v) => v.startsWith("CNV_") && !m.hiddenVariants.includes(v) : (v) => !v.startsWith("CNV_")
-  );
-  if (!order.length && sortSamples.ignoreEmptyFilteredOrder) return () => 0;
-  const nextRound = "z";
-  const cls = /* @__PURE__ */ new Map();
-  function setSortIndex(row) {
-    if (!($id in row)) {
-      cls.set(row.sample, nextRound);
-      return;
-    }
-    const values = row[$id].renderedValues || row[$id].filteredValues || row[$id].values;
-    if (sortSamples.filter && !findMatchingValue(values, sortSamples.filter.values)) {
-      cls.set(row.sample, nextRound);
-      return;
-    }
-    const vals = values.map((v) => v.class);
-    if (!order.find((mcls) => vals.includes(mcls))) {
-      cls.set(row.sample, nextRound);
-      return;
-    } else if (!sortSamples.isOrdered) {
-      cls.set(row.sample, "1");
-    } else {
-      const str = order.map((mcls) => vals.includes(mcls) ? "1" : "x");
-      cls.set(row.sample, str);
-    }
-  }
-  return (a, b) => {
-    if (!cls.has(a.sample)) setSortIndex(a);
-    if (!cls.has(b.sample)) setSortIndex(b);
-    const ca = cls.get(a.sample);
-    const cb = cls.get(b.sample);
-    return ca < cb ? -1 : ca > cb ? 1 : 0;
-  };
-}
-function findMatchingValue(annoValues, filterValues) {
-  for (const v of annoValues) {
-    for (const f of filterValues) {
-      if ((!f.dt || v.dt === f.dt) && (!f.mclassLst || f.mclassLst.includes(v.class)) && (!f.class || f.class === v.class) && (!f.origin || v.origin === f.origin)) {
-        return true;
-      }
-    }
-  }
-}
-function getTermSorter(self, s, grp) {
-  if (grp?.type == "hierCluster") return self.hcTermSorter;
-  if (s.sortTermsBy == "asListed") {
-    return (a, b) => a.index - b.index;
-  }
-  if (s.sortTermsBy != "sampleCount") {
-    throw `unsupported s.sortTermsBy='${s.sortTermsBy}'`;
-  }
-  return (a, b) => {
-    if (self.app.vocabApi.vocab?.dslabel === "GDC") {
-      if (a.tw?.term?.id && !b.tw?.term?.id) return -1;
-      if (!a.tw?.term?.id && b.tw?.term?.id) return 1;
-    }
-    if (b.counts.samples !== a.counts.samples) return b.counts.samples - a.counts.samples;
-    if (b.counts.hits !== a.counts.hits) return b.counts.hits - a.counts.hits;
-    return a.index - b.index;
-  };
-}
-function getSortOptions(termdbConfig, controlLabels = {}, matrixSettings) {
-  const s = matrixSettings || termdbConfig?.matrix?.settings || {};
-  const l = Object.assign({ sample: "sample" }, controlLabels, s.controlLabels || {});
-  const sortOptions = {};
-  if (s.sortPriority) {
-    const order = 1;
-    Object.values(sortOptions).forEach((d) => {
-      if (d.order >= order) d.order += 1;
-    });
-    sortOptions.custom = {
-      label: s.sortPriority.label || "Custom sort",
-      value: "custom",
-      order,
-      sortPriority: s.sortPriority
-    };
-  }
-  sortOptions.a = s.sortOptions?.a ? reshapeSortPriority(s.sortOptions.a, l) : {
-    //label: l.Mutation + ' categories', //'CNV+SSM > SSM-only > CNV-only',
-    // altLabels: {
-    // 	mutationOnly: 'SSM',
-    // 	cnvOnly: 'CNV',
-    // },
-    value: "a",
-    order: 1,
-    // this is used for list order as a sorter option in a dropdown
-    sortPriority: [
-      {
-        label: `For each gene mutation, sort ${l.samples} by matching data`,
-        types: ["geneVariant"],
-        tiebreakers: [
-          {
-            skip: !s.mutationClasses.includes("Fuserna"),
-            // not visible, cannot be enabled
-            label: `${l.Samples} with Fusion RNASeq > without`,
-            filter: {
-              values: [
-                {
-                  dt: dtfusionrna
-                }
-              ]
-            },
-            by: "class",
-            isOrdered: false,
-            order: [
-              "Fuserna"
-              /*'WT', 'Blank'*/
-            ]
-          },
-          {
-            label: `${l.Samples} with truncating mutations > without`,
-            filter: {
-              values: [
-                {
-                  dt: dtsnvindel
-                }
-              ]
-            },
-            by: "class",
-            isOrdered: false,
-            order: [
-              ...s.truncatingMutations
-              // // truncating
-              // 'F', // FRAMESHIFT
-              // 'N', // NONSENSE
-              // 'L', // SPLICE
-              // 'P', // SPLICE_REGION
-              // // indel
-              // 'D', // PROTEINDEL
-              // 'I', // PROTEININS
-              // 'ProteinAltering',
-              // // point
-              // 'M' // MISSENSE
-            ],
-            // do not have the option to add unused protein-changing mutations,
-            // because the "truncating" label for this tiebreaker will not make sense
-            notUsed: []
-          },
-          {
-            label: `${l.Samples} with CNV data > without`,
-            mayToggle: true,
-            filter: {
-              values: [
-                {
-                  dt: dtcnv
-                }
-              ]
-            },
-            by: "class",
-            isOrdered: true,
-            disabled: true,
-            // visible, can be enabled
-            order: [mclasscnvAmp, mclasscnvHomozygousDel, mclasscnvgain, mclasscnvloss, mclasscnvloh]
-          },
-          {
-            disabled: false,
-            mayToggle: true,
-            label: `${l.Samples} with protein-changing mutations > without`,
-            filter: {
-              values: [
-                {
-                  dt: dtsnvindel
-                }
-              ]
-            },
-            by: "class",
-            isOrdered: false,
-            // by default, do not include truncating mutations here since they may
-            // already be used in the tiebreaker with truncating mutations
-            order: s.proteinChangingMutations.filter((mcls) => !s.truncatingMutations.includes(mcls)),
-            notUsed: s.truncatingMutations
-          }
-        ]
-      },
-      {
-        label: `For each dictionary variable, sort ${l.samples} by matching data`,
-        types: ["categorical", "integer", "float", "survival"],
-        tiebreakers: [
-          {
-            label: "Values",
-            by: "values"
-          }
-        ]
-      }
-    ]
-  };
-  sortOptions.name = {
-    label: `By ${l.sample} name, ID, or label`,
-    value: "name",
-    order: Object.values(sortOptions).length
-  };
-  return sortOptions;
-}
-function getSampleGroupSorter(self) {
-  const s = self.settings.matrix;
-  if (s.sortSampleGrpsBy == "hits")
-    return (a, b) => {
-      if (a.lst.length && !b.lst.length) return -1;
-      if (!a.lst.length && b.lst.length) return 1;
-      return b.totalCountedValues - a.totalCountedValues;
-    };
-  if (s.sortSampleGrpsBy == "sampleCount")
-    return (a, b) => {
-      if (a.lst.length && !b.lst.length) return -1;
-      if (!a.lst.length && b.lst.length) return 1;
-      if (a.lst.length == b.lst.length) {
-        return defaultSorter(a, b);
-      }
-      return b.lst.length - a.lst.length;
-    };
-  if (!self.config.divideBy?.$id) return defaultSorter;
-  const ref = self.data.refs.byTermId[self.config.divideBy.$id];
-  if (ref && !ref.keyOrder) ref.keyOrder = ref.bins ? ref.bins.map((b) => b.name) : [];
-  const predefinedKeyOrder = self.data.refs.byTermId[self.config.divideBy.$id]?.keyOrder;
-  if (!predefinedKeyOrder) return defaultSorter;
-  return (a, b) => {
-    a.order = predefinedKeyOrder.indexOf(a.id);
-    if (a.order == -1) delete a.order;
-    b.order = predefinedKeyOrder.indexOf(b.id);
-    if (b.order == -1) delete b.order;
-    if ("order" in a && "order" in b) return a.order - b.order;
-    if ("order" in a) return -1;
-    if ("order" in b) return 1;
-    if (a.tw?.term?.values?.[a.id]?.order && b.tw?.term?.values?.[b.id]?.order) {
-      return a.tw.term.values[a.id].order - b.tw.term.values[b.id].order;
-    }
-    return defaultSorter(a, b);
-  };
-}
-function defaultSorter(a, b) {
-  return a.name < b.name ? -1 : 1;
-}
-function getMclassSorter(self) {
-  const s = self.settings.matrix;
-  const activeOption = s.sortOptions[s.sortSamplesBy].sortPriority ? s.sortOptions[s.sortSamplesBy] : s.sortOptions.a;
-  const mclassPriority = [];
-  activeOption.sortPriority.forEach((obj) => {
-    if (obj.types.includes("geneVariant")) {
-      obj.tiebreakers.forEach((tiebreaker) => {
-        if (tiebreaker.by == "class" && tiebreaker.order) {
-          mclassPriority.push(...tiebreaker.order.filter((t) => t !== "WT" && t !== "Blank"));
-        }
-      });
-    }
-  });
-  const sorter = (a, b) => {
-    const ai = mclassPriority.indexOf(a.class);
-    const bi = mclassPriority.indexOf(b.class);
-    return ai == -1 && bi == -1 ? 0 : mclassPriority.indexOf(a.class) == -1 ? 1 : mclassPriority.indexOf(b.class) == -1 ? -1 : mclassPriority.indexOf(a.class) - mclassPriority.indexOf(b.class);
-  };
-  return sorter;
-}
-function reshapeSortPriority(sortOption, labels) {
-  const l = labels;
-  let geneVariantsEntry;
-  for (const sp of sortOption.sortPriority) {
-    if (sp.types.includes("categorical")) {
-      if (!sp.label) sp.label = `For each dictionary variable, sort ${l.samples} by matching data`;
-      continue;
-    }
-    if (!sp.types?.includes("geneVariant")) continue;
-    if (!geneVariantsEntry) {
-      geneVariantsEntry = sp;
-      if (!sp.label) sp.label = `For each gene mutation, sort ${l.samples} by matching data`;
-    } else {
-      geneVariantsEntry.tiebreakers.push(...sp.tiebreakers);
-      sp.toBeDeleted = true;
-    }
-  }
-  for (const tb of geneVariantsEntry.tiebreakers) {
-    if (tb.filter?.values?.find((v) => v.dt == dtfusionrna)) {
-      const defaults = {
-        label: `${l.Samples} with Fusion RNASeq > without`,
-        isOrdered: true,
-        disabled: false,
-        mayToggle: true
-      };
-      Object.assign(tb, defaults, tb);
-    } else if (tb.filter?.values?.find((v) => v.dt == dtsnvindel)) {
-      const label = tb.order.includes(mclasscnvgain) || tb.order.includes(mclasscnvloss) ? `${l.Samples} with SSM + CNV > SSM only` : `${l.Samples} with mutations`;
-      const defaults = {
-        label,
-        isOrdered: true,
-        disabled: false,
-        mayToggle: true
-      };
-      Object.assign(tb, defaults, tb);
-    } else if (tb.order.length == 2 && tb.order.includes(mclasscnvgain) && tb.order.includes(mclasscnvloss)) {
-      const defaults = {
-        label: `${l.Samples} with CNV only > without`,
-        filter: { values: [{ dt: dtcnv }] },
-        by: "class",
-        isOrdered: true,
-        disabled: false,
-        mayToggle: true
-      };
-      Object.assign(tb, defaults, tb);
-    }
-  }
-  sortOption.sortPriority = sortOption.sortPriority.filter((sp) => !sp.toBeDeleted);
-  return sortOption;
-}
-
-export {
-  getSampleSorter,
-  getTermSorter,
-  getSortOptions,
-  getSampleGroupSorter,
-  getMclassSorter,
-  reshapeSortPriority
-};
-//# sourceMappingURL=chunk-IABWKPRK.js.map

package/dist/chunk-IPDH4FHY.js

@@ -1,54 +0,0 @@
-import {
-  addGeneSearchbox
-} from "./chunk-LN3QYBGI.js";
-import {
-  Menu
-} from "./chunk-HYOEWQ5P.js";
-
-// termdb/handlers/snp.ts
-var SearchHandler = class {
-  init(opts) {
-    this.callback = opts.callback;
-    const geneSearch = addGeneSearchbox({
-      tip: new Menu({ padding: "0px" }),
-      genome: opts.genomeObj,
-      row: opts.holder,
-      searchOnly: "snp",
-      allowVariant: true,
-      callback: () => this.selectSnp(geneSearch)
-    });
-  }
-  async selectSnp(geneSearch) {
-    const { chr, ref, alt, fromWhat } = geneSearch;
-    if (!chr || !ref || !alt || !fromWhat) throw "missing chr, ref, alt, or fromWhat of snp";
-    let start, stop;
-    if (!geneSearch.start && !geneSearch.stop) {
-      if (geneSearch.pos) {
-        start = geneSearch.pos - 1;
-        stop = geneSearch.pos;
-      } else {
-        throw "missing coordinate of snp";
-      }
-    } else {
-      start = geneSearch.start;
-      stop = geneSearch.stop;
-    }
-    const term = {
-      id: fromWhat,
-      chr,
-      start,
-      stop,
-      name: fromWhat,
-      ref,
-      alt: typeof alt == "string" ? [alt] : alt,
-      // is string if input to geneSearch was in variant or hgvs format // TODO: update genesearch.ts to parse alternative alleles from any input format into arrays
-      type: "snp"
-    };
-    this.callback(term);
-  }
-};
-
-export {
-  SearchHandler
-};
-//# sourceMappingURL=chunk-IPDH4FHY.js.map