@sjcrh/proteinpaint-client 2.224.2 → 2.226.0

package/dist/chunk-ECCXTB5S.js

@@ -0,0 +1,562 @@
+import {
+  getSortSamplesByAncestry
+} from "./chunk-C2MCQZWH.js";
+import {
+  isDictionaryType
+} from "./chunk-T2W4JHWJ.js";
+import {
+  dtcnv,
+  dtfusionrna,
+  dtsnvindel,
+  mclasscnvAmp,
+  mclasscnvHomozygousDel,
+  mclasscnvgain,
+  mclasscnvloh,
+  mclasscnvloss
+} from "./chunk-2N345NXD.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='${s.sortSamplesBy}'`;
+  self.selectedTermsToSortAgainst = self.termOrder.filter((t) => t.tw.sortSamples);
+  const selectedTerms = self.selectedTermsToSortAgainst.map((t) => t.tw).sort((a, b) => a.sortSamples.priority - b.sortSamples.priority);
+  const sorterTerms = [];
+  if (self.config.chartType == "matrix" && s.sortBySampleAncestry === "first")
+    sorterTerms.push(getSortSamplesByAncestry(self));
+  const sortPriority = activeOption.sortPriority;
+  if (sortPriority) {
+    for (const _tw of selectedTerms) {
+      const tw = structuredClone(_tw);
+      if (tw.sortSamples?.by) {
+        sorterTerms.push(Object.assign({}, tw));
+        continue;
+      }
+      for (const p of sortPriority) {
+        if (opts.skipSorter?.(p, tw)) continue;
+        const type = tw.term.type == "geneVariant" && tw.q.type != "values" ? "categorical" : tw.term.type;
+        if (!p.types.includes(type)) continue;
+        for (const tb of p.tiebreakers) {
+          const sortSamples = Object.assign(structuredClone(tw.sortSamples || {}), tb);
+          const sorter = Object.assign(structuredClone(tw), { sortSamples });
+          sorterTerms.push(sorter);
+        }
+      }
+    }
+  }
+  if (sortPriority) {
+    for (const p of sortPriority) {
+      for (const t of self.termOrder) {
+        if (selectedTerms.find((tw) => tw.$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;
+    }
+    const values = row[$id].filteredValues || row[$id].values;
+    if (sortSamples.filter && !findMatchingValue(values, sortSamples.filter.values)) {
+      dt.set(row.sample, nextRound);
+      return;
+    }
+    const indices = 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.termdbConfig?.matrix?.sortDictTermsFirst) {
+      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
+    };
+  }
+  const cnvClasses = [mclasscnvAmp, mclasscnvHomozygousDel, mclasscnvgain, mclasscnvloss, mclasscnvloh];
+  const proteinChangingClasses = (s.proteinChangingMutations || []).filter(
+    (mcls) => !s.truncatingMutations.includes(mcls)
+  );
+  const sortedClasses = ["Fuserna", ...s.truncatingMutations || [], ...cnvClasses, ...proteinChangingClasses];
+  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: cnvClasses
+          },
+          {
+            disabled: false,
+            mayToggle: true,
+            label: `${l.Samples} with protein-changing mutations > without`,
+            filter: {
+              values: [
+                {
+                  dt: dtsnvindel
+                }
+              ]
+            },
+            by: "class",
+            isOrdered: false,
+            // by default, do not include truncating mutations here since they may
+            // already be used in the tiebreaker with truncating mutations
+            order: proteinChangingClasses,
+            notUsed: s.truncatingMutations
+          },
+          {
+            disabled: false,
+            mayToggle: true,
+            label: `${l.Samples} with other classification > without`,
+            filter: {
+              values: [
+                {
+                  dt: dtsnvindel
+                }
+              ]
+            },
+            by: "class",
+            isOrdered: false,
+            order: s.mutationClasses.filter((cls) => !sortedClasses.includes(cls) && cls != "Blank"),
+            notUsed: []
+          }
+        ]
+      },
+      {
+        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 ${l.samples} by matching data`;
+    } else {
+      geneVariantsEntry.tiebreakers.push(...sp.tiebreakers);
+      sp.toBeDeleted = true;
+    }
+  }
+  for (const tb of geneVariantsEntry.tiebreakers) {
+    const origClone = structuredClone(tb);
+    if (tb.filter?.values?.find((v) => v.dt == dtfusionrna)) {
+      const defaults = {
+        label: `${l.Samples} with Fusion RNASeq > without`,
+        isOrdered: true,
+        disabled: false,
+        mayToggle: true
+      };
+      Object.assign(tb, defaults, origClone);
+    } 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, origClone);
+    } 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, origClone);
+    }
+  }
+  sortOption.sortPriority = sortOption.sortPriority.filter((sp) => !sp.toBeDeleted);
+  return sortOption;
+}
+
+export {
+  getSampleSorter,
+  getTermSorter,
+  getSortOptions,
+  getSampleGroupSorter,
+  getMclassSorter,
+  reshapeSortPriority
+};
+//# sourceMappingURL=chunk-ECCXTB5S.js.map

package/dist/chunk-ECTOEM7X.js

@@ -0,0 +1,96 @@
+import {
+  addGeneSearchbox,
+  first_genetrack_tolist,
+  getTermSampleTypes,
+  makeDNAMethRegionTerm,
+  mayRenderSampleTypeRow,
+  sayerror
+} from "./chunk-DPWSIN62.js";
+import {
+  Menu
+} from "./chunk-CNFTQSNE.js";
+
+// termdb/handlers/dnaMethylation.ts
+var SearchHandler = class {
+  init(opts) {
+    this.opts = opts;
+    this.callback = opts.callback;
+    this.app = opts.app;
+    const holder = opts.holder.append("div").style("margin", "10px 0px");
+    this.dom = {};
+    this.sampleTypeSelect = mayRenderSampleTypeRow(holder.append("div"), this.query, this.app.vocabApi.termdbConfig);
+    this.dom.errDiv = holder.append("div").style("margin", "5px 0px").style("display", "none");
+    this.dom.geneSearchDiv = holder.append("div");
+    this.dom.blockDiv = holder.append("div").style("display", "none").style("margin", "15px 4px");
+    const geneSearch = addGeneSearchbox({
+      tip: new Menu({ padding: "0px" }),
+      genome: opts.genomeObj,
+      row: this.dom.geneSearchDiv,
+      callback: async () => {
+        try {
+          this.dom.errDiv.style("display", "none");
+          await this.handleGeneSearch(geneSearch);
+        } catch (e) {
+          this.dom.errDiv.style("display", "block");
+          sayerror(this.dom.errDiv, "Error: " + (e.message || e));
+          if (e.stack) console.log(e.stack);
+        }
+      }
+    });
+  }
+  async handleGeneSearch(geneSearch) {
+    if (geneSearch.geneSymbol) {
+      const { chr, start, stop } = geneSearch;
+      if (!chr || !Number.isInteger(start) || !Number.isInteger(stop))
+        throw new Error("unable to retrieve gene coordinate");
+      this.dom.blockDiv.selectAll("*").remove();
+      this.dom.blockDiv.style("display", "block");
+      this.dom.blockDiv.append("div").style("opacity", 0.6).text("Navigate genome browser to desired region");
+      const arg = {
+        holder: this.dom.blockDiv,
+        genome: this.opts.genomeObj,
+        // genome obj
+        chr,
+        start,
+        stop,
+        tklst: [],
+        nobox: true,
+        width: 500,
+        hidegenelegend: true,
+        debugmode: this.opts.debug
+      };
+      first_genetrack_tolist(this.opts.genomeObj, arg.tklst);
+      const _ = await import("./block-YGQFUK5L.js");
+      this.blockInstance = new _.Block(arg);
+      this.dom.submitBtn = this.dom.blockDiv.append("div").attr("data-testid", "sjpp-dnaMethylation-submitDiv").style("margin", "10px 0px").append("button").style("border", "none").style("border-radius", "20px").style("padding", "10px 15px").text("Submit Region").on("click", async () => {
+        const { chr: chr2, start: start2, stop: stop2 } = this.blockInstance.rglst[0];
+        const term = this.makeTerm({ chr: chr2, start: start2, stop: stop2 });
+        if (term) await this.callback(term);
+      });
+    } else if (geneSearch.chr && Number.isInteger(geneSearch.start) && Number.isInteger(geneSearch.stop)) {
+      const { chr } = geneSearch;
+      let { start, stop } = geneSearch;
+      if (geneSearch.actualposition?.len <= 1) {
+        start = geneSearch.actualposition.position;
+        stop = start + 1;
+      }
+      const term = this.makeTerm({ chr, start, stop });
+      if (term) await this.callback(term);
+    } else {
+      throw new Error("invalid gene search input");
+    }
+  }
+  makeTerm(opts) {
+    const termSampleTypes = getTermSampleTypes(this.sampleTypeSelect, this.query, this.app.vocabApi.termdbConfig);
+    if (!termSampleTypes) return;
+    return makeDNAMethRegionTerm(opts, this.app.vocabApi, termSampleTypes);
+  }
+  get query() {
+    return this.app.vocabApi.termdbConfig?.queries.dnaMethylation;
+  }
+};
+
+export {
+  SearchHandler
+};
+//# sourceMappingURL=chunk-ECTOEM7X.js.map

package/dist/chunk-ECTOEM7X.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../termdb/handlers/dnaMethylation.ts"],
+  "sourcesContent": ["import { Menu, addGeneSearchbox, sayerror, mayRenderSampleTypeRow, getTermSampleTypes } from '#dom'\nimport { makeDNAMethRegionTerm } from '#tw/dnaMethylation'\nimport { first_genetrack_tolist } from '#common/1stGenetk'\n\n/** Coordinate note: both the genome browser and the HDF5 beta file use 0-based\n coordinates. Verified by cross-referencing 5 probes from the test H5 file\n (dnaMeth.h5) against UCSC hg38 using the search API:\n   https://api.genome.ucsc.edu/search?search=<probeId>&genome=hg38\n\n H5 positions were read with:\n   python3 -c \"import h5py; h5=h5py.File('proteinpaint/server/test/tp/files/hg38/TermdbTest/dnaMeth.h5','r'); \\\n     print(list(zip(h5['/meta/probe/probeID'].asstr()[:5], h5['/meta/start'][:5])))\"\n\n All matched the 0-based half-open (BED) position returned by UCSC:\n   cg22949073: H5=7669073, UCSC=chr17:7669073-7669074\n   cg16397722: H5=7673772, UCSC=chr17:7673772-7673773\n   cg04405586: H5=7675143, UCSC=chr17:7675143-7675144\n   cg15110538: H5=7675305, UCSC=chr17:7675305-7675306\n   cg10792831: H5=7675371, UCSC=chr17:7675371-7675372\nNo conversion is needed. Single-position inputs (e.g. chr17:7661778) are\nrecovered from actualposition to avoid the 400bp expansion that string2pos()\napplies for the genome browser. */\n\nexport class SearchHandler {\n\topts: any\n\tcallback: any\n\tapp: any\n\tdom: any\n\tblockInstance: any\n\tsampleTypeSelect?: any\n\tinit(opts) {\n\t\tthis.opts = opts\n\t\tthis.callback = opts.callback\n\t\tthis.app = opts.app\n\t\tconst holder = opts.holder.append('div').style('margin', '10px 0px')\n\t\tthis.dom = {}\n\t\tthis.sampleTypeSelect = mayRenderSampleTypeRow(holder.append('div'), this.query, this.app.vocabApi.termdbConfig)\n\t\tthis.dom.errDiv = holder.append('div').style('margin', '5px 0px').style('display', 'none')\n\t\tthis.dom.geneSearchDiv = holder.append('div')\n\t\tthis.dom.blockDiv = holder.append('div').style('display', 'none').style('margin', '15px 4px')\n\t\tconst geneSearch = addGeneSearchbox({\n\t\t\ttip: new Menu({ padding: '0px' }),\n\t\t\tgenome: opts.genomeObj,\n\t\t\trow: this.dom.geneSearchDiv,\n\t\t\tcallback: async () => {\n\t\t\t\ttry {\n\t\t\t\t\tthis.dom.errDiv.style('display', 'none')\n\t\t\t\t\tawait this.handleGeneSearch(geneSearch)\n\t\t\t\t} catch (e: any) {\n\t\t\t\t\tthis.dom.errDiv.style('display', 'block')\n\t\t\t\t\tsayerror(this.dom.errDiv, 'Error: ' + (e.message || e))\n\t\t\t\t\tif (e.stack) console.log(e.stack)\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t}\n\n\tasync handleGeneSearch(geneSearch) {\n\t\tif (geneSearch.geneSymbol) {\n\t\t\t// gene input\n\t\t\t// embed block of gene locus to allow navigation to region of interest\n\t\t\tconst { chr, start, stop } = geneSearch\n\t\t\tif (!chr || !Number.isInteger(start) || !Number.isInteger(stop))\n\t\t\t\tthrow new Error('unable to retrieve gene coordinate')\n\n\t\t\tthis.dom.blockDiv.selectAll('*').remove()\n\t\t\tthis.dom.blockDiv.style('display', 'block')\n\t\t\tthis.dom.blockDiv.append('div').style('opacity', 0.6).text('Navigate genome browser to desired region')\n\n\t\t\tconst arg: any = {\n\t\t\t\tholder: this.dom.blockDiv,\n\t\t\t\tgenome: this.opts.genomeObj, // genome obj\n\t\t\t\tchr,\n\t\t\t\tstart,\n\t\t\t\tstop,\n\t\t\t\ttklst: [],\n\t\t\t\tnobox: true,\n\t\t\t\twidth: 500,\n\t\t\t\thidegenelegend: true,\n\t\t\t\tdebugmode: this.opts.debug\n\t\t\t}\n\t\t\tfirst_genetrack_tolist(this.opts.genomeObj, arg.tklst)\n\t\t\tconst _ = await import('#src/block')\n\t\t\tthis.blockInstance = new _.Block(arg)\n\n\t\t\tthis.dom.submitBtn = this.dom.blockDiv\n\t\t\t\t.append('div')\n\t\t\t\t.attr('data-testid', 'sjpp-dnaMethylation-submitDiv')\n\t\t\t\t.style('margin', '10px 0px')\n\t\t\t\t.append('button')\n\t\t\t\t.style('border', 'none')\n\t\t\t\t.style('border-radius', '20px')\n\t\t\t\t.style('padding', '10px 15px')\n\t\t\t\t.text('Submit Region')\n\t\t\t\t.on('click', async () => {\n\t\t\t\t\tconst { chr, start, stop } = this.blockInstance.rglst[0]\n\t\t\t\t\tconst term = this.makeTerm({ chr, start, stop })\n\t\t\t\t\tif (term) await this.callback(term)\n\t\t\t\t})\n\t\t} else if (geneSearch.chr && Number.isInteger(geneSearch.start) && Number.isInteger(geneSearch.stop)) {\n\t\t\t// coordinate input\n\t\t\t// string2pos() expands single positions to a 400bp window for the\n\t\t\t// genome browser, but we need the exact position for CpG queries.\n\t\t\t// Use actualposition when it indicates a single-position input.\n\t\t\tconst { chr } = geneSearch\n\t\t\tlet { start, stop } = geneSearch\n\t\t\tif (geneSearch.actualposition?.len <= 1) {\n\t\t\t\tstart = geneSearch.actualposition.position\n\t\t\t\tstop = start + 1\n\t\t\t}\n\t\t\tconst term = this.makeTerm({ chr, start, stop })\n\t\t\tif (term) await this.callback(term)\n\t\t} else {\n\t\t\tthrow new Error('invalid gene search input')\n\t\t}\n\t}\n\n\tmakeTerm(opts) {\n\t\tconst termSampleTypes = getTermSampleTypes(this.sampleTypeSelect, this.query, this.app.vocabApi.termdbConfig)\n\t\tif (!termSampleTypes) return\n\t\treturn makeDNAMethRegionTerm(opts, this.app.vocabApi, termSampleTypes)\n\t}\n\n\tget query() {\n\t\treturn this.app.vocabApi.termdbConfig?.queries.dnaMethylation\n\t}\n}\n"],
+  "mappings": ";;;;;;;;;;;;;AAuBO,IAAM,gBAAN,MAAoB;AAAA,EAO1B,KAAK,MAAM;AACV,SAAK,OAAO;AACZ,SAAK,WAAW,KAAK;AACrB,SAAK,MAAM,KAAK;AAChB,UAAM,SAAS,KAAK,OAAO,OAAO,KAAK,EAAE,MAAM,UAAU,UAAU;AACnE,SAAK,MAAM,CAAC;AACZ,SAAK,mBAAmB,uBAAuB,OAAO,OAAO,KAAK,GAAG,KAAK,OAAO,KAAK,IAAI,SAAS,YAAY;AAC/G,SAAK,IAAI,SAAS,OAAO,OAAO,KAAK,EAAE,MAAM,UAAU,SAAS,EAAE,MAAM,WAAW,MAAM;AACzF,SAAK,IAAI,gBAAgB,OAAO,OAAO,KAAK;AAC5C,SAAK,IAAI,WAAW,OAAO,OAAO,KAAK,EAAE,MAAM,WAAW,MAAM,EAAE,MAAM,UAAU,UAAU;AAC5F,UAAM,aAAa,iBAAiB;AAAA,MACnC,KAAK,IAAI,KAAK,EAAE,SAAS,MAAM,CAAC;AAAA,MAChC,QAAQ,KAAK;AAAA,MACb,KAAK,KAAK,IAAI;AAAA,MACd,UAAU,YAAY;AACrB,YAAI;AACH,eAAK,IAAI,OAAO,MAAM,WAAW,MAAM;AACvC,gBAAM,KAAK,iBAAiB,UAAU;AAAA,QACvC,SAAS,GAAQ;AAChB,eAAK,IAAI,OAAO,MAAM,WAAW,OAAO;AACxC,mBAAS,KAAK,IAAI,QAAQ,aAAa,EAAE,WAAW,EAAE;AACtD,cAAI,EAAE,MAAO,SAAQ,IAAI,EAAE,KAAK;AAAA,QACjC;AAAA,MACD;AAAA,IACD,CAAC;AAAA,EACF;AAAA,EAEA,MAAM,iBAAiB,YAAY;AAClC,QAAI,WAAW,YAAY;AAG1B,YAAM,EAAE,KAAK,OAAO,KAAK,IAAI;AAC7B,UAAI,CAAC,OAAO,CAAC,OAAO,UAAU,KAAK,KAAK,CAAC,OAAO,UAAU,IAAI;AAC7D,cAAM,IAAI,MAAM,oCAAoC;AAErD,WAAK,IAAI,SAAS,UAAU,GAAG,EAAE,OAAO;AACxC,WAAK,IAAI,SAAS,MAAM,WAAW,OAAO;AAC1C,WAAK,IAAI,SAAS,OAAO,KAAK,EAAE,MAAM,WAAW,GAAG,EAAE,KAAK,2CAA2C;AAEtG,YAAM,MAAW;AAAA,QAChB,QAAQ,KAAK,IAAI;AAAA,QACjB,QAAQ,KAAK,KAAK;AAAA;AAAA,QAClB;AAAA,QACA;AAAA,QACA;AAAA,QACA,OAAO,CAAC;AAAA,QACR,OAAO;AAAA,QACP,OAAO;AAAA,QACP,gBAAgB;AAAA,QAChB,WAAW,KAAK,KAAK;AAAA,MACtB;AACA,6BAAuB,KAAK,KAAK,WAAW,IAAI,KAAK;AACrD,YAAM,IAAI,MAAM,OAAO,qBAAY;AACnC,WAAK,gBAAgB,IAAI,EAAE,MAAM,GAAG;AAEpC,WAAK,IAAI,YAAY,KAAK,IAAI,SAC5B,OAAO,KAAK,EACZ,KAAK,eAAe,+BAA+B,EACnD,MAAM,UAAU,UAAU,EAC1B,OAAO,QAAQ,EACf,MAAM,UAAU,MAAM,EACtB,MAAM,iBAAiB,MAAM,EAC7B,MAAM,WAAW,WAAW,EAC5B,KAAK,eAAe,EACpB,GAAG,SAAS,YAAY;AACxB,cAAM,EAAE,KAAAA,MAAK,OAAAC,QAAO,MAAAC,MAAK,IAAI,KAAK,cAAc,MAAM,CAAC;AACvD,cAAM,OAAO,KAAK,SAAS,EAAE,KAAAF,MAAK,OAAAC,QAAO,MAAAC,MAAK,CAAC;AAC/C,YAAI,KAAM,OAAM,KAAK,SAAS,IAAI;AAAA,MACnC,CAAC;AAAA,IACH,WAAW,WAAW,OAAO,OAAO,UAAU,WAAW,KAAK,KAAK,OAAO,UAAU,WAAW,IAAI,GAAG;AAKrG,YAAM,EAAE,IAAI,IAAI;AAChB,UAAI,EAAE,OAAO,KAAK,IAAI;AACtB,UAAI,WAAW,gBAAgB,OAAO,GAAG;AACxC,gBAAQ,WAAW,eAAe;AAClC,eAAO,QAAQ;AAAA,MAChB;AACA,YAAM,OAAO,KAAK,SAAS,EAAE,KAAK,OAAO,KAAK,CAAC;AAC/C,UAAI,KAAM,OAAM,KAAK,SAAS,IAAI;AAAA,IACnC,OAAO;AACN,YAAM,IAAI,MAAM,2BAA2B;AAAA,IAC5C;AAAA,EACD;AAAA,EAEA,SAAS,MAAM;AACd,UAAM,kBAAkB,mBAAmB,KAAK,kBAAkB,KAAK,OAAO,KAAK,IAAI,SAAS,YAAY;AAC5G,QAAI,CAAC,gBAAiB;AACtB,WAAO,sBAAsB,MAAM,KAAK,IAAI,UAAU,eAAe;AAAA,EACtE;AAAA,EAEA,IAAI,QAAQ;AACX,WAAO,KAAK,IAAI,SAAS,cAAc,QAAQ;AAAA,EAChD;AACD;",
+  "names": ["chr", "start", "stop"]
+}