@sjcrh/proteinpaint-client 2.181.0 → 2.182.0

package/dist/chunk-2UWHV2SB.js

@@ -1,261 +0,0 @@
-import {
-  TermTypeGroups,
-  dtTerms,
-  dtdnamethylation,
-  dtgeneexpression,
-  dtmetaboliteintensity,
-  dtproteomeabundance,
-  dtssgsea
-} from "./chunk-ZLH4PJKX.js";
-
-// ../shared/utils/src/terms.js
-var ROOT_SAMPLE_TYPE = 1;
-var DEFAULT_SAMPLE_TYPE = 2;
-var NumericModes = {
-  continuous: "continuous",
-  discrete: "discrete"
-};
-var CATEGORICAL = "categorical";
-var CONDITION = "condition";
-var DATE = "date";
-var DNA_METHYLATION = "dnaMethylation";
-var FLOAT = "float";
-var GENE_VARIANT = "geneVariant";
-var GENE_EXPRESSION = "geneExpression";
-var ISOFORM_EXPRESSION = "isoformExpression";
-var INTEGER = "integer";
-var METABOLITE_INTENSITY = "metaboliteIntensity";
-var MULTIVALUE = "multivalue";
-var SAMPLELST = "samplelst";
-var SINGLECELL_CELLTYPE = "singleCellCellType";
-var SINGLECELL_GENE_EXPRESSION = "singleCellGeneExpression";
-var SNP = "snp";
-var SNP_LIST = "snplst";
-var SNP_LOCUS = "snplocus";
-var SSGSEA = "ssGSEA";
-var SURVIVAL = "survival";
-var TERM_COLLECTION = "termCollection";
-var PROTEOME_ABUNDANCE = "proteomeAbundance";
-var TermTypes = {
-  GENE_VARIANT,
-  GENE_EXPRESSION,
-  ISOFORM_EXPRESSION,
-  SSGSEA,
-  DNA_METHYLATION,
-  CATEGORICAL,
-  INTEGER,
-  FLOAT,
-  SNP,
-  SNP_LIST,
-  SNP_LOCUS,
-  CONDITION,
-  SURVIVAL,
-  SAMPLELST,
-  METABOLITE_INTENSITY,
-  PROTEOME_ABUNDANCE,
-  SINGLECELL_CELLTYPE,
-  SINGLECELL_GENE_EXPRESSION,
-  MULTIVALUE,
-  DATE,
-  TERM_COLLECTION
-};
-var dtTermTypes = new Set(dtTerms.map((t) => t.type));
-for (const dtTermType of dtTermTypes) {
-  TermTypes[dtTermType.toUpperCase()] = dtTermType;
-}
-var TermTypes2Dt = {
-  [GENE_EXPRESSION]: dtgeneexpression,
-  [SSGSEA]: dtssgsea,
-  [DNA_METHYLATION]: dtdnamethylation,
-  [METABOLITE_INTENSITY]: dtmetaboliteintensity,
-  [PROTEOME_ABUNDANCE]: dtproteomeabundance
-};
-var typeGroup = {
-  [CATEGORICAL]: TermTypeGroups.DICTIONARY_VARIABLES,
-  [CONDITION]: TermTypeGroups.DICTIONARY_VARIABLES,
-  [FLOAT]: TermTypeGroups.DICTIONARY_VARIABLES,
-  [INTEGER]: TermTypeGroups.DICTIONARY_VARIABLES,
-  [SAMPLELST]: TermTypeGroups.DICTIONARY_VARIABLES,
-  [SURVIVAL]: TermTypeGroups.DICTIONARY_VARIABLES,
-  [DATE]: TermTypeGroups.DICTIONARY_VARIABLES,
-  [MULTIVALUE]: TermTypeGroups.DICTIONARY_VARIABLES,
-  [GENE_VARIANT]: TermTypeGroups.MUTATION_CNV_FUSION,
-  [SNP]: TermTypeGroups.SNP,
-  [SNP_LIST]: TermTypeGroups.SNP_LIST,
-  [SNP_LOCUS]: TermTypeGroups.SNP_LOCUS,
-  [GENE_EXPRESSION]: TermTypeGroups.GENE_EXPRESSION,
-  [ISOFORM_EXPRESSION]: TermTypeGroups.ISOFORM_EXPRESSION,
-  [SSGSEA]: TermTypeGroups.SSGSEA,
-  [DNA_METHYLATION]: TermTypeGroups.DNA_METHYLATION,
-  [METABOLITE_INTENSITY]: TermTypeGroups.METABOLITE_INTENSITY,
-  [PROTEOME_ABUNDANCE]: TermTypeGroups.PROTEOME_ABUNDANCE,
-  [TERM_COLLECTION]: TermTypeGroups.TERM_COLLECTION,
-  [SINGLECELL_CELLTYPE]: TermTypeGroups.SINGLECELL_CELLTYPE,
-  [SINGLECELL_GENE_EXPRESSION]: TermTypeGroups.SINGLECELL_GENE_EXPRESSION
-};
-var nonDictTypes = /* @__PURE__ */ new Set([
-  SNP,
-  SNP_LIST,
-  SNP_LOCUS,
-  GENE_EXPRESSION,
-  ISOFORM_EXPRESSION,
-  SSGSEA,
-  DNA_METHYLATION,
-  GENE_VARIANT,
-  METABOLITE_INTENSITY,
-  PROTEOME_ABUNDANCE,
-  SINGLECELL_CELLTYPE,
-  SINGLECELL_GENE_EXPRESSION
-]);
-for (const dtTermType of dtTermTypes) {
-  nonDictTypes.add(TermTypes[dtTermType.toUpperCase()]);
-}
-var numericTypes = /* @__PURE__ */ new Set([
-  INTEGER,
-  FLOAT,
-  GENE_EXPRESSION,
-  ISOFORM_EXPRESSION,
-  SSGSEA,
-  DNA_METHYLATION,
-  METABOLITE_INTENSITY,
-  PROTEOME_ABUNDANCE,
-  SINGLECELL_GENE_EXPRESSION,
-  DATE
-]);
-var categoricalTypes = /* @__PURE__ */ new Set([CATEGORICAL, SNP]);
-var singleCellTerms = /* @__PURE__ */ new Set([
-  SINGLECELL_CELLTYPE,
-  SINGLECELL_GENE_EXPRESSION
-]);
-function isSingleCellTerm(term) {
-  if (!term) return false;
-  return singleCellTerms.has(term.type);
-}
-function isNumericTerm(term) {
-  if (!term) return false;
-  return numericTypes.has(term.type);
-}
-function isCategoricalTerm(term) {
-  if (!term) return false;
-  return categoricalTypes.has(term.type);
-}
-function isDictionaryType(type) {
-  return !isNonDictionaryType(type);
-}
-function isNonDictionaryType(type) {
-  if (!type) throw new Error("Type is not defined");
-  return nonDictTypes.has(type);
-}
-function isNumTermCollection(term) {
-  if (!term || !term.type) throw new Error("Term or term type is not defined");
-  return term.type === TERM_COLLECTION;
-}
-function equals(t1, t2) {
-  if (!t1) throw new Error("First term is not defined ");
-  if (!t2) throw new Error("Second term is not defined ");
-  if (t1.type !== t2.type) return false;
-  if (isDictionaryType(t1.type) && isDictionaryType(t2.type) && t1.type != SAMPLELST)
-    return t1.id === t2.id;
-  switch (t1.type) {
-    case GENE_EXPRESSION:
-      return t1.gene == t2.gene;
-    case ISOFORM_EXPRESSION:
-      return t1.isoform == t2.isoform;
-    case SSGSEA:
-      return t1.id == t2.id;
-    case DNA_METHYLATION:
-      return t1.chr == t2.chr && t1.start == t2.start && t1.stop == t2.stop;
-    case METABOLITE_INTENSITY:
-    case PROTEOME_ABUNDANCE:
-      return t1.name == t2.name;
-    case GENE_VARIANT:
-      return t1.gene == t2.gene || t1.chr == t2.chr && t1.start == t2.start && t1.stop == t2.stop;
-    // TO DO: Add more cases
-    // case SNP_LIST:
-    // case SNP_LOCUS:
-    // case SAMPLELST:
-    default:
-      return false;
-  }
-}
-var typeMap = {
-  categorical: "Categorical",
-  condition: "Condition",
-  float: "Numerical",
-  integer: "Numerical",
-  geneExpression: "Gene Expression",
-  isoformExpression: "Isoform Expression",
-  ssGSEA: "Geneset Expression",
-  dnaMethylation: "DNA Methylation",
-  geneVariant: "Gene Variant",
-  metaboliteIntensity: "Metabolite Intensity",
-  proteomeAbundance: "Whole Proteome Abundance",
-  multivalue: "Multi Value",
-  singleCellGeneExpression: "Single Cell, Gene Expression",
-  singleCellCellType: "Single Cell, Cell Type",
-  snplocus: "SNP Locus",
-  snp: "SNP",
-  snplst: "SNP List",
-  termCollection: "Term Collection"
-};
-function termType2label(type) {
-  return typeMap[type] || "Unknown term type";
-}
-function getDateFromNumber(value) {
-  const year = Math.floor(value);
-  const january1st = new Date(year, 0, 1);
-  const totalDays = getDaysInYear(year);
-  const time = Math.round((value - year) * totalDays) * oneDayTime;
-  const date = new Date(january1st.getTime() + time);
-  return date;
-}
-var oneDayTime = 24 * 60 * 60 * 1e3;
-function getDateStrFromNumber(value) {
-  const date = getDateFromNumber(value);
-  return date.toLocaleDateString("en-US", {
-    year: "numeric",
-    month: "long"
-  });
-}
-function getDaysInYear(year) {
-  const isLeap = new Date(year, 1, 29).getMonth() === 1;
-  const days = isLeap ? 366 : 365;
-  return days;
-}
-
-export {
-  ROOT_SAMPLE_TYPE,
-  DEFAULT_SAMPLE_TYPE,
-  NumericModes,
-  CATEGORICAL,
-  DATE,
-  DNA_METHYLATION,
-  FLOAT,
-  GENE_VARIANT,
-  GENE_EXPRESSION,
-  ISOFORM_EXPRESSION,
-  INTEGER,
-  METABOLITE_INTENSITY,
-  SINGLECELL_CELLTYPE,
-  SINGLECELL_GENE_EXPRESSION,
-  SNP,
-  SSGSEA,
-  TERM_COLLECTION,
-  PROTEOME_ABUNDANCE,
-  TermTypes,
-  dtTermTypes,
-  TermTypes2Dt,
-  typeGroup,
-  numericTypes,
-  isSingleCellTerm,
-  isNumericTerm,
-  isCategoricalTerm,
-  isDictionaryType,
-  isNonDictionaryType,
-  isNumTermCollection,
-  equals,
-  termType2label,
-  getDateFromNumber,
-  getDateStrFromNumber
-};
-//# sourceMappingURL=chunk-2UWHV2SB.js.map

package/dist/chunk-2UWHV2SB.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../shared/utils/src/terms.js"],
-  "sourcesContent": ["import {\n\tdtgeneexpression,\n\tdtssgsea,\n\tdtdnamethylation,\n\tdtmetaboliteintensity,\n\tdtproteomeabundance,\n\tTermTypeGroups,\n\tdtTerms,\n} from \"./common.js\"\nimport { TermTypeGroups as TermTypeGroups2 } from \"./common.js\"\nconst ROOT_SAMPLE_TYPE = 1\nconst DEFAULT_SAMPLE_TYPE = 2\nconst NumericModes = {\n\tcontinuous: \"continuous\",\n\tdiscrete: \"discrete\",\n}\nconst CATEGORICAL = \"categorical\"\nconst CONDITION = \"condition\"\nconst DATE = \"date\"\nconst DNA_METHYLATION = \"dnaMethylation\"\nconst FLOAT = \"float\"\nconst GENE_VARIANT = \"geneVariant\"\nconst GENE_EXPRESSION = \"geneExpression\"\nconst ISOFORM_EXPRESSION = \"isoformExpression\"\nconst INTEGER = \"integer\"\nconst METABOLITE_INTENSITY = \"metaboliteIntensity\"\nconst MULTIVALUE = \"multivalue\"\nconst SAMPLELST = \"samplelst\"\nconst SINGLECELL_CELLTYPE = \"singleCellCellType\"\nconst SINGLECELL_GENE_EXPRESSION = \"singleCellGeneExpression\"\nconst SNP = \"snp\"\nconst SNP_LIST = \"snplst\"\nconst SNP_LOCUS = \"snplocus\"\nconst SSGSEA = \"ssGSEA\"\nconst SURVIVAL = \"survival\"\nconst TERM_COLLECTION = \"termCollection\"\nconst PROTEOME_ABUNDANCE = \"proteomeAbundance\"\nconst TermTypes = {\n\tGENE_VARIANT,\n\tGENE_EXPRESSION,\n\tISOFORM_EXPRESSION,\n\tSSGSEA,\n\tDNA_METHYLATION,\n\tCATEGORICAL,\n\tINTEGER,\n\tFLOAT,\n\tSNP,\n\tSNP_LIST,\n\tSNP_LOCUS,\n\tCONDITION,\n\tSURVIVAL,\n\tSAMPLELST,\n\tMETABOLITE_INTENSITY,\n\tPROTEOME_ABUNDANCE,\n\tSINGLECELL_CELLTYPE,\n\tSINGLECELL_GENE_EXPRESSION,\n\tMULTIVALUE,\n\tDATE,\n\tTERM_COLLECTION,\n}\nconst dtTermTypes = new Set(dtTerms.map((t) => t.type))\nfor (const dtTermType of dtTermTypes) {\n\tTermTypes[dtTermType.toUpperCase()] = dtTermType\n}\nconst TermTypes2Dt = {\n\t[GENE_EXPRESSION]: dtgeneexpression,\n\t[SSGSEA]: dtssgsea,\n\t[DNA_METHYLATION]: dtdnamethylation,\n\t[METABOLITE_INTENSITY]: dtmetaboliteintensity,\n\t[PROTEOME_ABUNDANCE]: dtproteomeabundance,\n}\nconst typeGroup = {\n\t[CATEGORICAL]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[CONDITION]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[FLOAT]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[INTEGER]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[SAMPLELST]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[SURVIVAL]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[DATE]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[MULTIVALUE]: TermTypeGroups.DICTIONARY_VARIABLES,\n\t[GENE_VARIANT]: TermTypeGroups.MUTATION_CNV_FUSION,\n\t[SNP]: TermTypeGroups.SNP,\n\t[SNP_LIST]: TermTypeGroups.SNP_LIST,\n\t[SNP_LOCUS]: TermTypeGroups.SNP_LOCUS,\n\t[GENE_EXPRESSION]: TermTypeGroups.GENE_EXPRESSION,\n\t[ISOFORM_EXPRESSION]: TermTypeGroups.ISOFORM_EXPRESSION,\n\t[SSGSEA]: TermTypeGroups.SSGSEA,\n\t[DNA_METHYLATION]: TermTypeGroups.DNA_METHYLATION,\n\t[METABOLITE_INTENSITY]: TermTypeGroups.METABOLITE_INTENSITY,\n\t[PROTEOME_ABUNDANCE]: TermTypeGroups.PROTEOME_ABUNDANCE,\n\t[TERM_COLLECTION]: TermTypeGroups.TERM_COLLECTION,\n\t[SINGLECELL_CELLTYPE]: TermTypeGroups.SINGLECELL_CELLTYPE,\n\t[SINGLECELL_GENE_EXPRESSION]: TermTypeGroups.SINGLECELL_GENE_EXPRESSION,\n}\nconst nonDictTypes = /* @__PURE__ */ new Set([\n\tSNP,\n\tSNP_LIST,\n\tSNP_LOCUS,\n\tGENE_EXPRESSION,\n\tISOFORM_EXPRESSION,\n\tSSGSEA,\n\tDNA_METHYLATION,\n\tGENE_VARIANT,\n\tMETABOLITE_INTENSITY,\n\tPROTEOME_ABUNDANCE,\n\tSINGLECELL_CELLTYPE,\n\tSINGLECELL_GENE_EXPRESSION,\n])\nfor (const dtTermType of dtTermTypes) {\n\tnonDictTypes.add(TermTypes[dtTermType.toUpperCase()])\n}\nconst numericTypes = /* @__PURE__ */ new Set([\n\tINTEGER,\n\tFLOAT,\n\tGENE_EXPRESSION,\n\tISOFORM_EXPRESSION,\n\tSSGSEA,\n\tDNA_METHYLATION,\n\tMETABOLITE_INTENSITY,\n\tPROTEOME_ABUNDANCE,\n\tSINGLECELL_GENE_EXPRESSION,\n\tDATE,\n])\nconst annoNumericTypes = /* @__PURE__ */ new Set([INTEGER, FLOAT, DATE])\nconst categoricalTypes = /* @__PURE__ */ new Set([CATEGORICAL, SNP])\nconst singleCellTerms = /* @__PURE__ */ new Set([\n\tSINGLECELL_CELLTYPE,\n\tSINGLECELL_GENE_EXPRESSION,\n])\nfunction isSingleCellTerm(term) {\n\tif (!term) return false\n\treturn singleCellTerms.has(term.type)\n}\nfunction isNumericTerm(term) {\n\tif (!term) return false\n\treturn numericTypes.has(term.type)\n}\nfunction isCategoricalTerm(term) {\n\tif (!term) return false\n\treturn categoricalTypes.has(term.type)\n}\nfunction isDictionaryType(type) {\n\treturn !isNonDictionaryType(type)\n}\nfunction isNonDictionaryType(type) {\n\tif (!type) throw new Error(\"Type is not defined\")\n\treturn nonDictTypes.has(type)\n}\nfunction isNumTermCollection(term) {\n\tif (!term || !term.type) throw new Error(\"Term or term type is not defined\")\n\treturn term.type === TERM_COLLECTION\n}\nfunction equals(t1, t2) {\n\tif (!t1) throw new Error(\"First term is not defined \")\n\tif (!t2) throw new Error(\"Second term is not defined \")\n\tif (t1.type !== t2.type) return false\n\tif (\n\t\tisDictionaryType(t1.type) &&\n\t\tisDictionaryType(t2.type) &&\n\t\tt1.type != SAMPLELST\n\t)\n\t\treturn t1.id === t2.id\n\tswitch (t1.type) {\n\t\tcase GENE_EXPRESSION:\n\t\t\treturn t1.gene == t2.gene\n\t\tcase ISOFORM_EXPRESSION:\n\t\t\treturn t1.isoform == t2.isoform\n\t\tcase SSGSEA:\n\t\t\treturn t1.id == t2.id\n\t\tcase DNA_METHYLATION:\n\t\t\treturn t1.chr == t2.chr && t1.start == t2.start && t1.stop == t2.stop\n\t\tcase METABOLITE_INTENSITY:\n\t\tcase PROTEOME_ABUNDANCE:\n\t\t\treturn t1.name == t2.name\n\t\tcase GENE_VARIANT:\n\t\t\treturn (\n\t\t\t\tt1.gene == t2.gene ||\n\t\t\t\t(t1.chr == t2.chr && t1.start == t2.start && t1.stop == t2.stop)\n\t\t\t)\n\t\t// TO DO: Add more cases\n\t\t// case SNP_LIST:\n\t\t// case SNP_LOCUS:\n\t\t// case SAMPLELST:\n\t\tdefault:\n\t\t\treturn false\n\t}\n}\nfunction getBin(lst, value) {\n\tlet bin = lst.findIndex(\n\t\t(b) =>\n\t\t\t(b.startunbounded && value < b.stop) ||\n\t\t\t(b.startunbounded && b.stopinclusive && value == b.stop)\n\t)\n\tif (bin == -1)\n\t\tbin = lst.findIndex(\n\t\t\t(b) =>\n\t\t\t\t(b.stopunbounded && value > b.start) ||\n\t\t\t\t(b.stopunbounded && b.startinclusive && value == b.start)\n\t\t)\n\tif (bin == -1)\n\t\tbin = lst.findIndex(\n\t\t\t(b) =>\n\t\t\t\t(value > b.start && value < b.stop) ||\n\t\t\t\t(b.startinclusive && value == b.start) ||\n\t\t\t\t(b.stopinclusive && value == b.stop)\n\t\t)\n\treturn bin\n}\nfunction getSampleType(term, ds) {\n\tif (!term) return null\n\tif (term.type && isNonDictionaryType(term.type)) return DEFAULT_SAMPLE_TYPE\n\tif (term.id) return ds.cohort.termdb.term2SampleType.get(term.id)\n\tif (term.type == \"samplelst\") {\n\t\tconst key = Object.keys(term.values)[0]\n\t\tconst sampleId = term.values[key].list[0]?.sampleId\n\t\tif (sampleId) return ds.sampleId2Type.get(Number(sampleId) || sampleId)\n\t\telse return DEFAULT_SAMPLE_TYPE\n\t}\n\treturn DEFAULT_SAMPLE_TYPE\n}\nfunction getParentType(types, ds) {\n\tif (Object.keys(ds.cohort.termdb.sampleTypes).length == 0) return null\n\tconst ids = Array.from(types)\n\tif (!ids || ids.length == 0) return null\n\tfor (const id of ids) {\n\t\tconst typeObj = ds.cohort.termdb.sampleTypes[id]\n\t\tif (!typeObj) continue\n\t\tif (typeObj.parent_id == null) return id\n\t\tif (ids.includes(typeObj.parent_id)) continue\n\t\telse return typeObj.parent_id\n\t}\n\treturn null\n}\nconst typeMap = {\n\tcategorical: \"Categorical\",\n\tcondition: \"Condition\",\n\tfloat: \"Numerical\",\n\tinteger: \"Numerical\",\n\tgeneExpression: \"Gene Expression\",\n\tisoformExpression: \"Isoform Expression\",\n\tssGSEA: \"Geneset Expression\",\n\tdnaMethylation: \"DNA Methylation\",\n\tgeneVariant: \"Gene Variant\",\n\tmetaboliteIntensity: \"Metabolite Intensity\",\n\tproteomeAbundance: \"Whole Proteome Abundance\",\n\tmultivalue: \"Multi Value\",\n\tsingleCellGeneExpression: \"Single Cell, Gene Expression\",\n\tsingleCellCellType: \"Single Cell, Cell Type\",\n\tsnplocus: \"SNP Locus\",\n\tsnp: \"SNP\",\n\tsnplst: \"SNP List\",\n\ttermCollection: \"Term Collection\",\n}\nfunction termType2label(type) {\n\treturn typeMap[type] || \"Unknown term type\"\n}\nfunction getDateFromNumber(value) {\n\tconst year = Math.floor(value)\n\tconst january1st = new Date(year, 0, 1)\n\tconst totalDays = getDaysInYear(year)\n\tconst time = Math.round((value - year) * totalDays) * oneDayTime\n\tconst date = new Date(january1st.getTime() + time)\n\treturn date\n}\nconst oneDayTime = 24 * 60 * 60 * 1e3\nfunction getDateStrFromNumber(value) {\n\tconst date = getDateFromNumber(value)\n\treturn date.toLocaleDateString(\"en-US\", {\n\t\tyear: \"numeric\",\n\t\tmonth: \"long\",\n\t})\n}\nfunction getNumberFromDateStr(str) {\n\tconst date = new Date(str)\n\treturn getNumberFromDate(date)\n}\nfunction getNumberFromDate(date) {\n\tconst year = date.getFullYear()\n\tconst january1st = new Date(year, 0, 1)\n\tconst diffDays = (date.getTime() - january1st.getTime()) / oneDayTime\n\tconst daysTotal = getDaysInYear(year)\n\tconst decimal = diffDays / daysTotal\n\treturn year + decimal\n}\nfunction getDaysInYear(year) {\n\tconst isLeap = new Date(year, 1, 29).getMonth() === 1\n\tconst days = isLeap ? 366 : 365\n\treturn days\n}\nexport {\n\tCATEGORICAL,\n\tCONDITION,\n\tDATE,\n\tDEFAULT_SAMPLE_TYPE,\n\tDNA_METHYLATION,\n\tFLOAT,\n\tGENE_EXPRESSION,\n\tGENE_VARIANT,\n\tINTEGER,\n\tISOFORM_EXPRESSION,\n\tMETABOLITE_INTENSITY,\n\tMULTIVALUE,\n\tNumericModes,\n\tPROTEOME_ABUNDANCE,\n\tROOT_SAMPLE_TYPE,\n\tSAMPLELST,\n\tSINGLECELL_CELLTYPE,\n\tSINGLECELL_GENE_EXPRESSION,\n\tSNP,\n\tSNP_LIST,\n\tSNP_LOCUS,\n\tSSGSEA,\n\tSURVIVAL,\n\tTERM_COLLECTION,\n\tTermTypeGroups2 as TermTypeGroups,\n\tTermTypes,\n\tTermTypes2Dt,\n\tannoNumericTypes,\n\tdtTermTypes,\n\tequals,\n\tgetBin,\n\tgetDateFromNumber,\n\tgetDateStrFromNumber,\n\tgetDaysInYear,\n\tgetNumberFromDate,\n\tgetNumberFromDateStr,\n\tgetParentType,\n\tgetSampleType,\n\tisCategoricalTerm,\n\tisDictionaryType,\n\tisNonDictionaryType,\n\tisNumTermCollection,\n\tisNumericTerm,\n\tisSingleCellTerm,\n\tnumericTypes,\n\ttermType2label,\n\ttypeGroup,\n}\n"],
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-}

package/dist/chunk-3656ZY4T.js

@@ -1,237 +0,0 @@
-import {
-  TermTypes
-} from "./chunk-2UWHV2SB.js";
-import {
-  __export
-} from "./chunk-HFNDKYVF.js";
-
-// plots/matrix/hierCluster.renderers.js
-var hierCluster_renderers_exports = {};
-__export(hierCluster_renderers_exports, {
-  maySetSandboxHeader: () => maySetSandboxHeader,
-  plotDendrogramHclust: () => plotDendrogramHclust,
-  renderImage: () => renderImage
-});
-function maySetSandboxHeader(appState) {
-  if (!this.dom.header) return;
-  switch (this.config.dataType) {
-    case TermTypes.GENE_EXPRESSION:
-      this.dom.header.text("Gene Expression Clustering");
-      break;
-    case TermTypes.METABOLITE_INTENSITY:
-      this.dom.header.text("Metabolite Intensity Clustering");
-      break;
-    case TermTypes.PROTEOME_ABUNDANCE:
-      this.dom.header.text(
-        this.config.assayCohortTitle ? `Protein Abundance Clustering (${this.config.assayCohortTitle})` : "Protein Abundance Clustering"
-      );
-      break;
-    default:
-      throw `dataType '${this.config.dataType}' not recognized`;
-  }
-}
-function plotDendrogramHclust(plotOnly) {
-  const d = this.dimensions;
-  const s = this.config.settings.matrix;
-  const xOffset = d.seriesXoffset;
-  const pxr = window.devicePixelRatio <= 1 ? 1 : window.devicePixelRatio;
-  const obj = this.hierClusterData.clustering;
-  const row = obj.row;
-  const col = obj.col;
-  const rowHeight = this.settings.matrix.clusterRowh, { xDendrogramHeight, yDendrogramHeight } = this.settings.hierCluster, colWidth = this.dimensions.dx;
-  if (plotOnly !== "left") {
-    if (!this.settings.hierCluster.clusterSamples) {
-      this.dom.topDendrogram.selectAll("*").remove();
-    } else {
-      const height2px = getHclustHeightScalefactor(col.height, yDendrogramHeight);
-      const height = yDendrogramHeight + 1e-7;
-      const width = colWidth * col.inputOrder.length;
-      const canvas = new OffscreenCanvas(width * pxr, height * pxr);
-      const ctx = canvas.getContext("2d");
-      ctx.scale(pxr, pxr);
-      ctx.imageSmoothingEnabled = false;
-      ctx.imageSmoothingQuality = "high";
-      ctx.strokeStyle = "black";
-      const mergedClusters = /* @__PURE__ */ new Map();
-      for (const [clusterid0, pair] of col.merge.entries()) {
-        const clusterid = clusterid0 + 1;
-        const children = [];
-        const childrenClusters = [];
-        let x1, x2, y1, y2;
-        if (pair.n1 < 0) {
-          const [name, columnNumber] = getLeafNumber(pair.n1, col.inputOrder, col.order);
-          x1 = colWidth * (columnNumber + 0.5);
-          y1 = yDendrogramHeight;
-          children.push({ name });
-        } else {
-          if (!mergedClusters.has(pair.n1)) throw "pair.n1 is positive but not seen before";
-          const c = mergedClusters.get(pair.n1);
-          x1 = c.x;
-          y1 = c.y;
-          children.push(...c.children);
-          childrenClusters.push(pair.n1);
-        }
-        if (pair.n2 < 0) {
-          const [name, columnNumber] = getLeafNumber(pair.n2, col.inputOrder, col.order);
-          x2 = colWidth * (columnNumber + 0.5);
-          y2 = yDendrogramHeight;
-          children.push({ name });
-        } else {
-          if (!mergedClusters.has(pair.n2)) throw "pair.n1 is positive but not seen before";
-          const c = mergedClusters.get(pair.n2);
-          x2 = c.x;
-          y2 = c.y;
-          children.push(...c.children);
-          childrenClusters.push(pair.n2);
-        }
-        const clusterY = yDendrogramHeight - col.height[clusterid0].height * height2px;
-        const highlight = this.clickedClusterIds?.includes(clusterid);
-        ctx.strokeStyle = highlight ? "red" : "black";
-        ctx.beginPath();
-        ctx.moveTo(x1, y1);
-        ctx.lineTo(x1, clusterY);
-        ctx.lineTo(x2, clusterY);
-        ctx.lineTo(x2, y2);
-        ctx.stroke();
-        ctx.closePath();
-        mergedClusters.set(clusterid, {
-          x: (x1 + x2) / 2,
-          y: clusterY,
-          children,
-          childrenClusters,
-          clusterPosition: {
-            x1,
-            x2,
-            y1,
-            y2,
-            clusterY
-          }
-        });
-      }
-      this.renderImage(
-        this.api,
-        this.dom.topDendrogram,
-        canvas,
-        width,
-        height,
-        xDendrogramHeight + 0.5 * colWidth,
-        s.margin.top + s.scrollHeight
-      );
-      col.mergedClusters = mergedClusters;
-    }
-  }
-  if (plotOnly !== "top") {
-    if (!this.settings.hierCluster.clusterRows) {
-      this.dom.leftDendrogram.selectAll("*").remove();
-    } else {
-      const height2px = getHclustHeightScalefactor(row.height, xDendrogramHeight);
-      const width = xDendrogramHeight + 1e-7;
-      const height = rowHeight * row.inputOrder.length;
-      const canvas = new OffscreenCanvas(width * pxr, height * pxr);
-      const ctx = canvas.getContext("2d");
-      ctx.scale(pxr, pxr);
-      ctx.imageSmoothingEnabled = false;
-      ctx.imageSmoothingQuality = "high";
-      ctx.strokeStyle = "black";
-      const mergedClusters = /* @__PURE__ */ new Map();
-      for (const [clusterid0, pair] of row.merge.entries()) {
-        const clusterid = clusterid0 + 1;
-        const children = [];
-        const childrenClusters = [];
-        let x1, x2, y1, y2;
-        if (pair.n1 < 0) {
-          const [name, rowNumber] = getLeafNumber(pair.n1, row.inputOrder, row.order);
-          y1 = rowHeight * (rowNumber + 0.5);
-          x1 = xDendrogramHeight;
-          children.push({ name });
-        } else {
-          if (!mergedClusters.has(pair.n1)) throw "pair.n1 is positive but not seen before";
-          const c = mergedClusters.get(pair.n1);
-          x1 = c.x;
-          y1 = c.y;
-          children.push(...c.children);
-          childrenClusters.push(pair.n1);
-        }
-        if (pair.n2 < 0) {
-          const [name, rowNumber] = getLeafNumber(pair.n2, row.inputOrder, row.order);
-          y2 = rowHeight * (rowNumber + 0.5);
-          x2 = xDendrogramHeight;
-          children.push({ name });
-        } else {
-          if (!mergedClusters.has(pair.n2)) throw "pair.n1 is positive but not seen before";
-          const c = mergedClusters.get(pair.n2);
-          x2 = c.x;
-          y2 = c.y;
-          children.push(...c.children);
-          childrenClusters.push(pair.n2);
-        }
-        const clusterX = xDendrogramHeight - row.height[clusterid0].height * height2px;
-        const highlight = this.clickedLeftClusterIds?.includes(clusterid);
-        ctx.strokeStyle = highlight ? "red" : "black";
-        ctx.beginPath();
-        ctx.moveTo(x1, y1);
-        ctx.lineTo(clusterX, y1);
-        ctx.lineTo(clusterX, y2);
-        ctx.lineTo(x2, y2);
-        ctx.stroke();
-        ctx.closePath();
-        mergedClusters.set(clusterid, {
-          x: clusterX,
-          y: (y1 + y2) / 2,
-          children,
-          childrenClusters,
-          clusterPosition: {
-            x1,
-            x2,
-            y1,
-            y2,
-            clusterX
-          }
-        });
-      }
-      const t = this.termOrder.find((t2) => t2.grp.type == "hierCluster" || t2.grp.name == this.hcTermGroup.name);
-      const y = (
-        // t.labelOffset is commented out because it is already handled in adjustSvgDimensions
-        t.grpIndex * s.rowgspace + t.prevGrpTotalIndex * s.rowh + t.totalHtAdjustments + s.margin.top + s.scrollHeight + // left dendrogram image must be lower than the top dendrogram image height
-        yDendrogramHeight
-      );
-      this.renderImage(this.api, this.dom.leftDendrogram, canvas, width, height, 0, y);
-      row.mergedClusters = mergedClusters;
-    }
-  }
-}
-async function renderImage(componentApi, g, canvas, width, height, x, y) {
-  const sequenceId = componentApi.getSequenceId();
-  const reader = new FileReader();
-  reader.addEventListener(
-    "load",
-    () => {
-      if (componentApi.isStaleSequenceId(sequenceId)) return;
-      g.selectAll("*").remove();
-      g.append("image").attr("x", x + 0.033).attr("y", y + 0.033).attr("xlink:href", reader.result).attr("width", width).attr("height", height);
-    },
-    false
-  );
-  const blob = await canvas.convertToBlob({ quality: 1 });
-  reader.readAsDataURL(blob);
-}
-function getHclustHeightScalefactor(lst, ph) {
-  let max = lst[0].height;
-  for (const h of lst) max = Math.max(max, h.height);
-  return ph / max;
-}
-function getLeafNumber(minus, inputOrder, order) {
-  const name = inputOrder[-minus - 1];
-  if (!name) throw "minus not in inputOrder";
-  const i = order.findIndex((j) => j.name == name);
-  if (i == -1) throw "name not found in hc$order";
-  return [name, i];
-}
-
-export {
-  maySetSandboxHeader,
-  plotDendrogramHclust,
-  renderImage,
-  hierCluster_renderers_exports
-};
-//# sourceMappingURL=chunk-3656ZY4T.js.map

package/dist/chunk-3TU6TRLQ.js

@@ -1,98 +0,0 @@
-import {
-  addGeneSearchbox,
-  first_genetrack_tolist,
-  sayerror
-} from "./chunk-XZZLEHWC.js";
-import {
-  Menu
-} from "./chunk-2SRMRC6L.js";
-import {
-  TermTypes
-} from "./chunk-2UWHV2SB.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.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-2QM37YSE.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 });
-        await this.callback(term);
-      });
-    } else if (geneSearch.chr && Number.isInteger(geneSearch.start) && Number.isInteger(geneSearch.stop)) {
-      const { chr, start, stop } = geneSearch;
-      const term = this.makeTerm({ chr, start, stop });
-      await this.callback(term);
-    } else {
-      throw new Error("invalid gene search input");
-    }
-  }
-  makeTerm(opts) {
-    const { chr, start, stop } = opts;
-    if (!chr || !Number.isInteger(start) || !Number.isInteger(stop)) throw new Error("invalid coordinate");
-    const coord = `${chr}:${start}-${stop}`;
-    const unit = this.app.vocabApi.termdbConfig.queries.dnaMethylation?.unit || "Average Beta Value";
-    const term = {
-      id: coord,
-      chr,
-      start,
-      stop,
-      name: `${coord} ${unit}`,
-      // will also allow to be user-assigned
-      type: TermTypes.DNA_METHYLATION
-    };
-    return term;
-  }
-};
-
-export {
-  SearchHandler
-};
-//# sourceMappingURL=chunk-3TU6TRLQ.js.map