@sjcrh/proteinpaint-shared 2.180.0 → 2.180.1

package/src/terms.js

@@ -1,309 +1,324 @@
 import {
-  dtgeneexpression,
-  dtssgsea,
-  dtdnamethylation,
-  dtmetaboliteintensity,
-  dtwholeproteomeabundance,
-  TermTypeGroups,
-  dtTerms
-} from "./common.js";
-import { TermTypeGroups as TermTypeGroups2 } from "./common.js";
-const ROOT_SAMPLE_TYPE = 1;
-const DEFAULT_SAMPLE_TYPE = 2;
+	dtgeneexpression,
+	dtssgsea,
+	dtdnamethylation,
+	dtmetaboliteintensity,
+	dtproteomeabundance,
+	TermTypeGroups,
+	dtTerms,
+} from "./common.js"
+import { TermTypeGroups as TermTypeGroups2 } from "./common.js"
+const ROOT_SAMPLE_TYPE = 1
+const DEFAULT_SAMPLE_TYPE = 2
 const NumericModes = {
-  continuous: "continuous",
-  discrete: "discrete"
-};
-const CATEGORICAL = "categorical";
-const CONDITION = "condition";
-const DATE = "date";
-const DNA_METHYLATION = "dnaMethylation";
-const FLOAT = "float";
-const GENE_VARIANT = "geneVariant";
-const GENE_EXPRESSION = "geneExpression";
-const INTEGER = "integer";
-const METABOLITE_INTENSITY = "metaboliteIntensity";
-const MULTIVALUE = "multivalue";
-const SAMPLELST = "samplelst";
-const SINGLECELL_CELLTYPE = "singleCellCellType";
-const SINGLECELL_GENE_EXPRESSION = "singleCellGeneExpression";
-const SNP = "snp";
-const SNP_LIST = "snplst";
-const SNP_LOCUS = "snplocus";
-const SSGSEA = "ssGSEA";
-const SURVIVAL = "survival";
-const TERM_COLLECTION = "termCollection";
-const WHOLE_PROTEOME_ABUNDANCE = "wholeProteomeAbundance";
+	continuous: "continuous",
+	discrete: "discrete",
+}
+const CATEGORICAL = "categorical"
+const CONDITION = "condition"
+const DATE = "date"
+const DNA_METHYLATION = "dnaMethylation"
+const FLOAT = "float"
+const GENE_VARIANT = "geneVariant"
+const GENE_EXPRESSION = "geneExpression"
+const INTEGER = "integer"
+const METABOLITE_INTENSITY = "metaboliteIntensity"
+const MULTIVALUE = "multivalue"
+const SAMPLELST = "samplelst"
+const SINGLECELL_CELLTYPE = "singleCellCellType"
+const SINGLECELL_GENE_EXPRESSION = "singleCellGeneExpression"
+const SNP = "snp"
+const SNP_LIST = "snplst"
+const SNP_LOCUS = "snplocus"
+const SSGSEA = "ssGSEA"
+const SURVIVAL = "survival"
+const TERM_COLLECTION = "termCollection"
+const PROTEOME_ABUNDANCE = "proteomeAbundance"
 const TermTypes = {
-  GENE_VARIANT,
-  GENE_EXPRESSION,
-  SSGSEA,
-  DNA_METHYLATION,
-  CATEGORICAL,
-  INTEGER,
-  FLOAT,
-  SNP,
-  SNP_LIST,
-  SNP_LOCUS,
-  CONDITION,
-  SURVIVAL,
-  SAMPLELST,
-  METABOLITE_INTENSITY,
-  WHOLE_PROTEOME_ABUNDANCE,
-  SINGLECELL_CELLTYPE,
-  SINGLECELL_GENE_EXPRESSION,
-  MULTIVALUE,
-  DATE,
-  TERM_COLLECTION
-};
-const dtTermTypes = new Set(dtTerms.map((t) => t.type));
+	GENE_VARIANT,
+	GENE_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,
+}
+const dtTermTypes = new Set(dtTerms.map((t) => t.type))
 for (const dtTermType of dtTermTypes) {
-  TermTypes[dtTermType.toUpperCase()] = dtTermType;
+	TermTypes[dtTermType.toUpperCase()] = dtTermType
 }
-const NUMERIC_DICTIONARY_TERM = "numericDictTerm";
 const TermTypes2Dt = {
-  [GENE_EXPRESSION]: dtgeneexpression,
-  [SSGSEA]: dtssgsea,
-  [DNA_METHYLATION]: dtdnamethylation,
-  [METABOLITE_INTENSITY]: dtmetaboliteintensity,
-  [WHOLE_PROTEOME_ABUNDANCE]: dtwholeproteomeabundance
-};
+	[GENE_EXPRESSION]: dtgeneexpression,
+	[SSGSEA]: dtssgsea,
+	[DNA_METHYLATION]: dtdnamethylation,
+	[METABOLITE_INTENSITY]: dtmetaboliteintensity,
+	[PROTEOME_ABUNDANCE]: dtproteomeabundance,
+}
 const 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,
-  [SSGSEA]: TermTypeGroups.SSGSEA,
-  [DNA_METHYLATION]: TermTypeGroups.DNA_METHYLATION,
-  [METABOLITE_INTENSITY]: TermTypeGroups.METABOLITE_INTENSITY,
-  [WHOLE_PROTEOME_ABUNDANCE]: TermTypeGroups.WHOLE_PROTEOME_ABUNDANCE,
-  [TERM_COLLECTION]: TermTypeGroups.TERM_COLLECTION,
-  [SINGLECELL_CELLTYPE]: TermTypeGroups.SINGLECELL_CELLTYPE,
-  [SINGLECELL_GENE_EXPRESSION]: TermTypeGroups.SINGLECELL_GENE_EXPRESSION
-};
+	[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,
+	[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,
+}
 const nonDictTypes = /* @__PURE__ */ new Set([
-  SNP,
-  SNP_LIST,
-  SNP_LOCUS,
-  GENE_EXPRESSION,
-  SSGSEA,
-  DNA_METHYLATION,
-  GENE_VARIANT,
-  METABOLITE_INTENSITY,
-  WHOLE_PROTEOME_ABUNDANCE,
-  SINGLECELL_CELLTYPE,
-  SINGLECELL_GENE_EXPRESSION
-]);
+	SNP,
+	SNP_LIST,
+	SNP_LOCUS,
+	GENE_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()]);
+	nonDictTypes.add(TermTypes[dtTermType.toUpperCase()])
 }
 const numericTypes = /* @__PURE__ */ new Set([
-  INTEGER,
-  FLOAT,
-  GENE_EXPRESSION,
-  SSGSEA,
-  DNA_METHYLATION,
-  METABOLITE_INTENSITY,
-  WHOLE_PROTEOME_ABUNDANCE,
-  SINGLECELL_GENE_EXPRESSION,
-  DATE
-]);
-const annoNumericTypes = /* @__PURE__ */ new Set([INTEGER, FLOAT, DATE]);
-const categoricalTypes = /* @__PURE__ */ new Set([CATEGORICAL, SNP]);
-const singleCellTerms = /* @__PURE__ */ new Set([SINGLECELL_CELLTYPE, SINGLECELL_GENE_EXPRESSION]);
+	INTEGER,
+	FLOAT,
+	GENE_EXPRESSION,
+	SSGSEA,
+	DNA_METHYLATION,
+	METABOLITE_INTENSITY,
+	PROTEOME_ABUNDANCE,
+	SINGLECELL_GENE_EXPRESSION,
+	DATE,
+])
+const annoNumericTypes = /* @__PURE__ */ new Set([INTEGER, FLOAT, DATE])
+const categoricalTypes = /* @__PURE__ */ new Set([CATEGORICAL, SNP])
+const singleCellTerms = /* @__PURE__ */ new Set([
+	SINGLECELL_CELLTYPE,
+	SINGLECELL_GENE_EXPRESSION,
+])
 function isSingleCellTerm(term) {
-  if (!term) return false;
-  return singleCellTerms.has(term.type);
+	if (!term) return false
+	return singleCellTerms.has(term.type)
 }
 function isNumericTerm(term) {
-  if (!term) return false;
-  return numericTypes.has(term.type);
+	if (!term) return false
+	return numericTypes.has(term.type)
 }
 function isCategoricalTerm(term) {
-  if (!term) return false;
-  return categoricalTypes.has(term.type);
+	if (!term) return false
+	return categoricalTypes.has(term.type)
 }
 function isDictionaryType(type) {
-  return !isNonDictionaryType(type);
+	return !isNonDictionaryType(type)
 }
 function isNonDictionaryType(type) {
-  if (!type) throw new Error("Type is not defined");
-  return nonDictTypes.has(type);
+	if (!type) throw new Error("Type is not defined")
+	return nonDictTypes.has(type)
 }
 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 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 WHOLE_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;
-  }
+	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 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
+	}
 }
 function getBin(lst, value) {
-  let bin = lst.findIndex(
-    (b) => b.startunbounded && value < b.stop || b.startunbounded && b.stopinclusive && value == b.stop
-  );
-  if (bin == -1)
-    bin = lst.findIndex(
-      (b) => b.stopunbounded && value > b.start || b.stopunbounded && b.startinclusive && value == b.start
-    );
-  if (bin == -1)
-    bin = lst.findIndex(
-      (b) => value > b.start && value < b.stop || b.startinclusive && value == b.start || b.stopinclusive && value == b.stop
-    );
-  return bin;
+	let bin = lst.findIndex(
+		(b) =>
+			(b.startunbounded && value < b.stop) ||
+			(b.startunbounded && b.stopinclusive && value == b.stop)
+	)
+	if (bin == -1)
+		bin = lst.findIndex(
+			(b) =>
+				(b.stopunbounded && value > b.start) ||
+				(b.stopunbounded && b.startinclusive && value == b.start)
+		)
+	if (bin == -1)
+		bin = lst.findIndex(
+			(b) =>
+				(value > b.start && value < b.stop) ||
+				(b.startinclusive && value == b.start) ||
+				(b.stopinclusive && value == b.stop)
+		)
+	return bin
 }
 function getSampleType(term, ds) {
-  if (!term) return null;
-  if (term.type && isNonDictionaryType(term.type)) return DEFAULT_SAMPLE_TYPE;
-  if (term.id) return ds.cohort.termdb.term2SampleType.get(term.id);
-  if (term.type == "samplelst") {
-    const key = Object.keys(term.values)[0];
-    const sampleId = term.values[key].list[0]?.sampleId;
-    if (sampleId) return ds.sampleId2Type.get(Number(sampleId) || sampleId);
-    else return DEFAULT_SAMPLE_TYPE;
-  }
-  return DEFAULT_SAMPLE_TYPE;
+	if (!term) return null
+	if (term.type && isNonDictionaryType(term.type)) return DEFAULT_SAMPLE_TYPE
+	if (term.id) return ds.cohort.termdb.term2SampleType.get(term.id)
+	if (term.type == "samplelst") {
+		const key = Object.keys(term.values)[0]
+		const sampleId = term.values[key].list[0]?.sampleId
+		if (sampleId) return ds.sampleId2Type.get(Number(sampleId) || sampleId)
+		else return DEFAULT_SAMPLE_TYPE
+	}
+	return DEFAULT_SAMPLE_TYPE
 }
 function getParentType(types, ds) {
-  if (Object.keys(ds.cohort.termdb.sampleTypes).length == 0) return null;
-  const ids = Array.from(types);
-  if (!ids || ids.length == 0) return null;
-  for (const id of ids) {
-    const typeObj = ds.cohort.termdb.sampleTypes[id];
-    if (!typeObj) continue;
-    if (typeObj.parent_id == null) return id;
-    if (ids.includes(typeObj.parent_id)) continue;
-    else return typeObj.parent_id;
-  }
-  return null;
+	if (Object.keys(ds.cohort.termdb.sampleTypes).length == 0) return null
+	const ids = Array.from(types)
+	if (!ids || ids.length == 0) return null
+	for (const id of ids) {
+		const typeObj = ds.cohort.termdb.sampleTypes[id]
+		if (!typeObj) continue
+		if (typeObj.parent_id == null) return id
+		if (ids.includes(typeObj.parent_id)) continue
+		else return typeObj.parent_id
+	}
+	return null
 }
 const typeMap = {
-  categorical: "Categorical",
-  condition: "Condition",
-  float: "Numerical",
-  integer: "Numerical",
-  geneExpression: "Gene Expression",
-  ssGSEA: "Geneset Expression",
-  dnaMethylation: "DNA Methylation",
-  geneVariant: "Gene Variant",
-  metaboliteIntensity: "Metabolite Intensity",
-  wholeProteomeAbundance: "Whole Proteome Abundance",
-  multivalue: "Multi Value",
-  singleCellGeneExpression: "Single Cell, Gene Expression",
-  singleCellCellType: "Single Cell, Cell Type",
-  snplocus: "SNP Locus",
-  snp: "SNP",
-  snplst: "SNP List",
-  numericDictTerm: "Numeric Dictionary Term",
-  termCollection: "Term Collection"
-};
+	categorical: "Categorical",
+	condition: "Condition",
+	float: "Numerical",
+	integer: "Numerical",
+	geneExpression: "Gene 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";
+	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;
+	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
 }
-const oneDayTime = 24 * 60 * 60 * 1e3;
+const oneDayTime = 24 * 60 * 60 * 1e3
 function getDateStrFromNumber(value) {
-  const date = getDateFromNumber(value);
-  return date.toLocaleDateString("en-US", {
-    year: "numeric",
-    month: "long"
-  });
+	const date = getDateFromNumber(value)
+	return date.toLocaleDateString("en-US", {
+		year: "numeric",
+		month: "long",
+	})
 }
 function getNumberFromDateStr(str) {
-  const date = new Date(str);
-  return getNumberFromDate(date);
+	const date = new Date(str)
+	return getNumberFromDate(date)
 }
 function getNumberFromDate(date) {
-  const year = date.getFullYear();
-  const january1st = new Date(year, 0, 1);
-  const diffDays = (date.getTime() - january1st.getTime()) / oneDayTime;
-  const daysTotal = getDaysInYear(year);
-  const decimal = diffDays / daysTotal;
-  return year + decimal;
+	const year = date.getFullYear()
+	const january1st = new Date(year, 0, 1)
+	const diffDays = (date.getTime() - january1st.getTime()) / oneDayTime
+	const daysTotal = getDaysInYear(year)
+	const decimal = diffDays / daysTotal
+	return year + decimal
 }
 function getDaysInYear(year) {
-  const isLeap = new Date(year, 1, 29).getMonth() === 1;
-  const days = isLeap ? 366 : 365;
-  return days;
+	const isLeap = new Date(year, 1, 29).getMonth() === 1
+	const days = isLeap ? 366 : 365
+	return days
 }
 export {
-  CATEGORICAL,
-  CONDITION,
-  DATE,
-  DEFAULT_SAMPLE_TYPE,
-  DNA_METHYLATION,
-  FLOAT,
-  GENE_EXPRESSION,
-  GENE_VARIANT,
-  INTEGER,
-  METABOLITE_INTENSITY,
-  MULTIVALUE,
-  NUMERIC_DICTIONARY_TERM,
-  NumericModes,
-  ROOT_SAMPLE_TYPE,
-  SAMPLELST,
-  SINGLECELL_CELLTYPE,
-  SINGLECELL_GENE_EXPRESSION,
-  SNP,
-  SNP_LIST,
-  SNP_LOCUS,
-  SSGSEA,
-  SURVIVAL,
-  TERM_COLLECTION,
-  TermTypeGroups2 as TermTypeGroups,
-  TermTypes,
-  TermTypes2Dt,
-  WHOLE_PROTEOME_ABUNDANCE,
-  annoNumericTypes,
-  dtTermTypes,
-  equals,
-  getBin,
-  getDateFromNumber,
-  getDateStrFromNumber,
-  getDaysInYear,
-  getNumberFromDate,
-  getNumberFromDateStr,
-  getParentType,
-  getSampleType,
-  isCategoricalTerm,
-  isDictionaryType,
-  isNonDictionaryType,
-  isNumericTerm,
-  isSingleCellTerm,
-  numericTypes,
-  termType2label,
-  typeGroup
-};
+	CATEGORICAL,
+	CONDITION,
+	DATE,
+	DEFAULT_SAMPLE_TYPE,
+	DNA_METHYLATION,
+	FLOAT,
+	GENE_EXPRESSION,
+	GENE_VARIANT,
+	INTEGER,
+	METABOLITE_INTENSITY,
+	MULTIVALUE,
+	NumericModes,
+	PROTEOME_ABUNDANCE,
+	ROOT_SAMPLE_TYPE,
+	SAMPLELST,
+	SINGLECELL_CELLTYPE,
+	SINGLECELL_GENE_EXPRESSION,
+	SNP,
+	SNP_LIST,
+	SNP_LOCUS,
+	SSGSEA,
+	SURVIVAL,
+	TERM_COLLECTION,
+	TermTypeGroups2 as TermTypeGroups,
+	TermTypes,
+	TermTypes2Dt,
+	annoNumericTypes,
+	dtTermTypes,
+	equals,
+	getBin,
+	getDateFromNumber,
+	getDateStrFromNumber,
+	getDaysInYear,
+	getNumberFromDate,
+	getNumberFromDateStr,
+	getParentType,
+	getSampleType,
+	isCategoricalTerm,
+	isDictionaryType,
+	isNonDictionaryType,
+	isNumericTerm,
+	isSingleCellTerm,
+	numericTypes,
+	termType2label,
+	typeGroup,
+}

package/src/tree.js

@@ -29,8 +29,8 @@ using Map for lp, nodes etc will cause memory issue, thus the use of simple obje
 to-do: verify this works after a reorg
 */
 
-const hardcode_root = 'root'
-const hierarchy_spacer = '...'
+const hardcode_root = "root"
+const hierarchy_spacer = "..."
 
 export function stratinput(lst, levels) {
 	const lp = Object.create(null)
@@ -75,7 +75,7 @@ export function stratinput(lst, levels) {
 			}
 			if (!(thisv in nodes)) {
 				const n = {
-					lst: []
+					lst: [],
 				}
 				if (lev.full) {
 					n.full = m[lev.full]
@@ -119,7 +119,7 @@ export function stratinput(lst, levels) {
 			id1: n.id1,
 			v1: n.v1,
 			id2: n.id2,
-			v2: n.v2
+			v2: n.v2,
 		})
 	}
 	return nlst

package/src/vcf.ann.js

@@ -1,12 +1,12 @@
-import { vepinfo } from './common.js'
+import { vepinfo } from "./common.js"
 
 export function parse_ANN(str, header, m) {
 	// snpEff
 	if (!header) {
 		return null
 	}
-	for (const thisannotation of str.split(',')) {
-		const lst = thisannotation.replace(/&/g, ',').split('|')
+	for (const thisannotation of str.split(",")) {
+		const lst = thisannotation.replace(/&/g, ",").split("|")
 
 		const o = {}
 
@@ -35,8 +35,8 @@ export function parse_ANN(str, header, m) {
 		allele.ann.push(o)
 		o._gene = o.Gene_Name
 		// isoform
-		if (o.Feature_Type && o.Feature_Type == 'transcript' && o.Feature_ID) {
-			o._isoform = o.Feature_ID.split('.')[0]
+		if (o.Feature_Type && o.Feature_Type == "transcript" && o.Feature_ID) {
+			o._isoform = o.Feature_ID.split(".")[0]
 		}
 		// class
 		if (o.Annotation) {
@@ -50,11 +50,11 @@ export function parse_ANN(str, header, m) {
 			o._class = mclassnonstandard
 		}
 		// mname
-		if (o['HGVS.p']) {
+		if (o["HGVS.p"]) {
 			//o._mname=decodeURIComponent(o.HGVSp.substr(o.HGVSp.indexOf(':')+1))
-			o._mname = o['HGVS.p']
-		} else if (o['HGVS.c']) {
-			o._mname = o['HGVS.c']
+			o._mname = o["HGVS.p"]
+		} else if (o["HGVS.c"]) {
+			o._mname = o["HGVS.c"]
 		} else {
 		}
 	}