@sjcrh/proteinpaint-client 2.181.0 → 2.182.1

package/dist/chunk-ZLH4PJKX.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../shared/utils/src/filter.js", "../../shared/utils/src/common.js"],
-  "sourcesContent": ["function getFilteredSamples(sampleAnno, filter) {\n\tsetDatasetAnnotations(filter)\n\tconst samples = /* @__PURE__ */ new Set()\n\tfor (const anno of sampleAnno) {\n\t\tif (samples.has(anno.sample)) continue\n\t\tconst data = anno.s || anno.data\n\t\tif (data && sample_match_termvaluesetting(data, filter)) {\n\t\t\tsamples.add(anno.sample)\n\t\t}\n\t}\n\treturn samples\n}\nfunction sample_match_termvaluesetting(\n\trow,\n\tfilter,\n\t_term = null,\n\tsample = null\n) {\n\tconst lst = filter.type == \"tvslst\" ? filter.lst : [filter]\n\tlet numberofmatchedterms = 0\n\tfor (const item of lst) {\n\t\tif (\"type\" in item && item.type == \"tvslst\") {\n\t\t\tif (sample_match_termvaluesetting(row, item, _term, sample)) {\n\t\t\t\tnumberofmatchedterms++\n\t\t\t}\n\t\t} else {\n\t\t\tconst itemCopy = JSON.parse(JSON.stringify(item))\n\t\t\tconst t = itemCopy.tvs\n\t\t\tif (_term && t.term) {\n\t\t\t\tif (!(_term.name == t.term.name && _term.type == t.term.type)) {\n\t\t\t\t\tnumberofmatchedterms++\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t}\n\t\t\tlet samplevalue\n\t\t\tif (_term && !t.term) {\n\t\t\t\tif (t.term$type && t.term$type !== _term.type) {\n\t\t\t\t\tnumberofmatchedterms++\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tt.term = _term\n\t\t\t\tsamplevalue =\n\t\t\t\t\ttypeof row === \"object\" && t.term.id in row ? row[t.term.id] : row\n\t\t\t} else if (sample && t.term.$id) {\n\t\t\t\tsamplevalue = sample[t.term.$id].value\n\t\t\t} else {\n\t\t\t\tsamplevalue = t.term.id in row ? row[t.term.id] : row\n\t\t\t}\n\t\t\tsetDatasetAnnotations(itemCopy)\n\t\t\tlet thistermmatch\n\t\t\tif (t.term.type == \"categorical\") {\n\t\t\t\tif (samplevalue === void 0) continue\n\t\t\t\tthistermmatch = t.valueset.has(samplevalue)\n\t\t\t} else if (t.term.type == \"integer\" || t.term.type == \"float\") {\n\t\t\t\tif (samplevalue === void 0) continue\n\t\t\t\tfor (const range of t.ranges) {\n\t\t\t\t\tif (\"value\" in range) {\n\t\t\t\t\t\tthistermmatch = samplevalue === range.value\n\t\t\t\t\t\tif (thistermmatch) break\n\t\t\t\t\t} else if (samplevalue == range.name) {\n\t\t\t\t\t\tthistermmatch = true\n\t\t\t\t\t\tbreak\n\t\t\t\t\t} else {\n\t\t\t\t\t\tif (t.term.values) {\n\t\t\t\t\t\t\tconst v = t.term.values[samplevalue.toString()]\n\t\t\t\t\t\t\tif (v && v.uncomputable) {\n\t\t\t\t\t\t\t\tcontinue\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tlet left, right\n\t\t\t\t\t\tif (range.startunbounded) {\n\t\t\t\t\t\t\tleft = true\n\t\t\t\t\t\t} else if (\"start\" in range) {\n\t\t\t\t\t\t\tif (range.startinclusive) {\n\t\t\t\t\t\t\t\tleft = samplevalue >= range.start\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tleft = samplevalue > range.start\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (range.stopunbounded) {\n\t\t\t\t\t\t\tright = true\n\t\t\t\t\t\t} else if (\"stop\" in range) {\n\t\t\t\t\t\t\tif (range.stopinclusive) {\n\t\t\t\t\t\t\t\tright = samplevalue <= range.stop\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tright = samplevalue < range.stop\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tthistermmatch = left && right\n\t\t\t\t\t}\n\t\t\t\t\tif (thistermmatch) break\n\t\t\t\t}\n\t\t\t} else if (t.term.type == \"condition\") {\n\t\t\t\tconst key = getPrecomputedKey(t)\n\t\t\t\tconst anno = samplevalue && samplevalue[key]\n\t\t\t\tif (anno) {\n\t\t\t\t\tthistermmatch = Array.isArray(anno)\n\t\t\t\t\t\t? t.values.find((d) => anno.includes(d.key))\n\t\t\t\t\t\t: t.values.find((d) => d.key == anno)\n\t\t\t\t}\n\t\t\t} else if (t.term.type == \"geneVariant\") {\n\t\t\t\tconst svalues = samplevalue.values || [samplevalue]\n\t\t\t\tfor (const sv of svalues) {\n\t\t\t\t\tthistermmatch =\n\t\t\t\t\t\tt.values.find(\n\t\t\t\t\t\t\t(v) =>\n\t\t\t\t\t\t\t\tv.dt == sv.dt &&\n\t\t\t\t\t\t\t\t(!v.origin || sv.origin == v.origin) &&\n\t\t\t\t\t\t\t\t(!v.mclasslst || v.mclasslst.includes(sv.class))\n\t\t\t\t\t\t) && true\n\t\t\t\t\tif (thistermmatch) break\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tthrow \"unknown term type [sample_match_termvaluesetting() shared/utils/src/filter.ts]\"\n\t\t\t}\n\t\t\tif (t.isnot) {\n\t\t\t\tthistermmatch = !thistermmatch\n\t\t\t}\n\t\t\tif (thistermmatch) numberofmatchedterms++\n\t\t}\n\t\tif (filter.join == \"or\") {\n\t\t\tif (numberofmatchedterms && filter.in) return true\n\t\t\tif (!numberofmatchedterms && !filter.in) return true\n\t\t}\n\t}\n\tif (!(\"in\" in filter)) filter.in = true\n\treturn filter.in == (numberofmatchedterms == lst.length)\n}\nfunction setDatasetAnnotations(item, ds = null) {\n\tif (item.type == \"tvslst\") {\n\t\tfor (const subitem of item.lst) {\n\t\t\tsetDatasetAnnotations(subitem, ds)\n\t\t}\n\t} else {\n\t\tif (ds && typeof ds.setAnnoByTermId == \"function\") {\n\t\t\tds.setAnnoByTermId(item.tvs.term.id)\n\t\t}\n\t\tif (item.tvs.term.type == \"categorical\") {\n\t\t\tconst tvsAny = item.tvs\n\t\t\ttvsAny.valueset = new Set(tvsAny.values.map((i) => i.key))\n\t\t}\n\t}\n}\nfunction getPrecomputedKey(q) {\n\tconst precomputedKey =\n\t\tq.bar_by_children && q.value_by_max_grade\n\t\t\t? \"childrenAtMaxGrade\"\n\t\t\t: q.bar_by_children && q.value_by_most_recent\n\t\t\t? \"childrenAtMostRecent\"\n\t\t\t: q.bar_by_children && q.value_by_computable_grade\n\t\t\t? \"children\"\n\t\t\t: q.bar_by_grade && q.value_by_max_grade\n\t\t\t? \"maxGrade\"\n\t\t\t: q.bar_by_grade && q.value_by_most_recent\n\t\t\t? \"mostRecentGrades\"\n\t\t\t: q.bar_by_grade && q.value_by_computable_grade\n\t\t\t? \"computableGrades\"\n\t\t\t: \"\"\n\tif (!precomputedKey) throw `unknown condition term bar_by_* and/or value_by_*`\n\treturn precomputedKey\n}\nfunction filterJoin(lst) {\n\tif (!lst || lst.length == 0) return\n\tlet f = JSON.parse(JSON.stringify(lst[0]))\n\tif (lst.length == 1) return f\n\tif (f.lst.length < 2) {\n\t\tif (f.join !== \"\")\n\t\t\tthrow 'filter.join must be an empty string \"\" when filter.lst.length < 2'\n\t\tf.join = \"and\"\n\t} else if (f.join == \"or\") {\n\t\tf = {\n\t\t\ttype: \"tvslst\",\n\t\t\tjoin: \"and\",\n\t\t\tin: true,\n\t\t\tlst: [f],\n\t\t}\n\t} else if (f.join != \"and\") {\n\t\tthrow 'filter.join must be either \"and\" or \"or\" when .lst length > 1'\n\t}\n\tfor (let i = 1; i < lst.length; i++) {\n\t\tconst f2 = JSON.parse(JSON.stringify(lst[i]))\n\t\tif (f2.join == \"or\") f.lst.push(f2)\n\t\telse f.lst.push(...f2.lst)\n\t}\n\tif (f.lst.length == 1 && f.lst[0].type == \"tvs\") {\n\t\tf.join = \"\"\n\t}\n\treturn f\n}\nfunction getWrappedTvslst(lst = [], join = \"\", $id = null) {\n\tconst filter = {\n\t\ttype: \"tvslst\",\n\t\tin: true,\n\t\tjoin,\n\t\tlst,\n\t}\n\tif ($id !== null) filter.$id = $id\n\treturn filter\n}\nfunction validateTermCollectionTvs(lst1, lst2) {\n\tif (!Array.isArray(lst1)) throw new Error(\"numerator not array\")\n\tif (!Array.isArray(lst2)) throw new Error(\"denominator not array\")\n\tif (lst1.length == 0) throw new Error(\"numerator empty\")\n\tif (lst2.length == 0) throw new Error(\"denominator empty\")\n\tif (lst1.length > lst2.length)\n\t\tthrow new Error(\"numerator longer than denominator\")\n\tfor (const s of lst1) {\n\t\tif (typeof s != \"string\") throw new Error(\"one of numerator not string\")\n\t\tif (!s) throw new Error(\"empty string in numerator\")\n\t\tif (!lst2.includes(s))\n\t\t\tthrow new Error(\"one of numerator not in denominator\")\n\t}\n}\nexport {\n\tfilterJoin,\n\tgetFilteredSamples,\n\tgetWrappedTvslst,\n\tsample_match_termvaluesetting,\n\tsetDatasetAnnotations,\n\tvalidateTermCollectionTvs,\n}\n", "/*\nshared between client and server\n\nexported functions\n- bplen()\n- mclasstester()\n- basecompliment()\n\n\n*/\nimport { rgb } from \"d3-color\"\nimport * as d3scale from \"d3-scale\"\nimport * as d3 from \"d3\"\nimport { getWrappedTvslst } from \"./filter.js\"\n\n// moved from `#shared/terms` to here, so that this can be passed as\n// part of 'common' argument to exported dataset js function, at server runtime\n// 3/30/2026 - changed from literal object to a class with static properties\n// to make it easier for IDEs and tsc compiler to catch typos in consumer code\nexport class TermTypeGroups {\n\tstatic DICTIONARY_VARIABLES = \"Dictionary Variables\"\n\tstatic DNA_METHYLATION = \"DNA Methylation\"\n\tstatic GENE_DEPENDENCY = \"Gene Dependency\"\n\tstatic GENE_EXPRESSION = \"Gene Expression\"\n\tstatic ISOFORM_EXPRESSION = \"Isoform Expression\"\n\tstatic GSEA = \"GSEA\"\n\tstatic METABOLITE_INTENSITY = \"Metabolite Intensity\"\n\tstatic PROTEOME_ABUNDANCE = \"Whole Proteome Abundance\"\n\tstatic MUTATION_CNV_FUSION = \"Mutation/CNV/Fusion\"\n\tstatic MUTATION_SIGNATURE = \"Mutation Signature\"\n\tstatic PROTEIN_EXPRESSION = \"Protein Expression\"\n\tstatic SINGLECELL_CELLTYPE = \"Single-cell Cell Type\"\n\tstatic SINGLECELL_GENE_EXPRESSION = \"Single-cell Gene Expression\"\n\tstatic SNP = \"SNP Genotype\"\n\tstatic SNP_LIST = \"SNP List\"\n\tstatic SNP_LOCUS = \"SNP Locus\"\n\tstatic SPLICE_JUNCTION = \"Splice Junction\"\n\tstatic SSGSEA = \"Geneset Expression\"\n\tstatic TERM_COLLECTION = \"Term Collection\"\n\tstatic VARIANT_GENOTYPE = \"Variant Genotype\"\n}\n// freeze so that mutating any of the static properties above will throw at runtime\nObject.freeze(TermTypeGroups)\n\nexport const defaultcolor = rgb(\"#8AB1D4\").darker()\nexport const default_text_color = rgb(\"#aaa\").darker().darker()\n\nexport const exoncolor = \"#4F8053\"\nexport const plotColor = \"#ce768e\"\n\n// something that has something to do with coding gene reading frame\nexport const IN_frame = true\nexport const OUT_frame = false\n\n/********************************\n*        on dt usage            *\n*********************************\n- once a dt value is decided and used with actual dataset,\n  the value must not be altered, since dataset file may hardcode such value and reassigning to a new integer will break!\n- never test dt value by range e.g. if(dt>10), it breaks! only test equality!\n- in code import variable from here and DO NOT use literal values, to make code tractable\n*/\nexport const dtsnvindel = 1\nexport const dtfusionrna = 2\nexport const dtgeneexpression = 3\nexport const dtcnv = 4\nexport const dtsv = 5\nexport const dtitd = 6\nexport const dtdel = 7\nexport const dtnloss = 8\nexport const dtcloss = 9\nexport const dtloh = 10\nexport const dtmetaboliteintensity = 11\nexport const dtssgsea = 12\nexport const dtdnamethylation = 13\nexport const dtproteomeabundance = 14\n// add new dt value here. !!!DO NOT change value of existing dt!!!\n\nexport const dt2label = {\n\t[dtsnvindel]: \"SNV/indel\",\n\t[dtfusionrna]: \"Fusion RNA\",\n\t[dtcnv]: \"CNV\",\n\t[dtsv]: \"SV\",\n\t[dtitd]: \"ITD\",\n\t[dtdel]: \"Deletion\",\n\t[dtnloss]: \"N-loss\",\n\t[dtcloss]: \"C-loss\",\n\t[dtloh]: \"LOH\",\n\t[dtgeneexpression]: \"Gene Expression\",\n\t[dtmetaboliteintensity]: \"Metabolite Intensity\",\n\t[dtproteomeabundance]: \"Whole Proteome Abundance\",\n}\n\n// Maps dt types to UI labels and lesion types for GRIN2\n// All dt types use lesionTypes array for consistency\nexport const dt2lesion = {\n\t[dtsnvindel]: {\n\t\tuilabel: \"SNV/INDEL (Mutation)\",\n\t\tlesionTypes: [\n\t\t\t{ name: \"Mutation\", lesionType: \"mutation\", color: \"#44AA44\" },\n\t\t],\n\t},\n\t[dtcnv]: {\n\t\tuilabel: \"CNV (Copy Number Variation)\",\n\t\tlesionTypes: [\n\t\t\t{ name: \"Loss\", lesionType: \"loss\", color: \"#4444FF\" },\n\t\t\t{ name: \"Gain\", lesionType: \"gain\", color: \"#FF4444\" },\n\t\t],\n\t},\n\t[dtsv]: {\n\t\tuilabel: \"SV (Structural Variation)\",\n\t\tlesionTypes: [{ name: \"SV\", lesionType: \"sv\", color: \"#9932CC\" }],\n\t},\n\t[dtfusionrna]: {\n\t\tuilabel: \"Fusion (RNA Fusion)\",\n\t\tlesionTypes: [{ name: \"Fusion\", lesionType: \"fusion\", color: \"#FFA500\" }],\n\t},\n}\n\n// Maps GRIN2 option types to their corresponding dt values\nexport const optionToDt = {\n\tsnvindelOptions: dtsnvindel,\n\tcnvOptions: dtcnv,\n\tfusionOptions: dtfusionrna,\n\tsvOptions: dtsv,\n}\n\nexport const mclass = {\n\tM: {\n\t\tlabel: \"MISSENSE\",\n\t\tcolor: \"#3987CC\",\n\t\tdt: dtsnvindel,\n\t\tdesc: \"A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved\",\n\t\tkey: \"M\",\n\t},\n\tE: {\n\t\tlabel: \"EXON\",\n\t\tcolor: \"#bcbd22\",\n\t\tdt: dtsnvindel,\n\t\tdesc: \"A variant in the exon of a non-coding RNA.\",\n\t\tkey: \"E\",\n\t},\n\tF: {\n\t\tlabel: \"FRAMESHIFT\",\n\t\tcolor: \"rgb(200, 61, 61)\",\n\t\tdt: dtsnvindel,\n\t\tdesc: \"A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three\",\n\t\tkey: \"F\",\n\t},\n\tN: {\n\t\tlabel: \"NONSENSE\",\n\t\tcolor: \"#ff7f0e\",\n\t\tdt: dtsnvindel,\n\t\tdesc: \"A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript\",\n\t\tkey: \"N\",\n\t},\n\tS: {\n\t\tlabel: \"SILENT\",\n\t\tcolor: \"#2ca02c\",\n\t\tdt: dtsnvindel,\n\t\tdesc: \"A sequence variant where there is no resulting change to the encoded amino acid\",\n\t\tkey: \"S\",\n\t},\n\tD: {\n\t\tlabel: \"PROTEINDEL\",\n\t\tcolor: \"rgb(100, 100, 100)\",\n\t\tdt: dtsnvindel,\n\t\tdesc: \"An inframe non synonymous variant that deletes bases from the coding sequence\",\n\t\tkey: \"D\",\n\t},\n\tI: {\n\t\tlabel: \"PROTEININS\",\n\t\tcolor: \"#8c564b\",\n\t\tdt: dtsnvindel,\n\t\tdesc: \"An inframe non synonymous variant that inserts bases into in the coding sequence\",\n\t\tkey: \"I\",\n\t},\n\tProteinAltering: {\n\t\tlabel: \"PROTEINALTERING\",\n\t\tcolor: \"#5a0034\",\n\t\tdt: dtsnvindel,\n\t\tdesc: \"An inframe complex change to the coding sequence\",\n\t\tkey: \"ProteinAltering\",\n\t},\n\tP: {\n\t\tlabel: \"SPLICE_REGION\",\n\t\tcolor: \"#9467bd\",\n\t\tdt: dtsnvindel,\n\t\tdesc: \"A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron\",\n\t\tkey: \"P\",\n\t},\n\tL: {\n\t\tlabel: \"SPLICE\",\n\t\tcolor: \"#6633FF\",\n\t\tdt: dtsnvindel,\n\t\tdesc: \"A variant near an exon edge that may affect splicing functionality\",\n\t\tkey: \"L\",\n\t},\n\tIntron: {\n\t\tlabel: \"INTRON\",\n\t\tcolor: \"#656565\",\n\t\tdt: dtsnvindel,\n\t\tdesc: \"An intronic variant.\",\n\t\tkey: \"Intron\",\n\t},\n\n\tStopLost: {\n\t\tlabel: \"Stop lost\",\n\t\tcolor: \"#ff7f0e\",\n\t\tdt: dtsnvindel,\n\t\tdesc: \"A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript\",\n\t\tkey: \"StopLost\",\n\t},\n\tStartLost: {\n\t\tlabel: \"Start lost\",\n\t\tcolor: \"#ff7f0e\",\n\t\tdt: dtsnvindel,\n\t\tdesc: \"A codon variant that changes at least one base of the canonical start codon\",\n\t\tkey: \"StartLost\",\n\t},\n\n\t// quick fix!! for showing genes that are not tested in samples (e.g. gene panels) in the heatmap\n\tBlank: {\n\t\tlabel: \"Not tested\",\n\t\tcolor: \"#fff\",\n\t\tdt: dtsnvindel,\n\t\tdesc: \"This gene is not tested.\",\n\t\tkey: \"Blank\",\n\t},\n\n\tWT: {\n\t\tlabel: \"Wildtype\",\n\t\tcolor: \"#D3D3D3\",\n\t\tdt: dtsnvindel,\n\t\tdesc: \"Wildtype\",\n\t\tkey: \"WT\",\n\t},\n}\nexport const mclassitd = \"ITD\"\nmclass[mclassitd] = {\n\tlabel: \"ITD\",\n\tcolor: \"#ff70ff\",\n\tdt: dtitd,\n\tdesc: \"In-frame internal tandem duplication.\",\n\tkey: mclassitd,\n}\n\nexport const mclassdel = \"DEL\"\nmclass[mclassdel] = {\n\tlabel: \"DELETION, intragenic\",\n\tcolor: \"#858585\",\n\tdt: dtdel,\n\tdesc: \"Intragenic deletion.\",\n\tkey: mclassdel,\n}\n\nexport const mclassnloss = \"NLOSS\"\nmclass[mclassnloss] = {\n\tlabel: \"N-terminus loss\",\n\tcolor: \"#545454\",\n\tdt: dtnloss,\n\tdesc: \"N-terminus loss due to translocation\",\n\tkey: mclassnloss,\n}\n\nexport const mclasscloss = \"CLOSS\"\nmclass[mclasscloss] = {\n\tlabel: \"C-terminus loss\",\n\tcolor: \"#545454\",\n\tdt: dtcloss,\n\tdesc: \"C-terminus loss due to translocation\",\n\tkey: mclasscloss,\n}\n\nexport const mclassutr3 = \"Utr3\"\nmclass[mclassutr3] = {\n\tlabel: \"UTR_3\",\n\tcolor: \"#998199\",\n\tdt: dtsnvindel,\n\tdesc: \"A variant in the 3' untranslated region.\",\n\tkey: mclassutr3,\n}\n\nexport const mclassutr5 = \"Utr5\"\nmclass[mclassutr5] = {\n\tlabel: \"UTR_5\",\n\tcolor: \"#819981\",\n\tdt: dtsnvindel,\n\tdesc: \"A variant in the 5' untranslated region.\",\n\tkey: mclassutr5,\n}\n\nexport const mclassnonstandard = \"X\"\nmclass[mclassnonstandard] = {\n\tlabel: \"NONSTANDARD\",\n\tcolor: \"black\",\n\tdt: dtsnvindel,\n\tdesc: \"A mutation class that either does not match our notation, or is unspecified.\",\n\tkey: mclassnonstandard,\n}\n\nexport const mclassnoncoding = \"noncoding\"\nmclass[mclassnoncoding] = {\n\tlabel: \"NONCODING\",\n\tcolor: \"black\",\n\tdt: dtsnvindel,\n\tdesc: \"Noncoding mutation.\",\n\tkey: mclassnoncoding,\n}\n\n/*\nincludes full list of consequences from\nhttps://www.ensembl.org/info/genome/variation/prediction/predicted_data.html\neach entry is SO term with matching pp class\nentries that cannot be mapped to dtsnvindel classes are commented off\norder of entries is severity\n\n* since source of data! *\nfrom this array derives multiple types of lookup tables to perform mapping on both ways\n*/\nconst SOterms = [\n\t//transcript_ablation // not supported: 1) do not expect this in maf/vcf 2) should be represented as cnv deletion but not the legacy unused value \"dtdel\"; if needed can reenable\n\t[\"splice_acceptor_variant\", \"L\"],\n\t[\"splice_donor_variant\", \"L\"],\n\t[\"stop_gained\", \"N\"],\n\t[\"frameshift_variant\", \"F\"],\n\t[\"stop_lost\", \"StopLost\"],\n\t[\"start_lost\", \"StartLost\"],\n\t//transcript_amplification // not supported, should be represented by cnv instead\n\t[\"feature_elongation\", mclassnoncoding],\n\t[\"feature_truncation\", mclassnoncoding],\n\t[\"inframe_insertion\", \"I\"],\n\t[\"inframe_deletion\", \"D\"],\n\t[\"missense_variant\", \"M\"],\n\t[\"protein_altering_variant\", \"ProteinAltering\"],\n\t[\"splice_donor_5th_base_variant\", \"P\"],\n\t[\"splice_region_variant\", \"P\"],\n\t[\"splice_donor_region_variant\", \"P\"],\n\t[\"splice_polypyrimidine_tract_variant\", \"P\"],\n\t[\"incomplete_terminal_codon_variant\", \"N\"],\n\t[\"start_retained_variant\", \"S\"],\n\t[\"stop_retained_variant\", \"S\"],\n\t[\"synonymous_variant\", \"S\"],\n\t[\"coding_sequence_variant\", \"E\"],\n\t[\"mature_miRNA_variant\", \"E\"],\n\t[\"5_prime_UTR_variant\", mclassutr5],\n\t[\"3_prime_UTR_variant\", mclassutr3],\n\t[\"non_coding_transcript_exon_variant\", \"E\"],\n\t[\"intron_variant\", \"Intron\"],\n\t[\"NMD_transcript_variant\", \"F\"],\n\t[\"non_coding_transcript_variant\", \"E\"],\n\t[\"coding_transcript_variant\", \"E\"],\n\t[\"upstream_gene_variant\", mclassnoncoding],\n\t[\"downstream_gene_variant\", mclassnoncoding],\n\t[\"TFBS_ablation\", mclassnoncoding],\n\t[\"TFBS_amplification\", mclassnoncoding],\n\t[\"TF_binding_site_variant\", mclassnoncoding],\n\t[\"regulatory_region_ablation\", mclassnoncoding],\n\t[\"regulatory_region_amplification\", mclassnoncoding],\n\t[\"regulatory_region_variant\", mclassnoncoding],\n\t[\"intergenic_variant\", mclassnoncoding],\n\t[\"sequence_variant\", mclassnonstandard],\n]\n\n// maps a pp class to an array of consequences\n// k: pp class, v: array of consequences. case sensitive\nexport const class2SOterm = new Map()\nfor (const [csq, cls] of SOterms) {\n\tif (!class2SOterm.has(cls)) class2SOterm.set(cls, [])\n\tclass2SOterm.get(cls).push(csq)\n}\n\n// maps a consequence to a pp class. no severity info. use vepinfo() if needs severity\n// k: consequence, v: pp class. case sensitive.\nexport const SOterm2class = new Map()\nfor (const [csq, cls] of SOterms) {\n\tSOterm2class.set(csq, cls)\n}\n\n// outdated function to match with adhoc nonstandard notations, only used in legacy code utils/src/bulk.snv.js\n// DO NOT USE to map vep consequences\nexport function mclasstester(s) {\n\tswitch (s.toLowerCase()) {\n\t\tcase \"missense_mutation\":\n\t\t\treturn \"M\"\n\t\tcase \"nonsense_mutation\":\n\t\t\treturn \"N\"\n\t\tcase \"splice_site\":\n\t\t\treturn \"L\"\n\t\tcase \"splice_region\":\n\t\t\treturn \"P\"\n\t\tcase \"rna\":\n\t\t\treturn mclassnoncoding\n\t\tcase \"frame_shift_del\":\n\t\t\treturn \"F\"\n\t\tcase \"frame_shift_ins\":\n\t\t\treturn \"F\"\n\t\tcase \"in_frame_del\":\n\t\t\treturn \"D\"\n\t\tcase \"in_frame_ins\":\n\t\t\treturn \"I\"\n\t\tcase \"protein_altering_variant\":\n\t\t\treturn \"ProteinAltering\"\n\t\tcase \"translation_start_site\":\n\t\t\treturn mclassnonstandard\n\t\tcase \"nonstop_mutation\":\n\t\t\treturn \"N\"\n\t\tcase \"3'utr\":\n\t\t\treturn mclassutr3\n\t\tcase \"3'flank\":\n\t\t\treturn mclassnoncoding\n\t\tcase \"5'utr\":\n\t\t\treturn mclassutr5\n\t\tcase \"5'flank\":\n\t\t\treturn mclassnoncoding\n\t\tcase \"silent\":\n\t\t\treturn \"S\"\n\t\tcase \"blank\":\n\t\t\treturn \"Blank\"\n\t\tdefault:\n\t\t\treturn null\n\t}\n}\n\nexport const mclassfusionrna = \"Fuserna\"\nmclass[mclassfusionrna] = {\n\tlabel: \"Fusion transcript\",\n\tcolor: \"#545454\",\n\tdt: dtfusionrna,\n\tdesc:\n\t\t\"Marks the break points leading to fusion transcripts.<br>\" +\n\t\t\"<span style=\\\"font-size:150%\\\">&#9680;</span> - 3' end of the break point is fused to the 5' end of another break point in a different gene.<br>\" +\n\t\t\"<span style=\\\"font-size:150%\\\">&#9681;</span> - 5' end of the break point is fused to the 3' end of another break point in a different gene.\",\n\tkey: mclassfusionrna,\n}\nexport const mclasssv = \"SV\"\nmclass[mclasssv] = {\n\tlabel: \"Structural variation\",\n\tcolor: \"#858585\",\n\tdt: dtsv,\n\tdesc:\n\t\t\"<span style=\\\"font-size:150%\\\">&#9680;</span> - 3' end of the break point is fused to the 5' end of another break point in a different gene.<br>\" +\n\t\t\"<span style=\\\"font-size:150%\\\">&#9681;</span> - 5' end of the break point is fused to the 3' end of another break point in a different gene.\",\n\tkey: mclasssv,\n}\n\n// \"CNV_amp\" represents \"CNV Gain\" and is used in both 2-category and 5-category CNV data representation\n// \"CNV_amplification\" represents CNV amplification and is used in 5-category CNV\n// \"CNV_amp\" have to stay as-is since it may be hardcoded in lots of data beyond portal code.\nexport const mclasscnvgain = \"CNV_amp\"\nmclass[mclasscnvgain] = {\n\tlabel: \"Copy number gain\", // TODO change to 'Gain'\n\tcolor: \"#e9a3c9\",\n\tdt: dtcnv,\n\tdesc: \"Copy number gain\",\n\tkey: mclasscnvgain,\n}\n\nexport const mclasscnvloss = \"CNV_loss\"\nmclass[mclasscnvloss] = {\n\tlabel: \"Copy number loss\",\n\tcolor: \"#a1d76a\",\n\tdt: dtcnv,\n\tdesc: \"Copy number loss\",\n\tkey: mclasscnvloss,\n}\n\n// mclasscnvAmp is next level above mclasscnvgain and is used in 5-category CNV data\nexport const mclasscnvAmp = \"CNV_amplification\"\nmclass[mclasscnvAmp] = {\n\tlabel: \"Copy number amplification\",\n\tcolor: \"#ff0000\",\n\tdt: dtcnv,\n\tdesc: \"Copy number amplification\",\n\tkey: mclasscnvAmp,\n}\n\nexport const mclasscnvHomozygousDel = \"CNV_homozygous_deletion\"\nmclass[mclasscnvHomozygousDel] = {\n\tlabel: \"Copy number homozygous deletion\",\n\tcolor: \"#0000ff\",\n\tdt: dtcnv,\n\tdesc: \"Copy number homozygous deletion\",\n\tkey: mclasscnvHomozygousDel,\n}\n\nexport const mclasscnvloh = \"CNV_loh\"\nmclass[mclasscnvloh] = {\n\tlabel: \"LOH\",\n\tcolor: \"#12EDFC\",\n\tdt: dtcnv,\n\tdesc: \"Loss of heterozygosity\",\n\tkey: mclasscnvloh,\n}\n\n// for VCF\nexport const mclasssnv = \"snv\"\nmclass[mclasssnv] = {\n\tlabel: \"SNV\",\n\tcolor: \"#92a2d4\",\n\tdt: dtsnvindel,\n\tdesc: \"Single nucleotide variation\",\n\tkey: mclasssnv,\n}\n\nexport const mclassmnv = \"mnv\"\nmclass[mclassmnv] = {\n\tlabel: \"MNV\",\n\tcolor: \"#92a2d4\",\n\tdt: dtsnvindel,\n\tdesc: \"Multiple nucleotide variation\",\n\tkey: mclassmnv,\n}\n\nexport const mclassinsertion = \"insertion\"\nmclass[mclassinsertion] = {\n\tlabel: \"Sequence insertion\",\n\tcolor: \"#bd8e91\",\n\tdt: dtsnvindel,\n\tdesc: \"Sequence insertion\",\n\tkey: mclassinsertion,\n}\n\nexport const mclassdeletion = \"deletion\"\nmclass[mclassdeletion] = {\n\tlabel: \"Sequence deletion\",\n\tcolor: \"#b5a174\",\n\tdt: dtsnvindel,\n\tdesc: \"Sequence deletion\",\n\tkey: mclassdeletion,\n}\n// TODO complex indel\n\n/* tricky\nwhen a mds3 tk uses numeric cnv, data points from tk.cnv.cnvLst[] has .class=dtcnv but no class!\na \"cnv\" entry needs to be present in mclass legend, and thus this wrapper function over mclass{} to allow dtcnv as key\nthe tricky case doesn't apply to other plots\n*/\nexport function mds3tkMclass(k) {\n\tif (k == dtcnv) {\n\t\treturn {\n\t\t\tcolor: \"#858585\",\n\t\t\tlabel: \"CNV\",\n\t\t\tdesc: \"Copy number variation\",\n\t\t}\n\t}\n\treturn mclass[k]\n}\n\nexport const dt2color = {\n\t[dtsnvindel]: mclass.M.color, // general color for snvindel irrespective of class (when class is not available)\n\t// add new dt as needed\n}\n\n// option to override mutation class attribute values\nexport function applyOverrides(overrides = {}) {\n\tif (overrides.mclass) {\n\t\tfor (const key in overrides.mclass) {\n\t\t\t// allow to fill-in mutation class that are missing from mclass;\n\t\t\t// may be useful for things like 'Not tested', etc, that may not be in mclass by default\n\t\t\t// but are used by a customer with its own PP server instance\n\t\t\tif (!mclass[key]) mclass[key] = {}\n\t\t\tfor (const subkey in overrides.mclass[key]) {\n\t\t\t\tmclass[key][subkey] = overrides.mclass[key][subkey]\n\t\t\t}\n\t\t}\n\t}\n}\n\n/* legacy function. input is comma-joined multiple consequences\nperforms case insensitive match and returns severity rank\nTODO share data with SOterms\n*/\nexport const vepinfo = function (s) {\n\tconst l = s.toLowerCase().split(\",\")\n\tlet rank = 1\n\tif (l.indexOf(\"transcript_ablation\") != -1) {\n\t\t// FIXME no class for whole gene deletion\n\t\treturn [dtdel, mclassdel, rank]\n\t}\n\trank++\n\tif (l.indexOf(\"splice_acceptor_variant\") != -1) return [dtsnvindel, \"L\", rank]\n\trank++\n\tif (l.indexOf(\"splice_donor_variant\") != -1) return [dtsnvindel, \"L\", rank]\n\trank++\n\tif (l.indexOf(\"stop_gained\") != -1) return [dtsnvindel, \"N\", rank]\n\trank++\n\tif (l.indexOf(\"frameshift_variant\") != -1) return [dtsnvindel, \"F\", rank]\n\trank++\n\tif (l.indexOf(\"stop_lost\") != -1) return [dtsnvindel, \"N\", rank]\n\trank++\n\tif (l.indexOf(\"start_lost\") != -1) return [dtsnvindel, \"N\", rank]\n\trank++\n\tif (l.indexOf(\"transcript_amplification\") != -1) {\n\t\t// FIXME no class for whole gene amp\n\t\treturn [dtsnvindel, mclassnonstandard, rank]\n\t}\n\trank++\n\tif (\n\t\tl.indexOf(\"inframe_insertion\") != -1 ||\n\t\tl.indexOf(\"conservative_inframe_insertion\") != -1 ||\n\t\tl.indexOf(\"disruptive_inframe_insertion\") != -1\n\t)\n\t\treturn [dtsnvindel, \"I\", rank]\n\trank++\n\tif (\n\t\tl.indexOf(\"inframe_deletion\") != -1 ||\n\t\tl.indexOf(\"conservative_inframe_deletion\") != -1 ||\n\t\tl.indexOf(\"disruptive_inframe_deletion\") != -1\n\t)\n\t\treturn [dtsnvindel, \"D\", rank]\n\trank++\n\tif (l.indexOf(\"missense_variant\") != -1) return [dtsnvindel, \"M\", rank]\n\trank++\n\tif (l.indexOf(\"protein_altering_variant\") != -1)\n\t\treturn [dtsnvindel, \"ProteinAltering\", rank]\n\trank++\n\tif (l.indexOf(\"splice_region_variant\") != -1) return [dtsnvindel, \"P\", rank]\n\trank++\n\tif (l.indexOf(\"incomplete_terminal_codon_variant\") != -1)\n\t\treturn [dtsnvindel, \"N\", rank]\n\trank++\n\tif (l.indexOf(\"stop_retained_variant\") != -1) return [dtsnvindel, \"S\", rank]\n\trank++\n\tif (l.indexOf(\"synonymous_variant\") != -1) return [dtsnvindel, \"S\", rank]\n\trank++\n\tif (l.indexOf(\"coding_sequence_variant\") != -1)\n\t\treturn [dtsnvindel, mclassnonstandard, rank]\n\trank++\n\tif (l.indexOf(\"mature_mirna_variant\") != -1) return [dtsnvindel, \"E\", rank]\n\trank++\n\tif (l.indexOf(\"5_prime_utr_variant\") != -1)\n\t\treturn [dtsnvindel, mclassutr5, rank]\n\trank++\n\tif (l.indexOf(\"3_prime_utr_variant\") != -1)\n\t\treturn [dtsnvindel, mclassutr3, rank]\n\trank++\n\tif (l.indexOf(\"non_coding_transcript_exon_variant\") != -1)\n\t\treturn [dtsnvindel, \"E\", rank]\n\trank++\n\tif (l.indexOf(\"intron_variant\") != -1) return [dtsnvindel, \"Intron\", rank]\n\trank++\n\tif (l.indexOf(\"nmd_transcript_variant\") != -1) return [dtsnvindel, \"S\", rank]\n\trank++\n\tif (l.indexOf(\"non_coding_transcript_variant\") != -1)\n\t\treturn [dtsnvindel, \"E\", rank]\n\trank++\n\tif (l.indexOf(\"upstream_gene_variant\") != -1)\n\t\treturn [dtsnvindel, mclassnoncoding, rank]\n\trank++\n\tif (l.indexOf(\"downstream_gene_variant\") != -1)\n\t\treturn [dtsnvindel, mclassnoncoding, rank]\n\trank++\n\tif (l.indexOf(\"tfbs_ablation\") != -1)\n\t\treturn [dtsnvindel, mclassnoncoding, rank]\n\trank++\n\tif (l.indexOf(\"tfbs_amplification\") != -1)\n\t\treturn [dtsnvindel, mclassnoncoding, rank]\n\trank++\n\tif (l.indexOf(\"tf_binding_site_variant\") != -1)\n\t\treturn [dtsnvindel, mclassnoncoding, rank]\n\trank++\n\tif (l.indexOf(\"regulatory_region_ablation\") != -1)\n\t\treturn [dtsnvindel, mclassnoncoding, rank]\n\trank++\n\tif (l.indexOf(\"regulatory_region_amplification\") != -1)\n\t\treturn [dtsnvindel, mclassnoncoding, rank]\n\trank++\n\tif (l.indexOf(\"feature_elongation\") != -1)\n\t\treturn [dtsnvindel, mclassnoncoding, rank]\n\trank++\n\tif (l.indexOf(\"regulatory_region_variant\") != -1)\n\t\treturn [dtsnvindel, mclassnoncoding, rank]\n\trank++\n\tif (l.indexOf(\"feature_truncation\") != -1)\n\t\treturn [dtsnvindel, mclassnoncoding, rank]\n\trank++\n\tif (l.indexOf(\"intergenic_variant\") != -1)\n\t\treturn [dtsnvindel, mclassnoncoding, rank]\n\trank++\n\treturn [dtsnvindel, mclassnonstandard, rank]\n}\n\n// m orgin\nexport const germlinelegend =\n\t'<circle cx=\"7\" cy=\"12\" r=\"7\" fill=\"#b1b1b1\"></circle><path d=\"M6.735557395310443e-16,-11A11,11 0 0,1 11,0L9,0A9,9 0 0,0 5.51091059616309e-16,-9Z\" transform=\"translate(7,12)\" fill=\"#858585\" stroke=\"none\"></path>'\n\nexport const morigin = {}\n\nexport const moriginsomatic = \"S\"\nmorigin[moriginsomatic] = {\n\tlabel: \"Somatic\",\n\tdesc: \"A variant found only in a tumor sample. The proportion is indicated by lack of any arc.\",\n\tlegend: '<circle cx=\"7\" cy=\"12\" r=\"7\" fill=\"#b1b1b1\"></circle>',\n}\nexport const morigingermline = \"G\"\nmorigin[morigingermline] = {\n\tlabel: \"Germline\",\n\tdesc: \"A constitutional variant found in a normal sample. The proportion is indicated by the span of the solid arc within the whole circle.\",\n\tlegend: germlinelegend,\n}\n\nmorigin.germline = morigin[morigingermline]\nmorigin.somatic = morigin[moriginsomatic]\n\nexport const moriginrelapse = \"R\"\nmorigin[moriginrelapse] = {\n\tlabel: \"Relapse\",\n\tdesc: \"A somatic variant found only in a relapse sample. The proportion is indicated by the span of the hollow arc within the whole circle.\",\n\tlegend:\n\t\t'<circle cx=\"7\" cy=\"12\" r=\"7\" fill=\"#b1b1b1\"></circle><path d=\"M6.735557395310443e-16,-11A11,11 0 0,1 11,0L9,0A9,9 0 0,0 5.51091059616309e-16,-9Z\" transform=\"translate(7,12)\" fill=\"none\" stroke=\"#858585\"></path>',\n}\nexport const morigingermlinepathogenic = \"GP\"\nmorigin[morigingermlinepathogenic] = {\n\tlabel: \"Germline pathogenic\",\n\tdesc: \"A constitutional variant with pathogenic allele.\",\n\tlegend: germlinelegend,\n}\nexport const morigingermlinenonpathogenic = \"GNP\"\nmorigin[morigingermlinenonpathogenic] = {\n\tlabel: \"Germline non-pathogenic\",\n\tdesc: \"A constitutional variant with non-pathogenic allele.\",\n\tlegend: germlinelegend,\n\thidden: true,\n}\n\nexport const tkt = {\n\tusegm: \"usegm\",\n\tds: \"dataset\",\n\tbigwig: \"bigwig\",\n\tbigwigstranded: \"bigwigstranded\",\n\tjunction: \"junction\",\n\tmdsjunction: \"mdsjunction\",\n\tmdssvcnv: \"mdssvcnv\", // replaced by mds3\n\tmdsexpressionrank: \"mdsexpressionrank\",\n\tmdsvcf: \"mdsvcf\", // for snv/indels, currently vcf, may include MAF\n\t//mdsgeneral:'mdsgeneral', // replaces mdssvcnv   ****** not ready yet\n\tbedj: \"bedj\",\n\tpgv: \"profilegenevalue\",\n\tbampile: \"bampile\",\n\thicstraw: \"hicstraw\",\n\texpressionrank: \"expressionrank\",\n\taicheck: \"aicheck\",\n\tase: \"ase\",\n\tmds3: \"mds3\", //\n\tbedgraphdot: \"bedgraphdot\",\n\tbam: \"bam\",\n\tld: \"ld\",\n}\n\nexport function validtkt(what) {\n\tfor (const k in tkt) {\n\t\tif (what == tkt[k]) {\n\t\t\treturn true\n\t\t}\n\t}\n\treturn false\n}\n\n/*\nmember track types from mdsvcf\nto get rid of hardcoded strings\nin future may include MAF format files\n*/\nexport const mdsvcftype = {\n\tvcf: \"vcf\",\n}\n\n/*\nfor custom mdssvcnv track\nor general track\nto avoid using hard-coded string\n*/\nexport const custommdstktype = {\n\tvcf: \"vcf\",\n\tsvcnvitd: \"svcnvitd\",\n\tgeneexpression: \"geneexpression\",\n}\n\n// codons that are not here are stop codon!!\nexport const codon = {\n\tGCT: \"A\",\n\tGCC: \"A\",\n\tGCA: \"A\",\n\tGCG: \"A\",\n\tCGT: \"R\",\n\tCGC: \"R\",\n\tCGA: \"R\",\n\tCGG: \"R\",\n\tAGA: \"R\",\n\tAGG: \"R\",\n\tAAT: \"N\",\n\tAAC: \"N\",\n\tGAT: \"D\",\n\tGAC: \"D\",\n\tTGT: \"C\",\n\tTGC: \"C\",\n\tCAA: \"Q\",\n\tCAG: \"Q\",\n\tGAA: \"E\",\n\tGAG: \"E\",\n\tGGT: \"G\",\n\tGGC: \"G\",\n\tGGA: \"G\",\n\tGGG: \"G\",\n\tCAT: \"H\",\n\tCAC: \"H\",\n\tATT: \"I\",\n\tATC: \"I\",\n\tATA: \"I\",\n\tTTA: \"L\",\n\tTTG: \"L\",\n\tCTT: \"L\",\n\tCTC: \"L\",\n\tCTA: \"L\",\n\tCTG: \"L\",\n\tAAA: \"K\",\n\tAAG: \"K\",\n\tATG: \"M\",\n\tTTT: \"F\",\n\tTTC: \"F\",\n\tCCT: \"P\",\n\tCCC: \"P\",\n\tCCA: \"P\",\n\tCCG: \"P\",\n\tTCT: \"S\",\n\tTCC: \"S\",\n\tTCA: \"S\",\n\tTCG: \"S\",\n\tAGT: \"S\",\n\tAGC: \"S\",\n\tACT: \"T\",\n\tACC: \"T\",\n\tACA: \"T\",\n\tACG: \"T\",\n\tTGG: \"W\",\n\tTAT: \"Y\",\n\tTAC: \"Y\",\n\tGTT: \"V\",\n\tGTC: \"V\",\n\tGTA: \"V\",\n\tGTG: \"V\",\n}\n\nexport const codon_stop = \"*\"\n\nexport function nt2aa(gm) {\n\t// must convert genome seq to upper case!!!\n\tif (!gm.genomicseq) return undefined\n\tconst enlst = []\n\tif (gm.coding) {\n\t\tfor (const [i, e] of gm.coding.entries()) {\n\t\t\tconst s = gm.genomicseq.substr(e[0] - gm.start, e[1] - e[0])\n\t\t\tif (gm.strand == \"-\") {\n\t\t\t\tenlst.push(reversecompliment(s))\n\t\t\t} else {\n\t\t\t\tenlst.push(s)\n\t\t\t}\n\t\t}\n\t}\n\tconst nt = enlst.join(\"\")\n\tconst pep = []\n\n\t/*\n\tif startCodonFrame is set, will not begin translation from first nt, but will skip 1 or 2 nt at the beginning\n\tin case of IGKC, frame=1 means it will borrow 1 nt from the previous IGKJ exons\n\tso the first two nucleotides from the current exon will have to be skipped when translating IGKC alone\n\t*/\n\tconst startntidx = gm.startCodonFrame ? 3 - gm.startCodonFrame : 0\n\tfor (let i = startntidx; i < nt.length; i += 3) {\n\t\tconst a = codon[nt.substr(i, 3)]\n\t\tpep.push(a || codon_stop)\n\t}\n\tgm.cdseq = nt\n\treturn pep.join(\"\")\n}\n\nexport function bplen(len, isfile) {\n\t// if \"isfile\" is true, to measure file size instead of basepair len\n\tif (len >= 1000000000) return (len / 1000000000).toFixed(1) + \" Gb\"\n\tif (len >= 10000000) return Math.ceil(len / 1000000) + \" Mb\"\n\tif (len >= 1000000) return (len / 1000000).toFixed(1) + \" Mb\"\n\tif (len >= 10000) return Math.ceil(len / 1000) + \" Kb\"\n\tif (len >= 1000) return (len / 1000).toFixed(1) + \" Kb\"\n\treturn len + (isfile ? \"bytes\" : \" bp\")\n}\n\nexport const basecolor = {\n\tA: \"#ca0020\",\n\tT: \"#f4a582\",\n\tC: \"#92c5de\",\n\tG: \"#0571b0\",\n}\n\nexport function basecompliment(nt) {\n\tswitch (nt) {\n\t\tcase \"A\":\n\t\t\treturn \"T\"\n\t\tcase \"T\":\n\t\t\treturn \"A\"\n\t\tcase \"C\":\n\t\t\treturn \"G\"\n\t\tcase \"G\":\n\t\t\treturn \"C\"\n\t\tcase \"a\":\n\t\t\treturn \"t\"\n\t\tcase \"t\":\n\t\t\treturn \"a\"\n\t\tcase \"c\":\n\t\t\treturn \"g\"\n\t\tcase \"g\":\n\t\t\treturn \"c\"\n\t\tdefault:\n\t\t\treturn nt\n\t}\n}\n\nexport function reversecompliment(s) {\n\tconst tmp = []\n\tfor (let i = s.length - 1; i >= 0; i--) {\n\t\ttmp.push(basecompliment(s[i]))\n\t}\n\treturn tmp.join(\"\")\n}\n\nexport function spliceeventchangegmexon(gm, evt) {\n\t/*\n\talter gm.coding[], by exon-skip/alt events\n\tfor frame checking\n\tgm must have coding\n\t*/\n\tconst gm2 = {\n\t\tchr: gm.chr,\n\t\tstart: gm.start,\n\t\tstop: gm.stop,\n\t\tstrand: gm.strand,\n\t\tcoding: [],\n\t}\n\tif (evt.isskipexon || evt.isaltexon) {\n\t\tfor (let i = 0; i < gm.exon.length; i++) {\n\t\t\tconst codingstart = Math.max(gm.codingstart, gm.exon[i][0])\n\t\t\tconst codingstop = Math.min(gm.codingstop, gm.exon[i][1])\n\t\t\tif (codingstart > codingstop) {\n\t\t\t\t// not coding exon\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tif (evt.skippedexon.indexOf(i) == -1) {\n\t\t\t\t// not skipped\n\t\t\t\tgm2.coding.push([codingstart, codingstop])\n\t\t\t} else {\n\t\t\t\t// skipped\n\t\t\t}\n\t\t}\n\t} else if (evt.a5ss || evt.a3ss) {\n\t\t// still equal number of exons\n\t\t// adjust the affected exon first, then figure out coding[]\n\t\tconst exons = gm.exon.map((e) => [e[0], e[1]])\n\t\tconst forward = gm.strand == \"+\"\n\t\tif (evt.a5ss) {\n\t\t\tif (forward) {\n\t\t\t\texons[evt.exon5idx][1] = evt.junctionB.start\n\t\t\t} else {\n\t\t\t\texons[evt.exon5idx + 1][0] = evt.junctionB.stop\n\t\t\t}\n\t\t} else {\n\t\t\tif (forward) {\n\t\t\t\texons[evt.exon5idx + 1][0] = evt.junctionB.stop\n\t\t\t} else {\n\t\t\t\texons[evt.exon5idx][1] = evt.junctionB.start\n\t\t\t}\n\t\t}\n\t\t// from new exons, figure out coding exons\n\t\tfor (const e of exons) {\n\t\t\tconst codingstart = Math.max(gm.codingstart, e[0])\n\t\t\tconst codingstop = Math.min(gm.codingstop, e[1])\n\t\t\tif (codingstart > codingstop) {\n\t\t\t\t// not coding exon\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tgm2.coding.push([codingstart, codingstop])\n\t\t}\n\t}\n\treturn gm2\n}\n\nexport function fasta2gmframecheck(gm, str) {\n\t/*\n\tgm{}\n\t\t.chr\n\t\t.start\n\t\t.stop\n\t\t\tstart/stop is transcript position\n\t\t.strand\n\t\t.coding[]\n\tstr\n\t\tsamtools faidx output\n\t*/\n\tconst lines = str.split(\"\\n\")\n\t// remove fasta header\n\tlines.shift()\n\tgm.genomicseq = lines.join(\"\").toUpperCase()\n\n\tconst aaseq = nt2aa(gm)\n\n\tlet thisframe = OUT_frame\n\tconst stopcodonidx = aaseq.indexOf(codon_stop)\n\tif (stopcodonidx == aaseq.length - 1) {\n\t\t// the first appearance of stop codon is at the last of translation\n\t\tthisframe = IN_frame\n\t}\n\treturn thisframe\n}\n\nexport function validate_vcfinfofilter(obj) {\n\t/*\n\tvalidate vcfinfofilter as from embedding api or dataset\n\t*/\n\n\tif (!obj.lst) return \".lst missing\"\n\n\tif (!Array.isArray(obj.lst)) return \"input is not an array\"\n\n\tfor (const set of obj.lst) {\n\t\tif (!set.name) return \"name missing from a set of .vcfinfofilter.lst\"\n\n\t\tif (set.autocategory || set.categories) {\n\t\t\t// categorical info, auto or defined\n\n\t\t\tif (!set.autocategory) {\n\t\t\t\tfor (const k in set.categories) {\n\t\t\t\t\tconst v = set.categories[k]\n\t\t\t\t\tif (!set.autocolor && !v.color)\n\t\t\t\t\t\treturn (\n\t\t\t\t\t\t\t\".color missing for class \" +\n\t\t\t\t\t\t\tk +\n\t\t\t\t\t\t\t\" from .categories of set \" +\n\t\t\t\t\t\t\tset.name\n\t\t\t\t\t\t)\n\t\t\t\t\tif (!v.label) {\n\t\t\t\t\t\tv.label = k\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tif (set.categoryhidden) {\n\t\t\t\tfor (const k in set.categoryhidden) {\n\t\t\t\t\tif (!set.categories[k])\n\t\t\t\t\t\treturn (\n\t\t\t\t\t\t\t\"unknown hidden-by-default category \" +\n\t\t\t\t\t\t\tk +\n\t\t\t\t\t\t\t\" from set \" +\n\t\t\t\t\t\t\tset.name\n\t\t\t\t\t\t)\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tset.categoryhidden = {}\n\t\t\t}\n\t\t} else if (set.numericfilter) {\n\t\t\t// otherwise, numerical value, the style of population frequency filter\n\t\t\tconst lst = []\n\t\t\tfor (const v of set.numericfilter) {\n\t\t\t\tif (typeof v == \"number\") {\n\t\t\t\t\t/*\n\t\t\t\t\tjust a number, defaults to 'lower-than'\n\t\t\t\t\t*/\n\t\t\t\t\tlst.push({ side: \"<\", value: v })\n\t\t\t\t} else {\n\t\t\t\t\tlst.push({\n\t\t\t\t\t\tside: v.side || \"<\",\n\t\t\t\t\t\tvalue: v.value,\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t}\n\t\t\tset.numericfilter = lst\n\n\t\t\t//return 'no .categories or .numericfilter from set '+set.name\n\t\t}\n\n\t\tif (set.altalleleinfo) {\n\t\t\tif (!set.altalleleinfo.key) {\n\t\t\t\treturn \".key missing from .altalleleinfo from set \" + set.name\n\t\t\t}\n\t\t} else if (set.locusinfo) {\n\t\t\tif (!set.locusinfo.key) {\n\t\t\t\treturn \".key missing from .locusinfo from set \" + set.name\n\t\t\t}\n\t\t} else {\n\t\t\treturn (\n\t\t\t\t\"neither .altalleleinfo or .locusinfo is available from set \" + set.name\n\t\t\t)\n\t\t}\n\t}\n}\n\nexport function contigNameNoChr(genome, chrlst) {\n\t/*\n\tFIXME hard-coded for human genome styled chromosome names\n\t*/\n\tfor (const n in genome.majorchr) {\n\t\tif (chrlst.indexOf(n.replace(\"chr\", \"\")) != -1) {\n\t\t\treturn true\n\t\t}\n\t}\n\tif (genome.minorchr) {\n\t\tfor (const n in genome.minorchr) {\n\t\t\tif (chrlst.indexOf(n.replace(\"chr\", \"\")) != -1) {\n\t\t\t\treturn true\n\t\t\t}\n\t\t}\n\t}\n\treturn false\n}\nexport function contigNameNoChr2(genome, chrlst) {\n\t// returns number of matching chr names that either includes \"chr\" or not\n\t// for detecting if chrlst entirely mismatch with what's in the genome build\n\t// TODO replace contigNameNoChr\n\tlet nochrcount = 0,\n\t\thaschrcount = 0\n\tfor (const n in genome.majorchr) {\n\t\tif (chrlst.includes(n)) {\n\t\t\thaschrcount++\n\t\t} else if (chrlst.includes(n.replace(\"chr\", \"\"))) {\n\t\t\tnochrcount++\n\t\t}\n\t}\n\tif (genome.minorchr) {\n\t\tfor (const n in genome.minorchr) {\n\t\t\tif (chrlst.includes(n)) {\n\t\t\t\thaschrcount++\n\t\t\t} else if (chrlst.includes(n.replace(\"chr\", \"\"))) {\n\t\t\t\tnochrcount++\n\t\t\t}\n\t\t}\n\t}\n\treturn [nochrcount, haschrcount]\n}\n\nexport function getMax_byiqr(lst, novaluemax) {\n\t/*\n\tlst: array of numbers\n\tnovaluemax: when lst is empty, return this value\n\tcutoff value based on IQR to exclude outlier values\n\t*/\n\tif (lst.length == 0) return novaluemax\n\tlst.sort((i, j) => i - j)\n\tconst max = lst[lst.length - 1]\n\tif (lst.length <= 5) return max\n\tconst q1 = lst[Math.floor(lst.length / 4)]\n\tconst q2 = lst[Math.floor((lst.length * 3) / 4)]\n\treturn Math.min(q2 + (q2 - q1) * 1.5, max)\n}\n\nexport function alleleInGenotypeStr(genotype, allele) {\n\tif (!genotype) return false\n\tif (genotype.indexOf(\"/\") != -1) {\n\t\treturn genotype.split(\"/\").indexOf(allele) != -1\n\t}\n\treturn genotype.split(\"|\").indexOf(allele) != -1\n}\n\nexport const gmmode = {\n\tgenomic: \"genomic\",\n\tsplicingrna: \"splicing RNA\", // if just 1 exon, use \"RNA\" as label\n\texononly: \"exon only\",\n\tprotein: \"protein\",\n\tgmsum: \"aggregated exons\",\n}\n\n/*\ninput:\n\nm={}\n\tm.csq=[]\n\t\telement: {\n\t\t\tAllele: str,\n\t\t\tConsequence: str,\n\t\t\tCANONICAL: str, // true if _isoform is canonical\n\t\t\t...\n\t\t\t_isoform: str,\n\t\t\t_class: str,\n\t\t\t_csqrank: int\n\t\t}\n\tm.ann=[]\n\t\tannovar output. may be derelict\nblock={}\n\tblock.usegm={ isoform }\n\tcan be a mock object when running this function in node!\n\ndoes:\n\tfind an annotation from m.csq[] that's fitting the circumstance\n\t- current gm isoform displayed in block gene mode\n\t- any canonical isoform from m.csq[] (can be missing if vep is not instructed to do it)\n\t- one with highest _csqrank\n\tthen, copy its class/mname to m{}\n\thas many fall-back and always try to assign class/mname\n\nno return\n*/\nexport function vcfcopymclass(m, block) {\n\tif (m.csq) {\n\t\tlet useone // point to the element of m.csq[], from this class/mname is copied to m{}\n\n\t\tif (block.usegm) {\n\t\t\t// block is in gm mode, find a csq matching with the genemodel isoform\n\t\t\tuseone = m.csq.find((i) => i._isoform == block.usegm.isoform)\n\t\t}\n\n\t\tif (!useone) {\n\t\t\t// no match to usegm isoform; can be due to in genomic mode and zoomed out, where this variant is from a neighboring gene near block.usegm\n\t\t\t// find one using canonical isoform\n\t\t\tuseone = m.csq.find((i) => i.CANONICAL)\n\n\t\t\tif (!useone) {\n\t\t\t\t// none of the elements in m.csq[] is using a canonical isoform, as that's a vep optional output\n\t\t\t\t// last method: choose *colorful* annotation based on if is canonical, _csqrank\n\t\t\t\tuseone = m.csq[0]\n\t\t\t\tfor (const q of m.csq) {\n\t\t\t\t\tif (q._csqrank < useone._csqrank) {\n\t\t\t\t\t\tuseone = q\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tif (useone) {\n\t\t\tm.gene = useone._gene\n\t\t\tm.isoform = useone._isoform\n\t\t\tm.class = useone._class\n\t\t\tm.dt = useone._dt\n\t\t\tm.mname = useone._mname\n\n\t\t\tif (m.class == mclassnoncoding) {\n\t\t\t\t// noncoding converted from csq is not a meaningful, drab color, has no mname label, delete so later will be converted to non-protein class\n\t\t\t\tdelete m.class\n\t\t\t}\n\t\t}\n\t} else if (m.ann) {\n\t\t// there could be many applicable annotations, the first one not always desirable\n\t\t// choose *colorful* annotation based on _csqrank\n\t\tlet useone = null\n\t\tif (block.usegm) {\n\t\t\tfor (const q of m.ann) {\n\t\t\t\tif (q._isoform != block.usegm.isoform) continue\n\t\t\t\tif (useone) {\n\t\t\t\t\tif (q._csqrank < useone._csqrank) {\n\t\t\t\t\t\tuseone = q\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\tuseone = q\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (!useone && block.gmmode == gmmode.genomic) {\n\t\t\t\t// no match to this gene, but in genomic mode, maybe from other genes?\n\t\t\t\tuseone = m.ann[0]\n\t\t\t}\n\t\t} else {\n\t\t\tuseone = m.ann[0]\n\t\t\tfor (const q of m.ann) {\n\t\t\t\tif (q._csqrank < useone._csqrank) {\n\t\t\t\t\tuseone = q\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tif (useone) {\n\t\t\tm.gene = useone._gene\n\t\t\tm.isoform = useone._isoform\n\t\t\tm.class = useone._class\n\t\t\tm.dt = useone._dt\n\t\t\tm.mname = useone._mname\n\n\t\t\tif (m.class == mclassnoncoding) {\n\t\t\t\tdelete m.class\n\t\t\t}\n\t\t}\n\t}\n\n\tif (m.class == undefined) {\n\t\t// infer class from m.type, which was assigned by vcf.js\n\t\tif (mclass[m.type]) {\n\t\t\tm.class = m.type\n\t\t\tm.dt = mclass[m.type].dt\n\t\t\tm.mname = m.id && m.id != \".\" ? m.id : m.ref + \">\" + m.alt\n\t\t\tif (m.mname.length > 15) {\n\t\t\t\t// avoid long indel\n\t\t\t\tm.mname = m.type\n\t\t\t}\n\t\t} else {\n\t\t\tm.class = mclassnonstandard\n\t\t\tm.dt = dtsnvindel\n\t\t\tm.mname = m.type\n\t\t}\n\t}\n\n\tdelete m.type\n}\n\n/*\nused in:\n\tmdssvcnv track, mutation attributes, items that are not annotated by an attribute for showing in legend, and server-side filtering\n*/\nexport const not_annotated = \"Unannotated\"\n\n// kernal density estimator as from https://www.d3-graph-gallery.com/graph/density_basic.html\n\nexport function kernelDensityEstimator(kernel, X) {\n\treturn function (V) {\n\t\treturn X.map((x) => {\n\t\t\treturn [\n\t\t\t\tx,\n\t\t\t\tV.map((v) => kernel(x - v)).reduce((i, j) => i + j, 0) / V.length,\n\t\t\t]\n\t\t})\n\t}\n}\n\nexport function kernelEpanechnikov(k) {\n\treturn function (v) {\n\t\treturn Math.abs((v /= k)) <= 1 ? (0.75 * (1 - v * v)) / k : 0\n\t}\n}\n\n/////////////////////// color sets /////////////////////////\n\nexport const schemeCategory20 = [\n\t\"#1f77b4\",\n\t\"#aec7e8\",\n\t\"#ff7f0e\",\n\t\"#ffbb78\",\n\t\"#2ca02c\",\n\t\"#98df8a\",\n\t\"#d62728\",\n\t\"#ff9896\",\n\t\"#9467bd\",\n\t\"#c5b0d5\",\n\t\"#8c564b\",\n\t\"#c49c94\",\n\t\"#e377c2\",\n\t\"#f7b6d2\",\n\t\"#7f7f7f\",\n\t\"#c7c7c7\",\n\t\"#bcbd22\",\n\t\"#dbdb8d\",\n\t\"#17becf\",\n\t\"#9edae5\",\n]\nexport const schemeCategory2 = [\"#e75480\", \"blue\"]\n\nexport function getColorScheme(number) {\n\tif (number > 20) {\n\t\tconst scheme = []\n\t\tfor (let i = 0; i < number; i++)\n\t\t\tscheme.push(d3.interpolateRainbow(i / number))\n\t\treturn scheme\n\t}\n\tif (number > 12) return schemeCategory20\n\telse if (number > 8) return d3.schemePaired\n\telse if (number > 2) return d3.schemeDark2\n\telse return schemeCategory2\n}\nexport function getColors(number) {\n\tconst scheme = getColorScheme(number)\n\treturn 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-  "names": ["tmp", "chr"]
-}

package/dist/chunk-ZZSDYKD5.js

@@ -1,14 +0,0 @@
-// src/block.lazyload.js
-var Block;
-async function blocklazyload(arg) {
-  if (!Block) {
-    const b = await import("./block-2QM37YSE.js");
-    Block = b.Block;
-  }
-  return new Block(arg);
-}
-
-export {
-  blocklazyload
-};
-//# sourceMappingURL=chunk-ZZSDYKD5.js.map

package/dist/condition-S52W57ZO.js

@@ -1,330 +0,0 @@
-import {
-  getPillNameDefault,
-  make_radios,
-  sayerror,
-  set_hiddenvalues,
-  throwMsgWithFilePathAndFnName
-} from "./chunk-XZZLEHWC.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-CJJ6LDZM.js";
-import "./chunk-2SRMRC6L.js";
-import "./chunk-QEHUEG4X.js";
-import "./chunk-XDI4UFCZ.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-5EF5U7MX.js";
-import "./chunk-2K5DSRBJ.js";
-import "./chunk-UCLS2SVB.js";
-import {
-  copyMerge
-} from "./chunk-MVTCBVSX.js";
-import "./chunk-SEQLC4AD.js";
-import "./chunk-L4QG7XZE.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-2TIYJ3PH.js";
-import "./chunk-RIGZHHCP.js";
-import "./chunk-AAEXTQT3.js";
-import "./chunk-2UWHV2SB.js";
-import "./chunk-ZLH4PJKX.js";
-import "./chunk-TV74I3Y5.js";
-import "./chunk-IH7ILDJS.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-SEEYV6P2.js";
-import "./chunk-NDWTN4U5.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-
-// termsetting/handlers/condition.ts
-var cutoffGrades = [1, 2, 3, 4, 5];
-function getHandler(self) {
-  return {
-    getPillName(d) {
-      return getPillNameDefault(self, d);
-    },
-    getPillStatus() {
-      return getPillStatus(self);
-    },
-    showEditMenu(div) {
-      if (self.q.mode == "discrete") {
-        return showMenu_discrete(self, div);
-      }
-      if (self.q.mode == "binary" || self.q.mode == "cuminc" || self.q.mode == "cox") {
-        return showMenu_cutoff(self, div);
-      }
-      console.error("invalid q.mode:", self.q.mode);
-      throw "invalid q.mode";
-    }
-    // async postMain() {
-    // 	const body = self.opts.getBodyParams?.() || {} //make sure term1_q is added
-    // 	const data = await self.vocabApi.getCategories(self.term, self.filter!, body)
-    // 	//not really sure this is necessary but it's consistent across other handlers
-    // 	self.category2samplecount = []
-    // 	for (const d of data.lst) {
-    // 		self.category2samplecount.push({
-    // 			key: d.key,
-    // 			label: d.label,
-    // 			count: d.samplecount
-    // 		})
-    // 		// }
-    // 	}
-    // }
-  };
-}
-function getPillStatus(self) {
-  const text = self.q?.name || self.q?.reuseId;
-  if (text) return { text };
-  if (self.q.mode == "discrete") {
-    if (self.q.breaks?.length) {
-      return { text: self.q.breaks.length + 1 + " groups" };
-    } else {
-      if (self.q.bar_by_grade) {
-        if (self.q.value_by_max_grade) return { text: "Max. Grade" };
-        if (self.q.value_by_most_recent) return { text: "Most Recent Grade" };
-        if (self.q.value_by_computable_grade) return { text: "Any Grade" };
-        return { text: "Error: unknown grade setting", bgcolor: "red" };
-      }
-      if (self.q.bar_by_children) return { text: "Sub-condition" };
-    }
-  }
-  if (self.q.mode == "binary") {
-    return {
-      text: self.usecase?.target == "regression" ? self.data.q.groups.find((x) => x.name != self.data.refGrp).name : "binary"
-    };
-  }
-  if (self.q.mode == "cuminc" || self.q.mode == "cox") {
-    if (!self.q.breaks || self.q.breaks.length == 0) throwMsgWithFilePathAndFnName("Missing q.breaks");
-    return { text: `Grades ${self.q.breaks[0]}-5` };
-  }
-  return {};
-}
-async function showMenu_discrete(self, div) {
-  const value_type_div = div.append("div").style("margin", "10px 0px 10px 5px").style("border-left", "solid 1px #ededed");
-  value_type_div.append("div").style("display", "inline-block").style("margin", "0px 0px 5px 5px").style("color", "rgb(136, 136, 136)").text("Grade type:");
-  const value_type_select = value_type_div.append("select").style("display", "inline").style("margin", "0px 10px").on("change", () => {
-    const i = value_type_select.property("selectedIndex");
-    self.q.bar_by_grade = i != 3;
-    self.q.bar_by_children = i == 3;
-    self.q.value_by_max_grade = i == 0;
-    self.q.value_by_most_recent = i == 1;
-    self.q.value_by_computable_grade = i == 2 || i == 3;
-    self.dom.tip.hide();
-    self.api.runCallback();
-  });
-  value_type_select.append("option").text("Max grade per patient");
-  value_type_select.append("option").text("Most recent grade per patient");
-  value_type_select.append("option").text("Any grade per patient");
-  if (self.term.subconditions) {
-    value_type_select.append("option").text("Sub-conditions");
-  }
-  value_type_select.property(
-    "selectedIndex",
-    self.q.bar_by_children ? 3 : self.q.value_by_computable_grade ? 2 : self.q.value_by_most_recent ? 1 : 0
-  );
-  if (self.q.bar_by_children) {
-    return;
-  }
-  const breaksSelectorDiv = div.append("div").style("margin", "20px 0px 10px 5px").style("border-left", "solid 1px #ededed");
-  breaksSelectorDiv.append("div").text("Divide grades into groups (optional):").style("margin", "0px 0px 10px 5px").style("color", "rgb(136, 136, 136)");
-  const holder = breaksSelectorDiv.append("div").style("display", "flex").style("align-items", "start").style("margin-left", "10px").style("width", "100%");
-  const gradeValuesDiv = holder.append("div").style("margin-right", "20px");
-  const rangeNameDiv = holder.append("div").style("display", "grid").style("grid-template-columns", "auto auto").style("column-gap", "20px").style("align-items", "center").style("margin-right", "5px");
-  gradeValuesDiv.append("div").style("margin-bottom", "5px").style("color", "rgb(136, 136, 136)").text("Cutoff grades");
-  const textarea = gradeValuesDiv.append("textarea").style("width", "100px").style("height", "70px").on("keyup", textarea2gradeUI);
-  gradeValuesDiv.append("div").style("font-size", ".6em").style("margin-left", "1px").style("color", "#858585").html("Enter numeric values </br>seperated by ENTER");
-  if (self.q.breaks?.length) {
-    textarea.property("value", self.q.breaks.join("\n"));
-  }
-  textarea2gradeUI();
-  function textarea2gradeUI() {
-    rangeNameDiv.selectAll("*").remove();
-    const breaks = textarea2breaks();
-    if (!breaks.length) {
-      delete self.q.breaks;
-      delete self.q.groups;
-      return;
-    }
-    if (!self.term.values) throwMsgWithFilePathAndFnName(`Missing term values`);
-    const grades = Object.keys(self.term.values).filter((g) => !self.term.values?.[g].uncomputable).map(Number).sort((a, b) => a - b);
-    const groups = getGroups(grades, breaks);
-    rangeNameDiv.append("div").style("margin-bottom", "3px").style("color", "rgb(136, 136, 136)").text("Range");
-    rangeNameDiv.append("div").style("margin-bottom", "3px").style("color", "rgb(136, 136, 136)").text("Label");
-    for (const [i, g] of groups.entries()) {
-      rangeNameDiv.append("div").text(g.name.replace(/Grades* /, ""));
-      rangeNameDiv.append("div").append("input").attr("type", "text").property("value", g.name).style("margin", "2px 0px").on("change", function() {
-        groups[i].name = this.value;
-      });
-    }
-    self.q.breaks = breaks;
-    self.q.groups = groups;
-  }
-  function textarea2breaks() {
-    const str = textarea.property("value").trim();
-    if (!str) return [];
-    const lst = [...new Set(str.split("\n"))];
-    const breaks = [];
-    for (const x of lst) {
-      const b = Number(x);
-      if (!Number.isInteger(b)) {
-        sayerror(div, "cutoff grade must be an integer value");
-        return [];
-      }
-      if (b < 1 || b > 5) {
-        sayerror(div, `cutoff grade must be within grades 1-5`);
-        return [];
-      }
-      breaks.push(b);
-    }
-    if (!breaks.length) return [];
-    return breaks.sort((i, j) => i - j);
-  }
-  div.append("button").text("Apply").style("margin", "10px").on("click", (event) => {
-    event.target.disabled = true;
-    event.target.innerHTML = "Loading...";
-    self.api.runCallback();
-  });
-}
-function showMenu_cutoff(self, div) {
-  const holder = div.append("div").style("margin", "10px").style("display", "grid").style("grid-template-columns", "auto auto").style("gap", "20px");
-  holder.append("div").text("Grade cutoff").style("opacity", 0.4);
-  const sd = holder.append("div");
-  const gradeSelect = sd.append("select").on("change", changeGradeSelect);
-  for (const i of cutoffGrades) {
-    gradeSelect.append("option").text(self.term.values?.[i].label);
-  }
-  gradeSelect.property("selectedIndex", self.q.breaks[0] - 1);
-  holder.append("div").text(self.q.mode == "binary" ? "Group 1" : "Censored").style("opacity", 0.4);
-  const g1n = holder.append("div").style("opacity", 0.4);
-  holder.append("div").text(self.q.mode == "binary" ? "Group 2" : "Event").style("opacity", 0.4);
-  const g2n = holder.append("div").style("opacity", 0.4);
-  changeGradeSelect();
-  function changeGradeSelect() {
-    const grade = gradeSelect.property("selectedIndex") + 1;
-    g1n.selectAll("*").remove();
-    g2n.selectAll("*").remove();
-    const grades = Object.keys(self.term.values).map(Number).sort((a, b) => a - b);
-    for (const i of grades) {
-      if (i < grade) {
-        g1n.append("div").text(self.term.values?.[i].label);
-      } else {
-        g2n.append("div").text(self.term.values?.[i].label);
-      }
-    }
-  }
-  const timeUnit = self.vocabApi.termdbConfig.timeUnit;
-  let timeScaleChoice;
-  if (self.q.mode == "cox") {
-    timeScaleChoice = self.q.timeScale;
-    holder.append("div").text("Time axis").style("opacity", 0.4);
-    const options = [
-      {
-        label: timeUnit.charAt(0).toUpperCase() + timeUnit.slice(1),
-        value: "time"
-      },
-      { label: "Age", value: "age" }
-    ];
-    if (self.q.timeScale == "age") {
-      options[1].checked = true;
-    } else {
-      options[0].checked = true;
-    }
-    make_radios({
-      holder: holder.append("div"),
-      options,
-      styles: { padding: "" },
-      callback: (v) => timeScaleChoice = v
-    });
-  }
-  div.append("button").text("Apply").style("margin", "10px").on("click", (event) => {
-    if (!self.q.breaks || self.q.breaks.length == 0) throwMsgWithFilePathAndFnName("Missing q.breaks");
-    const grade = gradeSelect.property("selectedIndex") + 1;
-    self.q.breaks[0] = grade;
-    if (self.q.mode == "binary") {
-      const grades = Object.keys(self.term.values).map(Number).sort((a, b) => a - b);
-      self.q.groups = getGroups(grades, self.q.breaks);
-      self.refGrp = self.q.groups[0].name;
-    }
-    if (self.q.mode == "cox") self.q.timeScale = timeScaleChoice;
-    event.target.disabled = true;
-    event.target.innerHTML = "Loading...";
-    self.api.runCallback();
-  });
-}
-function getGroups(grades, breaks) {
-  grades.sort((a, b2) => a - b2);
-  const groups = [];
-  let group = { values: [] };
-  let b;
-  for (const g of grades) {
-    if (breaks.includes(g)) {
-      b = g;
-      const max = Math.max(...group.values);
-      if (!groups.length) {
-        if (group.values.length == 1) {
-          if (group.values[0] !== 0) throw "unexpected group value";
-          group.name = "Grade 0";
-        } else {
-          if (group.values.length == 2 && group.values.includes(-1) && group.values.includes(0)) {
-            group.name = "Not tested/Grade 0";
-          } else {
-            group.name = group.values.includes(-1) ? `Not tested/Grade 0 - Grade ${max}` : `Grades 0-${max}`;
-          }
-        }
-      } else {
-        group.name = group.values.length == 1 ? `Grade ${group.values[0]}` : `${group.name}-${max}`;
-      }
-      groups.push(group);
-      group = {
-        name: `Grade ${b}`,
-        values: [g]
-      };
-    } else {
-      group.values.push(g);
-    }
-  }
-  group.name = `Grades ${b}-5`;
-  groups.push(group);
-  return groups;
-}
-function fillTW(tw, vocabApi, defaultQ) {
-  set_hiddenvalues(tw.q, tw.term);
-  if (defaultQ) {
-    copyMerge(tw.q, defaultQ);
-  }
-  if (!Object.keys(tw.q).includes("mode")) tw.q.mode = "discrete";
-  if (!tw.q.valueFor) {
-    const q = tw.q;
-    if (!q.bar_by_grade && !q.bar_by_children) q.bar_by_grade = true;
-    tw.q.valueFor = tw.q.bar_by_children ? "children" : "grade";
-  }
-  if (tw.q.valueFor == "grade") {
-    if (tw.q.value_by_max_grade || tw.q.value_by_most_recent || tw.q.value_by_computable_grade) {
-    } else {
-      tw.q.value_by_max_grade = true;
-    }
-  }
-  if (tw.q.mode == "binary" || tw.q.mode == "cox" || tw.q.mode == "cuminc") {
-    const defaultBreak = tw.q.mode == "binary" ? 1 : 3;
-    if (!tw.q.breaks?.length) tw.q.breaks = [defaultBreak];
-    if (tw.q.breaks.length != 1 || ![1, 2, 3, 4, 5].includes(tw.q.breaks[0])) throw "invalid tw.q.breaks";
-  }
-  if (tw.q.valueFor == "grade") {
-    if (tw.q.breaks?.length) {
-      if (!tw.term.values) throw "missing term.values";
-      if (tw.q.mode == "discrete" || tw.q.mode == "binary") {
-        const grades = Object.keys(tw.term.values).filter((g) => tw.q.mode == "discrete" ? !tw.term.values?.[g].uncomputable : g).map(Number).sort((a, b) => a - b);
-        tw.q.groups = getGroups(grades, tw.q.breaks);
-      }
-    }
-    if (tw.q.mode == "cox") {
-      if (!tw.q.timeScale) tw.q.timeScale = "time";
-      if (!["age", "time"].includes(tw.q.timeScale)) throw "invalid q.timeScale";
-    }
-  }
-}
-export {
-  fillTW,
-  getHandler
-};
-//# sourceMappingURL=condition-S52W57ZO.js.map

package/dist/controls-B4MTTPWO.js

@@ -1,39 +0,0 @@
-import {
-  controlsInit,
-  renderTerm1Label,
-  term0_term2_defaultQ
-} from "./chunk-XZZLEHWC.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-CJJ6LDZM.js";
-import "./chunk-2SRMRC6L.js";
-import "./chunk-QEHUEG4X.js";
-import "./chunk-XDI4UFCZ.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-5EF5U7MX.js";
-import "./chunk-2K5DSRBJ.js";
-import "./chunk-UCLS2SVB.js";
-import "./chunk-MVTCBVSX.js";
-import "./chunk-SEQLC4AD.js";
-import "./chunk-L4QG7XZE.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-2TIYJ3PH.js";
-import "./chunk-RIGZHHCP.js";
-import "./chunk-AAEXTQT3.js";
-import "./chunk-2UWHV2SB.js";
-import "./chunk-ZLH4PJKX.js";
-import "./chunk-TV74I3Y5.js";
-import "./chunk-IH7ILDJS.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-SEEYV6P2.js";
-import "./chunk-NDWTN4U5.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  controlsInit,
-  renderTerm1Label,
-  term0_term2_defaultQ
-};
-//# sourceMappingURL=controls-B4MTTPWO.js.map

package/dist/controls.config-6KBCTIPN.js

@@ -1,37 +0,0 @@
-import {
-  configUiInit,
-  initByInput
-} from "./chunk-XZZLEHWC.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-CJJ6LDZM.js";
-import "./chunk-2SRMRC6L.js";
-import "./chunk-QEHUEG4X.js";
-import "./chunk-XDI4UFCZ.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-5EF5U7MX.js";
-import "./chunk-2K5DSRBJ.js";
-import "./chunk-UCLS2SVB.js";
-import "./chunk-MVTCBVSX.js";
-import "./chunk-SEQLC4AD.js";
-import "./chunk-L4QG7XZE.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-2TIYJ3PH.js";
-import "./chunk-RIGZHHCP.js";
-import "./chunk-AAEXTQT3.js";
-import "./chunk-2UWHV2SB.js";
-import "./chunk-ZLH4PJKX.js";
-import "./chunk-TV74I3Y5.js";
-import "./chunk-IH7ILDJS.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-SEEYV6P2.js";
-import "./chunk-NDWTN4U5.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  configUiInit,
-  initByInput
-};
-//# sourceMappingURL=controls.config-6KBCTIPN.js.map