@sjcrh/proteinpaint-types 2.119.0 → 2.123.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/brainImaging.js +1 -1
- package/dist/{chunk-T2CSA2MC.js → chunk-3ZT4UCFM.js} +366 -512
- package/dist/{chunk-4V46EBDF.js → chunk-5XRJ5ATE.js} +916 -1264
- package/dist/{chunk-BM3JLR6T.js → chunk-AGSW7G4T.js} +905 -1253
- package/dist/{chunk-HURSYPTO.js → chunk-D5OG676D.js} +32 -1
- package/dist/{chunk-J6SJ4M3S.js → chunk-F64WJMRL.js} +1094 -1306
- package/dist/{chunk-YURGGHZI.js → chunk-K7P6C6KU.js} +731 -1079
- package/dist/{chunk-GI4NNB34.js → chunk-LBGUOJR3.js} +366 -512
- package/dist/{chunk-OL4OMJSP.js → chunk-NCFUZ5VV.js} +903 -1139
- package/dist/{chunk-GD3KAF6V.js → chunk-QMWUUGEK.js} +457 -603
- package/dist/{chunk-DL4UYYVE.js → chunk-RX5EB2HL.js} +366 -512
- package/dist/{chunk-ROPNHRVV.js → chunk-SQBZAOWB.js} +366 -512
- package/dist/{chunk-7NNYHDAK.js → chunk-XPOHYEAY.js} +917 -1265
- package/dist/{chunk-UVOO2LBD.js → chunk-ZMOSABYP.js} +916 -1264
- package/dist/correlationVolcano.js +1 -1
- package/dist/index.js +13 -13
- package/dist/samplewsimages.js +1 -1
- package/dist/termdb.boxplot.js +1 -1
- package/dist/termdb.categories.js +1 -1
- package/dist/termdb.cluster.js +1 -1
- package/dist/termdb.descrstats.js +1 -1
- package/dist/termdb.numericcategories.js +1 -1
- package/dist/termdb.percentile.js +1 -1
- package/dist/termdb.termsbyids.js +1 -1
- package/dist/termdb.topTermsByType.js +1 -1
- package/dist/termdb.topVariablyExpressedGenes.js +1 -1
- package/dist/termdb.violin.js +1 -1
- package/package.json +1 -1
- package/src/dataset.ts +11 -5
- package/src/filter.ts +12 -67
- package/src/genome.ts +1 -1
- package/src/routes/hicgenome.ts +1 -1
- package/src/routes/isoformlst.ts +1 -1
- package/src/routes/samplewsimages.ts +1 -0
- package/src/routes/termdb.cohorts.ts +1 -1
- package/src/routes/termdb.singlecellData.ts +1 -1
- package/src/terms/categorical.ts +3 -3
- package/src/terms/condition.ts +2 -2
- package/src/terms/geneExpression.ts +3 -3
- package/src/terms/geneVariant.ts +58 -19
- package/src/terms/metaboliteIntensity.ts +4 -4
- package/src/terms/q.ts +1 -1
- package/src/terms/samplelst.ts +3 -3
- package/src/terms/singleCellCellType.ts +2 -2
- package/src/terms/singleCellGeneExpression.ts +4 -5
- package/src/terms/snp.ts +3 -3
- package/src/terms/snps.ts +4 -4
- package/src/terms/term.ts +14 -8
- package/src/terms/tw.ts +7 -8
- package/src/terms/updated-types.ts +5 -4
- package/src/termsetting.ts +4 -4
- package/src/test/numeric.type.spec.ts +2 -2
package/dist/index.js
CHANGED
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@@ -2,7 +2,7 @@ import {
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termsByIdsPayload,
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validTermsByIdsRequest,
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validTermsByIdsResponse
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} from "./chunk-
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} from "./chunk-AGSW7G4T.js";
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import {
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topMutatedGenePayload,
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validTopMutatedGeneRequest,
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@@ -12,17 +12,17 @@ import {
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termdbTopTermsByTypePayload,
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validTermdbTopTermsByTypeRequest,
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validTermdbTopTermsByTypeResponse
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} from "./chunk-
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} from "./chunk-NCFUZ5VV.js";
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import {
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termdbTopVariablyExpressedGenesPayload,
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validTermdbTopVariablyExpressedGenesRequest,
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validTermdbTopVariablyExpressedGenesResponse
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} from "./chunk-
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} from "./chunk-SQBZAOWB.js";
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import {
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validViolinRequest,
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validViolinResponse,
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violinPayload
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} from "./chunk-
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} from "./chunk-RX5EB2HL.js";
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import {
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tilePayload,
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validTileRequest,
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@@ -42,7 +42,7 @@ import {
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percentilePayload,
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validPercentileRequest,
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validPercentileResponse
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} from "./chunk-
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} from "./chunk-3ZT4UCFM.js";
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import {
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rootTermPayload,
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validRootTermRequest,
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@@ -87,17 +87,17 @@ import {
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boxplotPayload,
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validBoxPlotRequest,
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validBoxPlotResponse
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} from "./chunk-
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} from "./chunk-XPOHYEAY.js";
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import {
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termdbCategoriesPayload,
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validCategoriesRequest,
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validCategoriesResponse
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} from "./chunk-
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} from "./chunk-ZMOSABYP.js";
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import {
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termdbClusterPayload,
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validTermdbClusterRequest,
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validTermdbClusterResponse
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} from "./chunk-
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} from "./chunk-F64WJMRL.js";
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import {
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termdbCohortSummaryPayload,
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validTermdbCohortSummaryRequest,
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@@ -112,12 +112,12 @@ import {
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descrStatsPayload,
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validDescrStatsRequest,
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validDescrStatsResponse
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} from "./chunk-
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} from "./chunk-5XRJ5ATE.js";
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import {
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numericCategoriesPayload,
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validNumericCategoriesRequest,
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validNumericCategoriesResponse
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} from "./chunk-
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} from "./chunk-LBGUOJR3.js";
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import {
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hicstatPayload,
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validHicstatRequest,
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@@ -147,7 +147,7 @@ import {
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sampleWSImagesPayload,
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validSampleWSImagesRequest,
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validSampleWSImagesResponse
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} from "./chunk-
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} from "./chunk-D5OG676D.js";
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import {
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snpPayload,
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validSnpRequest,
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@@ -197,7 +197,7 @@ import {
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brainImagingPayload,
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validBrainImagingRequest,
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validBrainImagingResponse
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} from "./chunk-
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} from "./chunk-QMWUUGEK.js";
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import {
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brainImagingSamplesPayload,
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validBrainImagingSamplesRequest,
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@@ -212,7 +212,7 @@ import {
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CorrelationVolcanoPayload,
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validCorrelationVolcanoRequest,
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validCorrelationVolcanoResponse
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} from "./chunk-
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} from "./chunk-K7P6C6KU.js";
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import {
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datasetPayload,
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validDatasetRequest,
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package/dist/samplewsimages.js
CHANGED
package/dist/termdb.boxplot.js
CHANGED
package/dist/termdb.cluster.js
CHANGED
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@@ -2,7 +2,7 @@ import {
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termdbTopVariablyExpressedGenesPayload,
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validTermdbTopVariablyExpressedGenesRequest,
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validTermdbTopVariablyExpressedGenesResponse
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} from "./chunk-
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} from "./chunk-SQBZAOWB.js";
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import "./chunk-CNSSF43V.js";
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export {
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termdbTopVariablyExpressedGenesPayload,
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package/dist/termdb.violin.js
CHANGED
package/package.json
CHANGED
package/src/dataset.ts
CHANGED
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@@ -600,9 +600,13 @@ type CnvSegment = {
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cnvMaxCopynumber?: number
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*/
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/**
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/** quick fix for gdc cnv tool:
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if not set, mds3 tk & matrix will load cnv segments and show them together with ssm & fusion
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if set:
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- for mds3 tk loading via mds3.load.js, only when tk.hardcodeCnvOnly=true, this will be loaded and shown
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- for others using mayGetGeneVariantData(), this is always disabled, as request won't have this flag
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*/
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requiresHardcodeCnvOnlyFlag?: true
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}
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/*
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getWSImages?: (sampleName: string) => Promise<WSImage[]>
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/** ds supplied */
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getWSIAnnotations?: (sampleName: string, wsiImage: string) => Promise<string[]>
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/** ds supplied */
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getZoomInPoints?: (sampleName: string, wsiImage: string) => Promise<Array<[number, number]>>
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}
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/*** types supporting Termdb ***/
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/** Terms */
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termIds?: TermIds
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/** if true, backend is allowed to send sample names to client in charts */
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displaySampleIds?: boolean
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displaySampleIds?: (clientAuthResult: any) => boolean
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converSampleIds?: boolean
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alwaysShowBranchTerms?: boolean
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minimumSampleAllowed4filter?: number
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/** colors for a category multivalues */
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}
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//terms
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//terms are shown in the dictionary based on term and user role.
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}
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type SampleType = {
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package/src/filter.ts
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import { NumericTerm, NumericBin } from './terms/numeric.ts'
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import { CategoricalTerm } from './terms/categorical.ts'
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import {
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import { ConditionTerm } from './terms/condition.ts'
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import type { BaseValue } from './terms/term.ts'
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import type { NumericTerm, NumericBin } from './terms/numeric.ts'
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import type { CategoricalTerm } from './terms/categorical.ts'
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import type { DtTerm } from './terms/geneVariant.ts'
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import type { ConditionTerm } from './terms/condition.ts'
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--------EXPORTED--------
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grade_and_child?: GradeAndChildEntry[]
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}
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type GeneVariantOrigin = 'somatic' | 'germline'
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type SNVIndelClasses =
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type SNVIndelTvsValue = {
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dt: 1
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mclassLst: SNVIndelClasses[]
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mclassExcludeLst: SNVIndelClasses[]
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origin?: GeneVariantOrigin
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}
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type CNVClasses = 'CNV_amp' | 'CNV_loss' | 'CNV_loh' | 'Blank' | 'WT' | 'CNV_amplification' | 'CNV_homozygous_deletion'
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type CNVTvsValue = {
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dt: 4
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mclassLst: CNVClasses[]
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mclassExcludeLst: CNVClasses[]
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origin?: GeneVariantOrigin
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}
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type SVClasses = 'SV' | 'Blank' | 'WT'
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type SVTvsValue = {
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dt: 5
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mclassLst: SVClasses[]
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mclassExcludeLst: SVClasses[]
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origin?: GeneVariantOrigin
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}
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type FusionRNAClasses = 'Fuserna' | 'Blank' | 'WT'
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type FusionTvsValue = {
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dt: 2
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mclassLst: FusionRNAClasses[]
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mclassExcludeLst: FusionRNAClasses[]
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origin?: GeneVariantOrigin
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}
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type GeneVariantTvsValue = SNVIndelTvsValue | CNVTvsValue | SVTvsValue | FusionTvsValue
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type GeneVariantTvs = BaseTvs & {
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term:
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values:
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term: DtTerm
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values: { key: string; label: string; value: string }[]
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/*** types supporting Filter type ***/
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export type Tvs = CategoricalTvs | NumericTvs | ConditionTvs | GeneVariantTvs // | SampleLstTvs ...
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export type Filter = {
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type: '
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in
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join:
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type: 'tvslst'
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in: boolean
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join: string
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tag?: string // client-side only
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lst: (
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lst: ({ type: 'tvs'; tvs: Tvs } | Filter)[]
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}
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package/src/genome.ts
CHANGED
package/src/routes/hicgenome.ts
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import type { BaseHicRequest, XYZCoord } from './hicdata.ts'
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import { RoutePayload } from './routeApi.ts'
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import type { RoutePayload } from './routeApi.ts'
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export type HicGenomeRequest = BaseHicRequest & {
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/** Entire chromosome list read from the file (see hicstate) */
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package/src/routes/isoformlst.ts
CHANGED
package/src/terms/categorical.ts
CHANGED
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import {
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import type {
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BaseTerm,
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TermValues,
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GroupSettingQ,
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PredefinedGroupSettingQ,
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CustomGroupSettingQ
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} from './term.ts'
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import { RawValuesQ, RawPredefinedGroupsetQ, RawCustomGroupsetQ, MinBaseQ } from './q.ts'
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import { TermSettingInstance } from '../termsetting.ts'
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import type { RawValuesQ, RawPredefinedGroupsetQ, RawCustomGroupsetQ, MinBaseQ } from './q.ts'
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import type { TermSettingInstance } from '../termsetting.ts'
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/**
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package/src/terms/condition.ts
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import { TermWrapper } from './tw.ts'
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import { NumericTerm, NumericQ } from './numeric.ts'
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3
|
-
import { TermSettingInstance } from '../termsetting.ts'
|
|
1
|
+
import type { TermWrapper } from './tw.ts'
|
|
2
|
+
import type { NumericTerm, NumericQ } from './numeric.ts'
|
|
3
|
+
import type { TermSettingInstance } from '../termsetting.ts'
|
|
4
4
|
|
|
5
5
|
/*
|
|
6
6
|
--------EXPORTED--------
|
package/src/terms/geneVariant.ts
CHANGED
|
@@ -1,24 +1,28 @@
|
|
|
1
|
-
import type { MinBaseQ, BaseTerm, TermGroupSetting, BaseTW,
|
|
1
|
+
import type { MinBaseQ, BaseTerm, TermGroupSetting, BaseTW, TermValues, BaseGroupSet, TermFilter } from '../index.ts'
|
|
2
2
|
import type { TermSettingInstance } from '../termsetting.ts'
|
|
3
3
|
|
|
4
|
-
|
|
5
|
-
|
|
6
|
-
// see fillTW() in termsetting/handlers/geneVariant.ts
|
|
4
|
+
// q types
|
|
5
|
+
export type GvBaseQ = MinBaseQ & {
|
|
7
6
|
cnvGainCutoff?: number
|
|
8
7
|
cnvMaxLength?: number
|
|
9
8
|
cnvMinAbsValue?: number
|
|
10
9
|
cnvLossCutoff?: number
|
|
11
|
-
exclude: string[]
|
|
12
10
|
}
|
|
13
11
|
|
|
14
|
-
|
|
12
|
+
type RawGvValuesQ = GvBaseQ & { type?: 'values' }
|
|
13
|
+
type RawGvCustomGsQ = GvBaseQ & { type: 'custom-groupset'; customset?: BaseGroupSet }
|
|
15
14
|
|
|
16
|
-
type
|
|
15
|
+
export type GvValuesQ = GvBaseQ & { type: 'values' }
|
|
16
|
+
export type GvCustomGsQ = GvBaseQ & { type: 'custom-groupset'; customset: BaseGroupSet }
|
|
17
|
+
|
|
18
|
+
export type GvQ = GvValuesQ | GvCustomGsQ
|
|
19
|
+
|
|
20
|
+
// term types
|
|
21
|
+
type GvBaseTerm = BaseTerm & {
|
|
17
22
|
type: 'geneVariant'
|
|
18
|
-
groupsetting: TermGroupSetting
|
|
19
23
|
}
|
|
20
24
|
|
|
21
|
-
export type
|
|
25
|
+
export type GvGene = {
|
|
22
26
|
kind: 'gene'
|
|
23
27
|
gene: string
|
|
24
28
|
// chr,start,stop should exist together as a separate type called
|
|
@@ -29,36 +33,71 @@ export type GeneVariantGeneTerm = GeneVariantBaseTerm & {
|
|
|
29
33
|
stop?: number
|
|
30
34
|
}
|
|
31
35
|
|
|
32
|
-
export type
|
|
36
|
+
export type GvCoord = {
|
|
33
37
|
kind: 'coord'
|
|
34
38
|
chr: string
|
|
35
39
|
start: number
|
|
36
40
|
stop: number
|
|
37
41
|
}
|
|
38
42
|
|
|
39
|
-
export type
|
|
43
|
+
export type RawGvTerm = GvBaseTerm &
|
|
44
|
+
(GvGene | GvCoord) & {
|
|
45
|
+
groupsetting?: TermGroupSetting
|
|
46
|
+
filter?: TermFilter
|
|
47
|
+
}
|
|
48
|
+
|
|
49
|
+
export type GvTerm = GvBaseTerm &
|
|
50
|
+
(GvGene | GvCoord) & {
|
|
51
|
+
groupsetting: TermGroupSetting
|
|
52
|
+
filter: TermFilter
|
|
53
|
+
}
|
|
54
|
+
|
|
55
|
+
// tw types
|
|
56
|
+
export type RawGvValuesTW = BaseTW & {
|
|
57
|
+
type?: 'GvValuesTW'
|
|
58
|
+
term: RawGvTerm
|
|
59
|
+
q: RawGvValuesQ
|
|
60
|
+
}
|
|
61
|
+
|
|
62
|
+
export type RawGvCustomGsTW = BaseTW & {
|
|
63
|
+
type?: 'GvCustomGsTW'
|
|
64
|
+
term: RawGvTerm
|
|
65
|
+
q: RawGvCustomGsQ
|
|
66
|
+
}
|
|
40
67
|
|
|
41
|
-
export type
|
|
42
|
-
|
|
43
|
-
|
|
68
|
+
export type GvValuesTW = BaseTW & {
|
|
69
|
+
type: 'GvValuesTW'
|
|
70
|
+
term: GvTerm
|
|
71
|
+
q: GvValuesQ
|
|
44
72
|
}
|
|
45
73
|
|
|
74
|
+
export type GvCustomGsTW = BaseTW & {
|
|
75
|
+
type: 'GvCustomGsTW'
|
|
76
|
+
term: GvTerm
|
|
77
|
+
q: GvCustomGsQ
|
|
78
|
+
}
|
|
79
|
+
|
|
80
|
+
export type RawGvTW = RawGvValuesTW | RawGvCustomGsTW
|
|
81
|
+
export type GvTW = GvValuesTW | GvCustomGsTW
|
|
82
|
+
|
|
83
|
+
// termsetting types
|
|
46
84
|
export type GeneVariantTermSettingInstance = TermSettingInstance & {
|
|
47
|
-
q:
|
|
48
|
-
term:
|
|
85
|
+
q: GvQ
|
|
86
|
+
term: GvTerm
|
|
49
87
|
category2samplecount: any
|
|
50
88
|
groupSettingInstance?: any
|
|
51
89
|
}
|
|
52
90
|
|
|
91
|
+
// miscellaneous types
|
|
53
92
|
export type DtTerm = {
|
|
54
93
|
id: string
|
|
94
|
+
query: string
|
|
55
95
|
name: string
|
|
96
|
+
name_noOrigin: string
|
|
56
97
|
parent_id: any
|
|
57
98
|
isleaf: boolean
|
|
58
99
|
type: string
|
|
59
100
|
dt: number
|
|
60
101
|
origin?: string
|
|
61
|
-
values
|
|
62
|
-
min?: number
|
|
63
|
-
max?: number
|
|
102
|
+
values: TermValues
|
|
64
103
|
}
|
|
@@ -1,7 +1,7 @@
|
|
|
1
|
-
import { TermWrapper } from './tw.ts'
|
|
2
|
-
import { BaseQ } from './term.ts'
|
|
3
|
-
import { NumericTerm } from './numeric.ts'
|
|
4
|
-
import { TermSettingInstance } from '../termsetting.ts'
|
|
1
|
+
import type { TermWrapper } from './tw.ts'
|
|
2
|
+
import type { BaseQ } from './term.ts'
|
|
3
|
+
import type { NumericTerm } from './numeric.ts'
|
|
4
|
+
import type { TermSettingInstance } from '../termsetting.ts'
|
|
5
5
|
|
|
6
6
|
/*
|
|
7
7
|
--------EXPORTED--------
|
package/src/terms/q.ts
CHANGED
package/src/terms/samplelst.ts
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
|
-
import { BaseTerm, BaseQ } from './term.ts'
|
|
2
|
-
import { TermWrapper } from './tw.ts'
|
|
3
|
-
import { TermSettingInstance } from '../termsetting.ts'
|
|
1
|
+
import type { BaseTerm, BaseQ } from './term.ts'
|
|
2
|
+
import type { TermWrapper } from './tw.ts'
|
|
3
|
+
import type { TermSettingInstance } from '../termsetting.ts'
|
|
4
4
|
|
|
5
5
|
/*
|
|
6
6
|
--------EXPORTED--------
|
|
@@ -1,5 +1,5 @@
|
|
|
1
|
-
import { BaseTerm, BaseTW, GroupSettingQ, TermGroupSetting, TermValues } from './term.ts'
|
|
2
|
-
import { MinBaseQ } from './q.ts'
|
|
1
|
+
import type { BaseTerm, BaseTW, GroupSettingQ, TermGroupSetting, TermValues } from './term.ts'
|
|
2
|
+
import type { MinBaseQ } from './q.ts'
|
|
3
3
|
|
|
4
4
|
type SingleCellCellTypeBaseQ = MinBaseQ & { mode: 'discrete' | 'binary' }
|
|
5
5
|
|
|
@@ -1,8 +1,7 @@
|
|
|
1
|
-
import { TermWrapper } from './tw.ts'
|
|
2
|
-
import {
|
|
3
|
-
import {
|
|
4
|
-
import {
|
|
5
|
-
import { NumericTerm } from './numeric.ts'
|
|
1
|
+
import type { TermWrapper } from './tw.ts'
|
|
2
|
+
import type { GeneExpressionQ } from './geneExpression.ts'
|
|
3
|
+
import type { TermSettingInstance } from '../termsetting.ts'
|
|
4
|
+
import type { NumericTerm } from './numeric.ts'
|
|
6
5
|
|
|
7
6
|
/*
|
|
8
7
|
--------EXPORTED--------
|
package/src/terms/snp.ts
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
|
-
import { TermWrapper } from './tw.ts'
|
|
2
|
-
import { BaseQ, BaseTerm, GroupSettingQ, TermGroupSetting } from './term.ts'
|
|
3
|
-
import { TermSettingInstance } from '../termsetting.ts'
|
|
1
|
+
import type { TermWrapper } from './tw.ts'
|
|
2
|
+
import type { BaseQ, BaseTerm, GroupSettingQ, TermGroupSetting } from './term.ts'
|
|
3
|
+
import type { TermSettingInstance } from '../termsetting.ts'
|
|
4
4
|
|
|
5
5
|
/*
|
|
6
6
|
For term type 'snp'
|
package/src/terms/snps.ts
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
|
-
import { BaseTW, BaseQ, BaseTerm } from './term.ts'
|
|
2
|
-
import { TermSettingInstance, InstanceDom, UseCase } from '../termsetting.ts'
|
|
3
|
-
import { VocabApi } from '../vocab.ts'
|
|
4
|
-
import { Tvs, Filter } from '../filter.ts'
|
|
1
|
+
import type { BaseTW, BaseQ, BaseTerm } from './term.ts'
|
|
2
|
+
import type { TermSettingInstance, InstanceDom, UseCase } from '../termsetting.ts'
|
|
3
|
+
import type { VocabApi } from '../vocab.ts'
|
|
4
|
+
import type { Tvs, Filter } from '../filter.ts'
|
|
5
5
|
|
|
6
6
|
/*
|
|
7
7
|
--------EXPORTED--------
|