@sjcrh/proteinpaint-types 2.146.4-1 → 2.147.2-0

package/src/terms/qualitative.ts

@@ -0,0 +1,73 @@
+import type {
+	GroupSettingQ,
+	ValuesQ,
+	BaseTW,
+	PredefinedGroupSettingQ,
+	CustomGroupSettingQ,
+	RawCategoricalTerm,
+	CategoricalTerm,
+	RawSnpTerm,
+	SnpTerm,
+	RawSingleCellCellTypeTerm,
+	SingleCellCellTypeTerm
+} from '../index.ts'
+import type { RawValuesQ, RawPredefinedGroupsetQ, RawCustomGroupsetQ, MinBaseQ } from './q.ts'
+
+/**
+ * A raw qualitative termwrapper object, before filling-in
+ *
+ * test:QualitativeQ:
+ *
+ * @category TW
+ */
+
+export type RawQualTerm = RawCategoricalTerm | RawSnpTerm | RawSingleCellCellTypeTerm
+export type QualTerm = CategoricalTerm | SnpTerm | SingleCellCellTypeTerm
+
+export type RawQualTWValues = BaseTW & {
+	type?: 'QualTWValues'
+	/** must already exist, for dictionary terms, TwRouter.fill() will use mayHydrateDictTwLst() */
+	term: RawQualTerm
+	q: RawValuesQ
+}
+
+export type RawQualTWPredefinedGS = BaseTW & {
+	type?: 'QualTWPredefinedGS'
+	term: RawQualTerm
+	q: RawPredefinedGroupsetQ
+}
+
+export type RawQualTWCustomGS = BaseTW & {
+	type?: 'QualTWCustomGS'
+	term: RawQualTerm
+	q: RawCustomGroupsetQ
+}
+
+export type RawQualTW = RawQualTWValues | RawQualTWPredefinedGS | RawQualTWCustomGS
+
+export type QualBaseQ = MinBaseQ & {
+	mode?: 'discrete' | 'binary'
+}
+
+export type QualQ = GroupSettingQ | ValuesQ
+
+export type QualTWValues = BaseTW & {
+	//id: string
+	term: QualTerm
+	q: ValuesQ
+	type: 'QualTWValues'
+}
+
+export type QualTWPredefinedGS = BaseTW & {
+	term: QualTerm
+	q: PredefinedGroupSettingQ
+	type: 'QualTWPredefinedGS'
+}
+
+export type QualTWCustomGS = BaseTW & {
+	term: QualTerm
+	q: CustomGroupSettingQ
+	type: 'QualTWCustomGS'
+}
+
+export type QualTW = QualTWValues | QualTWPredefinedGS | QualTWCustomGS

package/src/terms/singleCellCellType.ts

@@ -1,22 +1,18 @@
-import type { BaseTerm, BaseTW, GroupSettingQ, TermGroupSetting, TermValues } from '../index.ts'
-import type { MinBaseQ } from './q.ts'
-
-type SingleCellCellTypeBaseQ = MinBaseQ & { mode: 'discrete' | 'binary' }
-
-export type SingleCellCellTypeQ = SingleCellCellTypeBaseQ & GroupSettingQ
+import type { BaseTerm, TermGroupSetting, TermValues } from '../index.ts'
 
 export type SingleCellCellTypeTerm = BaseTerm & {
 	type: 'singleCellCellType'
 	/** the cell types may be also cell attributes like CNV, Fusion, etc */
-	values: TermValues
 	/** single cell terms require a sample to read the term values, they are associated with a sample */
 	sample: string
 	/** the plot defined in the dataset contains a column with the term values for the sample, it needs to be passed to read the sample values */
 	plot: string
 	groupsetting: TermGroupSetting
+	// may be used to hide
+	values: TermValues
 }
 
-export type SingleCellCellTypeTW = BaseTW & {
-	term: SingleCellCellTypeTerm
-	q: SingleCellCellTypeQ
+export type RawSingleCellCellTypeTerm = SingleCellCellTypeTerm & {
+	groupsetting?: TermGroupSetting
+	values?: TermValues
 }

package/src/terms/snp.ts

@@ -1,28 +1,24 @@
-import type { BaseTW, MinBaseQ, BaseTerm, GroupSettingQ, TermGroupSetting } from '../index.ts'
-import type { TermSettingInstance } from '../termsetting.ts'
+import type { TermGroupSetting, TermValues, BaseTerm } from '../index.ts'
 
 /*
 For term type 'snp'
 */
 
-export type SnpQ = MinBaseQ & GroupSettingQ
-
 export type SnpTerm = BaseTerm & {
+	type: 'snp'
+	id: string
+	name: string
 	chr: string
 	start: number
 	stop: number
 	ref: string
 	alt: string[]
 	groupsetting: TermGroupSetting
+	// may be used to hide
+	values: TermValues
 }
 
-export type SnpTW = BaseTW & {
-	type: 'SnpTW'
-	q: SnpQ
-	term: SnpTerm
-}
-
-export type SnpTermSettingInstance = TermSettingInstance & {
-	q: SnpQ
-	term: SnpTerm
+export type RawSnpTerm = SnpTerm & {
+	groupsetting?: TermGroupSetting
+	values?: TermValues
 }

package/src/terms/ssGSEA.ts

@@ -11,12 +11,16 @@ export type SsGSEATerm = NumericBaseTerm & {
 	/** term.name: geneset db term name for native term, and user-defined name for custom term */
 	/** custom term has list of gene names used for computing score */
 	genes?: string[]
-	name?: string
+	name: string
 	type: 'ssGSEA'
 	bins?: PresetNumericBins
 	unit?: string
 }
 
+export type RawSsGSEATerm = SsGSEATerm & {
+	name?: string
+}
+
 export type SsGSEATW = NumTW & { term: SsGSEATerm }
 
 export type RawSsGSEATW = RawNumTW & { term: SsGSEATerm }

package/src/terms/term.ts

@@ -1,10 +1,10 @@
 import type { Filter } from '../filter.js'
-import type { CategoricalTerm } from './categorical.js'
 import type { ConditionTerm } from './condition.js'
 import type { NumericTerm } from './numeric.js'
 import type { GvTerm } from './geneVariant.js'
 import type { SampleLstTerm } from './samplelst.js'
 import type { SnpsTerm } from './snps.js'
+import type { QualTerm } from './qualitative.ts'
 
 /**
  * @param id      term.id for dictionary terms, undefined for non-dictionary terms
@@ -42,7 +42,7 @@ export type BaseTerm = {
 }
 
 // NumericTerm includes integer, float, date, geneExpression, metaboliteIntensity, and other non-dict terms
-export type Term = BaseTerm & (NumericTerm | CategoricalTerm | ConditionTerm | SampleLstTerm | SnpsTerm | GvTerm)
+export type Term = BaseTerm & (NumericTerm | ConditionTerm | SampleLstTerm | SnpsTerm | GvTerm | QualTerm)
 
 /*** types supporting Term types ***/
 

package/src/terms/tw.ts

@@ -1,10 +1,9 @@
 import type { SnpsQ, SnpsTW } from './snps.ts'
-import type { SnpQ, SnpTW } from './snp.ts'
 import type { ConditionQ, ConditionTW } from './condition.ts'
 import type { SampleLstQ } from './samplelst.ts'
-import type { CatTWTypes, CategoricalQ } from './categorical.ts'
 import type { NumTW, NumericQ } from './numeric.ts'
 import type { GvTW, GvQ } from './geneVariant.ts'
+import type { QualTW, QualQ } from './qualitative.ts'
 
 export type BaseTW = {
 	id?: string
@@ -21,9 +20,9 @@ export type BaseTW = {
 	valueFilter?: any
 }
 
-export type TermWrapper = CatTWTypes | NumTW | GvTW | ConditionTW | SnpsTW | SnpTW
+export type TermWrapper = NumTW | GvTW | ConditionTW | SnpsTW | QualTW
 
-export type Q = CategoricalQ | NumericQ | GvQ | ConditionQ | SnpsQ | SnpQ | SampleLstQ // | other q
+export type Q = NumericQ | GvQ | ConditionQ | SnpsQ | SampleLstQ | QualQ // | other q
 
 //export type TermWrapper = CategoricalTW | NumericTW | SnpsTW | (BaseTW & { term: Term; q: Q })
 export type TwLst = TermWrapper[]