@sjcrh/proteinpaint-types 2.188.1 → 2.190.0

package/src/terms/isoformExpression.ts

@@ -1,36 +0,0 @@
-import type { PresetNumericBins, NumericBaseTerm, NumTW, RawNumTW } from '../index.ts'
-
-/*
---------EXPORTED--------
-IsoformExpressionTerm
-IsoformExpressionTermWrapper
-*/
-
-type Isoform = {
-	kind?: 'isoform'
-	isoform: string
-	gene?: string
-	chr?: string
-	start?: number
-	stop?: number
-}
-
-type Coord = {
-	kind?: 'coord'
-	isoform?: string
-	gene?: string
-	chr: string
-	start: number
-	stop: number
-}
-
-export type IsoformExpressionTerm = NumericBaseTerm & {
-	type: 'isoformExpression'
-	bins?: PresetNumericBins
-} & (Isoform | Coord)
-
-export type IsoformExpressionTW = NumTW & { term: IsoformExpressionTerm }
-
-export type RawIsoformExpTerm = IsoformExpressionTerm & { name?: string }
-
-export type RawIsoformExpTW = RawNumTW & { term: RawIsoformExpTerm }

package/src/terms/metaboliteIntensity.ts

@@ -1,30 +0,0 @@
-import type { NumericBaseTerm, PresetNumericBins, NumTW, RawNumTW } from '../index.ts'
-
-/*
---------EXPORTED--------
-MetaboliteIntensityTermWrapper
-MetaboliteIntensityTermSettingInstance
-
-*/
-
-export type MetaboliteIntensityTerm = NumericBaseTerm & {
-	id?: string
-	name: string
-	type: 'metaboliteIntensity'
-	metabolite: string
-	bins?: PresetNumericBins
-	unit?: string
-}
-
-export type MetaboliteIntensityTW = NumTW & { term: MetaboliteIntensityTerm }
-
-export type RawMetaboliteIntensityTerm = NumericBaseTerm & {
-	id?: string
-	type: 'metaboliteIntensity'
-	metabolite: string
-	name?: string
-	bins?: PresetNumericBins
-	unit?: string
-}
-
-export type RawMetaboliteIntensityTW = RawNumTW & { term: RawMetaboliteIntensityTerm }

package/src/terms/numeric.ts

@@ -1,278 +0,0 @@
-import type {
-	MinBaseQ,
-	BaseTW,
-	TermValues,
-	BaseTerm,
-	GeneExpressionTerm,
-	IsoformExpressionTerm,
-	MetaboliteIntensityTerm,
-	ProteomeAbundanceTerm,
-	DateTerm,
-	SsGSEATerm,
-	DnaMethylationTerm,
-	SingleCellGeneExpressionTerm
-} from '../index.ts'
-
-export type RawRegularBin = Partial<RegularNumericBinConfig> & { preferredBins?: string }
-
-export type RawNumTWRegularBin = BaseTW & {
-	type?: 'NumTWRegularBin'
-	term: NumericTerm
-	q: RawRegularBin
-}
-
-export type RawCustomBin = Partial<CustomNumericBinConfig> & { preferredBins?: string }
-
-export type RawNumTWCustomBin = BaseTW & {
-	type?: 'NumTWCustomBin'
-	term: NumericTerm
-	q: RawCustomBin
-}
-
-export type RawNumTWCont = BaseTW & {
-	type?: 'NumTWCont'
-	term: NumericTerm
-	q: ContinuousNumericQ
-}
-
-export type RawNumTWSpline = BaseTW & {
-	type?: 'NumTWSpline'
-	term: NumericTerm
-	q: SplineNumericQ
-}
-
-export type RawNumTW = RawNumTWCustomBin | RawNumTWRegularBin | RawNumTWCont | RawNumTWSpline
-
-export type NumericBaseTerm = BaseTerm & {
-	/** tailored color scale for this term, so that when the term is used for color gradient in scatter, this set of colors will be used by default */
-	continuousColorScale?: { minColor: string; maxColor: string }
-	unit?: string
-}
-
-export type NumericDictTerm = NumericBaseTerm & {
-	id: string
-	type: 'integer' | 'float'
-	bins: PresetNumericBins
-	values?: TermValues
-}
-
-export type RawNumericDictTerm = NumericDictTerm & {
-	id?: string
-}
-
-export type NumericTerm =
-	| NumericDictTerm
-	| GeneExpressionTerm
-	| IsoformExpressionTerm
-	| MetaboliteIntensityTerm
-	| ProteomeAbundanceTerm
-	| DateTerm
-	| SsGSEATerm
-	| DnaMethylationTerm
-	| SingleCellGeneExpressionTerm
-
-export type StartUnboundedBin = {
-	// where possible, assign a concrete value (true) when it is known in advance,
-	// in which case, do not use an abstract type (boolean) to startunbounded
-	startunbounded: true
-	startinclusive?: false // cannot include an infinite bound
-	stop: number
-	stopinclusive?: boolean
-	stopunbounded?: false
-	label?: string
-	range?: string // alternative bin label
-}
-
-export type StopUnboundedBin = {
-	start: number
-	stopunbounded: true
-	startinclusive?: boolean
-	startunbounded?: false
-	stopinclusive?: false // cannot include an infinite bound
-	label?: string
-	range?: string // alternative bin label
-}
-
-// TODO??? should separate a fully bounded bin by startinclusive, stopinclusive
-// since neighboring bins must not contain the same boundary value
-export type FullyBoundedBin = {
-	startunbounded?: false
-	startinclusive?: boolean
-	start: number
-	stop: number
-	stopinclusive?: boolean
-	stopunbounded?: false
-	label?: string
-	range?: string // alternative bin label
-}
-
-export type NumericBin = StartUnboundedBin | FullyBoundedBin | StopUnboundedBin
-
-export type RangeEntry = NumericBin | { value: number; label: string }
-
-export type RegularNumericBinConfig = MinBaseQ & {
-	type: 'regular-bin' // another concrete value being assigned, instead of `string`
-	//regular-sized bins
-	mode?: 'discrete'
-	bin_size: number
-	// first_bin.stop is always required
-	first_bin: StartUnboundedBin | FullyBoundedBin
-
-	// if last_bin?.start is set, then a fixed last bin is used; otherwise it's not fixed and computed from data
-	last_bin?: StopUnboundedBin | FullyBoundedBin
-	label_offset?: number
-	startinclusive?: boolean
-	stopinclusive?: boolean
-	/** a d3-format value to format the bin boundary values.
-	 * Defaults to none, in which case the computed bin start and stop values
-	 * (float numbers in javascript) will be used as-is for labels.
-	 * Or, when using the browser UI to edit the numeric bin, the number of decimals
-	 * in the bin_size will be used as the number of fixed decimals;
-	 * for example, bin_size = 0.25 and bin_size = 0.250 will imply a ‘.2f’ and ‘.3f’ d3-format value, respectively.
-	 * Note that the generated bin labels may use integer values in some cases for less clutter, such as when bins.size = 1.
-	 *  */
-	rounding?: string
-	/** indicates the bin config was set when not enough data is available to compute bins,
-	 * may trigger resetting term.bins to avoid using dummy presetBins in TermdbVocab.setTermBins()
-	 * when the cohort changes
-	 */
-	isDummyPreset?: boolean
-}
-
-export type CustomNumericBinConfigLst = [NumericBin, ...NumericBin[]]
-
-export type CustomNumericBinConfig = MinBaseQ & {
-	type: 'custom-bin'
-	mode?: 'discrete' | 'binary'
-	// since ts will allow NumericBin[] to be empty,
-	// use this workaround to define a non-empty array
-	lst: CustomNumericBinConfigLst
-	preferredBins?: 'median'
-	/** indicates the bin config was set when not enough data is available to compute bins,
-	 * may trigger resetting term.bins to avoid using dummy presetBins in TermdbVocab.setTermBins()
-	 * when the cohort changes
-	 */
-	isDummyPreset?: boolean
-}
-
-export type PresetNumericBins = {
-	default: RegularNumericBinConfig | CustomNumericBinConfig
-	less: RegularNumericBinConfig | CustomNumericBinConfig
-	label_offset?: number
-	label_offset_ignored?: boolean
-	rounding?: string
-	min?: number
-	max?: number
-}
-
-export type BinnedNumericQ = RegularNumericBinConfig | CustomNumericBinConfig
-
-export type DiscreteNumericQ = BinnedNumericQ //&
-// MinBaseQ & {
-// 	mode: 'discrete' | 'binary'
-// }
-
-// TODO: test with live code that defines an actual binary q object
-export type BinaryNumericQ = MinBaseQ & {
-	mode: 'binary'
-	type: 'custom-bin'
-	// tuple type with 2 members
-	lst: [StartUnboundedBin | FullyBoundedBin, StopUnboundedBin | FullyBoundedBin]
-	cutoffType?: 'normal' | 'percentile'
-	cutoffPercentile?: number
-}
-
-export type ContinuousNumericQ = MinBaseQ & {
-	mode?: 'continuous'
-	// TODO: do not use a boolean, convert to a `transform: 'zscore' | ...` option
-	convert2ZScore?: boolean
-	//scale?: string
-	// todo below: q.type is expected to be undefined for now,
-	// but may be used later like in other q.modes,
-	// making type optional here makes NumericQ operations/conditions
-	// work consistently within the TermWrapper union type
-	type?: undefined
-	scale?: number
-}
-
-export type SplineNumericQ = MinBaseQ & {
-	mode: 'spline'
-	knots: {
-		value: number
-	}[]
-	// todo below: q.type is expected to be undefined for now,
-	// but may be used later like in other q.modes,
-	// making type optional here makes NumericQ operations/conditions
-	// work consistently within the TermWrapper union type
-	type?: undefined
-}
-
-export type NumericQ = DiscreteNumericQ | BinaryNumericQ | ContinuousNumericQ | SplineNumericQ
-
-export type NumericTW = BaseTW & {
-	//id: string
-	term: NumericTerm
-	q: NumericQ
-}
-
-export type NumTWDiscrete = BaseTW & {
-	type: 'NumTWDiscrete'
-	term: NumericTerm
-	q: DiscreteNumericQ
-}
-
-export type NumTWRegularBin = BaseTW & {
-	type: 'NumTWRegularBin'
-	term: NumericTerm
-	q: RegularNumericBinConfig
-}
-
-export type NumTWCustomBin = BaseTW & {
-	type: 'NumTWCustomBin'
-	term: NumericTerm
-	q: CustomNumericBinConfig
-}
-
-export type NumTWBinaryBin = BaseTW & {
-	type: 'NumTWBinaryBin'
-	term: NumericTerm
-	q: BinaryNumericQ
-}
-
-export type NumTWBinary = BaseTW & {
-	type: 'NumTWBinary'
-	term: NumericTerm
-	q: BinaryNumericQ
-}
-
-export type NumTWCont = BaseTW & {
-	type: 'NumTWCont'
-	term: NumericTerm
-	q: ContinuousNumericQ
-}
-
-export type NumTWSpline = BaseTW & {
-	type: 'NumTWSpline'
-	term: NumericTerm
-	q: SplineNumericQ
-}
-
-export type NumTW = NumTWRegularBin | NumTWCustomBin | NumTWBinary | NumTWCont | NumTWSpline
-export type NumTWDiscreteTypes = NumTWRegularBin | NumTWCustomBin //| NumTWBinary
-
-export type DefaultMedianQ = {
-	isAtomic?: true
-	mode: 'discrete'
-	type: 'custom-bin'
-	preferredBins: 'median'
-	lst: []
-}
-
-export type DefaultBinnedQ = {
-	isAtomic: true
-	mode: 'discrete'
-	type: 'regular-bin' | 'custom-bin'
-	preferredBins: 'default' | 'less'
-}
-
-export type DefaultNumericQ = NumericQ | DefaultBinnedQ | DefaultMedianQ

package/src/terms/proteomeAbundance.ts

@@ -1,38 +0,0 @@
-import type { NumericBaseTerm, PresetNumericBins, NumTW, RawNumTW } from '../index.ts'
-
-/*
---------EXPORTED--------
-ProteomeTermWrapper
-ProteomeTermSettingInstance
-
-*/
-
-export type ProteomeDetails = {
-	organism: string
-	assay: string
-	cohort: string
-}
-
-export type ProteomeAbundanceTerm = NumericBaseTerm & {
-	id?: string
-	name: string
-	type: 'proteomeAbundance'
-	protein: string
-	bins?: PresetNumericBins
-	unit?: string
-	/** organism, assay and cohort this term belongs to */
-	dataTypeDetails: ProteomeDetails
-}
-
-export type ProteomeAbundanceTW = NumTW & { term: ProteomeAbundanceTerm }
-
-export type RawProteomeAbundanceTerm = NumericBaseTerm & {
-	id?: string
-	type: 'proteomeAbundance'
-	protein: string
-	name?: string
-	bins?: PresetNumericBins
-	unit?: string
-}
-
-export type RawProteomeAbundanceTW = RawNumTW & { term: RawProteomeAbundanceTerm }

package/src/terms/q.ts

@@ -1,105 +0,0 @@
-//import type { CategoricalQ } from './q.ts'
-import type { Filter } from '../filter.js'
-
-// MinBaseQ is BaseQ without .mode and .type
-// MinBaseQ should eventually replace BaseQ because .mode and .type
-// should be specified in a term-type-specific manner
-export type MinBaseQ = {
-	/**Automatically set by fillTermWrapper()
-	Applies to barchart, survival plot, and cuminc plot.
-	Contains categories of a term to be hidden in its chart. This should only apply to client-side rendering, and should not be part of “dataName” when requesting data from server. Server will always provide a summary for all categories. It’s up to the client to show/hide categories.
-	This allows the key visibility to be stored in state, while toggling visibility will not trigger data re-request.
-	Currently termsetting menu does not manage this attribute. It’s managed by barchart legend.
-	*/
-	hiddenValues?: HiddenValues
-	/**indicates this object should not be extended by a copy-merge tool */
-	isAtomic?: true
-	name?: string
-	reuseId?: string
-}
-
-export type CategoricalBaseQ = MinBaseQ & {
-	mode?: 'discrete' | 'binary'
-}
-
-export type RawValuesQ = MinBaseQ & {
-	type?: 'values'
-	mode?: 'binary' | 'discrete' | 'values' // legacy support for 'values', will be converted to 'discrete'
-}
-
-export type RawPredefinedGroupsetQ = MinBaseQ & {
-	type: 'predefined-groupset'
-	mode?: 'binary' | 'discrete'
-	predefined_groupset_idx: number
-	/** deprecated nested object, will be handled by reshapeLegacyTW() in TwRouter */
-	groupsetting?: { inuse?: boolean } & GroupSettingQ
-}
-
-export type RawCustomGroupsetQ = MinBaseQ & {
-	type: 'custom-groupset'
-	mode?: 'binary' | 'discrete'
-	customset: {
-		groups: GroupEntry[]
-	}
-	/** deprecated nested object, will be handled by reshapeLegacyTW() in TwRouter */
-	groupsetting?: { inuse?: boolean } & GroupSettingQ
-	sampleCounts?: { key: string; value?: number; label?: string }[]
-}
-
-export type HiddenValues = {
-	[index: string]: number
-}
-
-/*** types supporting termwrapper q ***/
-
-export type ValuesQ = CategoricalBaseQ & {
-	type: 'values'
-}
-
-export type PredefinedGroupSettingQ = CategoricalBaseQ & {
-	type: 'predefined-groupset'
-	predefined_groupset_idx: number
-}
-
-export type CustomGroupSettingQ = CategoricalBaseQ & {
-	type: 'custom-groupset'
-	customset: BaseGroupSet
-}
-
-export type FilterQ = MinBaseQ & {
-	type: 'filter'
-}
-
-export type GroupSettingQ = ValuesQ | FilterQ | PredefinedGroupSettingQ | CustomGroupSettingQ
-
-export type ValuesGroup = {
-	name: string
-	type: 'values' | string // can remove boolean fallback once problematic js files are converted to .ts and can declare `type: 'values' as const`
-	values: { key: number | string; label: string }[]
-	uncomputable?: boolean // if true, do not include this group in computations
-}
-
-export type FilterGroup = {
-	name: string
-	type: 'filter'
-	filter: Filter
-	color: string
-}
-
-export type GroupEntry = ValuesGroup | FilterGroup
-
-export type BaseGroupSet = {
-	groups: GroupEntry[]
-}
-
-type Groupset = {
-	name: string
-	is_grade?: boolean
-	is_subcondition?: boolean
-	dt?: number // dt of groupset, used by geneVariant term
-} & BaseGroupSet
-
-export type TermGroupSetting = {
-	disabled: boolean // true when term has <= 2 values, otherwise false
-	lst?: Groupset[] // array of predefined groupsets
-}

package/src/terms/qualitative.ts

@@ -1,73 +0,0 @@
-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/samplelst.ts

@@ -1,34 +0,0 @@
-import type { BaseTerm, MinBaseQ } from '../index.ts'
-import type { TermWrapper } from './tw.ts'
-
-/*
---------EXPORTED--------
-SampleLstTermValues
-SampleLstQ
-SampleLstTerm
-SampleLstTW
-SampleLstSettingInstance
-
-*/
-
-export type SampleLstTermValues = {
-	[index: string | number]: {
-		name: string
-		inuse: boolean
-		list: { sampleId: string; sample: string }[]
-		values: any
-	}
-}
-
-export type SampleLstQ = MinBaseQ & {
-	groups: SampleLstTermValues
-}
-
-export type SampleLstTerm = BaseTerm & {
-	values: SampleLstTermValues
-}
-
-export type SampleLstTW = TermWrapper & {
-	q: SampleLstQ
-	term: SampleLstTerm
-}

package/src/terms/singleCellCellType.ts

@@ -1,18 +0,0 @@
-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 */
-	/** single cell terms require a sample to read the term values, they are associated with a sample */
-	sample: object
-	/** 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 RawSingleCellCellTypeTerm = SingleCellCellTypeTerm & {
-	groupsetting?: TermGroupSetting
-	values?: TermValues
-}

package/src/terms/singleCellGeneExpression.ts

@@ -1,32 +0,0 @@
-// import type { BaseTerm } from '../index.ts'
-import type { PresetNumericBins, NumericBaseTerm, NumTW, RawNumTW } from '../index.ts'
-
-type Gene = {
-	kind?: 'gene'
-	gene: string
-	chr?: string
-	start?: number
-	stop?: number
-}
-
-type Coord = {
-	kind?: 'coord'
-	gene?: string
-	chr: string
-	start: number
-	stop: number
-}
-
-export type SingleCellGeneExpressionTerm = NumericBaseTerm & {
-	type: 'singleCellGeneExpression'
-	gene: string
-	sample: string
-	unit: string
-	bins?: PresetNumericBins
-} & (Gene | Coord)
-
-export type SingleCellGeneExpressionTermTW = NumTW & { term: SingleCellGeneExpressionTerm }
-
-export type RawSingleCellGeneExpTerm = SingleCellGeneExpressionTerm & { name?: string }
-
-export type RawSingleCellGeneExpTW = RawNumTW & { term: RawSingleCellGeneExpTerm }

package/src/terms/snp.ts

@@ -1,24 +0,0 @@
-import type { TermGroupSetting, TermValues, BaseTerm } from '../index.ts'
-
-/*
-For term type 'snp'
-*/
-
-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 RawSnpTerm = SnpTerm & {
-	groupsetting?: TermGroupSetting
-	values?: TermValues
-}