@sjcrh/proteinpaint-types 2.182.0 → 2.183.0

package/src/index.ts

@@ -50,6 +50,7 @@ export * from './routes/termdb.dmr.ts'
 export * from './routes/termdb.isoformAvailability.ts'
 export * from './routes/termdb.numericcategories.ts'
 export * from './routes/termdb.percentile.ts'
+export * from './routes/termdb.proteome.ts'
 export * from './routes/termdb.runChart.ts'
 export * from './routes/termdb.rootterm.ts'
 export * from './routes/termdb.termchildren.ts'

package/src/routes/termdb.proteome.ts

@@ -0,0 +1,13 @@
+import type { RoutePayload } from './routeApi.js'
+
+export type TermdbProteomeRequest = any
+export type TermdbProteomeResponse = any
+
+export const termdbProteomePayload: RoutePayload = {
+	request: {
+		typeId: 'TermdbProteomeRequest'
+	},
+	response: {
+		typeId: 'TermdbProteomeResponse'
+	}
+}

package/src/terms/dnaMethylation.ts

@@ -3,16 +3,25 @@ import type { NumericBaseTerm, NumericQ, PresetNumericBins, NumTW, RawNumTW } fr
 export type DnaMethylationQ = NumericQ & { dt?: number }
 
 export type DnaMethylationTerm = NumericBaseTerm & {
-	/** term.id: plan to be concatenated string value "chr:start-stop" */
-	/** term.name: can be user-assigned */
 	type: 'dnaMethylation'
+	/** concatenated string value "chr:start-stop" */
+	id?: string
 	chr: string
 	start: number
 	stop: number
+	/** Type used to categorize the genomic feature */
+	genomicFeatureType: 'gene' | 'promoter' | 'region' | 'enhancer'
 	bins?: PresetNumericBins
 }
 
-export type RawDnaMethylationTerm = DnaMethylationTerm & { name?: string }
+export type RawDnaMethylationTerm = DnaMethylationTerm & {
+	/** Name of the genomic feature, e.g., gene name or promoter id/name, etc.
+	 * Different than .name, which includes the genomic coordinates and unit,
+	 * and is used for display purposes.*/
+	featureName?: string
+	name?: string
+	unit?: string
+}
 
 export type DnaMethylationTW = NumTW & { term: DnaMethylationTerm }
 

package/src/terms/termCollection.ts

@@ -10,7 +10,7 @@ type BaseTermCollection = BaseTerm & {
 	type: 'termCollection'
 	/** list of term.ids that are available in this collection. this is used in request payload and server side */
 	termIds?: string[]
-	/** list of term objs corresponding to termIds[]. 
+	/** list of term objs corresponding to termIds[].
 	this is generated on server init, and sent to client, so client has easy access to show name of every term */
 	termlst: BaseTerm[]
 	/** TODO purpose */
@@ -20,6 +20,10 @@ type BaseTermCollection = BaseTerm & {
 			[prop: string]: any
 		}
 	}
+	/** When true, member terms are non-dictionary terms (e.g. isoformExpression).
+	 *  getData() expands them into individual tws for existing handlers, then
+	 *  reconstitutes the grouped shape after data is returned. */
+	isCustom?: boolean
 }
 
 export type NumericTermCollection = BaseTermCollection & {
@@ -60,6 +64,7 @@ export type RawNumericTermCollection = {
 		}
 	}
 	numerators?: string[]
+	isCustom?: boolean
 }
 
 /** Pre-fill shape for a categorical termCollection (memberType set by TermCollection.fill()) */
@@ -75,6 +80,7 @@ export type RawCategoricalTermCollection = {
 		}
 	}
 	categoryKeys?: CategoryKey[]
+	isCustom?: boolean
 }
 
 export type RawTermCollection = RawNumericTermCollection | RawCategoricalTermCollection