@sjcrh/proteinpaint-types 2.123.0 → 2.124.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.123.0",
+  "version": "2.124.0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -607,6 +607,13 @@ type CnvSegment = {
 		- for others using mayGetGeneVariantData(), this is always disabled, as request won't have this flag
 	*/
 	requiresHardcodeCnvOnlyFlag?: true
+
+	/** CNV cutoffs (such as cnvGainCutoff, cnvLossCutoff, cnvMaxLength) that are applied to specific genes */
+	cnvCutoffsByGene?: {
+		[geneName: string]: {
+			[key: string]: any
+		}
+	}
 }
 
 /*
@@ -1172,9 +1179,12 @@ type Matrix = {
 	settings?: MatrixSettings
 	/** matrix-specific mclass override? */
 	mclass?: Mclass
-	// TODO: improve definitions below
+	/** filter to hide entire legend group, e.g. hide all CNV */
 	legendGrpFilter?: any
+	/** filter to hide categories or mclass, e.g. hide male, hide MISSENSE */
 	legendValueFilter?: any
+	/** matrix criteria for a CNV alteration */
+	cnvCutoffs?: any
 }
 
 // specific hierCluster type settings, should be named as "dataTYpe + Cluster"
@@ -1970,11 +1980,6 @@ export type Mds3 = BaseMds & {
 	// !!! TODO: improve these type definitions below !!!
 	getHostHeaders?: (q?: any) => any
 	serverconfigFeatures?: any
-	customTwQByType?: {
-		[termType: string]: {
-			[key: string]: any
-		}
-	}
 	getHealth?: (ds: any) => {
 		[key: string]: any
 	}

package/src/genome.ts

@@ -19,6 +19,12 @@ type TermDbs = {
 type TermDbsEntry = {
 	label: string
 	cohort: Cohort
+	/** list of geneset groups in db; required for geneORA and gsea
+	later allow ds override so ds can enable/disable some genesets..
+	*/
+	analysisGenesetGroups: { label: string; value: string }[]
+	/** required for gsea */
+	geneORAparam: { minCutoff: number; maxCutoff: number }
 }
 
 type DbStatement = {