@sjcrh/proteinpaint-types 2.185.0 → 2.187.0

package/dist/termdb.percentile.js

@@ -2,7 +2,7 @@ import {
   percentilePayload,
   validPercentileRequest,
   validPercentileResponse
-} from "./chunk-ONNT3XV7.js";
+} from "./chunk-I3QGRA7O.js";
 import "./chunk-YNHC5SXO.js";
 export {
   percentilePayload,

package/dist/termdb.profileForms2Scores.js

@@ -0,0 +1,11 @@
+import {
+  ProfileForms2ScoresPayload,
+  validProfileForms2ScoresRequest,
+  validProfileForms2ScoresResponse
+} from "./chunk-5N7V62ZL.js";
+import "./chunk-YNHC5SXO.js";
+export {
+  ProfileForms2ScoresPayload,
+  validProfileForms2ScoresRequest,
+  validProfileForms2ScoresResponse
+};

package/dist/termdb.singlecellDEgenes.js

@@ -2,7 +2,7 @@ import {
   termdbSingleCellDEgenesPayload,
   validTermdbSingleCellDEgenesRequest,
   validTermdbSingleCellDEgenesResponse
-} from "./chunk-NLANDPY7.js";
+} from "./chunk-OCH5BJCV.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbSingleCellDEgenesPayload,

package/dist/termdb.termsbyids.js

@@ -2,7 +2,7 @@ import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-UWK6LBTQ.js";
+} from "./chunk-F2QRI6B2.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termsByIdsPayload,

package/dist/termdb.topTermsByType.js

@@ -2,7 +2,7 @@ import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-2NINVZOB.js";
+} from "./chunk-AYTV7V46.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbTopTermsByTypePayload,

package/dist/termdb.topVariablyExpressedGenes.js

@@ -2,7 +2,7 @@ import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
-} from "./chunk-QMEKJW2A.js";
+} from "./chunk-DPJUULKQ.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbTopVariablyExpressedGenesPayload,

package/dist/termdb.violinBox.js

@@ -2,7 +2,7 @@ import {
   validViolinBoxRequest,
   validViolinBoxResponse,
   violinBoxPayload
-} from "./chunk-WNUWRPXG.js";
+} from "./chunk-IIWTMQJZ.js";
 import "./chunk-YNHC5SXO.js";
 export {
   validViolinBoxRequest,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.185.0",
+  "version": "2.187.0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -734,9 +734,21 @@ type ProteomeAssayConfig = {
 export type ProteomeAbundanceQuery = {
 	/** database file path */
 	dbfile?: string
-	overlayTerm?: BaseTerm
-	/** document structure */
-	assays: {
+	/** organism-keyed structure (new format) */
+	organisms?: {
+		[organism: string]: {
+			overlayTerm: BaseTerm
+			columnIdx: number
+			columnValue?: string
+			/** genome assembly name for this organism, e.g. 'hg38' or 'mm10' */
+			genomeName?: string
+			assays: {
+				[assayName: string]: ProteomeAssayConfig
+			}
+		}
+	}
+	/** flat assays structure (legacy format) */
+	assays?: {
 		[assayName: string]: ProteomeAssayConfig
 	}
 	samples?: number[]
@@ -1377,6 +1389,8 @@ type MatrixSettings = {
 	cnvUnit?: 'log2ratio' | 'segmedian'
 	/** whether to show white cell border for SNVindel in oncoPrint mode */
 	oncoPrintSNVindelCellBorder?: boolean
+	/** use a geneset edit UI without or with initial radio inputs */
+	genesetEditUiVersion?: '' | 'withTabs'
 }
 
 type NumericDictTermClusterSettings = {

package/src/routes/termdb.DE.ts

@@ -94,13 +94,23 @@ export type VolcanoData<T extends DataEntry> = {
 /** Coordinate metadata returned by the `volcano` renderer, used by the client to overlay
  * interactive top-significant circles on top of the server-drawn PNG. */
 export type PlotExtent = {
-	/** Data-space x domain used during rendering. */
+	/** Padded data-space x domain — used to position overlay dots so points near
+	 * the real-data edges stay fully visible (mirror of manhattan's yPlot domain). */
 	xMin: number
 	xMax: number
-	/** Data-space y domain used during rendering (on -log10 p-value scale). */
+	/** Padded data-space y domain (on -log10 p-value scale). */
 	yMin: number
 	yMax: number
-	/** PNG canvas dimensions. */
+	/** Unpadded data-space x domain — used for the visible axis labels/ticks
+	 * so the axis only spans the real data region. */
+	xMinUnpadded: number
+	xMaxUnpadded: number
+	/** Unpadded data-space y domain. */
+	yMinUnpadded: number
+	yMaxUnpadded: number
+	/** Dot radius in pixels (echoed back so overlay rings match the PNG). */
+	dotRadiusPx: number
+	/** PNG canvas dimensions (already include 2*dotRadiusPx of padding). */
 	pixelWidth: number
 	pixelHeight: number
 	/** Inner drawing rect inside the PNG (after axis margins). Client overlay circles

package/src/routes/termdb.cluster.ts

@@ -66,7 +66,7 @@ export type TermdbClusterRequestProteomeAbundance = TermdbClusterRequestBase & {
 	terms: ProteomeAbundanceTW[]
 	/** perform z-score transformation on values */
 	zScoreTransformation?: string
-	/** assay type and cohort for the selected proteome data */
+	/** organism, assay type and cohort for the selected proteome data */
 	proteomeDetails: ProteomeDetails
 }
 

package/src/routes/termdb.profileForms2Scores.ts

@@ -0,0 +1,25 @@
+import type { RoutePayload } from './routeApi.js'
+
+export type ProfileForms2ScoresRequest = {
+	// q is optional: term wrappers from getMultivalueTWs() carry no q field,
+	// and JSON.stringify drops `q: undefined`, so the field may be absent on the wire.
+	scoreTerms: { term: { id: string }; q?: any }[]
+	scScoreTerms?: { term: { id: string }; q?: any }[]
+	filter?: any
+	filterByUserSites?: boolean
+}
+
+export type ProfileForms2ScoresResponse = {
+	term2Score: { [termId: string]: { [category: string]: number } }
+	sites: { label: string; value: string }[]
+	n: number
+}
+
+export const ProfileForms2ScoresPayload: RoutePayload = {
+	request: {
+		typeId: 'ProfileForms2ScoresRequest'
+	},
+	response: {
+		typeId: 'ProfileForms2ScoresResponse'
+	}
+}

package/src/terms/proteomeAbundance.ts

@@ -8,6 +8,7 @@ ProteomeTermSettingInstance
 */
 
 export type ProteomeDetails = {
+	organism: string
 	assay: string
 	cohort: string
 }
@@ -19,7 +20,7 @@ export type ProteomeAbundanceTerm = NumericBaseTerm & {
 	protein: string
 	bins?: PresetNumericBins
 	unit?: string
-	/** assay and cohort this term belongs to */
+	/** organism, assay and cohort this term belongs to */
 	proteomeDetails: ProteomeDetails
 }