@sjcrh/proteinpaint-types 2.117.0 → 2.118.2

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.117.0",
+  "version": "2.118.2",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -522,33 +522,57 @@ type TrackLst = {
 	activeTracks: string[]
 }
 
+/** cnv segments are queried by coordinates, and can be filtered by segment length and/or value
+configs for types of cnv data
+- log(ratio)
+	{
+		cnvMaxLength:10000000
+		cnvGainCutoff:5
+		cnvLossCutoff:-5
+	}
+- copy number
+	{
+		cnvMaxLength:1000000
+		cnvMaxCopynumber:10
+		cnvMinCopynumber:1
+	}
+important: presence of filtering properties indiate the type of cnv quantification
+and will trigger rendering of ui controls
+*/
 type CnvSegment = {
-	byrange: CnvSegmentByRange
+	/** ds supplied ordynamically added getter */
+	get?: (q: any) => any
+	/** either file or get is required. file is bgzipped with columns:
+	1. chr
+	2. start, 0-based
+	3. stop
+	4. {"dt": 4, "mattr": {"origin": "somatic"}, "sample": "3332", "value": -1.0}
+	*/
+	file?: string
+
 	/****** rendering parameters ****
-not used as query parameter to filter segments
-value range for color scaling. default to 5. cnv segment value>this will use solid color
-*/
+	not used as query parameter to filter segments
+	value range for color scaling. default to 5. cnv segment value>this will use solid color
+	*/
 	absoluteValueRenderMax?: number
 	gainColor?: string
 	lossColor?: string
 
-	/*** filtering parameters ***
-default max length setting to restrict to focal events; if missing show all */
+	/** filter segments by max length to restrict to focal events; set to -1 to show all
+	allow to be missing, in such case will always show all */
 	cnvMaxLength?: number
 
-	/** TODO define value type, if logratio, or copy number */
-
-	/** following two cutoffs only apply to log ratio, cnv gain value is positive, cnv loss value is negative
-if cnv is gain, skip if value<this cutoff */
+	/** if cnv is quantified as log(ratio) or similar, must set these two properties
+	filter segments by following two cutoffs only apply to log ratio, cnv gain value is positive, cnv loss value is negative
+	*/
+	/** if value>0, skip if value<this cutoff, set to a large value e.g. 100 for not filtering */
 	cnvGainCutoff?: number
-	/** if cnv is loss, skip if value>this cutoff */
+	/** if value<0, skip if value>this cutoff, set to a large negative value e.g. -100 for not filtering */
 	cnvLossCutoff?: number
-}
-
-type CnvSegmentByRange = {
-	src: 'native' | 'gdcapi' | string
-	/** only for src=native */
-	file?: string
+	/** TODO if cnv is quantified as integer copy number, must set these properties; do not use for log(ratio)
+	 */
+	cnvMinCopynumber?: number
+	cnvMaxCopynumber?: number
 }
 
 /*
@@ -563,11 +587,11 @@ type Probe2Cnv = {
 */
 
 type RnaseqGeneCount = {
-	/** Name of the HDF5 or text file */
+	/** Name of the HDF5 file */
 	file: string
 	samplesFile?: string
-	/** Storage_type for storing data (HDF5 or text). Will deprecate text files in the future */
-	storage_type: 'text' | 'HDF5'
+	/** Storage_type for storing data (HDF5) */
+	storage_type: 'HDF5'
 }
 
 /** the metabolite query */
@@ -599,8 +623,6 @@ export type GeneExpressionQueryNative = {
 	samples?: number[]
 	/** dynamically added flag during launch */
 	nochr?: boolean
-	/** if true, the file is in HDF5 format */
-	hdf5File?: boolean
 	/** dynamically added getter */
 	get?: (param: any) => void
 	/** This dictionary is used to store/cache the default bins calculated for a geneExpression term when initialized in the fillTermWrapper */
@@ -611,7 +633,7 @@ export type GeneExpressionQuery = GeneExpressionQueryGdc | GeneExpressionQueryNa
 
 export type SingleCellGeneExpressionNative = {
 	src: 'native'
-	/** path to HDF5 files. for now only hdf5 is supported.
+	/** path to HDF5 files. for now only HDF5 is supported.
 	each is a gene-by-cell matrix for a sample, with ".h5" suffix. missing files are detected and handled */
 	folder: string
 	/** dynamically added getter */