finish drafting all supported tracks; browser events API

Signed-off-by: eternal-flame-AD <[email protected]>
igvteam · Sep 2, 2024 · 2fd541c · 2fd541c
1 parent 6efe242
commit 2fd541c
Showing 1 changed file with 97 additions and 9 deletions.
diff --git a/js/igv.d.ts b/js/igv.d.ts
@@ -6,31 +6,41 @@ declare class Opaque<N extends string> {
     private readonly __opaque_brand: N;
 }
 
-export type TrackType = "annotation" | "alignment" | "variant" | "seg" | "cnvpytor" | "wig" | "merged" | "gwas" | "mut";
+export type TrackType =
+    "annotation" | "wig" | "alignment" | "variant" | "mut" | "seg" |
+    "gwas" | "interact" | "qtl" | "junction" | "cnvpytor" | "merged" | "arc";
 
 export type TrackLoad<T extends TrackType> =
     Tracks.TrackCommonOptions &
     (T extends "annotation" ? (Tracks.AnnotationTrackOptions & Tracks.TypeFormatPair<'annotation', Tracks.AnnotationFormat>) :
         T extends "wig" ? (Tracks.WigTrackOptions & Tracks.TypeFormatPair<'wig', Tracks.WigFormat>) :
-        T extends "merged" ? (Tracks.WigMergedTrackOptions & { type: 'merged' }) :
         T extends "alignment" ? (Tracks.AlignmentTrackOptions & Tracks.TypeFormatPair<'alignment', Tracks.AlignmentFormat>) :
-        T extends "variabt" ? (Tracks.VariantTrackOptions & Tracks.TypeFormatPair<'variant', Tracks.VariantFormat>) :
+        T extends "variant" ? (Tracks.VariantTrackOptions & Tracks.TypeFormatPair<'variant', Tracks.VariantFormat>) :
+        T extends "mut" ? (Tracks.MutationTrackOptions & Tracks.TypeFormatPair<'mut', Tracks.MutationFormat>) :
         T extends "seg" ? (Tracks.SegTrackOptions & Tracks.TypeFormatPair<'seg', Tracks.SegFormat>) :
-        T extends "cnvpytor" ? (Tracks.CnvPyTorTrackOptions & Tracks.TypeFormatPair<'cnvpytor', Tracks.CnvPyTorFormat>) :
         T extends "gwas" ? (Tracks.GWASTrackOptions<Tracks.GWASFormat> & Tracks.TypeFormatPair<'gwas', Tracks.GWASFormat>) :
-        T extends "mut" ? (Tracks.MutationTrackOptions & Tracks.TypeFormatPair<'mut', Tracks.MutationFormat>) :
+        T extends "interact" ? (Tracks.InteractTrackOptions & Tracks.TypeFormatPair<'interact', Tracks.InteractFormat>) :
+        T extends "qtl" ? (Tracks.QTLTrackOptions & Tracks.TypeFormatPair<'qtl', Tracks.QTLFormat>) :
+        T extends "junction" ? (Tracks.JunctionTrackOptions & Tracks.TypeFormatPair<'junction', Tracks.JunctionFormat>) :
+        T extends "cnvpytor" ? (Tracks.CnvPyTorTrackOptions & Tracks.TypeFormatPair<'cnvpytor', Tracks.CnvPyTorFormat>) :
+        T extends "merged" ? (Tracks.WigMergedTrackOptions & { type: 'merged' }) :
+        T extends "arc" ? (Tracks.ArcTrackOptions & Tracks.TypeFormatPair<'arc', Tracks.ArcFormat>) :
         never);
 
 export type TrackOf<T extends TrackType> =
     T extends "annotation" ? Tracks.Track :
+    T extends "wig" ? Tracks.Track :
     T extends "alignment" ? Tracks.AlignmentTrack :
     T extends "variant" ? Tracks.Track :
+    T extends "mut" ? Tracks.Track :
     T extends "seg" ? Tracks.Track :
+    T extends "gwas" ? Tracks.Track :
+    T extends "interact" ? Tracks.Track :
+    T extends "qtl" ? Tracks.Track :
+    T extends "junction" ? Tracks.Track :
     T extends "cnvpytor" ? Tracks.Track :
-    T extends "wig" ? Tracks.Track :
     T extends "merged" ? Tracks.Track :
-    T extends "gwas" ? Tracks.Track :
-    T extends "mut" ? Tracks.Track :
+    T extends "arc" ? Tracks.Track :
     never;
 
 
@@ -391,6 +401,59 @@ export namespace Tracks {
             attribute: string;
         });
     }
+
+    export type InteractFormat = "interact" | "bedpe" | "bigInteract";
+
+    export type InteractTrackOptions = {
+        arcType?: "nested" | "proportional" | "inView" | "partialInView";
+        arcOrientation?: "UP" | "DOWN";
+        alpha?: number;
+        thickness?: number;
+    }
+
+    export type QTLFormat = "qtl";
+
+    export type QTLTrackOptions = {
+        min?: number;
+        max?: number;
+        autoscalePercentile?: number;
+    }
+
+    export type JunctionFormat = "bed";
+
+    export type JunctionTrackFilteringOptions = {
+        minUniquelyMappedReads?: number;
+        minTotalReads?: number;
+        maxFractionMultiMappedReads?: number;
+        minSplicedAlignmentOverhang?: number;
+        hideStrand?: "+" | "-";
+        hideAnnotatedJunctions?: boolean;
+        hideUnannotatedJunctions?: boolean;
+        hideMotifs?: string[];
+    }
+
+    export type JunctionTrackOptions = ({
+        colorBy?: "numUniqueReads" | "numReads";
+        colorByNumReadsThreshold: number;
+    } | {
+        colorBy: "isAnnotatedJunction" | "strand" | "motif";
+        colorByNumReadsThreshold?: never;
+    }) & {
+        thicknessBasedOn?: "numUniqueReads" | "numReads" | "isAnnotatedJunction";
+        bounceHeightBasedOn?: "random" | "distance" | "thickness";
+        labelUniqueReadCount?: boolean;
+        labelMultiMappedReadCount?: boolean;
+        labelTotalReadCount?: boolean;
+        labelMotif?: boolean;
+        labelAnnotatedJunction?: string | null;
+        minSplicedAlignmentOverhang?: number;
+    } & JunctionTrackFilteringOptions;
+
+    export type ArcFormat = "bp";
+
+    export type ArcTrackOptions = {
+        arcOrientation?: "UP" | "DOWN";
+    }
 }
 
 type Nucleotide = 'A' | 'C' | 'G' | 'T' | 'N';
@@ -542,6 +605,29 @@ interface CreateOptExtras {
     tracks: TrackLoad<TrackType>[];
 }
 
+export namespace BrowserEvents {
+    export type EventType = "trackremoved" | "trackdrag" | "trackdragend" | "locuschange" | "trackclick" | "trackorderchanged";
+
+    export type EventPayload<T extends EventType> =
+        T extends "trackremoved" ? Tracks.Track[] :
+        T extends "locusChange" ? {
+            chr: string;
+            start: number;
+            end: number;
+            getLocusString: () => string;
+        }[] :
+        T extends "trackclick" ? {
+            name: string;
+            value: string;
+        } :
+        T extends "trackorderchanged" ? string[] :
+        never;
+
+    export type EventReturn<T extends EventType> =
+        T extends "trackclick" ? boolean :
+        void;
+}
+
 export type CreateOpt = GenomeOpt & CreateOptExtras;
 
 declare class ROISet {
@@ -566,7 +652,6 @@ declare class _Browser {
     loadGenome(genome: string | ReferenceGenome): Promise<void>;
     loadSessionObject(session: Opaque<'igv.js session JSON'>): void;
     loadSession(session: string): void;
-    // TODO: check the return type
     loadTrack<T extends TrackType>(track: TrackLoad<T>): Promise<TrackOf<T>>;
     loadSampleInfo({ url: string }): void;
     findTracks(func: (track: Tracks.Track) => boolean): Tracks.Track[];
@@ -589,6 +674,9 @@ declare class _Browser {
         end: number,
         interpolant: number,
     }) => void): void;
+
+    on<T extends BrowserEvents.EventType>(event: T, handler: (payload: BrowserEvents.EventPayload<T>) => BrowserEvents.EventReturn<T>): void;
+    off(event: BrowserEvents.EventType): void;
 }
 
 export type Browser = _Browser;