gosling.js 2.0.0-alpha.1 → 2.0.0-alpha.11

package/dist/demo/gosling-component.d.ts

@@ -1,4 +1,4 @@
-import { type RefObject } from 'react';
+import { type Ref, type ReactElement } from 'react';
 import { PixiManager } from '@pixi-manager';
 import { type UrlToFetchOptions } from '../src/compiler/compile';
 import type { TrackInfo } from 'src/compiler/bounding-box';
@@ -14,14 +14,17 @@ interface GoslingComponentProps {
     padding?: number;
     theme?: Theme;
     urlToFetchOptions?: UrlToFetchOptions;
-    ref?: RefObject<GoslingRef>;
+    ref?: Ref<GoslingRef>;
+    /** A callback function to notify that visualization has been rendered for the first time */
     visualized?: () => void;
+    /** A callback function to notify that visualization has been resized. Only called when responsive design is used. */
+    resized?: () => void;
 }
-export declare function GoslingComponent(props: GoslingComponentProps): JSX.Element;
+export declare function GoslingComponent(props: GoslingComponentProps): ReactElement;
 /**
  * This is the main function. It takes a Gosling spec and renders it using the PixiManager
  */
-export declare function renderGosling(gs: GoslingSpec, container: HTMLDivElement, pixiManager: PixiManager, theme: Theme, urlToFetchOptions?: UrlToFetchOptions): {
+export declare function renderGosling(gs: GoslingSpec, container: HTMLDivElement, pixiManager: PixiManager, theme: Theme, urlToFetchOptions?: UrlToFetchOptions, resized?: () => void): {
     plots: {};
     pixiManager: PixiManager;
     size: import("src/compiler/bounding-box").Size;

package/dist/demo/gosling-component.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"gosling-component.d.ts","sourceRoot":"","sources":["../../demo/gosling-component.tsx"],"names":[],"mappings":"AAAA,OAAc,EAAuB,KAAK,GAAG,EAAE,KAAK,YAAY,EAAuB,MAAM,OAAO,CAAC;AACrG,OAAO,EAAE,WAAW,EAAE,MAAM,eAAe,CAAC;AAC5C,OAAO,EAAW,KAAK,iBAAiB,EAAE,MAAM,yBAAyB,CAAC;AAI1E,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,2BAA2B,CAAC;AAC3D,OAAO,KAAK,EAAE,WAAW,EAAE,KAAK,EAAE,MAAM,YAAY,CAAC;AAErD,OAAO,EAAE,WAAW,EAAE,MAAM,gBAAgB,CAAC;AAG7C,MAAM,MAAM,UAAU,GAAG;IAAE,GAAG,EAAE,UAAU,CAAC,OAAO,WAAW,CAAC,CAAA;CAAE,CAAC;AAIjE,UAAU,qBAAqB;IAC3B,IAAI,CAAC,EAAE,WAAW,CAAC;IACnB,EAAE,CAAC,EAAE,MAAM,CAAC;IACZ,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,KAAK,CAAC,EAAE,KAAK,CAAC;IACd,iBAAiB,CAAC,EAAE,iBAAiB,CAAC;IACtC,GAAG,CAAC,EAAE,GAAG,CAAC,UAAU,CAAC,CAAC;IACtB,4FAA4F;IAC5F,UAAU,CAAC,EAAE,MAAM,IAAI,CAAC;IACxB,qHAAqH;IACrH,OAAO,CAAC,EAAE,MAAM,IAAI,CAAC;CACxB;AAED,wBAAgB,gBAAgB,CAAC,KAAK,EAAE,qBAAqB,GAAG,YAAY,CAwD3E;AAED;;GAEG;AACH,wBAAgB,aAAa,CACzB,EAAE,EAAE,WAAW,EACf,SAAS,EAAE,cAAc,EACzB,WAAW,EAAE,WAAW,EACxB,KAAK,EAAE,KAAK,EACZ,iBAAiB,CAAC,EAAE,iBAAiB,EACrC,OAAO,CAAC,EAAE,MAAM,IAAI;;;;;;;;EA2DvB"}

package/dist/demo/linking/linkedEncoding.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"linkedEncoding.d.ts","sourceRoot":"","sources":["../../../demo/linking/linkedEncoding.ts"],"names":[],"mappings":"AAWA,OAAO,EAAU,KAAK,MAAM,EAAE,MAAM,sBAAsB,CAAC;AAC3D,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,YAAY,CAAC;AAK9C;;GAEG;AACH,MAAM,WAAW,cAAc;IAC3B,SAAS,EAAE,MAAM,CAAC;IAClB,MAAM,EAAE,MAAM,CAAC;IACf,MAAM,EAAE;QACJ,EAAE,EAAE,MAAM,CAAC;QACX,QAAQ,EAAE,GAAG,GAAG,GAAG,GAAG,OAAO,CAAC;KACjC,EAAE,CAAC;CACP;AAkCD;;GAEG;AACH,wBAAgB,kBAAkB,CAAC,EAAE,EAAE,WAAW,oBAwBjD"}
+{"version":3,"file":"linkedEncoding.d.ts","sourceRoot":"","sources":["../../../demo/linking/linkedEncoding.ts"],"names":[],"mappings":"AAUA,OAAO,EAAU,KAAK,MAAM,EAAE,MAAM,sBAAsB,CAAC;AAC3D,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,YAAY,CAAC;AAK9C;;GAEG;AACH,MAAM,WAAW,cAAc;IAC3B,SAAS,EAAE,MAAM,CAAC;IAClB,MAAM,EAAE,MAAM,CAAC;IACf,MAAM,EAAE;QACJ,EAAE,EAAE,MAAM,CAAC;QACX,QAAQ,EAAE,GAAG,GAAG,GAAG,GAAG,OAAO,CAAC;KACjC,EAAE,CAAC;CACP;AAkCD;;GAEG;AACH,wBAAgB,kBAAkB,CAAC,EAAE,EAAE,WAAW,oBAwBjD"}

package/dist/demo/renderer/dataFetcher.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"dataFetcher.d.ts","sourceRoot":"","sources":["../../../demo/renderer/dataFetcher.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAC;AAEnD,OAAO,EACH,iBAAiB,EACjB,cAAc,EACd,cAAc,EACd,eAAe,EACf,cAAc,EACd,cAAc,EACd,cAAc,EACjB,MAAM,gBAAgB,CAAC;AACxB,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,sBAAsB,CAAC;AAM9D,OAAO,KAAK,EAAE,aAAa,EAAE,WAAW,EAAE,MAAM,8BAA8B,CAAC;AAE/E,wBAAgB,cAAc,CAAC,IAAI,EAAE,WAAW,GAAG,aAAa,EAAE,iBAAiB,CAAC,EAAE,iBAAiB;;;;;;;;;;;eA0CtG"}
+{"version":3,"file":"dataFetcher.d.ts","sourceRoot":"","sources":["../../../demo/renderer/dataFetcher.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAC;AAEnD,OAAO,EACH,iBAAiB,EACjB,cAAc,EACd,cAAc,EACd,eAAe,EACf,cAAc,EACd,cAAc,EACd,cAAc,EACjB,MAAM,gBAAgB,CAAC;AACxB,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,sBAAsB,CAAC;AAM9D,OAAO,KAAK,EAAE,aAAa,EAAE,WAAW,EAAE,MAAM,8BAA8B,CAAC;AAE/E,wBAAgB,cAAc,CAAC,IAAI,EAAE,WAAW,GAAG,aAAa,EAAE,iBAAiB,CAAC,EAAE,iBAAiB;;;;;;;;;;;eA4CtG"}

package/dist/demo/renderer/main.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"main.d.ts","sourceRoot":"","sources":["../../../demo/renderer/main.ts"],"names":[],"mappings":"AAOA,OAAO,EAAE,KAAK,SAAS,EAAa,MAAM,mBAAmB,CAAC;AAE9D,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,2BAA2B,CAAC;AAGhE,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,eAAe,CAAC;AAEjD,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,sBAAsB,CAAC;AAK9D;;;;GAIG;AACH,wBAAgB,eAAe,CAC3B,SAAS,EAAE,SAAS,EAAE,EACtB,eAAe,EAAE,cAAc,EAAE,EACjC,WAAW,EAAE,WAAW,EACxB,iBAAiB,CAAC,EAAE,iBAAiB,2BAiHxC"}
+{"version":3,"file":"main.d.ts","sourceRoot":"","sources":["../../../demo/renderer/main.ts"],"names":[],"mappings":"AASA,OAAO,EAAE,KAAK,SAAS,EAAa,MAAM,mBAAmB,CAAC;AAE9D,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,2BAA2B,CAAC;AAGhE,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,eAAe,CAAC;AAEjD,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,sBAAsB,CAAC;AAO9D;;;;GAIG;AACH,wBAAgB,eAAe,CAC3B,SAAS,EAAE,SAAS,EAAE,EACtB,eAAe,EAAE,cAAc,EAAE,EACjC,WAAW,EAAE,WAAW,EACxB,iBAAiB,CAAC,EAAE,iBAAiB,2BAyIxC"}

package/dist/demo/track-def/axis.d.ts

@@ -13,7 +13,7 @@ export declare function getAxisTrackDef(track: ProcessedTrack, boundingBox: {
     y: number;
     width: number;
     height: number;
-}, theme: Required<CompleteThemeDeep>): [trackBbox: {
+}, theme: Required<CompleteThemeDeep>): [{
     x: number;
     y: number;
     width: number;

package/dist/demo/track-def/axis.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"axis.d.ts","sourceRoot":"","sources":["../../../demo/track-def/axis.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,gBAAgB,EAAE,MAAM,4BAA4B,CAAC;AAQnE,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,4BAA4B,CAAC;AAEpE,OAAO,EAAa,KAAK,QAAQ,EAAE,MAAM,QAAQ,CAAC;AAClD,OAAO,KAAK,EAA0B,cAAc,EAAE,MAAM,SAAS,CAAC;AAGtE;;;;;GAKG;AACH,wBAAgB,eAAe,CAC3B,KAAK,EAAE,cAAc,EACrB,WAAW,EAAE;IAAE,CAAC,EAAE,MAAM,CAAC;IAAC,CAAC,EAAE,MAAM,CAAC;IAAC,KAAK,EAAE,MAAM,CAAC;IAAC,MAAM,EAAE,MAAM,CAAA;CAAE,EACpE,KAAK,EAAE,QAAQ,CAAC,iBAAiB,CAAC,GACnC,CAAC,SAAS,EAAE;IAAE,CAAC,EAAE,MAAM,CAAC;IAAC,CAAC,EAAE,MAAM,CAAC;IAAC,KAAK,EAAE,MAAM,CAAC;IAAC,MAAM,EAAE,MAAM,CAAA;CAAE,EAAE,QAAQ,CAAC,gBAAgB,CAAC,EAAE,GAAG,SAAS,CAAC,CA8DhH"}
+{"version":3,"file":"axis.d.ts","sourceRoot":"","sources":["../../../demo/track-def/axis.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,gBAAgB,EAAE,MAAM,4BAA4B,CAAC;AAQnE,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,4BAA4B,CAAC;AAEpE,OAAO,EAAa,KAAK,QAAQ,EAAE,MAAM,QAAQ,CAAC;AAClD,OAAO,KAAK,EAA0B,cAAc,EAAE,MAAM,SAAS,CAAC;AAGtE;;;;;GAKG;AACH,wBAAgB,eAAe,CAC3B,KAAK,EAAE,cAAc,EACrB,WAAW,EAAE;IAAE,CAAC,EAAE,MAAM,CAAC;IAAC,CAAC,EAAE,MAAM,CAAC;IAAC,KAAK,EAAE,MAAM,CAAC;IAAC,MAAM,EAAE,MAAM,CAAA;CAAE,EACpE,KAAK,EAAE,QAAQ,CAAC,iBAAiB,CAAC,GACnC,CAAC;IAAE,CAAC,EAAE,MAAM,CAAC;IAAC,CAAC,EAAE,MAAM,CAAC;IAAC,KAAK,EAAE,MAAM,CAAC;IAAC,MAAM,EAAE,MAAM,CAAA;CAAE,EAAE,QAAQ,CAAC,gBAAgB,CAAC,EAAE,GAAG,SAAS,CAAC,CA8DrG"}

package/dist/demo/track-def/dummy.d.ts

@@ -1,10 +1,12 @@
 import type { DummyTrackOptions } from '@gosling-lang/dummy-track';
 import { type TrackDef } from './main';
 import { type ProcessedDummyTrack } from './types';
+import type { CompleteThemeDeep } from 'src/core/utils/theme';
+import type { AxisTrackOptions } from '@gosling-lang/genomic-axis';
 export declare function processDummyTrack(track: ProcessedDummyTrack, boundingBox: {
     x: number;
     y: number;
     width: number;
     height: number;
-}): TrackDef<DummyTrackOptions>[];
+}, theme: Required<CompleteThemeDeep>): (TrackDef<DummyTrackOptions> | TrackDef<AxisTrackOptions>)[];
 //# sourceMappingURL=dummy.d.ts.map

package/dist/demo/track-def/dummy.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"dummy.d.ts","sourceRoot":"","sources":["../../../demo/track-def/dummy.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,2BAA2B,CAAC;AACnE,OAAO,EAAE,KAAK,QAAQ,EAAa,MAAM,QAAQ,CAAC;AAClD,OAAO,EAAE,KAAK,mBAAmB,EAAE,MAAM,SAAS,CAAC;AAEnD,wBAAgB,iBAAiB,CAC7B,KAAK,EAAE,mBAAmB,EAC1B,WAAW,EAAE;IAAE,CAAC,EAAE,MAAM,CAAC;IAAC,CAAC,EAAE,MAAM,CAAC;IAAC,KAAK,EAAE,MAAM,CAAC;IAAC,MAAM,EAAE,MAAM,CAAA;CAAE,GACrE,QAAQ,CAAC,iBAAiB,CAAC,EAAE,CAa/B"}
+{"version":3,"file":"dummy.d.ts","sourceRoot":"","sources":["../../../demo/track-def/dummy.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,2BAA2B,CAAC;AACnE,OAAO,EAAE,KAAK,QAAQ,EAAa,MAAM,QAAQ,CAAC;AAClD,OAAO,EAAE,KAAK,mBAAmB,EAAE,MAAM,SAAS,CAAC;AAEnD,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,sBAAsB,CAAC;AAC9D,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,4BAA4B,CAAC;AAEnE,wBAAgB,iBAAiB,CAC7B,KAAK,EAAE,mBAAmB,EAC1B,WAAW,EAAE;IAAE,CAAC,EAAE,MAAM,CAAC;IAAC,CAAC,EAAE,MAAM,CAAC;IAAC,KAAK,EAAE,MAAM,CAAC;IAAC,MAAM,EAAE,MAAM,CAAA;CAAE,EACpE,KAAK,EAAE,QAAQ,CAAC,iBAAiB,CAAC,GACnC,CAAC,QAAQ,CAAC,iBAAiB,CAAC,GAAG,QAAQ,CAAC,gBAAgB,CAAC,CAAC,EAAE,CA8B9D"}

package/dist/demo/track-def/main.d.ts

@@ -6,6 +6,7 @@ import { type BrushLinearTrackOptions } from '@gosling-lang/brush-linear';
 import type { TrackInfo } from '../../src/compiler/bounding-box';
 import type { CompleteThemeDeep } from '../../src/core/utils/theme';
 import type { GoslingTrackOptions } from '../../src/tracks/gosling-track/gosling-track';
+import type { SpatialTrackOptions } from 'src/tracks/spatial-track/spatial-track';
 import { type BrushCircularTrackOptions } from '@gosling-lang/brush-circular';
 import { type HeatmapTrackOptions } from '@gosling-lang/heatmap';
 /**
@@ -18,7 +19,8 @@ export declare enum TrackType {
     Axis = 3,
     BrushLinear = 4,
     BrushCircular = 5,
-    Heatmap = 6
+    Heatmap = 6,
+    Spatial = 7
 }
 /**
  * Associate options to each track type
@@ -31,6 +33,7 @@ interface TrackOptionsMap {
     [TrackType.BrushLinear]: BrushLinearTrackOptions;
     [TrackType.BrushCircular]: BrushCircularTrackOptions;
     [TrackType.Heatmap]: HeatmapTrackOptions;
+    [TrackType.Spatial]: SpatialTrackOptions;
 }
 /**
  *  This interface contains all of the information needed to render each track type.

package/dist/demo/track-def/main.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"main.d.ts","sourceRoot":"","sources":["../../../demo/track-def/main.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,eAAe,CAAC;AACjD,OAAO,EAAE,KAAK,gBAAgB,EAAE,MAAM,0BAA0B,CAAC;AACjE,OAAO,EAAE,KAAK,iBAAiB,EAAE,MAAM,2BAA2B,CAAC;AACnE,OAAO,EAAE,KAAK,gBAAgB,EAAE,MAAM,4BAA4B,CAAC;AACnE,OAAO,EAAE,KAAK,uBAAuB,EAAE,MAAM,4BAA4B,CAAC;AAC1E,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,4BAA4B,CAAC;AACpE,OAAO,KAAK,EAAE,mBAAmB,EAAE,MAAM,8CAA8C,CAAC;AACxF,OAAO,KAAK,EAAE,mBAAmB,EAAE,MAAM,wCAAwC,CAAC;AAKlF,OAAO,EAAE,KAAK,yBAAyB,EAAE,MAAM,8BAA8B,CAAC;AAC9E,OAAO,EAAE,KAAK,mBAAmB,EAAE,MAAM,uBAAuB,CAAC;AAIjE;;GAEG;AACH,oBAAY,SAAS;IACjB,IAAI,IAAA;IACJ,KAAK,IAAA;IACL,OAAO,IAAA;IACP,IAAI,IAAA;IACJ,WAAW,IAAA;IACX,aAAa,IAAA;IACb,OAAO,IAAA;IACP,OAAO,IAAA;CACV;AAED;;GAEG;AACH,UAAU,eAAe;IACrB,CAAC,SAAS,CAAC,OAAO,CAAC,EAAE,mBAAmB,CAAC;IACzC,CAAC,SAAS,CAAC,IAAI,CAAC,EAAE,gBAAgB,CAAC;IACnC,CAAC,SAAS,CAAC,KAAK,CAAC,EAAE,iBAAiB,CAAC;IACrC,CAAC,SAAS,CAAC,IAAI,CAAC,EAAE,gBAAgB,CAAC;IACnC,CAAC,SAAS,CAAC,WAAW,CAAC,EAAE,uBAAuB,CAAC;IACjD,CAAC,SAAS,CAAC,aAAa,CAAC,EAAE,yBAAyB,CAAC;IACrD,CAAC,SAAS,CAAC,OAAO,CAAC,EAAE,mBAAmB,CAAC;IACzC,CAAC,SAAS,CAAC,OAAO,CAAC,EAAE,mBAAmB,CAAC;CAC5C;AAED;;GAEG;AACH,MAAM,WAAW,QAAQ,CAAC,CAAC;IACvB,IAAI,EAAE,SAAS,CAAC;IAChB,OAAO,EAAE,MAAM,CAAC;IAChB,WAAW,EAAE;QAAE,CAAC,EAAE,MAAM,CAAC;QAAC,CAAC,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAC;QAAC,MAAM,EAAE,MAAM,CAAA;KAAE,CAAC;IACrE,OAAO,EAAE,CAAC,CAAC;CACd;AAED;;GAEG;AACH,MAAM,MAAM,SAAS,GAAG;KACnB,CAAC,IAAI,MAAM,eAAe,GAAG,QAAQ,CAAC,eAAe,CAAC,CAAC,CAAC,CAAC;CAC7D,CAAC,MAAM,eAAe,CAAC,CAAC;AAEzB;;;;;;GAMG;AACH,wBAAgB,eAAe,CAAC,UAAU,EAAE,SAAS,EAAE,EAAE,KAAK,EAAE,QAAQ,CAAC,iBAAiB,CAAC,GAAG,SAAS,EAAE,CAoCxG;AAED;;GAEG;AACH,wBAAgB,sBAAsB,CAAC,UAAU,EAAE,SAAS,EAAE,EAAE,WAAW,EAAE,WAAW,QAQvF"}

package/dist/demo/track-def/types.d.ts

@@ -11,15 +11,15 @@ import type { DataDeep, Assembly, DummyTrackStyle, Mark, X, Y } from '@gosling-l
  * TODO: this file is incomplete. It should be updated to include all the properties that a processed spec can have.
  */
 /** A Track after it has been compiled */
-export type ProcessedTrack = ProcessedLinearTrack | ProcessedCircularTrack | ProcessedDummyTrack;
+export type ProcessedTrack = ProcessedLinearTrack | ProcessedCircularTrack | ProcessedDummyTrack | ProcessedSpatialTrack;
 /** All tracks potentially have these properties */
 export interface ProcessedTrackBase {
-    layout?: 'linear' | 'circular';
+    layout?: 'linear' | 'circular' | 'spatial';
     id: string;
     height: number;
     width: number;
     static: boolean;
-    mark?: string;
+    mark?: Mark;
     orientation: 'horizontal' | 'vertical';
     title?: string;
     subtitle?: string;
@@ -53,9 +53,20 @@ export type ProcessedCircularTrack = ProcessedTrackBase & {
     outerRadius: number;
     innerRadius: number;
 };
-export type ProcessedDummyTrack = ProcessedTrackBase & {
-    type?: string;
+export type ProcessedSpatialTrack = ProcessedTrackBase & {
+    layout: 'spatial';
+    spatial: {
+        x: string;
+        y: string;
+        z: string;
+        chr: string;
+        coord: string;
+    };
+};
+export type ProcessedDummyTrack = (ProcessedLinearTrack | ProcessedCircularTrack) & {
+    type: 'dummy-track';
     style?: DummyTrackStyle;
+    x?: X;
 };
 /** Tracks in the _overlay */
 export interface OverlayTrack {

package/dist/demo/track-def/types.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../../../demo/track-def/types.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,QAAQ,EAAE,QAAQ,EAAE,eAAe,EAAE,IAAI,EAAE,CAAC,EAAE,CAAC,EAAE,MAAM,8BAA8B,CAAC;AAEpG;;;;;;;;;;GAUG;AAEH,yCAAyC;AACzC,MAAM,MAAM,cAAc,GACpB,oBAAoB,GACpB,sBAAsB,GACtB,mBAAmB,GACnB,qBAAqB,CAAC;AAC5B,mDAAmD;AACnD,MAAM,WAAW,kBAAkB;IAC/B,MAAM,CAAC,EAAE,QAAQ,GAAG,UAAU,GAAG,SAAS,CAAC;IAC3C,EAAE,EAAE,MAAM,CAAC;IACX,MAAM,EAAE,MAAM,CAAC;IACf,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,EAAE,OAAO,CAAC;IAChB,IAAI,CAAC,EAAE,IAAI,CAAC;IACZ,WAAW,EAAE,YAAY,GAAG,UAAU,CAAC;IACvC,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,IAAI,CAAC,EAAE,QAAQ,CAAC;IAChB,QAAQ,CAAC,EAAE,QAAQ,CAAC;IACpB,sBAAsB,CAAC,EAAE,OAAO,CAAC;IACjC,QAAQ,CAAC,EAAE,YAAY,EAAE,CAAC;IAC1B,KAAK,CAAC,EAAE;QAAE,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC;IAC1B,MAAM,CAAC,EAAE;QAAE,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC;IAC3B,OAAO,CAAC,EAAE;QAAE,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC;IAC5B,WAAW,CAAC,EAAE;QAAE,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC;IAChC,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,OAAO,CAAC,EAAE,MAAM,CAAC;CACpB;AAED,MAAM,MAAM,oBAAoB,GAAG,kBAAkB,GAAG;IACpD,MAAM,EAAE,QAAQ,CAAC;CACpB,CAAC;AAEF,MAAM,MAAM,sBAAsB,GAAG,kBAAkB,GAAG;IACtD,EAAE,EAAE,MAAM,CAAC;IACX,MAAM,EAAE,UAAU,CAAC;IACnB,UAAU,EAAE,MAAM,CAAC;IACnB,QAAQ,EAAE,MAAM,CAAC;IACjB,WAAW,EAAE,MAAM,CAAC;IACpB,WAAW,EAAE,MAAM,CAAC;CACvB,CAAC;AAIF,MAAM,MAAM,qBAAqB,GAAG,kBAAkB,GAAG;IACrD,MAAM,EAAE,SAAS,CAAC;IAClB,OAAO,EAAE;QACL,CAAC,EAAE,MAAM,CAAC;QACV,CAAC,EAAE,MAAM,CAAC;QACV,CAAC,EAAE,MAAM,CAAC;QACV,GAAG,EAAE,MAAM,CAAC;QACZ,KAAK,EAAE,MAAM,CAAC;KACjB,CAAC;CACL,CAAC;AAEF,MAAM,MAAM,mBAAmB,GAAG,CAAC,oBAAoB,GAAG,sBAAsB,CAAC,GAAG;IAChF,IAAI,EAAE,aAAa,CAAC;IACpB,KAAK,CAAC,EAAE,eAAe,CAAC;IACxB,CAAC,CAAC,EAAE,CAAC,CAAC;CACT,CAAC;AAEF,6BAA6B;AAC7B,MAAM,WAAW,YAAY;IACzB,EAAE,EAAE,MAAM,CAAC;IACX,IAAI,CAAC,EAAE,IAAI,CAAC;IACZ,CAAC,CAAC,EAAE,CAAC,CAAC;IACN,CAAC,CAAC,EAAE,CAAC,CAAC;IACN,KAAK,CAAC,EAAE;QAAE,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC;IAC1B,MAAM,CAAC,EAAE;QAAE,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC;CAC9B"}

package/dist/{exported-utils-b3ea2b1e.js → exported-utils-bca41fe4.js}

@@ -2975,6 +2975,7 @@ function getChannelKeysByType(spec, t) {
   return keys;
 }
 function IsXAxis(_) {
+  var _a;
   if ((IsSingleTrack(_) || IsOverlaidTrack(_)) && IsChannelDeep(_.x) && _.x.axis && _.x.axis !== "none") {
     return true;
   } else if (IsOverlaidTrack(_)) {
@@ -2987,6 +2988,8 @@ function IsXAxis(_) {
       }
     });
     return isFound;
+  } else if (IsDummyTrack(_)) {
+    return ((_a = _.x) == null ? void 0 : _a.axis) && _.x.axis !== "none";
   }
   return false;
 }
@@ -9162,6 +9165,41 @@ function uuid() {
   var _a, _b, _c;
   return (_c = (_b = (_a = globalThis.crypto).randomUUID) == null ? void 0 : _b.call(_a)) != null ? _c : fallback();
 }
+function propagateSpatialLayoutInfo(t) {
+  var _a, _b, _c, _d, _e, _f, _g;
+  const { layout } = t;
+  if (typeof layout == "object" && "type" in layout && layout.type === "spatial") {
+    const { model } = layout;
+    const [x, y, z] = model.xyz;
+    const { url, chromosome: chr, position: coord } = model;
+    t.spatial = {
+      x,
+      y,
+      z,
+      chr,
+      coord
+    };
+    t.layout = "spatial";
+    const dataTransform = {
+      type: "join",
+      from: { url, chromosomeField: chr, genomicField: coord }
+    };
+    let to = { startField: "start", endField: "end" };
+    if (((_a = t.data) == null ? void 0 : _a.type) === "bigwig") {
+      to = { startField: "start", endField: "end" };
+    } else if (((_b = t.data) == null ? void 0 : _b.type) === "csv") {
+      const startField = (_d = (_c = t.data.genomicFields) == null ? void 0 : _c[0]) != null ? _d : "unknown";
+      const endField = (_f = (_e = t.data.genomicFields) == null ? void 0 : _e[1]) != null ? _f : void 0;
+      to = { startField, endField };
+    }
+    t.dataTransform = [{ ...dataTransform, to }, ...(_g = t.dataTransform) != null ? _g : []];
+  } else if (typeof layout == "object") {
+    t.layout = layout.type;
+  }
+  if (t.locus && !t.x) {
+    t.x = { ...t.locus, type: "genomic" };
+  }
+}
 function traverseTracks(spec, callback) {
   if ("tracks" in spec) {
     spec.tracks.forEach((t, i, ts) => {
@@ -9313,9 +9351,10 @@ function traverseToFixSpecDownstream(spec, parentDef) {
         track.static = spec.static !== void 0 ? spec.static : false;
       if (!track.zoomLimits)
         track.zoomLimits = spec.zoomLimits;
-      if (track.layout == "circular" && IsDummyTrack(track)) {
-        track._invalidTrack = true;
-        return;
+      if (track.layout && typeof track.layout === "object" && track.layout.type === "spatial") {
+        if (!("template" in track)) {
+          propagateSpatialLayoutInfo(track);
+        }
       }
       track.style = getStyleOverridden(spec.style, track.style);
       if (IsOverlaidTrack(track)) {
@@ -9366,7 +9405,7 @@ function traverseToFixSpecDownstream(spec, parentDef) {
       if (i === 0) {
         track.overlayOnPreviousTrack = false;
       }
-      if (i === 0 || i !== 0 && tracks.slice(0, i).filter((d) => !d.overlayOnPreviousTrack).length === 1 && track.overlayOnPreviousTrack === true) {
+      if (i === 0 && !IsDummyTrack(track) || i !== 0 && tracks.slice(0, i).filter((d) => !d.overlayOnPreviousTrack).length === 1 && track.overlayOnPreviousTrack === true) {
         if ((IsSingleTrack(track) || IsOverlaidTrack(track)) && IsChannelDeep(track.x) && !track.x.axis) {
           if (track.orientation === "vertical") {
             track.x.axis = "left";
@@ -9384,6 +9423,11 @@ function traverseToFixSpecDownstream(spec, parentDef) {
             }
           });
         }
+      } else if (i === 0 && IsDummyTrack(track)) {
+        const nextNonDummyTrack = array.slice(i).find((d) => !IsDummyTrack(d));
+        if (nextNonDummyTrack && "x" in nextNonDummyTrack) {
+          track.x = { ...nextNonDummyTrack.x, axis: "top" };
+        }
       }
       if ((IsSingleTrack(track) || IsOverlaidTrack(track)) && IsChannelDeep(track.x) && track.x.axis && track.x.axis !== "none") {
         if (track.orientation === "vertical") {
@@ -9729,6 +9773,24 @@ const CHROM_SIZE_MM9 = {
   chrY: 15902555,
   chrM: 16299
 };
+const CHROM_SIZE_SACCER3 = {
+  chrI: 230218,
+  chrII: 813184,
+  chrIII: 316620,
+  chrIV: 1531933,
+  chrV: 576874,
+  chrVI: 270161,
+  chrVII: 1090940,
+  chrVIII: 562643,
+  chrIX: 439888,
+  chrX: 745751,
+  chrXI: 666816,
+  chrXII: 1078177,
+  chrXIII: 924431,
+  chrXIV: 784333,
+  chrXV: 1091291,
+  chrXVI: 948066
+};
 function getRelativeGenomicPosition(absPos, assembly, returnWithinAssembly = false) {
   const chrSizes = Object.entries(computeChromSizes(assembly).interval);
   const minPosChr = { chromosome: "unknown", position: Infinity };
@@ -9822,6 +9884,12 @@ const CRHOM_SIZES = Object.freeze({
     total: getChromTotalSize(CHROM_SIZE_MM9),
     path: basePath("mm9")
   },
+  sacCer3: {
+    size: CHROM_SIZE_SACCER3,
+    interval: getChromInterval(CHROM_SIZE_SACCER3),
+    total: getChromTotalSize(CHROM_SIZE_SACCER3),
+    path: "https://gosling-lang.s3.us-east-1.amazonaws.com/data/sacCer3.chrom.sizes"
+  },
   // `unknown` assembly contains only one chromosome with max length
   unknown: {
     size: { chr: Number.MAX_VALUE },
@@ -9843,8 +9911,25 @@ function getChromTotalSize(chromSize) {
   return Object.values(chromSize).reduce((sum, current) => sum + current, 0);
 }
 function parseGenomicPosition(position) {
-  const [chromosome, intervalString] = position.split(":");
-  if (intervalString) {
+  const firstColonIndex = position.indexOf(":");
+  if (firstColonIndex === -1) {
+    return { chromosome: position };
+  }
+  const chromosome = position.substring(0, firstColonIndex);
+  const intervalString = position.substring(firstColonIndex + 1);
+  if (intervalString.includes(":")) {
+    const dashIndex = intervalString.indexOf("-");
+    if (dashIndex !== -1) {
+      const startPosStr = intervalString.substring(0, dashIndex);
+      const endPart = intervalString.substring(dashIndex + 1);
+      const [chromosomeEnd, endPosStr] = endPart.split(":");
+      const start = +startPosStr.replace(/,/g, "");
+      const end = +endPosStr.replace(/,/g, "");
+      if (!Number.isNaN(start) && !Number.isNaN(end)) {
+        return { chromosome, start, chromosomeEnd, end };
+      }
+    }
+  } else {
     const [start, end] = intervalString.split("-").map((s) => +s.replace(/,/g, ""));
     if (!Number.isNaN(start) && !Number.isNaN(end)) {
       return { chromosome, start, end };
@@ -9853,14 +9938,15 @@ function parseGenomicPosition(position) {
   return { chromosome };
 }
 class GenomicPositionHelper {
-  constructor(chromosome, start, end) {
+  constructor(chromosome, start, end, chromosomeEnd) {
     this.chromosome = chromosome;
     this.start = start;
     this.end = end;
+    this.chromosomeEnd = chromosomeEnd;
   }
   static fromString(str) {
     const result = parseGenomicPosition(str);
-    return new GenomicPositionHelper(result.chromosome, result.start, result.end);
+    return new GenomicPositionHelper(result.chromosome, result.start, result.end, result.chromosomeEnd);
   }
   toAbsoluteCoordinates(assembly, padding = 0) {
     const info = computeChromSizes(assembly);
@@ -9874,6 +9960,15 @@ class GenomicPositionHelper {
       [start, end] = [1, size];
     }
     const offset = interval[0];
+    if (this.chromosomeEnd && this.chromosomeEnd !== this.chromosome) {
+      const endSize = info.size[this.chromosomeEnd];
+      const endInterval = info.interval[this.chromosomeEnd];
+      if (endSize === void 0 || endInterval === void 0) {
+        throw new Error(`End chromosome name ${this.chromosomeEnd} is not valid`);
+      }
+      const endOffset = endInterval[0];
+      return [start + offset - padding, end + endOffset + padding];
+    }
     return [start + offset - padding, end + offset + padding];
   }
 }
@@ -9927,18 +10022,18 @@ export {
   Is2DTrack as e,
   DEFAULT_VIEW_SPACING as f,
   DEFAULT_INNER_RADIUS_PROP as g,
-  IsDummyTrack as h,
-  IsOverlaidTrack as i,
-  IsXAxis as j,
-  IsYAxis as k,
-  DEFAULT_CIRCULAR_VIEW_PADDING as l,
-  traverseToFixSpecDownstream as m,
-  absToChr as n,
-  colorToHex as o,
-  getTextStyle as p,
-  computeChromSizes as q,
+  IsOverlaidTrack as h,
+  IsXAxis as i,
+  IsYAxis as j,
+  DEFAULT_CIRCULAR_VIEW_PADDING as k,
+  traverseToFixSpecDownstream as l,
+  absToChr as m,
+  colorToHex as n,
+  getTextStyle as o,
+  computeChromSizes as p,
+  cartesianToPolar as q,
   resolveSuperposedTracks as r,
-  cartesianToPolar as s,
+  IsDummyTrack as s,
   traverseTracks as t,
   uuid as u,
   getHiGlassColorRange as v,
@@ -9947,4 +10042,4 @@ export {
   commonjsGlobal as y,
   RemoteFile as z
 };
-//# sourceMappingURL=exported-utils-b3ea2b1e.js.map
+//# sourceMappingURL=exported-utils-bca41fe4.js.map