gosling.js 2.0.0-alpha.6 → 2.0.0-alpha.8

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

@@ -1 +1 @@
-{"version":3,"file":"gosling-component.d.ts","sourceRoot":"","sources":["../../demo/gosling-component.tsx"],"names":[],"mappings":"AAAA,OAAc,EAAuB,KAAK,SAAS,EAAuB,MAAM,OAAO,CAAC;AACxF,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,SAAS,CAAC,UAAU,CAAC,CAAC;IAC5B,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,eAwD5D;AACD;;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"}
+{"version":3,"file":"gosling-component.d.ts","sourceRoot":"","sources":["../../demo/gosling-component.tsx"],"names":[],"mappings":"AAAA,OAAc,EAAuB,KAAK,SAAS,EAAuB,MAAM,OAAO,CAAC;AACxF,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,SAAS,CAAC,UAAU,CAAC,CAAC;IAC5B,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,eAwD5D;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/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":"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;AAK9D;;;;GAIG;AACH,wBAAgB,eAAe,CAC3B,SAAS,EAAE,SAAS,EAAE,EACtB,eAAe,EAAE,cAAc,EAAE,EACjC,WAAW,EAAE,WAAW,EACxB,iBAAiB,CAAC,EAAE,iBAAiB,2BAwHxC"}
+{"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/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 @@
-{"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;AAKxF,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;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;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,CAuBxG;AAED;;GAEG;AACH,wBAAgB,sBAAsB,CAAC,UAAU,EAAE,SAAS,EAAE,EAAE,WAAW,EAAE,WAAW,QAQvF"}
+{"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;
@@ -53,6 +53,16 @@ export type ProcessedCircularTrack = ProcessedTrackBase & {
     outerRadius: number;
     innerRadius: number;
 };
+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;

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

@@ -1 +1 @@
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package/dist/{exported-utils-b3cf08ff.js → exported-utils-9e651c40.js}

@@ -9165,6 +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) => {
@@ -9316,6 +9351,11 @@ function traverseToFixSpecDownstream(spec, parentDef) {
         track.static = spec.static !== void 0 ? spec.static : false;
       if (!track.zoomLimits)
         track.zoomLimits = spec.zoomLimits;
+      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)) {
         track._overlay = track._overlay.filter((overlayTrack) => {
@@ -9733,6 +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 };
@@ -9826,6 +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 },
@@ -9951,4 +10015,4 @@ export {
   commonjsGlobal as y,
   RemoteFile as z
 };
-//# sourceMappingURL=exported-utils-b3cf08ff.js.map
+//# sourceMappingURL=exported-utils-9e651c40.js.map