@genome-spy/core 0.41.0 → 0.42.1

package/dist/src/utils/binnedIndex.test.js

@@ -152,4 +152,50 @@ describe("Binning Indexer", () => {
         expect(index(115, 116)).toEqual([4, 8]);
         expect(index(135, 145)).toEqual([6, 10]);
     });
+
+    test("Unordered ranges disable the index", () => {
+        const items = [
+            [10, 30],
+            [25, 50],
+
+            [112, 139],
+            [102, 129], // <- Unordered!
+            [121, 149],
+        ];
+        const indexer = createBinningRangeIndexer(
+            100,
+            [0, 1000],
+            (x) => x[0],
+            (x) => x[1]
+        );
+
+        items.forEach((x, i) => indexer(x, i * 2, (i + 1) * 2));
+
+        const index = indexer.getIndex();
+
+        expect(index).toBeUndefined();
+    });
+
+    test("Inverted ranges disable the index", () => {
+        const items = [
+            [10, 30],
+            [25, 50],
+
+            [102, 129],
+            [139, 112], // <- Inverted!
+            [121, 149],
+        ];
+        const indexer = createBinningRangeIndexer(
+            100,
+            [0, 1000],
+            (x) => x[0],
+            (x) => x[1]
+        );
+
+        items.forEach((x, i) => indexer(x, i * 2, (i + 1) * 2));
+
+        const index = indexer.getIndex();
+
+        expect(index).toBeUndefined();
+    });
 });

package/dist/src/utils/indexer.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"indexer.d.ts","sourceRoot":"","sources":["../../../src/utils/indexer.js"],"names":[],"mappings":"AAAA;;;;;;GAMG;AACH;;IAgBI,oCAAoC;;IAOpC,4BAA4B;kBAAhB,MAAM;;EAYrB"}
+{"version":3,"file":"indexer.d.ts","sourceRoot":"","sources":["../../../src/utils/indexer.js"],"names":[],"mappings":"AAAA;;;;;;GAMG;AACH;;IAyBI,oCAAoC;;IAOpC,4BAA4B;kBAAhB,MAAM;;EAYrB"}

package/dist/src/utils/indexer.js

@@ -8,16 +8,25 @@
 export default function createIndexer() {
     let counter = 0;
 
+    /** @type {any} */
+    let previousValue;
+    let index = 0;
+
     /** @type {Map<T, number>} */
     const values = new Map();
 
     /** @param {T} value */
     const indexer = (value) => {
-        let index = values.get(value);
+        if (value === previousValue) {
+            return index;
+        }
+
+        index = values.get(value);
         if (index === undefined) {
             index = counter++;
             values.set(value, index);
         }
+        previousValue = value;
         return index;
     };
 

package/dist/src/utils/indexer.test.js

@@ -8,6 +8,8 @@ test("Index values one by one", () => {
     expect(indexer("b")).toEqual(1);
     expect(indexer("c")).toEqual(2);
     expect(indexer("a")).toEqual(0);
+    expect(indexer("a")).toEqual(0);
+    expect(indexer("c")).toEqual(2);
     expect(indexer("c")).toEqual(2);
 });
 

package/dist/src/view/gridView.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"gridView.d.ts","sourceRoot":"","sources":["../../../src/view/gridView.js"],"names":[],"mappings":"AAkwBA;;;GAGG;AACH,iDAHW,OAAO,iBAAiB,EAAE,cAAc,GACtC,OAAO,iBAAiB,EAAE,QAAQ,CAwB9C;AAED;;;GAGG;AACH,uDAHW,OAAO,iBAAiB,EAAE,cAAc,GACtC,OAAO,iBAAiB,EAAE,QAAQ,CA6C9C;AA2BD;;GAEG;AACH,8EAUC;AAED;;;;;GAKG;AACH,4CAJW,OAAO,uBAAuB,EAAE,OAAO,UACvC,OAAO,iBAAiB,EAAE,UAAU,YACpC,QAAQ,aAmBlB;AAz3BD;;;;;;;;;;;;;;;GAeG;AACH;IA6BI;;;;;;;;;OASG;IACH,kBARW,OAAO,iBAAiB,EAAE,aAAa,WACvC,OAAO,yBAAyB,EAAE,OAAO,gBACzC,aAAa,iDAEb,MAAM,WACN,MAAM,YACN,OAAO,WAAW,EAAE,WAAW,EAoBzC;IARG,8CAAgB;IAOhB,uBAA0B;IAG9B;;OAEG;IACH,qDAIC;IAeD;;OAEG;IACH,wDAKC;IAqBD;;OAEG;IACH,8CAEC;IAED,yBAEC;IAED;;OAEG;IACH,wCAmCC;IA2OD;;;;OAIG;IAEH,gBALW,OAAO,4CAA4C,EAAE,OAAO,UAC5D,OAAO,uBAAuB,EAAE,OAAO,YACvC,OAAO,uBAAuB,EAAE,gBAAgB,QA2O1D;;CAmGJ;AAgJD;IACI;;;;OAIG;IACH,6DAHW,aAAa,UACb,MAAM,EAoFhB;IAjFG,4BAAgC;IAChC,kCAAgB;IAChB,eAAoB;IAEpB,uBAAuB;IACvB,YADW,QAAQ,CACQ;IAE3B,uBAAuB;IACvB,kBADW,QAAQ,CACc;IAEjC,mFAAmF;IACnF,MADW,QAAQ,OAAO,OAAO,iBAAiB,EAAE,UAAU,EAAE,QAAQ,CAAC,CAAC,CAC5D;IAEd,4FAA4F;IAC5F,WADW,QAAQ,OAAO,OAAO,iBAAiB,EAAE,UAAU,EAAE,YAAY,CAAC,CAAC,CAC3D;IAEnB,0DAA0D;IAC1D,kEAAoB;IAEpB,uBAAuB;IACvB,OADW,QAAQ,CACG;IAEtB,wBAAwB;IACxB,QADW,SAAS,CACQ;IA4DhC,uEAcC;IAED;;OAEG;IACH,4BAkKC;IAED,uBAqBC;IAED,iCAEC;CACJ;qBA9qC0D,eAAe;sBAFpD,uBAAuB;0BAGnB,oBAAoB;qBAGzB,eAAe;yBALX,mBAAmB;AAirC5C;IACI;;;OAGG;IACH,uBAHW,SAAS,8CAyFnB;IAtDG;;;MAAoB;IACpB,2CAAsC;IAKtC,uBAAuB;IAEvB,wBAAwB;IACxB,2BAAqC;IA+CzC,0BAKC;IAWD;;;;OAIG;IACH,gCAHW,SAAS,UACT,SAAS,QA8CnB;IA7BG,0BAAsE;CA8B7E;oBAl1CmB,qBAAqB"}
+{"version":3,"file":"gridView.d.ts","sourceRoot":"","sources":["../../../src/view/gridView.js"],"names":[],"mappings":"AAowBA;;;GAGG;AACH,iDAHW,OAAO,iBAAiB,EAAE,cAAc,GACtC,OAAO,iBAAiB,EAAE,QAAQ,CAwB9C;AAED;;;GAGG;AACH,uDAHW,OAAO,iBAAiB,EAAE,cAAc,GACtC,OAAO,iBAAiB,EAAE,QAAQ,CA6C9C;AA2BD;;GAEG;AACH,8EAUC;AAED;;;;;GAKG;AACH,4CAJW,OAAO,uBAAuB,EAAE,OAAO,UACvC,OAAO,iBAAiB,EAAE,UAAU,YACpC,QAAQ,aAmBlB;AA33BD;;;;;;;;;;;;;;;GAeG;AACH;IA6BI;;;;;;;;;OASG;IACH,kBARW,OAAO,iBAAiB,EAAE,aAAa,WACvC,OAAO,yBAAyB,EAAE,OAAO,gBACzC,aAAa,iDAEb,MAAM,WACN,MAAM,YACN,OAAO,WAAW,EAAE,WAAW,EAoBzC;IARG,8CAAgB;IAOhB,uBAA0B;IAG9B;;OAEG;IACH,qDAIC;IAeD;;OAEG;IACH,wDAKC;IAqBD;;OAEG;IACH,8CAEC;IAED,yBAEC;IAED;;OAEG;IACH,wCAmCC;IA2OD;;;;OAIG;IAEH,gBALW,OAAO,4CAA4C,EAAE,OAAO,UAC5D,OAAO,uBAAuB,EAAE,OAAO,YACvC,OAAO,uBAAuB,EAAE,gBAAgB,QA6O1D;;CAmGJ;AAgJD;IACI;;;;OAIG;IACH,6DAHW,aAAa,UACb,MAAM,EAoFhB;IAjFG,4BAAgC;IAChC,kCAAgB;IAChB,eAAoB;IAEpB,uBAAuB;IACvB,YADW,QAAQ,CACQ;IAE3B,uBAAuB;IACvB,kBADW,QAAQ,CACc;IAEjC,mFAAmF;IACnF,MADW,QAAQ,OAAO,OAAO,iBAAiB,EAAE,UAAU,EAAE,QAAQ,CAAC,CAAC,CAC5D;IAEd,4FAA4F;IAC5F,WADW,QAAQ,OAAO,OAAO,iBAAiB,EAAE,UAAU,EAAE,YAAY,CAAC,CAAC,CAC3D;IAEnB,0DAA0D;IAC1D,kEAAoB;IAEpB,uBAAuB;IACvB,OADW,QAAQ,CACG;IAEtB,wBAAwB;IACxB,QADW,SAAS,CACQ;IA4DhC,uEAcC;IAED;;OAEG;IACH,4BAkKC;IAED,uBAqBC;IAED,iCAEC;CACJ;qBAhrC0D,eAAe;sBAFpD,uBAAuB;0BAGnB,oBAAoB;qBAGzB,eAAe;yBALX,mBAAmB;AAmrC5C;IACI;;;OAGG;IACH,uBAHW,SAAS,8CAyFnB;IAtDG;;;MAAoB;IACpB,2CAAsC;IAKtC,uBAAuB;IAEvB,wBAAwB;IACxB,2BAAqC;IA+CzC,0BAKC;IAWD;;;;OAIG;IACH,gCAHW,SAAS,UACT,SAAS,QA8CnB;IA7BG,0BAAsE;CA8B7E;oBAp1CmB,qBAAqB"}

package/dist/src/view/gridView.js

@@ -436,6 +436,8 @@ export default class GridView extends ContainerView {
      */
     // eslint-disable-next-line complexity
     render(context, coords, options = {}) {
+        super.render(context, coords, options);
+
         if (!this.isConfiguredVisible()) {
             return;
         }

package/dist/src/view/layerView.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"layerView.d.ts","sourceRoot":"","sources":["../../../src/view/layerView.js"],"names":[],"mappings":"AAIA;IAQI;;;;;;;;OAQG;IACH,kBAPW,OAAO,iBAAiB,EAAE,SAAS,WACnC,OAAO,yBAAyB,EAAE,OAAO,gBACzC,aAAa,cACb,OAAO,WAAW,EAAE,OAAO,QAC3B,MAAM,YACN,OAAO,WAAW,EAAE,WAAW,EAQzC;IAHG,0CAAgB;IAoCpB,gEAEC;IAWD;;;;OAIG;IACH,gBAJW,OAAO,4CAA4C,EAAE,OAAO,UAC5D,OAAO,uBAAuB,EAAE,OAAO,YACvC,OAAO,uBAAuB,EAAE,gBAAgB,QAc1D;;CAeJ;0BAxGyB,oBAAoB"}
+{"version":3,"file":"layerView.d.ts","sourceRoot":"","sources":["../../../src/view/layerView.js"],"names":[],"mappings":"AAIA;IAQI;;;;;;;;OAQG;IACH,kBAPW,OAAO,iBAAiB,EAAE,SAAS,WACnC,OAAO,yBAAyB,EAAE,OAAO,gBACzC,aAAa,cACb,OAAO,WAAW,EAAE,OAAO,QAC3B,MAAM,YACN,OAAO,WAAW,EAAE,WAAW,EAQzC;IAHG,0CAAgB;IAoCpB,gEAEC;IAWD;;;;OAIG;IACH,gBAJW,OAAO,4CAA4C,EAAE,OAAO,UAC5D,OAAO,uBAAuB,EAAE,OAAO,YACvC,OAAO,uBAAuB,EAAE,gBAAgB,QAgB1D;;CAeJ;0BA1GyB,oBAAoB"}

package/dist/src/view/layerView.js

@@ -77,6 +77,8 @@ export default class LayerView extends ContainerView {
      * @param {import("../types/rendering.js").RenderingOptions} [options]
      */
     render(context, coords, options = {}) {
+        super.render(context, coords, options);
+
         if (!this.isConfiguredVisible()) {
             return;
         }

package/dist/src/view/unitView.d.ts

@@ -28,12 +28,6 @@ export default class UnitView extends ContainerView {
     spec: import("../spec/view.js").UnitSpec;
     /** @type {import("../marks/mark.js").default} */
     mark: import("../marks/mark.js").default;
-    /**
-     * Not nice! Inconsistent when faceting!
-     * TODO: Something. Maybe store only width/height
-     * @type {import("./layout/rectangle.js").default}
-     */
-    coords: import("./layout/rectangle.js").default;
     /**
      * @param {import("./renderingContext/viewRenderingContext.js").default} context
      * @param {import("./layout/rectangle.js").default} coords
@@ -60,7 +54,7 @@ export default class UnitView extends ContainerView {
     /**
      * @param {Channel} channel A primary channel
      */
-    _validateDomainQuery(channel: import("../spec/channel.js").Channel): import("../spec/channel.js").ChromPosDef | import("../spec/channel.js").PositionDatumDef | import("../spec/channel.js").MarkPropExprDef<import("../spec/channel.js").Type> | import("../spec/channel.js").MarkPropDatumDef<import("../spec/channel.js").Type> | import("../spec/channel.js").MarkPropDatumDef<import("../spec/channel.js").TypeForShape> | import("../spec/channel.js").PositionFieldDef<string> | import("../spec/channel.js").MarkPropFieldDef<string, import("../spec/channel.js").Type> | import("../spec/channel.js").MarkPropFieldDef<string, import("../spec/channel.js").TypeForShape>;
+    _validateDomainQuery(channel: import("../spec/channel.js").Channel): import("../spec/channel.js").MarkPropExprDef<import("../spec/channel.js").Type> | import("../spec/channel.js").MarkPropDatumDef<import("../spec/channel.js").Type> | import("../spec/channel.js").ChromPosDef | import("../spec/channel.js").PositionDatumDef | import("../spec/channel.js").MarkPropDatumDef<import("../spec/channel.js").TypeForShape> | import("../spec/channel.js").MarkPropFieldDef<string, import("../spec/channel.js").Type> | import("../spec/channel.js").PositionFieldDef<string> | import("../spec/channel.js").MarkPropFieldDef<string, import("../spec/channel.js").TypeForShape>;
     /**
      * Returns the domain of the specified channel of this domain/mark.
      *

package/dist/src/view/unitView.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"unitView.d.ts","sourceRoot":"","sources":["../../../src/view/unitView.js"],"names":[],"mappings":"AAqBA;;;;GAIG;AACH;QAHkB,MAAM,GAAE,cAAc,kBAAkB,EAAE,OAAO;EASjE;AAEF;IACI;;;;;;;OAOG;IACH;;;;;;;;OAQG;IACH,kBAPW,OAAO,iBAAiB,EAAE,QAAQ,WAClC,OAAO,yBAAyB,EAAE,OAAO,gBACzC,OAAO,oBAAoB,EAAE,OAAO,cACpC,OAAO,WAAW,EAAE,OAAO,QAC3B,MAAM,YACN,OAAO,WAAW,EAAE,WAAW,EAyBzC;IApBG,yCAAgB;IAIZ,iDAAiD;IACjD,MADW,OAAO,kBAAkB,EAAE,OAAO,CACnB;IAO9B;;;;OAIG;IACH,QAFU,OAAO,uBAAuB,EAAE,OAAO,CAE1B;IAK3B;;;;OAIG;IACH,gBAJW,OAAO,4CAA4C,EAAE,OAAO,UAC5D,OAAO,uBAAuB,EAAE,OAAO,YACvC,OAAO,uBAAuB,EAAE,gBAAgB,QAY1D;IAED,kDAIC;IAED;;;;;OAKG;IACH,iEAyEC;IAED;;;OAGG;IACH,mGASC;IAkBD;;OAEG;IACH,uDAEC;IAED;;OAEG;IACH,opBAcC;IAED;;;;;OAKG;IACH,6BAHW,OAAO,oBAAoB,EAAE,gBAAgB,iDAkBvD;IAED;;;;;;;;;;;;OAYG;IACH,gHA2CC;IAED,uBAQC;IAgBD;;;;OAIG;IACH,8BAJW,MAAM,+DAEJ,OAAO,iBAAiB,EAAE,kBAAkB,CAKxD;CACJ;0BA1VyB,oBAAoB"}
+{"version":3,"file":"unitView.d.ts","sourceRoot":"","sources":["../../../src/view/unitView.js"],"names":[],"mappings":"AAqBA;;;;GAIG;AACH;QAHkB,MAAM,GAAE,cAAc,kBAAkB,EAAE,OAAO;EASjE;AAEF;IACI;;;;;;;OAOG;IACH;;;;;;;;OAQG;IACH,kBAPW,OAAO,iBAAiB,EAAE,QAAQ,WAClC,OAAO,yBAAyB,EAAE,OAAO,gBACzC,OAAO,oBAAoB,EAAE,OAAO,cACpC,OAAO,WAAW,EAAE,OAAO,QAC3B,MAAM,YACN,OAAO,WAAW,EAAE,WAAW,EAkBzC;IAbG,yCAAgB;IAIZ,iDAAiD;IACjD,MADW,OAAO,kBAAkB,EAAE,OAAO,CACnB;IAUlC;;;;OAIG;IACH,gBAJW,OAAO,4CAA4C,EAAE,OAAO,UAC5D,OAAO,uBAAuB,EAAE,OAAO,YACvC,OAAO,uBAAuB,EAAE,gBAAgB,QAY1D;IAED,kDAIC;IAED;;;;;OAKG;IACH,iEAyEC;IAED;;;OAGG;IACH,mGASC;IAkBD;;OAEG;IACH,uDAEC;IAED;;OAEG;IACH,opBAcC;IAED;;;;;OAKG;IACH,6BAHW,OAAO,oBAAoB,EAAE,gBAAgB,iDAkBvD;IAED;;;;;;;;;;;;OAYG;IACH,gHA2CC;IAED,uBAQC;IAgBD;;;;OAIG;IACH,8BAJW,MAAM,+DAEJ,OAAO,iBAAiB,EAAE,kBAAkB,CAKxD;CACJ;0BAnVyB,oBAAoB"}

package/dist/src/view/unitView.js

@@ -1,5 +1,5 @@
-import RectMark from "../marks/rectMark.js";
-import PointMark from "../marks/pointMark.js";
+import RectMark from "../marks/rect.js";
+import PointMark from "../marks/point.js";
 import RuleMark from "../marks/rule.js";
 import LinkMark from "../marks/link.js";
 import TextMark from "../marks/text.js";
@@ -65,13 +65,6 @@ export default class UnitView extends ContainerView {
 
         this.resolve();
 
-        /**
-         * Not nice! Inconsistent when faceting!
-         * TODO: Something. Maybe store only width/height
-         * @type {import("./layout/rectangle.js").default}
-         */
-        this.coords = undefined;
-
         this.needsAxes = { x: true, y: true };
     }
 
@@ -81,12 +74,12 @@ export default class UnitView extends ContainerView {
      * @param {import("../types/rendering.js").RenderingOptions} [options]
      */
     render(context, coords, options = {}) {
+        super.render(context, coords, options);
+
         if (!this.isConfiguredVisible()) {
             return;
         }
 
-        this.coords = coords;
-
         context.pushView(this, coords);
         context.renderMark(this.mark, options);
         context.popView(this);

package/dist/src/view/view.d.ts

@@ -46,6 +46,12 @@ export default class View {
      * @type {function(number):number}
      */
     opacityFunction: (arg0: number) => number;
+    /**
+     * Not nice! Inconsistent when faceting!
+     * TODO: Something. Maybe store only width/height
+     * @type {import("./layout/rectangle.js").default}
+     */
+    coords: import("./layout/rectangle.js").default;
     context: import("../types/viewContext.js").default;
     layoutParent: import("./containerView.js").default;
     dataParent: View;

package/dist/src/view/view.d.ts.map

@@ -1 +1 @@
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package/dist/src/view/view.js

@@ -74,6 +74,13 @@ export default class View {
      */
     opacityFunction = defaultOpacityFunction;
 
+    /**
+     * Not nice! Inconsistent when faceting!
+     * TODO: Something. Maybe store only width/height
+     * @type {import("./layout/rectangle.js").default}
+     */
+    coords;
+
     /**
      *
      * @param {import("../spec/view.js").ViewSpec} spec
@@ -462,6 +469,10 @@ export default class View {
      * @type {import("../types/rendering.js").RenderMethod}
      */
     render(context, coords, options = {}) {
+        this.coords = options.clipRect
+            ? coords.intersect(options.clipRect)
+            : coords;
+
         // override
     }
 

package/dist/src/view/view.test.js

@@ -4,7 +4,7 @@ import UnitView from "./unitView.js";
 import { create, createAndInitialize } from "./testUtils.js";
 import { toRegularArray as r } from "../utils/domainArray.js";
 import ConcatView from "./concatView.js";
-import PointMark from "../marks/pointMark.js";
+import PointMark from "../marks/point.js";
 import View from "./view.js";
 import LayerView from "./layerView.js";
 

package/package.json

@@ -7,7 +7,7 @@
   },
   "contributors": [],
   "license": "MIT",
-  "version": "0.41.0",
+  "version": "0.42.1",
   "jsdelivr": "dist/bundle/index.js",
   "unpkg": "dist/bundle/index.js",
   "browser": "dist/bundle/index.js",
@@ -42,7 +42,7 @@
     "@gmod/bgzf-filehandle": "^1.4.7",
     "@gmod/gff": "^1.3.0",
     "@gmod/indexedfasta": "^2.0.4",
-    "@gmod/tabix": "^1.5.10",
+    "@gmod/tabix": "^1.5.13",
     "@types/d3-array": "^3.0.2",
     "@types/d3-dsv": "^3.0.0",
     "@types/d3-ease": "^3.0.0",
@@ -65,5 +65,5 @@
     "vega-scale": "^7.1.1",
     "vega-util": "^1.16.0"
   },
-  "gitHead": "b9e91be6b770d888429a3dc970c6468f776c76d4"
+  "gitHead": "46e64ce03c6beef54bc8d2d30b2b49816b82de33"
 }