@genome-spy/core 0.65.0 → 0.66.1

package/dist/schema.json

@@ -2353,7 +2353,9 @@
       "type": "object"
     },
     "FieldOrDatumDefWithCondition<MarkPropFieldDef<Type>,(string|null)>": {
-      "additionalProperties": false,
+      "additionalProperties": {
+        "not": {}
+      },
       "description": "A FieldDef with Condition<ValueDef> {   condition: {value: ...},   field: ...,   ... }",
       "properties": {
         "condition": {
@@ -2410,7 +2412,9 @@
       "type": "object"
     },
     "FieldOrDatumDefWithCondition<MarkPropFieldDef<Type>,number>": {
-      "additionalProperties": false,
+      "additionalProperties": {
+        "not": {}
+      },
       "description": "A FieldDef with Condition<ValueDef> {   condition: {value: ...},   field: ...,   ... }",
       "properties": {
         "condition": {
@@ -2467,7 +2471,9 @@
       "type": "object"
     },
     "FieldOrDatumDefWithCondition<MarkPropFieldDef<TypeForShape>,(string|null)>": {
-      "additionalProperties": false,
+      "additionalProperties": {
+        "not": {}
+      },
       "description": "A FieldDef with Condition<ValueDef> {   condition: {value: ...},   field: ...,   ... }",
       "properties": {
         "condition": {
@@ -8667,6 +8673,10 @@
           "description": "The alignment of the steps within the scale range.\n\nThis value must lie in the range `[0,1]`. A value of `0.5` indicates that the steps should be centered within the range. A value of `0` or `1` may be used to shift the bands to one side, say to position them adjacent to an axis.\n\n__Default value:__ `0.5`",
           "type": "number"
         },
+        "assembly": {
+          "description": "The genome assembly name for locus scales. If undefined, the default genome from the genome store is used.",
+          "type": "string"
+        },
         "base": {
           "description": "The logarithm base of the `log` scale (default `10`).",
           "type": "number"

package/dist/src/config/scaleDefaults.d.ts

@@ -0,0 +1,8 @@
+/**
+ * @param {import("../spec/channel.js").Channel} channel
+ * @param {import("../spec/channel.js").Type} dataType
+ * @param {boolean} isExplicitDomain
+ * @returns {import("../spec/scale.js").Scale}
+ */
+export function getDefaultScaleProperties(channel: import("../spec/channel.js").Channel, dataType: import("../spec/channel.js").Type, isExplicitDomain: boolean): import("../spec/scale.js").Scale;
+//# sourceMappingURL=scaleDefaults.d.ts.map

package/dist/src/config/scaleDefaults.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"scaleDefaults.d.ts","sourceRoot":"","sources":["../../../src/config/scaleDefaults.js"],"names":[],"mappings":"AAOA;;;;;GAKG;AACH,mDALW,OAAO,oBAAoB,EAAE,OAAO,YACpC,OAAO,oBAAoB,EAAE,IAAI,oBACjC,OAAO,GACL,OAAO,kBAAkB,EAAE,KAAK,CAiC5C"}

package/dist/src/config/scaleDefaults.js

@@ -0,0 +1,45 @@
+import {
+    isColorChannel,
+    isDiscreteChannel,
+    isPositionalChannel,
+} from "../encoder/encoder.js";
+import { NOMINAL, ORDINAL } from "../scales/scaleResolutionConstants.js";
+
+/**
+ * @param {import("../spec/channel.js").Channel} channel
+ * @param {import("../spec/channel.js").Type} dataType
+ * @param {boolean} isExplicitDomain
+ * @returns {import("../spec/scale.js").Scale}
+ */
+export function getDefaultScaleProperties(channel, dataType, isExplicitDomain) {
+    /** @type {import("../spec/scale.js").Scale} */
+    const props = {};
+
+    if (isExplicitDomain) {
+        props.zero = false;
+    }
+
+    if (isPositionalChannel(channel)) {
+        props.nice = !isExplicitDomain;
+    } else if (isColorChannel(channel)) {
+        // TODO: Named ranges
+        props.scheme =
+            dataType == NOMINAL
+                ? "tableau10"
+                : dataType == ORDINAL
+                  ? "blues"
+                  : "viridis";
+    } else if (isDiscreteChannel(channel)) {
+        // Shapes of point mark, for example
+        props.range =
+            channel == "shape"
+                ? ["circle", "square", "triangle-up", "cross", "diamond"]
+                : [];
+    } else if (channel == "size") {
+        props.range = [0, 400]; // TODO: Configurable default. This is currently optimized for points.
+    } else if (channel == "angle") {
+        props.range = [0, 360];
+    }
+
+    return props;
+}

package/dist/src/data/flowInit.js

@@ -2,7 +2,7 @@ import UnitView from "../view/unitView.js";
 import { buildDataFlow } from "../view/flowBuilder.js";
 import { optimizeDataFlow } from "./flowOptimizer.js";
 import { VISIT_SKIP } from "../view/view.js";
-import { reconfigureScales } from "../view/scaleResolution.js";
+import { reconfigureScaleDomains } from "../scales/scaleResolution.js";
 
 /** @type {WeakMap<import("./sources/dataSource.js").default, Promise<void>>} */
 const inFlightLoads = new WeakMap();
@@ -215,7 +215,7 @@ export function loadViewSubtreeData(
             loadDataSourceOnce(dataSource)
         )
     ).then((results) => {
-        reconfigureScales(subtreeRoot);
+        reconfigureScaleDomains(subtreeRoot);
         broadcastSubtreeDataReady(subtreeRoot);
         return results;
     });

package/dist/src/data/sources/lazy/axisTickSource.js

@@ -50,7 +50,7 @@ export default class AxisTickSource extends SingleAxisLazySource {
         // Note, although this function is async, it is not awaited. Data are updated
         // synchronously to ensure that the new ticks are available before the next frame is drawn.
 
-        const scale = this.scaleResolution.scale;
+        const scale = this.scaleResolution.getScale();
         const axisLength = this.scaleResolution.getAxisLength();
         const axisParams = this.params.axis;
 

package/dist/src/data/sources/lazy/singleAxisLazySource.d.ts

@@ -16,7 +16,7 @@ export default class SingleAxisLazySource extends DataSource {
     protected initializedPromise: Promise<void>;
     /** @type {import("../../../spec/channel.js").PrimaryPositionalChannel}  */
     channel: import("../../../spec/channel.js").PrimaryPositionalChannel;
-    scaleResolution: import("../../../view/scaleResolution.js").default;
+    scaleResolution: import("../../../scales/scaleResolution.js").default;
     /**
      * Convenience getter for genome.
      *

package/dist/src/data/sources/lazy/singleAxisLazySource.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"singleAxisLazySource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/singleAxisLazySource.js"],"names":[],"mappings":"AAIA;;;;GAIG;AACH;IAOI;;;OAGG;IACH,kBAHW,OAAO,uBAAuB,EAAE,OAAO,WACvC,OAAO,0BAA0B,EAAE,wBAAwB,EA+CrE;IAvDD;;;OAGG;IACH,4CAAuC;IAmBnC,2EAA2E;IAC3E,SADW,OAAO,0BAA0B,EAAE,wBAAwB,CAChD;IAEtB,oEAA4D;IA+BhE;;;;OAIG;IACH,oEAEC;IAED;;;;;;OAMG;IACH,wBAJW,MAAM,EAAE,iBACR,OAAO,yBAAyB,EAAE,gBAAgB,EAAE,QAK9D;IAED;;;;;OAKG;IACH,gCAGC;IAQD;;;;;;;;OAQG;IACH,8BAHW,OAAO,mBAAmB,EAAE,KAAK,EAAE,EAAE,QAgB/C;CACJ;uBA9HsB,kBAAkB"}
+{"version":3,"file":"singleAxisLazySource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/singleAxisLazySource.js"],"names":[],"mappings":"AAIA;;;;GAIG;AACH;IAOI;;;OAGG;IACH,kBAHW,OAAO,uBAAuB,EAAE,OAAO,WACvC,OAAO,0BAA0B,EAAE,wBAAwB,EA+CrE;IAvDD;;;OAGG;IACH,4CAAuC;IAmBnC,2EAA2E;IAC3E,SADW,OAAO,0BAA0B,EAAE,wBAAwB,CAChD;IAEtB,sEAA4D;IA+BhE;;;;OAIG;IACH,oEASC;IAED;;;;;;OAMG;IACH,wBAJW,MAAM,EAAE,iBACR,OAAO,yBAAyB,EAAE,gBAAgB,EAAE,QAK9D;IAED;;;;;OAKG;IACH,gCAGC;IAQD;;;;;;;;OAQG;IACH,8BAHW,OAAO,mBAAmB,EAAE,KAAK,EAAE,EAAE,QAgB/C;CACJ;uBArIsB,kBAAkB"}

package/dist/src/data/sources/lazy/singleAxisLazySource.js

@@ -1,6 +1,6 @@
 import UnitView from "../../../view/unitView.js";
 import DataSource from "../dataSource.js";
-import { reconfigureScales } from "../../../view/scaleResolution.js";
+import { reconfigureScaleDomains } from "../../../scales/scaleResolution.js";
 
 /**
  * Base class for data sources that listen a domain and propagate data lazily.
@@ -71,7 +71,14 @@ export default class SingleAxisLazySource extends DataSource {
      * @protected
      */
     get genome() {
-        return this.scaleResolution.getGenome();
+        const scale = this.scaleResolution.getScale();
+        if ("genome" in scale) {
+            const genome = scale.genome();
+            if (genome) {
+                return genome;
+            }
+        }
+        throw new Error("No genome has been defined!");
     }
 
     /**
@@ -123,6 +130,6 @@ export default class SingleAxisLazySource extends DataSource {
 
         this.complete();
 
-        reconfigureScales(this.view);
+        reconfigureScaleDomains(this.view);
     }
 }

package/dist/src/data/sources/lazy/singleAxisWindowedSource.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"singleAxisWindowedSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/singleAxisWindowedSource.js"],"names":[],"mappings":"AAIA;;;;;GAKG;AACH;IAWI;;;OAGG;IACH,kBAHU;QAAC,UAAU,CAAC,EAAE,MAAM,GAAG,OAAO,4BAA4B,EAAE,OAAO,CAAA;KAAC,CAGvE;IAEP;;;OAGG;IACH,0CAHW,OAAO,uBAAuB,EAAE,aAAa,QAqBvD;IAED;;;;OAIG;IACH,wBAFW,MAAM,EAAE,QAqBlB;IAcD;;;;;OAKG;IACH,iCAHW,MAAM,EAAE,iBAKlB;IApBD;;OAEG;IACH,mCAOC;IAYD;;;;;;;;;OASG;IACH,4BAHa,CAAC,YAHH,MAAM,EAAE,UACR,CAAC,eAAe,EAAE,OAAO,mCAAmC,EAAE,0BAA0B,EAAE,MAAM,EAAE,WAAW,KAAK,OAAO,CAAC,CAAC,CAAC,GAC3H,OAAO,CAAC,CAAC,EAAE,CAAC,CAoCvB;IAED;;;;;;OAMG;IACH,yCALW,MAAM,EAAE,cACR,MAAM,YACN,CAAS,IAAQ,EAAR,MAAM,EAAE,KAAE,IAAI,QAyBjC;;CACJ;iCA3KgC,2BAA2B"}
+{"version":3,"file":"singleAxisWindowedSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/lazy/singleAxisWindowedSource.js"],"names":[],"mappings":"AAIA;;;;;GAKG;AACH;IAWI;;;OAGG;IACH,kBAHU;QAAC,UAAU,CAAC,EAAE,MAAM,GAAG,OAAO,4BAA4B,EAAE,OAAO,CAAA;KAAC,CAGvE;IAEP;;;OAGG;IACH,0CAHW,OAAO,uBAAuB,EAAE,aAAa,QAqBvD;IAED;;;;OAIG;IACH,wBAFW,MAAM,EAAE,QAqBlB;IAcD;;;;;OAKG;IACH,iCAHW,MAAM,EAAE,iBAKlB;IApBD;;OAEG;IACH,mCAOC;IAYD;;;;;;;;;OASG;IACH,4BAHa,CAAC,YAHH,MAAM,EAAE,UACR,CAAC,eAAe,EAAE,OAAO,mCAAmC,EAAE,0BAA0B,EAAE,MAAM,EAAE,WAAW,KAAK,OAAO,CAAC,CAAC,CAAC,GAC3H,OAAO,CAAC,CAAC,EAAE,CAAC,CAwCvB;IAED;;;;;;OAMG;IACH,yCALW,MAAM,EAAE,cACR,MAAM,YACN,CAAS,IAAQ,EAAR,MAAM,EAAE,KAAE,IAAI,QAyBjC;;CACJ;iCA/KgC,2BAA2B"}

package/dist/src/data/sources/lazy/singleAxisWindowedSource.js

@@ -125,7 +125,11 @@ export default class SingleAxisWindowedSource extends SingleAxisLazySource {
 
         try {
             const resultByChrom = await Promise.all(
-                discreteChromosomeIntervals.map(async (d) => loader(d, signal))
+                discreteChromosomeIntervals.map(
+                    async (
+                        /** @type {import("@genome-spy/core/genome/genome.js").DiscreteChromosomeInterval} */ d
+                    ) => loader(d, signal)
+                )
             );
 
             if (!signal.aborted) {

package/dist/src/data/transforms/filterScoredLabels.d.ts

@@ -20,7 +20,7 @@ export default class FilterScoredLabelsTransform extends Transform {
     padding: number;
     /** @type {Map<any, ReservationMap>} */
     reservationMaps: Map<any, ReservationMap>;
-    resolution: import("../../view/scaleResolution.js").default;
+    resolution: import("../../scales/scaleResolution.js").default;
     schedule: () => void;
     _filterAndPropagate(): void;
     groups: Map<any, any>;

package/dist/src/data/transforms/filterScoredLabels.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"filterScoredLabels.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/filterScoredLabels.js"],"names":[],"mappings":"AAOA;IAKI;;;;OAIG;IACH,oBAHW,OAAO,yBAAyB,EAAE,wBAAwB,QAC1D,OAAO,oBAAoB,EAAE,OAAO,EA6C9C;IAxCG,mEAAoB;IAEpB,oBAAoB;IACpB,OADW,GAAG,EAAE,CACD;IAEf,mBAAoC;IAMpC,sDAA8C;IAC9C,oDAAgE;IAChE,wDAAuD;IACvD,sDAAmD;IACnD,mDAA6C;IAC7C,mDAA6C;IAC7C,gCAAgC;IAChC,cADW,CAAS,IAAG,EAAH,GAAG,KAAE,GAAG,CAGd;IACd,gBAAuC;IAEvC,uCAAuC;IACvC,iBADW,GAAG,CAAC,GAAG,EAAE,cAAc,CAAC,CACH;IAEhC,4DAAuD;IAIvD,qBAAuE;IAyB3E,4BAsEC;IAKG,sBAAuB;CAU9B;sBA3JqB,gBAAgB;2BAFX,+BAA+B"}
+{"version":3,"file":"filterScoredLabels.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/filterScoredLabels.js"],"names":[],"mappings":"AAOA;IAKI;;;;OAIG;IACH,oBAHW,OAAO,yBAAyB,EAAE,wBAAwB,QAC1D,OAAO,oBAAoB,EAAE,OAAO,EA6C9C;IAxCG,mEAAoB;IAEpB,oBAAoB;IACpB,OADW,GAAG,EAAE,CACD;IAEf,mBAAoC;IAMpC,sDAA8C;IAC9C,oDAAgE;IAChE,wDAAuD;IACvD,sDAAmD;IACnD,mDAA6C;IAC7C,mDAA6C;IAC7C,gCAAgC;IAChC,cADW,CAAS,IAAG,EAAH,GAAG,KAAE,GAAG,CAGd;IACd,gBAAuC;IAEvC,uCAAuC;IACvC,iBADW,GAAG,CAAC,GAAG,EAAE,cAAc,CAAC,CACH;IAEhC,8DAAuD;IAIvD,qBAAuE;IAyB3E,4BAsEC;IAKG,sBAAuB;CAU9B;sBA3JqB,gBAAgB;2BAFX,+BAA+B"}

package/dist/src/data/transforms/filterScoredLabels.js

@@ -76,7 +76,7 @@ export default class FilterScoredLabelsTransform extends Transform {
     _filterAndPropagate() {
         super.reset();
 
-        const scale = this.resolution.scale;
+        const scale = this.resolution.getScale();
         const rangeSpan = this.resolution.getAxisLength();
         if (!rangeSpan) {
             // The view size is not (yet) available

package/dist/src/data/transforms/linearizeGenomicCoordinate.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"linearizeGenomicCoordinate.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/linearizeGenomicCoordinate.js"],"names":[],"mappings":"AAKA;IAKI;;;;OAIG;IACH,oBAHW,OAAO,yBAAyB,EAAE,gCAAgC,QAClE,OAAO,oBAAoB,EAAE,OAAO,EAgG9C;IAvFG,2EAAoB;CAwF3B;sBA3GqB,gBAAgB"}
+{"version":3,"file":"linearizeGenomicCoordinate.d.ts","sourceRoot":"","sources":["../../../../src/data/transforms/linearizeGenomicCoordinate.js"],"names":[],"mappings":"AAKA;IAKI;;;;OAIG;IACH,oBAHW,OAAO,yBAAyB,EAAE,gCAAgC,QAClE,OAAO,oBAAoB,EAAE,OAAO,EAiG9C;IAxFG,2EAAoB;CAyF3B;sBA5GqB,gBAAgB"}

package/dist/src/data/transforms/linearizeGenomicCoordinate.js

@@ -28,7 +28,8 @@ export default class LinearizeGenomicCoordinate extends Transform {
             throw new Error("Invalid channel: " + channel);
         }
 
-        const genome = view.getScaleResolution(channel).getGenome();
+        const scale = view.getScaleResolution(channel).getScale();
+        const genome = "genome" in scale ? scale.genome() : undefined;
         if (!genome) {
             throw new Error(
                 "LinearizeGenomicCoordinate transform requires a locus scale!"

package/dist/src/encoder/encoder.d.ts

@@ -109,7 +109,7 @@ export function getPrimaryChannel(channel: import("../spec/channel.js").Channel)
  *
  * @param {import("../spec/channel.js").Channel} channel
  */
-export function getChannelWithSecondarys(channel: import("../spec/channel.js").Channel): ("search" | "fill" | "stroke" | "angle" | "sample" | "color" | "fillOpacity" | "opacity" | "strokeOpacity" | "strokeWidth" | "x" | "y" | "text" | "size" | "x2" | "y2" | "shape" | "dx" | "dy" | "uniqueId" | "facetIndex" | "semanticScore")[];
+export function getChannelWithSecondarys(channel: import("../spec/channel.js").Channel): import("../spec/channel.js").Channel[];
 /**
  * @param {import("../spec/channel.js").Channel} channel
  */

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

@@ -1 +1 @@
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+{"version":3,"file":"encoder.d.ts","sourceRoot":"","sources":["../../../src/encoder/encoder.js"],"names":[],"mappings":"AAwDA;;;;;;;;GAQG;AACH,iDAJW,OAAO,qBAAqB,EAAE,OAAO,YACrC,OAAO,oBAAoB,EAAE,QAAQ,GACnC,OAAO,CAAC,MAAM,6EAAkB,CAAC,CAgC7C;AAED;;;;GAIG;AACH,4DAJW,OAAO,qBAAqB,EAAE,QAAQ,EAAE,eACxC,CAAC,OAAO,EAAE,OAAO,oBAAoB,EAAE,gBAAgB,KAAK,OAAO,qBAAqB,EAAE,SAAS,yCAqC7G;AAED;;;;GAIG;AACH,kIAHW,CAAC,OAAO,EAAE,OAAO,oBAAoB,EAAE,gBAAgB,KAAK,OAAO,qBAAqB,EAAE,SAAS,yCAqC7G;AAED;;;;;GAKG;AACH,uCAHW,OAAO,oBAAoB,EAAE,UAAU,GACrC,UAAU,IAAI,OAAO,oBAAoB,EAAE,QAAQ,CAI/D;AAED;;;GAGG;AACH,uCAHW,OAAO,oBAAoB,EAAE,UAAU,GACrC,UAAU,IAAI,OAAO,oBAAoB,EAAE,YAAY,CAInE;AAED;;;GAGG;AACH,uCAHW,OAAO,oBAAoB,EAAE,UAAU,GACrC,UAAU,IAAI,OAAO,oBAAoB,EAAE,QAAQ,CAI/D;AAED;;;GAGG;AACH,kDAHW,OAAO,oBAAoB,EAAE,UAAU,GACrC,UAAU,IAAI,OAAO,oBAAoB,EAAE,mBAAmB,CAU1E;AAED;;GAEG;AACH,oDAFW,OAAO,oBAAoB,EAAE,UAAU,qkDAWjD;AAED;;;GAGG;AACH,6CAHW,OAAO,qBAAqB,EAAE,OAAO,WACrC,OAAO,oBAAoB,EAAE,OAAO,s9CAS9C;AAED;;;GAGG;AACH,iDAHW,OAAO,oBAAoB,EAAE,UAAU,GACrC,UAAU,IAAI,OAAO,oBAAoB,EAAE,UAAU,CAAC,OAAO,oBAAoB,EAAE,IAAI,CAAC,CAIpG;AAED;;;GAGG;AACH,0CAHW,OAAO,oBAAoB,EAAE,UAAU,GACrC,UAAU,IAAI,OAAO,oBAAoB,EAAE,WAAW,CAIlE;AAED;;;GAGG;AACH,sCAHW,OAAO,oBAAoB,EAAE,UAAU,GACrC,UAAU,IAAI,OAAO,oBAAoB,EAAE,OAAO,CAI9D;AAED;;;GAGG;AACH,2DAHW,OAAO,oBAAoB,EAAE,UAAU,GACrC,UAAU,IAAI,OAAO,oBAAoB,EAAE,4BAA4B,CAOnF;AAED;;;GAGG;AACH,oDAHW,OAAO,oBAAoB,EAAE,UAAU,GACrC,UAAU,IAAI,OAAO,oBAAoB,EAAE,qBAAqB,CAI5E;AAoBD;;;GAGG;AACH,oDAHW,OAAO,oBAAoB,EAAE,OAAO,GAClC,OAAO,IAAI,OAAO,oBAAoB,EAAE,wBAAwB,CAK5E;AAED;;;GAGG;AACH,6CAHW,OAAO,oBAAoB,EAAE,OAAO,GAClC,OAAO,IAAI,OAAO,oBAAoB,EAAE,iBAAiB,CAKrE;AAqBD;;;GAGG;AACH,4CAFW,MAAM,WAIhB;AAED;;;;GAIG;AACH,oDAFW,OAAO,oBAAoB,EAAE,OAAO,2DAS9C;AAED;;;;;GAKG;AACH,2CAFW,OAAO,oBAAoB,EAAE,OAAO,wCAI9C;AAED;;;;GAIG;AACH,kDAFW,OAAO,oBAAoB,EAAE,OAAO,0CAM9C;AAED;;GAEG;AACH,wCAFW,OAAO,oBAAoB,EAAE,OAAO,WAI9C;AAED;;;;GAIG;AACH,2CAFW,OAAO,oBAAoB,EAAE,OAAO,WAI9C;AAED;;;GAGG;AACH,4CAHW,OAAO,oBAAoB,EAAE,OAAO,GAClC,OAAO,IAAI,OAAO,oBAAoB,EAAE,gBAAgB,CAsBpE;AAED;;;;;GAKG;AACH,0CAHW,OAAO,oBAAoB,EAAE,OAAO,GAClC,GAAG,EAAE,CAsBjB;AAED;;;GAGG;AACH,gDAHW,OAAO,oBAAoB,EAAE,OAAO,GAClC,CAAS,IAAG,EAAH,GAAG,KAAE,MAAM,CAmBhC;AA7LD;;GAEG;AACH,wCAFU,OAAO,oBAAoB,EAAE,wBAAwB,EAAE,CAEb;AAEpD;;GAEG;AACH,0CAFU,OAAO,oBAAoB,EAAE,0BAA0B,EAAE,CAEX;AAExD;;GAEG;AACH,iCAFU,OAAO,oBAAoB,EAAE,iBAAiB,EAAE,CAKxD;AAoBF;;;;GAIG;AACH,gCAFU,OAAO,CAAC,MAAM,CAAC,OAAO,oBAAoB,EAAE,OAAO,EAAE,OAAO,oBAAoB,EAAE,0BAA0B,CAAC,CAAC,CAKtH;AAEF;;;;GAIG;AACH,8BAFU,OAAO,CAAC,MAAM,CAAC,OAAO,oBAAoB,EAAE,OAAO,EAAE,OAAO,oBAAoB,EAAE,OAAO,CAAC,CAAC,CAInG"}

package/dist/src/encoder/encoder.js

@@ -75,7 +75,7 @@ export default function createEncoders(unitView, encoding) {
     /**
      * @param {import("../spec/channel.js").ChannelWithScale} channel */
     const scaleSource = (channel) =>
-        unitView.getScaleResolution(channel)?.scale;
+        unitView.getScaleResolution(channel)?.getScale();
 
     for (const [channel, channelDef] of Object.entries(encoding)) {
         if (!channelDef) {

package/dist/src/genome/scaleLocus.d.ts

@@ -1,3 +1,42 @@
 export default function scaleLocus(): import("./scaleLocus.js").ScaleLocus;
 export function isScaleLocus(scale: any): scale is import("./scaleLocus.js").ScaleLocus;
+/**
+ * @param {import("./genome.js").default | { genome?: () => import("./genome.js").default } | undefined} scaleOrGenome
+ * @param {number} value
+ * @returns {number | import("./genome.js").ChromosomalLocus}
+ */
+export function toComplexValue(scaleOrGenome: import("./genome.js").default | {
+    genome?: () => import("./genome.js").default;
+} | undefined, value: number): number | import("./genome.js").ChromosomalLocus;
+/**
+ * @param {import("./genome.js").default | { genome?: () => import("./genome.js").default } | undefined} scaleOrGenome
+ * @param {number | import("./genome.js").ChromosomalLocus} complex
+ * @returns {number}
+ */
+export function fromComplexValue(scaleOrGenome: import("./genome.js").default | {
+    genome?: () => import("./genome.js").default;
+} | undefined, complex: number | import("./genome.js").ChromosomalLocus): number;
+/**
+ * @param {import("./genome.js").default | { genome?: () => import("./genome.js").default } | undefined} scaleOrGenome
+ * @param {import("../spec/scale.js").ScalarDomain | import("../spec/scale.js").ComplexDomain} interval
+ * @returns {number[]}
+ */
+export function fromComplexInterval(scaleOrGenome: import("./genome.js").default | {
+    genome?: () => import("./genome.js").default;
+} | undefined, interval: import("../spec/scale.js").ScalarDomain | import("../spec/scale.js").ComplexDomain): number[];
+/**
+ * @param {import("./genome.js").default | { genome?: () => import("./genome.js").default } | undefined} scaleOrGenome
+ * @param {import("../spec/scale.js").ScalarDomain | import("../spec/scale.js").ComplexDomain} interval
+ * @returns {import("../spec/scale.js").ScalarDomain | import("../spec/scale.js").ComplexDomain}
+ */
+export function toComplexInterval(scaleOrGenome: import("./genome.js").default | {
+    genome?: () => import("./genome.js").default;
+} | undefined, interval: import("../spec/scale.js").ScalarDomain | import("../spec/scale.js").ComplexDomain): import("../spec/scale.js").ScalarDomain | import("../spec/scale.js").ComplexDomain;
+/**
+ * @param {import("./genome.js").default | { genome?: () => import("./genome.js").default } | undefined} scaleOrGenome
+ * @returns {number[]}
+ */
+export function getGenomeExtent(scaleOrGenome: import("./genome.js").default | {
+    genome?: () => import("./genome.js").default;
+} | undefined): number[];
 //# sourceMappingURL=scaleLocus.d.ts.map

package/dist/src/genome/scaleLocus.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"scaleLocus.d.ts","sourceRoot":"","sources":["../../../src/genome/scaleLocus.js"],"names":[],"mappings":"AAIA,2EAyFC"}
+{"version":3,"file":"scaleLocus.d.ts","sourceRoot":"","sources":["../../../src/genome/scaleLocus.js"],"names":[],"mappings":"AAMA,2EAyFC;;AASD;;;;GAIG;AACH,8CAJW,OAAO,aAAa,EAAE,OAAO,GAAG;IAAE,MAAM,CAAC,EAAE,MAAM,OAAO,aAAa,EAAE,OAAO,CAAA;CAAE,GAAG,SAAS,SAC5F,MAAM,GACJ,MAAM,GAAG,OAAO,aAAa,EAAE,gBAAgB,CAK3D;AAED;;;;GAIG;AACH,gDAJW,OAAO,aAAa,EAAE,OAAO,GAAG;IAAE,MAAM,CAAC,EAAE,MAAM,OAAO,aAAa,EAAE,OAAO,CAAA;CAAE,GAAG,SAAS,WAC5F,MAAM,GAAG,OAAO,aAAa,EAAE,gBAAgB,GAC7C,MAAM,CAQlB;AAED;;;;GAIG;AACH,mDAJW,OAAO,aAAa,EAAE,OAAO,GAAG;IAAE,MAAM,CAAC,EAAE,MAAM,OAAO,aAAa,EAAE,OAAO,CAAA;CAAE,GAAG,SAAS,YAC5F,OAAO,kBAAkB,EAAE,YAAY,GAAG,OAAO,kBAAkB,EAAE,aAAa,GAChF,MAAM,EAAE,CAQpB;AAED;;;;GAIG;AACH,iDAJW,OAAO,aAAa,EAAE,OAAO,GAAG;IAAE,MAAM,CAAC,EAAE,MAAM,OAAO,aAAa,EAAE,OAAO,CAAA;CAAE,GAAG,SAAS,YAC5F,OAAO,kBAAkB,EAAE,YAAY,GAAG,OAAO,kBAAkB,EAAE,aAAa,GAChF,OAAO,kBAAkB,EAAE,YAAY,GAAG,OAAO,kBAAkB,EAAE,aAAa,CAO9F;AAED;;;GAGG;AACH,+CAHW,OAAO,aAAa,EAAE,OAAO,GAAG;IAAE,MAAM,CAAC,EAAE,MAAM,OAAO,aAAa,EAAE,OAAO,CAAA;CAAE,GAAG,SAAS,GAC1F,MAAM,EAAE,CAQpB"}

package/dist/src/genome/scaleLocus.js

@@ -1,6 +1,8 @@
 import { tickStep } from "d3-array";
 import { format as d3format } from "d3-format";
+
 import scaleIndex from "./scaleIndex.js";
+import { isChromosomalLocus, isChromosomalLocusInterval } from "./genome.js";
 
 export default function scaleLocus() {
     /** @type {import("./scaleLocus.js").ScaleLocus} */
@@ -99,3 +101,77 @@ export default function scaleLocus() {
 export function isScaleLocus(scale) {
     return scale.type == "locus";
 }
+
+/**
+ * @param {import("./genome.js").default | { genome?: () => import("./genome.js").default } | undefined} scaleOrGenome
+ * @param {number} value
+ * @returns {number | import("./genome.js").ChromosomalLocus}
+ */
+export function toComplexValue(scaleOrGenome, value) {
+    const genome = resolveGenome(scaleOrGenome);
+    return genome ? genome.toChromosomal(value) : value;
+}
+
+/**
+ * @param {import("./genome.js").default | { genome?: () => import("./genome.js").default } | undefined} scaleOrGenome
+ * @param {number | import("./genome.js").ChromosomalLocus} complex
+ * @returns {number}
+ */
+export function fromComplexValue(scaleOrGenome, complex) {
+    const genome = resolveGenome(scaleOrGenome);
+    if (genome && isChromosomalLocus(complex)) {
+        return genome.toContinuous(complex.chrom, complex.pos);
+    }
+    return /** @type {number} */ (complex);
+}
+
+/**
+ * @param {import("./genome.js").default | { genome?: () => import("./genome.js").default } | undefined} scaleOrGenome
+ * @param {import("../spec/scale.js").ScalarDomain | import("../spec/scale.js").ComplexDomain} interval
+ * @returns {number[]}
+ */
+export function fromComplexInterval(scaleOrGenome, interval) {
+    const genome = resolveGenome(scaleOrGenome);
+    if (genome && isChromosomalLocusInterval(interval)) {
+        return genome.toContinuousInterval(interval);
+    }
+    return /** @type {number[]} */ (interval);
+}
+
+/**
+ * @param {import("./genome.js").default | { genome?: () => import("./genome.js").default } | undefined} scaleOrGenome
+ * @param {import("../spec/scale.js").ScalarDomain | import("../spec/scale.js").ComplexDomain} interval
+ * @returns {import("../spec/scale.js").ScalarDomain | import("../spec/scale.js").ComplexDomain}
+ */
+export function toComplexInterval(scaleOrGenome, interval) {
+    const genome = resolveGenome(scaleOrGenome);
+    return genome
+        ? genome.toChromosomalInterval(/** @type {number[]} */ (interval))
+        : interval;
+}
+
+/**
+ * @param {import("./genome.js").default | { genome?: () => import("./genome.js").default } | undefined} scaleOrGenome
+ * @returns {number[]}
+ */
+export function getGenomeExtent(scaleOrGenome) {
+    const genome = resolveGenome(scaleOrGenome);
+    if (!genome) {
+        throw new Error("No genome has been defined!");
+    }
+    return genome.getExtent();
+}
+
+/**
+ * @param {import("./genome.js").default | { genome?: () => import("./genome.js").default } | undefined} scaleOrGenome
+ * @returns {import("./genome.js").default | undefined}
+ */
+function resolveGenome(scaleOrGenome) {
+    if (scaleOrGenome && "toChromosomal" in scaleOrGenome) {
+        return scaleOrGenome;
+    }
+    if (scaleOrGenome && "genome" in scaleOrGenome) {
+        return scaleOrGenome.genome();
+    }
+    return undefined;
+}

package/dist/src/genomeSpy/canvasExport.d.ts

@@ -0,0 +1,19 @@
+/**
+ * @param {object} options
+ * @param {import("../gl/webGLHelper.js").default} options.glHelper
+ * @param {import("../view/view.js").default} options.viewRoot
+ * @param {number} [options.logicalWidth]
+ * @param {number} [options.logicalHeight]
+ * @param {number} [options.devicePixelRatio]
+ * @param {string} [options.clearColor]
+ * @returns {string}
+ */
+export function exportCanvas({ glHelper, viewRoot, logicalWidth, logicalHeight, devicePixelRatio, clearColor, }: {
+    glHelper: import("../gl/webGLHelper.js").default;
+    viewRoot: import("../view/view.js").default;
+    logicalWidth?: number;
+    logicalHeight?: number;
+    devicePixelRatio?: number;
+    clearColor?: string;
+}): string;
+//# sourceMappingURL=canvasExport.d.ts.map

package/dist/src/genomeSpy/canvasExport.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"canvasExport.d.ts","sourceRoot":"","sources":["../../../src/genomeSpy/canvasExport.js"],"names":[],"mappings":"AAMA;;;;;;;;;GASG;AACH,iHARG;IAAwD,QAAQ,EAAxD,OAAO,sBAAsB,EAAE,OAAO;IACK,QAAQ,EAAnD,OAAO,iBAAiB,EAAE,OAAO;IAChB,YAAY,GAA7B,MAAM;IACW,aAAa,GAA9B,MAAM;IACW,gBAAgB,GAAjC,MAAM;IACW,UAAU,GAA3B,MAAM;CACd,GAAU,MAAM,CAmDlB"}

package/dist/src/genomeSpy/canvasExport.js

@@ -0,0 +1,66 @@
+import { createFramebufferInfo } from "twgl.js";
+
+import BufferedViewRenderingContext from "../view/renderingContext/bufferedViewRenderingContext.js";
+import Rectangle from "../view/layout/rectangle.js";
+import { framebufferToDataUrl } from "../gl/webGLHelper.js";
+
+/**
+ * @param {object} options
+ * @param {import("../gl/webGLHelper.js").default} options.glHelper
+ * @param {import("../view/view.js").default} options.viewRoot
+ * @param {number} [options.logicalWidth]
+ * @param {number} [options.logicalHeight]
+ * @param {number} [options.devicePixelRatio]
+ * @param {string} [options.clearColor]
+ * @returns {string}
+ */
+export function exportCanvas({
+    glHelper,
+    viewRoot,
+    logicalWidth,
+    logicalHeight,
+    devicePixelRatio,
+    clearColor = "white",
+}) {
+    logicalWidth ??= glHelper.getLogicalCanvasSize().width;
+    logicalHeight ??= glHelper.getLogicalCanvasSize().height;
+    devicePixelRatio ??= window.devicePixelRatio ?? 1;
+
+    const gl = glHelper.gl;
+
+    const width = Math.floor(logicalWidth * devicePixelRatio);
+    const height = Math.floor(logicalHeight * devicePixelRatio);
+
+    const framebufferInfo = createFramebufferInfo(
+        gl,
+        [
+            {
+                format: gl.RGBA,
+                type: gl.UNSIGNED_BYTE,
+                minMag: gl.LINEAR,
+                wrap: gl.CLAMP_TO_EDGE,
+            },
+        ],
+        width,
+        height
+    );
+
+    const renderingContext = new BufferedViewRenderingContext(
+        { picking: false },
+        {
+            webGLHelper: glHelper,
+            canvasSize: { width: logicalWidth, height: logicalHeight },
+            devicePixelRatio,
+            clearColor,
+            framebufferInfo,
+        }
+    );
+
+    viewRoot.render(
+        renderingContext,
+        Rectangle.create(0, 0, logicalWidth, logicalHeight)
+    );
+    renderingContext.render();
+
+    return framebufferToDataUrl(gl, framebufferInfo, "image/png");
+}

package/dist/src/genomeSpy/containerUi.d.ts

@@ -0,0 +1,17 @@
+/**
+ * @param {HTMLElement} container
+ */
+export function createContainerUi(container: HTMLElement): {
+    canvasWrapper: HTMLElement;
+    loadingMessageElement: HTMLElement;
+    loadingIndicatorsElement: HTMLElement;
+    tooltip: Tooltip;
+    styleElement: HTMLStyleElement;
+};
+/**
+ * @param {HTMLElement} container
+ * @param {string} message
+ */
+export function createMessageBox(container: HTMLElement, message: string): void;
+import Tooltip from "../utils/ui/tooltip.js";
+//# sourceMappingURL=containerUi.d.ts.map

package/dist/src/genomeSpy/containerUi.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"containerUi.d.ts","sourceRoot":"","sources":["../../../src/genomeSpy/containerUi.js"],"names":[],"mappings":"AAGA;;GAEG;AACH,6CAFW,WAAW;;;;;;EA2CrB;AAED;;;GAGG;AACH,4CAHW,WAAW,WACX,MAAM,QAUhB;oBA5DmB,wBAAwB"}

package/dist/src/genomeSpy/containerUi.js

@@ -0,0 +1,78 @@
+import css from "../styles/genome-spy.css.js";
+import Tooltip from "../utils/ui/tooltip.js";
+
+/**
+ * @param {HTMLElement} container
+ */
+export function createContainerUi(container) {
+    container.classList.add("genome-spy");
+
+    const styleElement = document.createElement("style");
+    styleElement.innerHTML = css;
+    container.appendChild(styleElement);
+
+    const canvasWrapper = element("div", {
+        class: "canvas-wrapper",
+    });
+    container.appendChild(canvasWrapper);
+
+    canvasWrapper.classList.add("loading");
+
+    const loadingMessageElement = element("div", {
+        class: "loading-message",
+        innerHTML: `<div class="message">Loading<span class="ellipsis">...</span></div>`,
+    });
+    canvasWrapper.appendChild(loadingMessageElement);
+
+    const loadingIndicatorsElement = element("div", {
+        class: "loading-indicators",
+    });
+    canvasWrapper.appendChild(loadingIndicatorsElement);
+
+    const tooltip = new Tooltip(container);
+
+    loadingMessageElement
+        .querySelector(".message")
+        .addEventListener("transitionend", () => {
+            /** @type {HTMLElement} */ (loadingMessageElement).style.display =
+                "none";
+        });
+
+    return {
+        canvasWrapper,
+        loadingMessageElement,
+        loadingIndicatorsElement,
+        tooltip,
+        styleElement,
+    };
+}
+
+/**
+ * @param {HTMLElement} container
+ * @param {string} message
+ */
+export function createMessageBox(container, message) {
+    // Uh, need a templating thingy
+    const messageBox = document.createElement("div");
+    messageBox.className = "message-box";
+    const messageText = document.createElement("div");
+    messageText.textContent = message;
+    messageBox.appendChild(messageText);
+    container.appendChild(messageBox);
+}
+
+/**
+ * @param {string} tag
+ * @param {Record<string, any>} attrs
+ */
+function element(tag, attrs) {
+    const el = document.createElement(tag);
+    for (const [key, value] of Object.entries(attrs)) {
+        if (["innerHTML", "innerText", "className"].includes(key)) {
+            // @ts-ignore
+            el[key] = value;
+        }
+        el.setAttribute(key, value);
+    }
+    return el;
+}

package/dist/src/genomeSpy/eventListenerRegistry.d.ts

@@ -0,0 +1,19 @@
+export default class EventListenerRegistry {
+    /**
+     * @param {string} type
+     * @param {(event: any) => void} listener
+     */
+    add(type: string, listener: (event: any) => void): void;
+    /**
+     * @param {string} type
+     * @param {(event: any) => void} listener
+     */
+    remove(type: string, listener: (event: any) => void): void;
+    /**
+     * @param {string} type
+     * @param {any} event
+     */
+    emit(type: string, event: any): void;
+    #private;
+}
+//# sourceMappingURL=eventListenerRegistry.d.ts.map

package/dist/src/genomeSpy/eventListenerRegistry.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"eventListenerRegistry.d.ts","sourceRoot":"","sources":["../../../src/genomeSpy/eventListenerRegistry.js"],"names":[],"mappings":"AAAA;IAQI;;;OAGG;IACH,UAHW,MAAM,YACN,CAAC,KAAK,EAAE,GAAG,KAAK,IAAI,QAU9B;IAED;;;OAGG;IACH,aAHW,MAAM,YACN,CAAC,KAAK,EAAE,GAAG,KAAK,IAAI,QAI9B;IAED;;;OAGG;IACH,WAHW,MAAM,SACN,GAAG,QAIb;;CACJ"}