@genome-spy/core 0.18.1 → 0.19.0

package/package.json

@@ -7,7 +7,7 @@
   },
   "contributors": [],
   "license": "BSD-2-Clause",
-  "version": "0.18.1",
+  "version": "0.19.0",
   "main": "dist/index.js",
   "module": "src/index.js",
   "exports": {
@@ -52,5 +52,5 @@
     "vega-scale": "^7.1.1",
     "vega-util": "^1.16.0"
   },
-  "gitHead": "5f4867844fa8b52f5e7df41b72be698550777f94"
+  "gitHead": "282eb640bf4c29be3755ef5de3992b8d76ad5f4c"
 }

package/src/data/collector.js

@@ -27,7 +27,7 @@ export default class Collector extends FlowNode {
         /** @type {(function(Collector):void)[]} */
         this.observers = [];
 
-        /** @type {Map<any | any[], Data>} */
+        /** @type {Map<any | any[], Data>} TODO: proper type for key */
         this.facetBatches = undefined;
 
         this._init();
@@ -59,8 +59,6 @@ export default class Collector extends FlowNode {
      * @param {import("./flowBatch").FlowBatch} flowBatch
      */
     beginBatch(flowBatch) {
-        // TODO: Propagate batches to children(?)
-
         if (isFacetBatch(flowBatch)) {
             this._data = [];
             this.facetBatches.set(asArray(flowBatch.facetId), this._data);
@@ -103,7 +101,14 @@ export default class Collector extends FlowNode {
         }
 
         if (this.children.length) {
-            for (const data of this.facetBatches.values()) {
+            for (const [key, data] of this.facetBatches.entries()) {
+                if (key) {
+                    /** @type {import("./flowBatch").FacetBatch} */
+                    const facetBatch = { type: "facet", facetId: key };
+                    for (const child of this.children) {
+                        child.beginBatch(facetBatch);
+                    }
+                }
                 for (const datum of data) {
                     this._propagate(datum);
                 }

package/src/data/flowOptimizer.js

@@ -1,3 +1,4 @@
+import Collector from "./collector";
 import { BEHAVIOR_CLONES } from "./flowNode";
 import CloneTransform from "./transforms/clone";
 
@@ -31,6 +32,11 @@ export function validateLinks(node, parent = undefined) {
  * @param {FlowNode} node
  */
 export function removeRedundantCloneTransforms(node, cloneRequired = false) {
+    if (node instanceof Collector) {
+        // If an object is modified downstream of Collector, it must be cloned
+        cloneRequired = true;
+    }
+
     if (node instanceof CloneTransform) {
         if (cloneRequired) {
             cloneRequired = false;

package/src/genome/genome.js

@@ -257,15 +257,27 @@ export default class Genome {
     parseInterval(str) {
         // TODO: consider changing [0-9XY] to support other species besides humans
         const matches = str.match(
-            /^(chr[0-9A-Z]+):([0-9,]+)-(?:(chr[0-9A-Z]+):)?([0-9,]+)$/
+            /^(chr[0-9A-Z]+)(?::([0-9,]+)(?:-(?:(chr[0-9A-Z]+):)?([0-9,]+))?)?$/
         );
 
         if (matches) {
             const startChr = matches[1];
+
+            if (matches.slice(2).every((x) => x === undefined)) {
+                const chrom = this.getChromosome(startChr);
+                if (chrom) {
+                    return [chrom.continuousStart, chrom.continuousEnd];
+                }
+                return;
+            }
+
             const endChr = matches[3] || startChr;
 
             const startIndex = parseInt(matches[2].replace(/,/g, ""));
-            const endIndex = parseInt(matches[4].replace(/,/g, ""));
+            const endIndex =
+                matches[4] !== undefined
+                    ? parseInt(matches[4].replace(/,/g, ""))
+                    : startIndex;
 
             return [
                 this.toContinuous(startChr, startIndex - 1),

package/src/genome/genome.test.js

@@ -150,3 +150,38 @@ describe("C. elegans genome, chromosome names prefixed with 'chr'", () => {
         expect(g.toContinuous("III", 10)).toEqual(30351865);
     });
 });
+
+describe("Parse interval strings", () => {
+    const chromosomes = [
+        { name: "chr1", size: 1000 },
+        { name: "chr2", size: 2000 },
+        { name: "chr3", size: 3000 },
+        { name: "chrX", size: 4000 },
+    ];
+
+    const g = new Genome({ name: "random", contigs: chromosomes });
+
+    test("Parses a single chromosome, returns an interval spanning the chromosome", () => {
+        expect(g.parseInterval("chr2")).toEqual([1000, 3000]);
+    });
+
+    test("Returns undefined on unknown chromosome", () => {
+        expect(g.parseInterval("chrZ")).toBeUndefined();
+    });
+
+    test("Parses a single coordinate without a thousand separator", () => {
+        expect(g.parseInterval("chr2:1500")).toEqual([2499, 2500]);
+    });
+
+    test("Parses a single coordinate with a thousand separator", () => {
+        expect(g.parseInterval("chr2:1,500")).toEqual([2499, 2500]);
+    });
+
+    test("Parses an interval within a single chromosome", () => {
+        expect(g.parseInterval("chr2:1,500-1,700")).toEqual([2499, 2700]);
+    });
+
+    test("Parses an interval spanning multiple chromosomes", () => {
+        expect(g.parseInterval("chr2:1,500-chr3:1,500")).toEqual([2499, 4500]);
+    });
+});

package/src/view/unitView.js

@@ -17,6 +17,7 @@ import {
 import createDomain from "../utils/domainArray";
 import AxisResolution from "./axisResolution";
 import { isAggregateSamplesSpec } from "./viewFactory";
+import { peek } from "../utils/arrayUtils";
 
 /**
  *
@@ -337,10 +338,13 @@ export default class UnitView extends ContainerView {
         if (isAggregateSamplesSpec(this.spec)) {
             // TODO: Support multiple
             for (const sumSpec of this.spec.aggregateSamples) {
-                sumSpec.transform = [
-                    ...(sumSpec.transform ?? []),
-                    { type: "mergeFacets" },
-                ];
+                const transform = sumSpec.transform ?? [];
+                if (transform.length && peek(transform).type != "collect") {
+                    // MergeFacets must be a direct child of Collector
+                    transform.push({ type: "collect" });
+                }
+                transform.push({ type: "mergeFacets" });
+                sumSpec.transform = transform;
 
                 sumSpec.encoding = {
                     ...(sumSpec.encoding ?? {}),