@genome-spy/core 0.18.1 → 0.20.0

package/dist/schema.json

@@ -478,6 +478,9 @@
         "baseUrl": {
           "type": "string"
         },
+        "columns": {
+          "type": "number"
+        },
         "concat": {
           "items": {
             "anyOf": [
@@ -575,7 +578,14 @@
           "type": "number"
         },
         "title": {
-          "type": "string"
+          "anyOf": [
+            {
+              "type": "string"
+            },
+            {
+              "$ref": "#/definitions/Title"
+            }
+          ]
         },
         "transform": {
           "items": {
@@ -606,7 +616,8 @@
         }
       },
       "required": [
-        "concat"
+        "concat",
+        "columns"
       ],
       "type": "object"
     },
@@ -1335,7 +1346,14 @@
           "type": "number"
         },
         "title": {
-          "type": "string"
+          "anyOf": [
+            {
+              "type": "string"
+            },
+            {
+              "$ref": "#/definitions/Title"
+            }
+          ]
         },
         "transform": {
           "items": {
@@ -1624,7 +1642,14 @@
           "type": "object"
         },
         "title": {
-          "type": "string"
+          "anyOf": [
+            {
+              "type": "string"
+            },
+            {
+              "$ref": "#/definitions/Title"
+            }
+          ]
         },
         "transform": {
           "items": {
@@ -1633,7 +1658,7 @@
           "type": "array"
         },
         "view": {
-          "$ref": "#/definitions/ViewConfig"
+          "$ref": "#/definitions/ViewBackground"
         },
         "visible": {
           "description": "Visibility of the view. An invisible view is removed from the layout and not rendered.\n\n**Default:** `true`",
@@ -2972,7 +2997,14 @@
               "type": "object"
             },
             "title": {
-              "type": "string"
+              "anyOf": [
+                {
+                  "type": "string"
+                },
+                {
+                  "$ref": "#/definitions/Title"
+                }
+              ]
             },
             "transform": {
               "items": {
@@ -2981,7 +3013,7 @@
               "type": "array"
             },
             "view": {
-              "$ref": "#/definitions/ViewConfig"
+              "$ref": "#/definitions/ViewBackground"
             },
             "visible": {
               "description": "Visibility of the view. An invisible view is removed from the layout and not rendered.\n\n**Default:** `true`",
@@ -3137,7 +3169,14 @@
               "type": "object"
             },
             "title": {
-              "type": "string"
+              "anyOf": [
+                {
+                  "type": "string"
+                },
+                {
+                  "$ref": "#/definitions/Title"
+                }
+              ]
             },
             "transform": {
               "items": {
@@ -3146,7 +3185,7 @@
               "type": "array"
             },
             "view": {
-              "$ref": "#/definitions/ViewConfig"
+              "$ref": "#/definitions/ViewBackground"
             },
             "visible": {
               "description": "Visibility of the view. An invisible view is removed from the layout and not rendered.\n\n**Default:** `true`",
@@ -3292,7 +3331,14 @@
               "type": "boolean"
             },
             "title": {
-              "type": "string"
+              "anyOf": [
+                {
+                  "type": "string"
+                },
+                {
+                  "$ref": "#/definitions/Title"
+                }
+              ]
             },
             "transform": {
               "items": {
@@ -3432,7 +3478,14 @@
               "type": "number"
             },
             "title": {
-              "type": "string"
+              "anyOf": [
+                {
+                  "type": "string"
+                },
+                {
+                  "$ref": "#/definitions/Title"
+                }
+              ]
             },
             "transform": {
               "items": {
@@ -3597,7 +3650,14 @@
               "type": "number"
             },
             "title": {
-              "type": "string"
+              "anyOf": [
+                {
+                  "type": "string"
+                },
+                {
+                  "$ref": "#/definitions/Title"
+                }
+              ]
             },
             "transform": {
               "items": {
@@ -3641,6 +3701,9 @@
             "baseUrl": {
               "type": "string"
             },
+            "columns": {
+              "type": "number"
+            },
             "concat": {
               "items": {
                 "anyOf": [
@@ -3749,7 +3812,14 @@
               "type": "number"
             },
             "title": {
-              "type": "string"
+              "anyOf": [
+                {
+                  "type": "string"
+                },
+                {
+                  "$ref": "#/definitions/Title"
+                }
+              ]
             },
             "transform": {
               "items": {
@@ -3780,6 +3850,7 @@
             }
           },
           "required": [
+            "columns",
             "concat"
           ],
           "type": "object"
@@ -3947,7 +4018,14 @@
           "type": "boolean"
         },
         "title": {
-          "type": "string"
+          "anyOf": [
+            {
+              "type": "string"
+            },
+            {
+              "$ref": "#/definitions/Title"
+            }
+          ]
         },
         "transform": {
           "items": {
@@ -4062,10 +4140,6 @@
           "description": "The exponent of the `pow` scale.",
           "type": "number"
         },
-        "fp64": {
-          "description": "Use emulated 64bit floating points on the GPU to increase precision.\n\nEmulation has a performance cost when compared to the native 32bit processing, but the effect is negligible in the most cases.\n\n__Default value:__ `true` for `\"locus\"` scale, `false` for others.",
-          "type": "boolean"
-        },
         "interpolate": {
           "anyOf": [
             {
@@ -4502,6 +4576,109 @@
         }
       ]
     },
+    "Title": {
+      "additionalProperties": false,
+      "properties": {
+        "align": {
+          "$ref": "#/definitions/Align",
+          "description": "Horizontal text alignment for title text. One of `\"left\"`, `\"center\"`, or `\"right\"`."
+        },
+        "anchor": {
+          "$ref": "#/definitions/TitleAnchor",
+          "description": "The anchor position for placing the title and subtitle text. One of `\"start\"`, `\"middle\"`, or `\"end\"`. For example, with an orientation of top these anchor positions map to a left-, center-, or right-aligned title."
+        },
+        "angle": {
+          "description": "Angle in degrees of title and subtitle text.",
+          "type": "number"
+        },
+        "baseline": {
+          "$ref": "#/definitions/Baseline",
+          "description": "Vertical text baseline for title and subtitle text. One of `\"alphabetic\"` (default), `\"top\"`, `\"middle\"`, or `\"bottom\"`."
+        },
+        "color": {
+          "description": "Text color for title text.",
+          "type": "string"
+        },
+        "dx": {
+          "description": "Delta offset for title and subtitle text x-coordinate.",
+          "type": "number"
+        },
+        "dy": {
+          "description": "Delta offset for title and subtitle text y-coordinate.",
+          "type": "number"
+        },
+        "font": {
+          "description": "Font name for title text.",
+          "type": "string"
+        },
+        "fontSize": {
+          "description": "Font size in pixels for title text.",
+          "minimum": 0,
+          "type": "number"
+        },
+        "fontStyle": {
+          "$ref": "#/definitions/FontStyle",
+          "description": "Font style for title text."
+        },
+        "fontWeight": {
+          "$ref": "#/definitions/FontWeight",
+          "description": "Font weight for title text. This can be either a string (e.g `\"bold\"`, `\"normal\"`) or a number (`100`, `200`, `300`, ..., `900` where `\"normal\"` = `400` and `\"bold\"` = `700`)."
+        },
+        "frame": {
+          "$ref": "#/definitions/TitleFrame",
+          "description": "The reference frame for the anchor position, one of `\"bounds\"` (to anchor relative to the full bounding box) or `\"group\"` (to anchor relative to the group width or height)."
+        },
+        "offset": {
+          "description": "The orthogonal offset in pixels by which to displace the title group from its position along the edge of the chart.",
+          "type": "number"
+        },
+        "orient": {
+          "$ref": "#/definitions/TitleOrient",
+          "description": "Default title orientation (`\"top\"`, `\"bottom\"`, `\"left\"`, or `\"right\"`)"
+        },
+        "style": {
+          "description": "A mark style property to apply to the title text mark. If not specified, a default style of `\"group-title\"` is applied.",
+          "type": "string"
+        },
+        "text": {
+          "description": "The title text.",
+          "type": "string"
+        }
+      },
+      "required": [
+        "text"
+      ],
+      "type": "object"
+    },
+    "TitleAnchor": {
+      "enum": [
+        null,
+        "start",
+        "middle",
+        "end"
+      ],
+      "type": [
+        "null",
+        "string"
+      ]
+    },
+    "TitleFrame": {
+      "enum": [
+        "bounds",
+        "group"
+      ],
+      "type": "string"
+    },
+    "TitleOrient": {
+      "enum": [
+        "none",
+        "left",
+        "right",
+        "top",
+        "bottom"
+      ],
+      "type": "string"
+    },
     "Tooltip": {
       "anyOf": [
         {
@@ -4700,7 +4877,14 @@
           "type": "object"
         },
         "title": {
-          "type": "string"
+          "anyOf": [
+            {
+              "type": "string"
+            },
+            {
+              "$ref": "#/definitions/Title"
+            }
+          ]
         },
         "transform": {
           "items": {
@@ -4709,7 +4893,7 @@
           "type": "array"
         },
         "view": {
-          "$ref": "#/definitions/ViewConfig"
+          "$ref": "#/definitions/ViewBackground"
         },
         "visible": {
           "description": "Visibility of the view. An invisible view is removed from the layout and not rendered.\n\n**Default:** `true`",
@@ -4859,7 +5043,14 @@
           "type": "number"
         },
         "title": {
-          "type": "string"
+          "anyOf": [
+            {
+              "type": "string"
+            },
+            {
+              "$ref": "#/definitions/Title"
+            }
+          ]
         },
         "transform": {
           "items": {
@@ -4936,7 +5127,7 @@
       ],
       "type": "object"
     },
-    "ViewConfig": {
+    "ViewBackground": {
       "additionalProperties": false,
       "properties": {
         "cornerRadius": {

package/package.json

@@ -7,7 +7,7 @@
   },
   "contributors": [],
   "license": "BSD-2-Clause",
-  "version": "0.18.1",
+  "version": "0.20.0",
   "main": "dist/index.js",
   "module": "src/index.js",
   "exports": {
@@ -28,6 +28,7 @@
     "dev": "node dev-server.js",
     "build": "vite build && npm run build:schema",
     "prepublishOnly": "npm run build",
+    "test:vitest": "vitest run",
     "test:tsc": "tsc -p tsconfig.json",
     "checkSpec": "tsc --allowJs --checkJs --strict --noEmit --moduleResolution node --target es6 src/spec/root.d.ts",
     "build:schema": "mkdir -p dist && ts-json-schema-generator --path 'src/spec/*.ts' --type RootSpec > dist/schema.json"
@@ -43,7 +44,7 @@
     "d3-color": "^3.0.1",
     "d3-ease": "^3.0.1",
     "d3-format": "^3.0.1",
-    "flatqueue": "^1.2.1",
+    "flatqueue": "^2.0.3",
     "internmap": "^2.0.3",
     "lit-html": "^2.0.2",
     "twgl.js": "^4.19.1",
@@ -52,5 +53,5 @@
     "vega-scale": "^7.1.1",
     "vega-util": "^1.16.0"
   },
-  "gitHead": "5f4867844fa8b52f5e7df41b72be698550777f94"
+  "gitHead": "dfeadc37891908cf775423c61a566358ecada9fa"
 }

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/collector.test.js

@@ -1,3 +1,5 @@
+import { expect, test } from "vitest";
+
 import Collector from "./collector";
 
 const data = [1, 5, 2, 4, 3].map((x) => ({ x }));

package/src/data/dataFlow.test.js

@@ -1,3 +1,5 @@
+import { describe, test } from "vitest";
+
 describe("DataFlow", () => {
     test.todo("TODO");
 });

package/src/data/flow.test.js

@@ -1,3 +1,4 @@
+import { describe, expect, test } from "vitest";
 import FilterTransform from "./transforms/filter";
 import FormulaTransform from "./transforms/formula";
 import Collector from "./collector";

package/src/data/flowNode.test.js

@@ -1,3 +1,4 @@
+import { describe, expect, test } from "vitest";
 import FlowNode from "./flowNode";
 import { validateLinks } from "./flowOptimizer";
 

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/data/flowOptimizer.test.js

@@ -1,3 +1,4 @@
+import { describe, expect, test } from "vitest";
 import FlowNode, { BEHAVIOR_CLONES } from "./flowNode";
 import { removeRedundantCloneTransforms, validateLinks } from "./flowOptimizer";
 import CloneTransform from "./transforms/clone";

package/src/data/formats/fasta.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import fasta from "./fasta";
 
 test("fasta", () => {

package/src/data/sources/inlineSource.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import Collector from "../collector";
 import InlineSource from "./inlineSource";
 

package/src/data/sources/sequenceSource.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import Collector from "../collector";
 import SequenceSource from "./sequenceSource";
 

package/src/data/transforms/clone.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import { processData } from "../flowTestUtils";
 import CloneTransform from "./clone";
 

package/src/data/transforms/coverage.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import CoverageTransform from "./coverage";
 import { processData } from "../flowTestUtils";
 

package/src/data/transforms/filter.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import { processData } from "../flowTestUtils";
 import FilterTransform from "./filter";
 

package/src/data/transforms/flattenDelimited.test.js

@@ -1,3 +1,4 @@
+import { describe, expect, test } from "vitest";
 import { processData } from "../flowTestUtils";
 import FlattenDelimitedTransform from "./flattenDelimited";
 

package/src/data/transforms/flattenSequence.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import { processData } from "../flowTestUtils";
 import FlattenSequenceTransform from "./flattenSequence";
 

package/src/data/transforms/formula.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import { processData } from "../flowTestUtils";
 import FormulaTransform from "./formula";
 

package/src/data/transforms/identifier.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import { range } from "d3-array";
 import { processData } from "../flowTestUtils";
 import IdentifierTransform, { BLOCK_SIZE, DEFAULT_AS } from "./identifier";

package/src/data/transforms/pileup.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import PileupTransform from "./pileup";
 import { processData } from "../flowTestUtils";
 

package/src/data/transforms/project.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import { processData } from "../flowTestUtils";
 import ProjectTransform from "./project";
 

package/src/data/transforms/regexExtract.test.js

@@ -1,3 +1,4 @@
+import { describe, expect, test } from "vitest";
 import { processData } from "../flowTestUtils";
 
 import RegexExtractTransform from "./regexExtract";

package/src/data/transforms/regexFold.test.js

@@ -1,3 +1,4 @@
+import { describe, expect, test } from "vitest";
 import { processData } from "../flowTestUtils";
 import RegexFoldTransform from "./regexFold";
 

package/src/data/transforms/sample.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import SampleTransform from "./sample";
 import { extent } from "d3-array";
 import { createChain } from "../../view/flowBuilder";

package/src/data/transforms/stack.test.js

@@ -1,3 +1,4 @@
+import { describe, expect, test } from "vitest";
 import { processData } from "../flowTestUtils";
 import StackTransform from "./stack";
 

package/src/encoder/accessor.test.js

@@ -1,3 +1,4 @@
+import { expect, test } from "vitest";
 import AccessorFactory from "./accessor";
 
 const af = new AccessorFactory();

package/src/encoder/encoder.test.js

@@ -1,3 +1,4 @@
+import { describe, expect, test } from "vitest";
 import AccessorFactory from "./accessor";
 import { scale as vegaScale } from "vega-scale";
 

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),