@genome-spy/core 0.14.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/index.js +224 -0
- package/dist/style.css +1 -0
- package/package.json +54 -0
- package/src/data/collector.js +178 -0
- package/src/data/collector.test.js +82 -0
- package/src/data/dataFlow.js +109 -0
- package/src/data/dataFlow.test.js +3 -0
- package/src/data/facetNode.js +17 -0
- package/src/data/flow.test.js +71 -0
- package/src/data/flowBatch.d.ts +40 -0
- package/src/data/flowNode.js +283 -0
- package/src/data/flowNode.test.js +49 -0
- package/src/data/flowOptimizer.js +117 -0
- package/src/data/flowOptimizer.test.js +192 -0
- package/src/data/flowTestUtils.js +63 -0
- package/src/data/formats/fasta.js +32 -0
- package/src/data/formats/fasta.test.js +26 -0
- package/src/data/sources/dataSource.js +22 -0
- package/src/data/sources/dataSourceFactory.js +24 -0
- package/src/data/sources/dataUtils.js +31 -0
- package/src/data/sources/dynamicCallbackSource.js +56 -0
- package/src/data/sources/dynamicSource.js +36 -0
- package/src/data/sources/inlineSource.js +69 -0
- package/src/data/sources/inlineSource.test.js +55 -0
- package/src/data/sources/namedSource.js +74 -0
- package/src/data/sources/sequenceSource.js +46 -0
- package/src/data/sources/sequenceSource.test.js +45 -0
- package/src/data/sources/urlSource.js +74 -0
- package/src/data/transforms/aggregate.js +69 -0
- package/src/data/transforms/clone.js +40 -0
- package/src/data/transforms/clone.test.js +10 -0
- package/src/data/transforms/coverage.js +187 -0
- package/src/data/transforms/coverage.test.js +122 -0
- package/src/data/transforms/filter.js +37 -0
- package/src/data/transforms/filter.test.js +17 -0
- package/src/data/transforms/filterScoredLabels.js +134 -0
- package/src/data/transforms/flattenCompressedExons.js +57 -0
- package/src/data/transforms/flattenDelimited.js +68 -0
- package/src/data/transforms/flattenDelimited.test.js +86 -0
- package/src/data/transforms/flattenSequence.js +39 -0
- package/src/data/transforms/flattenSequence.test.js +33 -0
- package/src/data/transforms/formula.js +39 -0
- package/src/data/transforms/formula.test.js +18 -0
- package/src/data/transforms/identifier.js +108 -0
- package/src/data/transforms/identifier.test.js +82 -0
- package/src/data/transforms/linearizeGenomicCoordinate.js +101 -0
- package/src/data/transforms/measureText.js +44 -0
- package/src/data/transforms/pileup.js +128 -0
- package/src/data/transforms/pileup.test.js +69 -0
- package/src/data/transforms/project.js +41 -0
- package/src/data/transforms/project.test.js +31 -0
- package/src/data/transforms/regexExtract.js +61 -0
- package/src/data/transforms/regexExtract.test.js +66 -0
- package/src/data/transforms/regexFold.js +141 -0
- package/src/data/transforms/regexFold.test.js +159 -0
- package/src/data/transforms/sample.js +101 -0
- package/src/data/transforms/sample.test.js +37 -0
- package/src/data/transforms/stack.js +137 -0
- package/src/data/transforms/stack.test.js +90 -0
- package/src/data/transforms/transformFactory.js +60 -0
- package/src/encoder/accessor.js +82 -0
- package/src/encoder/accessor.test.js +46 -0
- package/src/encoder/encoder.js +369 -0
- package/src/encoder/encoder.test.js +97 -0
- package/src/fonts/Lato-Regular.json +1267 -0
- package/src/fonts/Lato-Regular.png +0 -0
- package/src/fonts/OFL.txt +93 -0
- package/src/fonts/README.md +3 -0
- package/src/fonts/bmFont.d.ts +58 -0
- package/src/fonts/bmFontManager.js +357 -0
- package/src/fonts/bmFontMetrics.js +108 -0
- package/src/genome/genome.js +305 -0
- package/src/genome/genome.test.js +152 -0
- package/src/genome/genomeStore.js +54 -0
- package/src/genome/locusFormat.js +31 -0
- package/src/genome/scaleIndex.js +199 -0
- package/src/genome/scaleIndex.test.js +61 -0
- package/src/genome/scaleLocus.js +112 -0
- package/src/genome/scaleLocus.test.js +3 -0
- package/src/genomeSpy.js +753 -0
- package/src/gl/arrayBuilder.js +199 -0
- package/src/gl/dataToVertices.js +621 -0
- package/src/gl/includes/common.glsl +63 -0
- package/src/gl/includes/fp64-arithmetic.glsl +187 -0
- package/src/gl/includes/fp64-utils.js +132 -0
- package/src/gl/includes/picking.fragment.glsl +3 -0
- package/src/gl/includes/picking.vertex.glsl +29 -0
- package/src/gl/includes/sampleFacet.glsl +107 -0
- package/src/gl/includes/scales.glsl +79 -0
- package/src/gl/includes/scales_fp64.glsl +30 -0
- package/src/gl/link.fragment.glsl +18 -0
- package/src/gl/link.vertex.glsl +111 -0
- package/src/gl/point.fragment.glsl +123 -0
- package/src/gl/point.vertex.glsl +128 -0
- package/src/gl/rect.fragment.glsl +51 -0
- package/src/gl/rect.vertex.glsl +114 -0
- package/src/gl/rule.fragment.glsl +52 -0
- package/src/gl/rule.vertex.glsl +89 -0
- package/src/gl/text.fragment.glsl +31 -0
- package/src/gl/text.vertex.glsl +246 -0
- package/src/gl/webGLHelper.js +490 -0
- package/src/img/bowtie.svg +1 -0
- package/src/img/genomespy-favicon.svg +34 -0
- package/src/index.html +11 -0
- package/src/index.js +151 -0
- package/src/marks/link.js +189 -0
- package/src/marks/mark.js +867 -0
- package/src/marks/markUtils.js +109 -0
- package/src/marks/pointMark.js +279 -0
- package/src/marks/rectMark.js +236 -0
- package/src/marks/rule.js +231 -0
- package/src/marks/text.js +274 -0
- package/src/options.d.ts +9 -0
- package/src/scale/colorUtils.js +184 -0
- package/src/scale/glslScaleGenerator.js +462 -0
- package/src/scale/scale.js +441 -0
- package/src/scale/scale.test.js +323 -0
- package/src/scale/ticks.js +198 -0
- package/src/scale/ticks.test.js +39 -0
- package/src/singlePageApp.js +13 -0
- package/src/spec/axis.d.ts +296 -0
- package/src/spec/channel.d.ts +127 -0
- package/src/spec/data.d.ts +185 -0
- package/src/spec/font.d.ts +15 -0
- package/src/spec/genome.d.ts +35 -0
- package/src/spec/mark.d.ts +432 -0
- package/src/spec/root.d.ts +22 -0
- package/src/spec/scale.d.ts +265 -0
- package/src/spec/tooltip.d.ts +9 -0
- package/src/spec/transform.d.ts +479 -0
- package/src/spec/view.d.ts +215 -0
- package/src/styles/genome-spy.scss +153 -0
- package/src/tooltip/dataTooltipHandler.js +59 -0
- package/src/tooltip/refseqGeneTooltipHandler.js +77 -0
- package/src/tooltip/tooltipHandler.ts +12 -0
- package/src/types/filetypes.d.ts +4 -0
- package/src/types/flatqueue.d.ts +53 -0
- package/src/types/glsl.d.ts +4 -0
- package/src/types/object.d.ts +21 -0
- package/src/types/vega-scale.d.ts +60 -0
- package/src/utils/animator.js +83 -0
- package/src/utils/arrayUtils.js +55 -0
- package/src/utils/binnedRangeIndex.js +83 -0
- package/src/utils/clamp.js +8 -0
- package/src/utils/cloner.js +32 -0
- package/src/utils/cloner.test.js +23 -0
- package/src/utils/coalesce.js +11 -0
- package/src/utils/coalesce.test.js +15 -0
- package/src/utils/concatIterables.js +26 -0
- package/src/utils/concatIterables.test.js +7 -0
- package/src/utils/debounce.js +37 -0
- package/src/utils/domainArray.js +224 -0
- package/src/utils/domainArray.test.js +129 -0
- package/src/utils/eerp.js +13 -0
- package/src/utils/expression.js +32 -0
- package/src/utils/field.js +28 -0
- package/src/utils/fisheye.js +60 -0
- package/src/utils/formatObject.js +31 -0
- package/src/utils/html.js +23 -0
- package/src/utils/html.test.js +13 -0
- package/src/utils/indexer.js +43 -0
- package/src/utils/indexer.test.js +46 -0
- package/src/utils/inertia.js +124 -0
- package/src/utils/interactionEvent.js +33 -0
- package/src/utils/iterateNestedMaps.js +21 -0
- package/src/utils/iterateNestedMaps.test.js +32 -0
- package/src/utils/kWayMerge.js +42 -0
- package/src/utils/kWayMerge.test.js +25 -0
- package/src/utils/layout/flexLayout.js +336 -0
- package/src/utils/layout/flexLayout.test.js +296 -0
- package/src/utils/layout/padding.js +107 -0
- package/src/utils/layout/point.js +23 -0
- package/src/utils/layout/rectangle.js +282 -0
- package/src/utils/layout/rectangle.test.js +171 -0
- package/src/utils/mergeObjects.js +99 -0
- package/src/utils/mergeObjects.test.js +41 -0
- package/src/utils/numberExtractor.js +24 -0
- package/src/utils/numberExtractor.test.js +5 -0
- package/src/utils/point.js +14 -0
- package/src/utils/propertyCacher.js +70 -0
- package/src/utils/propertyCacher.test.js +84 -0
- package/src/utils/propertyCoalescer.js +37 -0
- package/src/utils/propertyCoalescer.test.js +21 -0
- package/src/utils/reservationMap.js +103 -0
- package/src/utils/reservationMap.test.js +19 -0
- package/src/utils/scaleNull.js +19 -0
- package/src/utils/setOperations.js +75 -0
- package/src/utils/smoothstep.js +10 -0
- package/src/utils/throttle.js +34 -0
- package/src/utils/topK.js +76 -0
- package/src/utils/topK.test.js +63 -0
- package/src/utils/transition.js +74 -0
- package/src/utils/ui/tooltip.js +189 -0
- package/src/utils/url.js +22 -0
- package/src/utils/variableTools.js +24 -0
- package/src/utils/variableTools.test.js +12 -0
- package/src/view/axisResolution.js +135 -0
- package/src/view/axisResolution.test.js +200 -0
- package/src/view/axisView.js +746 -0
- package/src/view/channel.js +5 -0
- package/src/view/concatView.js +296 -0
- package/src/view/containerView.js +141 -0
- package/src/view/decoratorView.js +510 -0
- package/src/view/facetView.js +488 -0
- package/src/view/flowBuilder.js +362 -0
- package/src/view/flowBuilder.test.js +124 -0
- package/src/view/importView.js +19 -0
- package/src/view/layerView.js +60 -0
- package/src/view/rendering.d.ts +44 -0
- package/src/view/renderingContext/compositeViewRenderingContext.js +51 -0
- package/src/view/renderingContext/deferredViewRenderingContext.js +174 -0
- package/src/view/renderingContext/layoutRecorderViewRenderingContext.js +128 -0
- package/src/view/renderingContext/simpleViewRenderingContext.js +62 -0
- package/src/view/renderingContext/svgViewRenderingContext.js +121 -0
- package/src/view/renderingContext/viewRenderingContext.js +41 -0
- package/src/view/scaleResolution.js +756 -0
- package/src/view/scaleResolution.test.js +571 -0
- package/src/view/scaleResolutionApi.d.ts +40 -0
- package/src/view/testUtils.js +48 -0
- package/src/view/unitView.js +368 -0
- package/src/view/view.js +589 -0
- package/src/view/view.test.js +213 -0
- package/src/view/viewContext.d.ts +57 -0
- package/src/view/viewFactory.js +179 -0
- package/src/view/viewFactory.test.js +16 -0
- package/src/view/viewUtils.js +420 -0
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import { createAndInitialize } from "./testUtils";
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import UnitView from "./unitView";
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import View from "./view";
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/** @type {import("../spec/view").LayerSpec} */
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const spec = {
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data: { values: [] },
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layer: [
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{
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mark: "point",
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encoding: {
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x: { field: "a", type: "quantitative" },
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y: {
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field: "a",
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type: "quantitative",
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scale: { domain: [1, 2] },
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},
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color: { value: "red" },
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},
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},
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{
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mark: "point",
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encoding: {
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x: { field: "a", type: "quantitative" },
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y: {
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field: "b",
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type: "quantitative",
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scale: { domain: [4, 5] },
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},
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color: { value: "green" },
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],
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};
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describe("Axes resolve properly", () => {
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const sharedSpec = {
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...spec,
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resolve: { scale: { y: "shared" }, axis: { y: "shared" } },
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};
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test("Independent axes are independent", async () => {
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const independentSpec = {
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...spec,
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resolve: { scale: { y: "shared" }, axis: { y: "independent" } },
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};
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const view = await createAndInitialize(independentSpec, View);
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const [r0, r1] = [0, 1].map((i) =>
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view.children[i].getAxisResolution("y")
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);
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expect(r0).toBeDefined();
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expect(r1).toBeDefined();
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expect(r0).not.toBe(r1);
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});
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test("Shared axes have joined titles", async () => {
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const view = await createAndInitialize(sharedSpec, View);
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expect(view.children[0].getAxisResolution("y").getTitle()).toEqual(
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"a, b"
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);
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});
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test("Title is taken from axis title, encoding title, and field name, in that order.", async () => {
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let view = await createAndInitialize(
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{
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data: { values: [] },
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mark: "point",
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encoding: {
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x: { field: "a", type: "quantitative" },
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y: {
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field: "a",
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type: "quantitative",
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},
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},
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},
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);
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expect(view.getAxisResolution("y").getTitle()).toEqual("a");
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view = await createAndInitialize(
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{
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data: { values: [] },
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mark: "point",
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encoding: {
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x: { field: "a", type: "quantitative" },
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y: {
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field: "a",
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title: "x",
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type: "quantitative",
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},
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},
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},
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);
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expect(view.getAxisResolution("y").getTitle()).toEqual("x");
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view = await createAndInitialize(
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{
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data: { values: [] },
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mark: "point",
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encoding: {
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x: { field: "a", type: "quantitative" },
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y: {
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field: "a",
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title: "x",
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type: "quantitative",
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axis: {
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title: "z",
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},
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},
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);
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expect(view.getAxisResolution("y").getTitle()).toEqual("z");
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});
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test("Primary and secondary channels are included in the title", async () => {
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let view = await createAndInitialize(
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{
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data: { values: [] },
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mark: "rule",
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encoding: {
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x: { field: "a", type: "quantitative" },
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x2: { field: "b" },
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},
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expect(view.getAxisResolution("x").getTitle()).toEqual("a, b");
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});
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test("Secondary channel's field name is hidden if primary channel has an explicit title", async () => {
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data: { values: [] },
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mark: "rule",
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encoding: {
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x: { field: "a", type: "quantitative", title: "foo" },
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x2: { field: "b" },
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},
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},
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);
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expect(view.getAxisResolution("x").getTitle()).toEqual("foo");
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let view2 = await createAndInitialize(
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{
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data: { values: [] },
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mark: "rule",
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encoding: {
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x: {
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field: "a",
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type: "quantitative",
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axis: { title: "foo" },
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},
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x2: { field: "b" },
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expect(view2.getAxisResolution("x").getTitle()).toEqual("foo");
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let view3 = await createAndInitialize(
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{
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data: { values: [] },
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mark: "rule",
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encoding: {
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171
|
+
x: {
|
|
172
|
+
field: "a",
|
|
173
|
+
type: "quantitative",
|
|
174
|
+
axis: { title: "foo" },
|
|
175
|
+
},
|
|
176
|
+
x2: { field: "b", title: "bar" },
|
|
177
|
+
},
|
|
178
|
+
},
|
|
179
|
+
UnitView
|
|
180
|
+
);
|
|
181
|
+
expect(view3.getAxisResolution("x").getTitle()).toEqual("foo, bar");
|
|
182
|
+
|
|
183
|
+
let view4 = await createAndInitialize(
|
|
184
|
+
{
|
|
185
|
+
data: { values: [] },
|
|
186
|
+
mark: "rule",
|
|
187
|
+
encoding: {
|
|
188
|
+
x: {
|
|
189
|
+
field: "a",
|
|
190
|
+
type: "quantitative",
|
|
191
|
+
title: null,
|
|
192
|
+
},
|
|
193
|
+
x2: { field: "b" },
|
|
194
|
+
},
|
|
195
|
+
},
|
|
196
|
+
UnitView
|
|
197
|
+
);
|
|
198
|
+
expect(view4.getAxisResolution("x").getTitle()).toBeNull();
|
|
199
|
+
});
|
|
200
|
+
});
|