@genome-spy/core 0.36.0 → 0.37.0
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/README.md +1 -0
- package/dist/{index.es.js → bundled/index.es.js} +4227 -4085
- package/dist/{index.js → bundled/index.js} +191 -55
- package/dist/src/data/collector.d.ts +36 -0
- package/dist/src/data/collector.d.ts.map +1 -0
- package/dist/src/data/collector.js +184 -0
- package/dist/src/data/collector.test.js +84 -0
- package/dist/src/data/dataFlow.d.ts +65 -0
- package/dist/src/data/dataFlow.d.ts.map +1 -0
- package/dist/src/data/dataFlow.js +142 -0
- package/dist/src/data/dataFlow.test.js +5 -0
- package/dist/src/data/facetNode.d.ts +17 -0
- package/dist/src/data/facetNode.d.ts.map +1 -0
- package/dist/src/data/facetNode.js +17 -0
- package/dist/src/data/flow.test.js +72 -0
- package/dist/src/data/flowNode.d.ts +136 -0
- package/dist/src/data/flowNode.d.ts.map +1 -0
- package/dist/src/data/flowNode.js +286 -0
- package/dist/src/data/flowNode.test.js +50 -0
- package/dist/src/data/flowOptimizer.d.ts +27 -0
- package/dist/src/data/flowOptimizer.d.ts.map +1 -0
- package/dist/src/data/flowOptimizer.js +133 -0
- package/dist/src/data/flowOptimizer.test.js +193 -0
- package/dist/src/data/flowTestUtils.d.ts +30 -0
- package/dist/src/data/flowTestUtils.d.ts.map +1 -0
- package/dist/src/data/flowTestUtils.js +63 -0
- package/dist/src/data/formats/fasta.d.ts +20 -0
- package/dist/src/data/formats/fasta.d.ts.map +1 -0
- package/dist/src/data/formats/fasta.js +32 -0
- package/dist/src/data/formats/fasta.test.js +27 -0
- package/dist/src/data/sources/dataSource.d.ts +12 -0
- package/dist/src/data/sources/dataSource.d.ts.map +1 -0
- package/dist/src/data/sources/dataSource.js +25 -0
- package/dist/src/data/sources/dataSourceFactory.d.ts +16 -0
- package/dist/src/data/sources/dataSourceFactory.d.ts.map +1 -0
- package/dist/src/data/sources/dataSourceFactory.js +127 -0
- package/dist/src/data/sources/dataUtils.d.ts +50 -0
- package/dist/src/data/sources/dataUtils.d.ts.map +1 -0
- package/dist/src/data/sources/dataUtils.js +83 -0
- package/dist/src/data/sources/dynamic/README.md +3 -0
- package/dist/src/data/sources/dynamic/axisGenomeSource.d.ts +13 -0
- package/dist/src/data/sources/dynamic/axisGenomeSource.d.ts.map +1 -0
- package/dist/src/data/sources/dynamic/axisGenomeSource.js +19 -0
- package/dist/src/data/sources/dynamic/axisTickSource.d.ts +18 -0
- package/dist/src/data/sources/dynamic/axisTickSource.d.ts.map +1 -0
- package/dist/src/data/sources/dynamic/axisTickSource.js +73 -0
- package/dist/src/data/sources/dynamic/bamSource.d.ts +46 -0
- package/dist/src/data/sources/dynamic/bamSource.d.ts.map +1 -0
- package/dist/src/data/sources/dynamic/bamSource.js +115 -0
- package/dist/src/data/sources/dynamic/bigBedSource.d.ts +51 -0
- package/dist/src/data/sources/dynamic/bigBedSource.d.ts.map +1 -0
- package/dist/src/data/sources/dynamic/bigBedSource.js +128 -0
- package/dist/src/data/sources/dynamic/bigWigSource.d.ts +58 -0
- package/dist/src/data/sources/dynamic/bigWigSource.d.ts.map +1 -0
- package/dist/src/data/sources/dynamic/bigWigSource.js +166 -0
- package/dist/src/data/sources/dynamic/gff3Source.d.ts +8 -0
- package/dist/src/data/sources/dynamic/gff3Source.d.ts.map +1 -0
- package/dist/src/data/sources/dynamic/gff3Source.js +19 -0
- package/dist/src/data/sources/dynamic/indexedFastaSource.d.ts +30 -0
- package/dist/src/data/sources/dynamic/indexedFastaSource.d.ts.map +1 -0
- package/dist/src/data/sources/dynamic/indexedFastaSource.js +86 -0
- package/dist/src/data/sources/dynamic/singleAxisLazySource.d.ts +42 -0
- package/dist/src/data/sources/dynamic/singleAxisLazySource.d.ts.map +1 -0
- package/dist/src/data/sources/dynamic/singleAxisLazySource.js +129 -0
- package/dist/src/data/sources/dynamic/tabixSource.d.ts +54 -0
- package/dist/src/data/sources/dynamic/tabixSource.d.ts.map +1 -0
- package/dist/src/data/sources/dynamic/tabixSource.js +140 -0
- package/dist/src/data/sources/dynamic/windowedMixin.d.ts +32 -0
- package/dist/src/data/sources/dynamic/windowedMixin.d.ts.map +1 -0
- package/dist/src/data/sources/dynamic/windowedMixin.js +53 -0
- package/dist/src/data/sources/inlineSource.d.ts +16 -0
- package/dist/src/data/sources/inlineSource.d.ts.map +1 -0
- package/dist/src/data/sources/inlineSource.js +68 -0
- package/dist/src/data/sources/inlineSource.test.js +56 -0
- package/dist/src/data/sources/namedSource.d.ts +25 -0
- package/dist/src/data/sources/namedSource.d.ts.map +1 -0
- package/dist/src/data/sources/namedSource.js +80 -0
- package/dist/src/data/sources/sequenceSource.d.ts +17 -0
- package/dist/src/data/sources/sequenceSource.d.ts.map +1 -0
- package/dist/src/data/sources/sequenceSource.js +47 -0
- package/dist/src/data/sources/sequenceSource.test.js +46 -0
- package/dist/src/data/sources/urlSource.d.ts +16 -0
- package/dist/src/data/sources/urlSource.d.ts.map +1 -0
- package/dist/src/data/sources/urlSource.js +74 -0
- package/dist/src/data/transforms/aggregate.d.ts +18 -0
- package/dist/src/data/transforms/aggregate.d.ts.map +1 -0
- package/dist/src/data/transforms/aggregate.js +67 -0
- package/dist/src/data/transforms/clone.d.ts +15 -0
- package/dist/src/data/transforms/clone.d.ts.map +1 -0
- package/dist/src/data/transforms/clone.js +40 -0
- package/dist/src/data/transforms/clone.test.js +11 -0
- package/dist/src/data/transforms/coverage.d.ts +30 -0
- package/dist/src/data/transforms/coverage.d.ts.map +1 -0
- package/dist/src/data/transforms/coverage.js +183 -0
- package/dist/src/data/transforms/coverage.test.js +123 -0
- package/dist/src/data/transforms/filter.d.ts +12 -0
- package/dist/src/data/transforms/filter.d.ts.map +1 -0
- package/dist/src/data/transforms/filter.js +33 -0
- package/dist/src/data/transforms/filter.test.js +18 -0
- package/dist/src/data/transforms/filterScoredLabels.d.ts +29 -0
- package/dist/src/data/transforms/filterScoredLabels.d.ts.map +1 -0
- package/dist/src/data/transforms/filterScoredLabels.js +134 -0
- package/dist/src/data/transforms/flatten.d.ts +10 -0
- package/dist/src/data/transforms/flatten.d.ts.map +1 -0
- package/dist/src/data/transforms/flatten.js +68 -0
- package/dist/src/data/transforms/flatten.test.js +93 -0
- package/dist/src/data/transforms/flattenCompressedExons.d.ts +19 -0
- package/dist/src/data/transforms/flattenCompressedExons.d.ts.map +1 -0
- package/dist/src/data/transforms/flattenCompressedExons.js +53 -0
- package/dist/src/data/transforms/flattenDelimited.d.ts +10 -0
- package/dist/src/data/transforms/flattenDelimited.d.ts.map +1 -0
- package/dist/src/data/transforms/flattenDelimited.js +66 -0
- package/dist/src/data/transforms/flattenDelimited.test.js +87 -0
- package/dist/src/data/transforms/flattenSequence.d.ts +11 -0
- package/dist/src/data/transforms/flattenSequence.d.ts.map +1 -0
- package/dist/src/data/transforms/flattenSequence.js +35 -0
- package/dist/src/data/transforms/flattenSequence.test.js +34 -0
- package/dist/src/data/transforms/formula.d.ts +13 -0
- package/dist/src/data/transforms/formula.d.ts.map +1 -0
- package/dist/src/data/transforms/formula.js +35 -0
- package/dist/src/data/transforms/formula.test.js +19 -0
- package/dist/src/data/transforms/identifier.d.ts +40 -0
- package/dist/src/data/transforms/identifier.d.ts.map +1 -0
- package/dist/src/data/transforms/identifier.js +106 -0
- package/dist/src/data/transforms/identifier.test.js +83 -0
- package/dist/src/data/transforms/linearizeGenomicCoordinate.d.ts +10 -0
- package/dist/src/data/transforms/linearizeGenomicCoordinate.d.ts.map +1 -0
- package/dist/src/data/transforms/linearizeGenomicCoordinate.js +97 -0
- package/dist/src/data/transforms/measureText.d.ts +18 -0
- package/dist/src/data/transforms/measureText.d.ts.map +1 -0
- package/dist/src/data/transforms/measureText.js +42 -0
- package/dist/src/data/transforms/pileup.d.ts +10 -0
- package/dist/src/data/transforms/pileup.d.ts.map +1 -0
- package/dist/src/data/transforms/pileup.js +126 -0
- package/dist/src/data/transforms/pileup.test.js +70 -0
- package/dist/src/data/transforms/project.d.ts +13 -0
- package/dist/src/data/transforms/project.d.ts.map +1 -0
- package/dist/src/data/transforms/project.js +38 -0
- package/dist/src/data/transforms/project.test.js +32 -0
- package/dist/src/data/transforms/regexExtract.d.ts +13 -0
- package/dist/src/data/transforms/regexExtract.d.ts.map +1 -0
- package/dist/src/data/transforms/regexExtract.js +57 -0
- package/dist/src/data/transforms/regexExtract.test.js +67 -0
- package/dist/src/data/transforms/regexFold.d.ts +14 -0
- package/dist/src/data/transforms/regexFold.d.ts.map +1 -0
- package/dist/src/data/transforms/regexFold.js +139 -0
- package/dist/src/data/transforms/regexFold.test.js +160 -0
- package/dist/src/data/transforms/sample.d.ts +42 -0
- package/dist/src/data/transforms/sample.d.ts.map +1 -0
- package/dist/src/data/transforms/sample.js +99 -0
- package/dist/src/data/transforms/sample.test.js +38 -0
- package/dist/src/data/transforms/stack.d.ts +11 -0
- package/dist/src/data/transforms/stack.d.ts.map +1 -0
- package/dist/src/data/transforms/stack.js +134 -0
- package/dist/src/data/transforms/stack.test.js +91 -0
- package/dist/src/data/transforms/transformFactory.d.ts +12 -0
- package/dist/src/data/transforms/transformFactory.d.ts.map +1 -0
- package/dist/src/data/transforms/transformFactory.js +59 -0
- package/dist/src/encoder/accessor.d.ts +15 -0
- package/dist/src/encoder/accessor.d.ts.map +1 -0
- package/dist/src/encoder/accessor.js +76 -0
- package/dist/src/encoder/accessor.test.js +47 -0
- package/dist/src/encoder/encoder.d.ts +144 -0
- package/dist/src/encoder/encoder.d.ts.map +1 -0
- package/dist/src/encoder/encoder.js +400 -0
- package/dist/src/encoder/encoder.test.js +98 -0
- package/dist/src/fonts/Lato-Regular.json +1267 -0
- package/dist/src/fonts/Lato-Regular.png +0 -0
- package/dist/src/fonts/OFL.txt +93 -0
- package/dist/src/fonts/README.md +3 -0
- package/dist/src/fonts/bmFontManager.d.ts +182 -0
- package/dist/src/fonts/bmFontManager.d.ts.map +1 -0
- package/dist/src/fonts/bmFontManager.js +359 -0
- package/dist/src/fonts/bmFontMetrics.d.ts +45 -0
- package/dist/src/fonts/bmFontMetrics.d.ts.map +1 -0
- package/dist/src/fonts/bmFontMetrics.js +108 -0
- package/dist/src/genome/genome.d.ts +172 -0
- package/dist/src/genome/genome.d.ts.map +1 -0
- package/dist/src/genome/genome.js +379 -0
- package/dist/src/genome/genome.test.js +226 -0
- package/dist/src/genome/genomeStore.d.ts +20 -0
- package/dist/src/genome/genomeStore.d.ts.map +1 -0
- package/dist/src/genome/genomeStore.js +54 -0
- package/dist/src/genome/locusFormat.d.ts +14 -0
- package/dist/src/genome/locusFormat.d.ts.map +1 -0
- package/dist/src/genome/locusFormat.js +37 -0
- package/dist/src/genome/scaleIndex.d.ts +6 -0
- package/dist/src/genome/scaleIndex.d.ts.map +1 -0
- package/dist/src/genome/scaleIndex.js +165 -0
- package/dist/src/genome/scaleIndex.test.js +78 -0
- package/dist/src/genome/scaleLocus.d.ts +3 -0
- package/dist/src/genome/scaleLocus.d.ts.map +1 -0
- package/dist/src/genome/scaleLocus.js +101 -0
- package/dist/src/genome/scaleLocus.test.js +4 -0
- package/dist/src/genomeSpy.d.ts +141 -0
- package/dist/src/genomeSpy.d.ts.map +1 -0
- package/dist/src/genomeSpy.js +788 -0
- package/dist/src/gl/arrayBuilder.d.ts +71 -0
- package/dist/src/gl/arrayBuilder.d.ts.map +1 -0
- package/dist/src/gl/arrayBuilder.js +199 -0
- package/dist/src/gl/dataToVertices.d.ts +194 -0
- package/dist/src/gl/dataToVertices.d.ts.map +1 -0
- package/dist/src/gl/dataToVertices.js +639 -0
- package/dist/src/gl/includes/common.glsl.js +2 -0
- package/dist/src/gl/includes/picking.fragment.glsl.js +2 -0
- package/dist/src/gl/includes/picking.vertex.glsl.js +2 -0
- package/dist/src/gl/includes/sampleFacet.glsl.js +2 -0
- package/dist/src/gl/includes/scales.glsl.js +2 -0
- package/dist/src/gl/link.fragment.glsl.js +2 -0
- package/dist/src/gl/link.vertex.glsl.js +2 -0
- package/dist/src/gl/point.fragment.glsl.js +2 -0
- package/dist/src/gl/point.vertex.glsl.js +2 -0
- package/dist/src/gl/rect.fragment.glsl.js +2 -0
- package/dist/src/gl/rect.vertex.glsl.js +2 -0
- package/dist/src/gl/rule.fragment.glsl.js +2 -0
- package/dist/src/gl/rule.vertex.glsl.js +2 -0
- package/dist/src/gl/text.fragment.glsl.js +2 -0
- package/dist/src/gl/text.vertex.glsl.js +2 -0
- package/dist/src/gl/webGLHelper.d.ts +118 -0
- package/dist/src/gl/webGLHelper.d.ts.map +1 -0
- package/dist/src/gl/webGLHelper.js +513 -0
- package/dist/src/img/bowtie.svg +1 -0
- package/dist/src/img/genomespy-favicon.svg +34 -0
- package/dist/src/index.d.ts +15 -0
- package/dist/src/index.d.ts.map +1 -0
- package/dist/src/index.html +11 -0
- package/dist/src/index.js +129 -0
- package/dist/src/marks/link.d.ts +11 -0
- package/dist/src/marks/link.d.ts.map +1 -0
- package/dist/src/marks/link.js +175 -0
- package/dist/src/marks/mark.d.ts +226 -0
- package/dist/src/marks/mark.d.ts.map +1 -0
- package/dist/src/marks/mark.js +1004 -0
- package/dist/src/marks/markUtils.d.ts +23 -0
- package/dist/src/marks/markUtils.d.ts.map +1 -0
- package/dist/src/marks/markUtils.js +125 -0
- package/dist/src/marks/pointMark.d.ts +11 -0
- package/dist/src/marks/pointMark.d.ts.map +1 -0
- package/dist/src/marks/pointMark.js +251 -0
- package/dist/src/marks/rectMark.d.ts +18 -0
- package/dist/src/marks/rectMark.d.ts.map +1 -0
- package/dist/src/marks/rectMark.js +255 -0
- package/dist/src/marks/rule.d.ts +6 -0
- package/dist/src/marks/rule.d.ts.map +1 -0
- package/dist/src/marks/rule.js +250 -0
- package/dist/src/marks/text.d.ts +13 -0
- package/dist/src/marks/text.d.ts.map +1 -0
- package/dist/src/marks/text.js +279 -0
- package/dist/src/scale/colorUtils.d.ts +34 -0
- package/dist/src/scale/colorUtils.d.ts.map +1 -0
- package/dist/src/scale/colorUtils.js +184 -0
- package/dist/src/scale/glslScaleGenerator.d.ts +45 -0
- package/dist/src/scale/glslScaleGenerator.d.ts.map +1 -0
- package/dist/src/scale/glslScaleGenerator.js +506 -0
- package/dist/src/scale/scale.d.ts +10 -0
- package/dist/src/scale/scale.d.ts.map +1 -0
- package/dist/src/scale/scale.js +456 -0
- package/dist/src/scale/scale.test.js +324 -0
- package/dist/src/scale/ticks.d.ts +47 -0
- package/dist/src/scale/ticks.d.ts.map +1 -0
- package/dist/src/scale/ticks.js +203 -0
- package/dist/src/scale/ticks.test.js +40 -0
- package/dist/src/singlePageApp.d.ts +2 -0
- package/dist/src/singlePageApp.d.ts.map +1 -0
- package/dist/src/singlePageApp.js +13 -0
- package/dist/src/spec/axis.d.ts +402 -0
- package/dist/src/spec/channel.d.ts +440 -0
- package/dist/src/spec/data.d.ts +370 -0
- package/dist/src/spec/font.d.ts +15 -0
- package/dist/src/spec/genome.d.ts +35 -0
- package/dist/src/spec/mark.d.ts +435 -0
- package/dist/src/spec/root.d.ts +22 -0
- package/dist/src/spec/sampleView.d.ts +185 -0
- package/dist/src/spec/scale.d.ts +273 -0
- package/dist/src/spec/title.d.ts +102 -0
- package/dist/src/spec/tooltip.d.ts +9 -0
- package/dist/src/spec/transform.d.ts +504 -0
- package/dist/src/spec/view.d.ts +214 -0
- package/dist/src/styles/genome-spy.css.d.ts +3 -0
- package/dist/src/styles/genome-spy.css.d.ts.map +1 -0
- package/dist/src/styles/genome-spy.css.js +114 -0
- package/dist/src/styles/genome-spy.scss +153 -0
- package/dist/src/tooltip/dataTooltipHandler.d.ts +2 -0
- package/dist/src/tooltip/dataTooltipHandler.d.ts.map +1 -0
- package/dist/src/tooltip/dataTooltipHandler.js +64 -0
- package/dist/src/tooltip/refseqGeneTooltipHandler.d.ts +2 -0
- package/dist/src/tooltip/refseqGeneTooltipHandler.d.ts.map +1 -0
- package/dist/src/tooltip/refseqGeneTooltipHandler.js +78 -0
- package/dist/src/tooltip/tooltipHandler.d.ts +9 -0
- package/dist/src/tooltip/tooltipHandler.d.ts.map +1 -0
- package/dist/src/tooltip/tooltipHandler.ts +12 -0
- package/dist/src/types/bmFont.d.ts +58 -0
- package/dist/src/types/embedApi.d.ts +67 -0
- package/dist/src/types/encoder.d.ts +84 -0
- package/dist/src/types/flowBatch.d.ts +40 -0
- package/dist/src/types/rendering.d.ts +65 -0
- package/dist/src/types/scaleResolutionApi.d.ts +40 -0
- package/dist/src/types/viewContext.d.ts +85 -0
- package/dist/src/utils/addBaseUrl.d.ts +6 -0
- package/dist/src/utils/addBaseUrl.d.ts.map +1 -0
- package/dist/src/utils/addBaseUrl.js +19 -0
- package/dist/src/utils/addBaseUrl.test.js +22 -0
- package/dist/src/utils/animator.d.ts +41 -0
- package/dist/src/utils/animator.d.ts.map +1 -0
- package/dist/src/utils/animator.js +83 -0
- package/dist/src/utils/arrayUtils.d.ts +34 -0
- package/dist/src/utils/arrayUtils.d.ts.map +1 -0
- package/dist/src/utils/arrayUtils.js +61 -0
- package/dist/src/utils/binnedIndex.d.ts +23 -0
- package/dist/src/utils/binnedIndex.d.ts.map +1 -0
- package/dist/src/utils/binnedIndex.js +167 -0
- package/dist/src/utils/binnedIndex.test.js +155 -0
- package/dist/src/utils/clamp.d.ts +7 -0
- package/dist/src/utils/clamp.d.ts.map +1 -0
- package/dist/src/utils/clamp.js +8 -0
- package/dist/src/utils/cloner.d.ts +16 -0
- package/dist/src/utils/cloner.d.ts.map +1 -0
- package/dist/src/utils/cloner.js +34 -0
- package/dist/src/utils/cloner.test.js +24 -0
- package/dist/src/utils/coalesce.d.ts +6 -0
- package/dist/src/utils/coalesce.d.ts.map +1 -0
- package/dist/src/utils/coalesce.js +11 -0
- package/dist/src/utils/coalesce.test.js +16 -0
- package/dist/src/utils/concatIterables.d.ts +8 -0
- package/dist/src/utils/concatIterables.d.ts.map +1 -0
- package/dist/src/utils/concatIterables.js +26 -0
- package/dist/src/utils/concatIterables.test.js +8 -0
- package/dist/src/utils/debounce.d.ts +8 -0
- package/dist/src/utils/debounce.d.ts.map +1 -0
- package/dist/src/utils/debounce.js +37 -0
- package/dist/src/utils/domainArray.d.ts +61 -0
- package/dist/src/utils/domainArray.d.ts.map +1 -0
- package/dist/src/utils/domainArray.js +216 -0
- package/dist/src/utils/domainArray.test.js +130 -0
- package/dist/src/utils/eerp.d.ts +12 -0
- package/dist/src/utils/eerp.d.ts.map +1 -0
- package/dist/src/utils/eerp.js +13 -0
- package/dist/src/utils/expression.d.ts +9 -0
- package/dist/src/utils/expression.d.ts.map +1 -0
- package/dist/src/utils/expression.js +32 -0
- package/dist/src/utils/field.d.ts +17 -0
- package/dist/src/utils/field.d.ts.map +1 -0
- package/dist/src/utils/field.js +28 -0
- package/dist/src/utils/formatObject.d.ts +7 -0
- package/dist/src/utils/formatObject.d.ts.map +1 -0
- package/dist/src/utils/formatObject.js +37 -0
- package/dist/src/utils/indexer.d.ts +16 -0
- package/dist/src/utils/indexer.d.ts.map +1 -0
- package/dist/src/utils/indexer.js +43 -0
- package/dist/src/utils/indexer.test.js +47 -0
- package/dist/src/utils/inertia.d.ts +42 -0
- package/dist/src/utils/inertia.d.ts.map +1 -0
- package/dist/src/utils/inertia.js +124 -0
- package/dist/src/utils/interactionEvent.d.ts +26 -0
- package/dist/src/utils/interactionEvent.d.ts.map +1 -0
- package/dist/src/utils/interactionEvent.js +33 -0
- package/dist/src/utils/iterateNestedMaps.d.ts +11 -0
- package/dist/src/utils/iterateNestedMaps.d.ts.map +1 -0
- package/dist/src/utils/iterateNestedMaps.js +21 -0
- package/dist/src/utils/iterateNestedMaps.test.js +33 -0
- package/dist/src/utils/kWayMerge.d.ts +9 -0
- package/dist/src/utils/kWayMerge.d.ts.map +1 -0
- package/dist/src/utils/kWayMerge.js +42 -0
- package/dist/src/utils/kWayMerge.test.js +26 -0
- package/dist/src/utils/layout/flexLayout.d.ts +182 -0
- package/dist/src/utils/layout/flexLayout.d.ts.map +1 -0
- package/dist/src/utils/layout/flexLayout.js +381 -0
- package/dist/src/utils/layout/flexLayout.test.js +323 -0
- package/dist/src/utils/layout/grid.d.ts +29 -0
- package/dist/src/utils/layout/grid.d.ts.map +1 -0
- package/dist/src/utils/layout/grid.js +95 -0
- package/dist/src/utils/layout/grid.test.js +71 -0
- package/dist/src/utils/layout/padding.d.ts +83 -0
- package/dist/src/utils/layout/padding.d.ts.map +1 -0
- package/dist/src/utils/layout/padding.js +155 -0
- package/dist/src/utils/layout/point.d.ts +16 -0
- package/dist/src/utils/layout/point.d.ts.map +1 -0
- package/dist/src/utils/layout/point.js +23 -0
- package/dist/src/utils/layout/rectangle.d.ts +142 -0
- package/dist/src/utils/layout/rectangle.d.ts.map +1 -0
- package/dist/src/utils/layout/rectangle.js +296 -0
- package/dist/src/utils/layout/rectangle.test.js +172 -0
- package/dist/src/utils/mergeObjects.d.ts +15 -0
- package/dist/src/utils/mergeObjects.d.ts.map +1 -0
- package/dist/src/utils/mergeObjects.js +99 -0
- package/dist/src/utils/mergeObjects.test.js +42 -0
- package/dist/src/utils/numberExtractor.d.ts +9 -0
- package/dist/src/utils/numberExtractor.d.ts.map +1 -0
- package/dist/src/utils/numberExtractor.js +24 -0
- package/dist/src/utils/numberExtractor.test.js +6 -0
- package/dist/src/utils/point.d.ts +9 -0
- package/dist/src/utils/point.d.ts.map +1 -0
- package/dist/src/utils/point.js +14 -0
- package/dist/src/utils/propertyCacher.d.ts +30 -0
- package/dist/src/utils/propertyCacher.d.ts.map +1 -0
- package/dist/src/utils/propertyCacher.js +70 -0
- package/dist/src/utils/propertyCacher.test.js +85 -0
- package/dist/src/utils/propertyCoalescer.d.ts +15 -0
- package/dist/src/utils/propertyCoalescer.d.ts.map +1 -0
- package/dist/src/utils/propertyCoalescer.js +42 -0
- package/dist/src/utils/propertyCoalescer.test.js +22 -0
- package/dist/src/utils/reservationMap.d.ts +42 -0
- package/dist/src/utils/reservationMap.d.ts.map +1 -0
- package/dist/src/utils/reservationMap.js +103 -0
- package/dist/src/utils/reservationMap.test.js +20 -0
- package/dist/src/utils/scaleNull.d.ts +13 -0
- package/dist/src/utils/scaleNull.d.ts.map +1 -0
- package/dist/src/utils/scaleNull.js +21 -0
- package/dist/src/utils/setOperations.d.ts +31 -0
- package/dist/src/utils/setOperations.d.ts.map +1 -0
- package/dist/src/utils/setOperations.js +75 -0
- package/dist/src/utils/smoothstep.d.ts +7 -0
- package/dist/src/utils/smoothstep.d.ts.map +1 -0
- package/dist/src/utils/smoothstep.js +10 -0
- package/dist/src/utils/throttle.d.ts +8 -0
- package/dist/src/utils/throttle.d.ts.map +1 -0
- package/dist/src/utils/throttle.js +34 -0
- package/dist/src/utils/topK.d.ts +22 -0
- package/dist/src/utils/topK.d.ts.map +1 -0
- package/dist/src/utils/topK.js +76 -0
- package/dist/src/utils/topK.test.js +64 -0
- package/dist/src/utils/transition.d.ts +44 -0
- package/dist/src/utils/transition.d.ts.map +1 -0
- package/dist/src/utils/transition.js +74 -0
- package/dist/src/utils/trees.d.ts +56 -0
- package/dist/src/utils/trees.d.ts.map +1 -0
- package/dist/src/utils/trees.js +92 -0
- package/dist/src/utils/trees.test.js +130 -0
- package/dist/src/utils/ui/tooltip.d.ts +50 -0
- package/dist/src/utils/ui/tooltip.d.ts.map +1 -0
- package/dist/src/utils/ui/tooltip.js +189 -0
- package/dist/src/utils/url.d.ts +9 -0
- package/dist/src/utils/url.d.ts.map +1 -0
- package/dist/src/utils/url.js +22 -0
- package/dist/src/utils/variableTools.d.ts +14 -0
- package/dist/src/utils/variableTools.d.ts.map +1 -0
- package/dist/src/utils/variableTools.js +24 -0
- package/dist/src/utils/variableTools.test.js +13 -0
- package/dist/src/view/axisGridView.d.ts +39 -0
- package/dist/src/view/axisGridView.d.ts.map +1 -0
- package/dist/src/view/axisGridView.js +246 -0
- package/dist/src/view/axisResolution.d.ts +24 -0
- package/dist/src/view/axisResolution.d.ts.map +1 -0
- package/dist/src/view/axisResolution.js +141 -0
- package/dist/src/view/axisResolution.test.js +201 -0
- package/dist/src/view/axisView.d.ts +49 -0
- package/dist/src/view/axisView.d.ts.map +1 -0
- package/dist/src/view/axisView.js +629 -0
- package/dist/src/view/concatView.d.ts +16 -0
- package/dist/src/view/concatView.d.ts.map +1 -0
- package/dist/src/view/concatView.js +84 -0
- package/dist/src/view/containerView.d.ts +43 -0
- package/dist/src/view/containerView.d.ts.map +1 -0
- package/dist/src/view/containerView.js +137 -0
- package/dist/src/view/facetView.d.ts +71 -0
- package/dist/src/view/facetView.d.ts.map +1 -0
- package/dist/src/view/facetView.js +492 -0
- package/dist/src/view/flowBuilder.d.ts +37 -0
- package/dist/src/view/flowBuilder.d.ts.map +1 -0
- package/dist/src/view/flowBuilder.js +383 -0
- package/dist/src/view/flowBuilder.test.js +125 -0
- package/dist/src/view/gridView.d.ts +111 -0
- package/dist/src/view/gridView.d.ts.map +1 -0
- package/dist/src/view/gridView.js +1086 -0
- package/dist/src/view/implicitRootView.d.ts +9 -0
- package/dist/src/view/implicitRootView.d.ts.map +1 -0
- package/dist/src/view/implicitRootView.js +23 -0
- package/dist/src/view/importView.d.ts +17 -0
- package/dist/src/view/importView.d.ts.map +1 -0
- package/dist/src/view/importView.js +22 -0
- package/dist/src/view/layerView.d.ts +25 -0
- package/dist/src/view/layerView.d.ts.map +1 -0
- package/dist/src/view/layerView.js +77 -0
- package/dist/src/view/renderingContext/bufferedViewRenderingContext.d.ts +30 -0
- package/dist/src/view/renderingContext/bufferedViewRenderingContext.d.ts.map +1 -0
- package/dist/src/view/renderingContext/bufferedViewRenderingContext.js +175 -0
- package/dist/src/view/renderingContext/compositeViewRenderingContext.d.ts +14 -0
- package/dist/src/view/renderingContext/compositeViewRenderingContext.d.ts.map +1 -0
- package/dist/src/view/renderingContext/compositeViewRenderingContext.js +51 -0
- package/dist/src/view/renderingContext/debuggingViewRenderingContext.d.ts +51 -0
- package/dist/src/view/renderingContext/debuggingViewRenderingContext.d.ts.map +1 -0
- package/dist/src/view/renderingContext/debuggingViewRenderingContext.js +94 -0
- package/dist/src/view/renderingContext/layoutRecorderViewRenderingContext.d.ts +60 -0
- package/dist/src/view/renderingContext/layoutRecorderViewRenderingContext.d.ts.map +1 -0
- package/dist/src/view/renderingContext/layoutRecorderViewRenderingContext.js +128 -0
- package/dist/src/view/renderingContext/simpleViewRenderingContext.d.ts +19 -0
- package/dist/src/view/renderingContext/simpleViewRenderingContext.d.ts.map +1 -0
- package/dist/src/view/renderingContext/simpleViewRenderingContext.js +64 -0
- package/dist/src/view/renderingContext/svgViewRenderingContext.d.ts +22 -0
- package/dist/src/view/renderingContext/svgViewRenderingContext.d.ts.map +1 -0
- package/dist/src/view/renderingContext/svgViewRenderingContext.js +125 -0
- package/dist/src/view/renderingContext/viewRenderingContext.d.ts +33 -0
- package/dist/src/view/renderingContext/viewRenderingContext.d.ts.map +1 -0
- package/dist/src/view/renderingContext/viewRenderingContext.js +41 -0
- package/dist/src/view/scaleResolution.d.ts +170 -0
- package/dist/src/view/scaleResolution.d.ts.map +1 -0
- package/dist/src/view/scaleResolution.js +874 -0
- package/dist/src/view/scaleResolution.test.js +658 -0
- package/dist/src/view/testUtils.d.ts +30 -0
- package/dist/src/view/testUtils.d.ts.map +1 -0
- package/dist/src/view/testUtils.js +101 -0
- package/dist/src/view/title.d.ts +6 -0
- package/dist/src/view/title.d.ts.map +1 -0
- package/dist/src/view/title.js +165 -0
- package/dist/src/view/unitView.d.ts +93 -0
- package/dist/src/view/unitView.d.ts.map +1 -0
- package/dist/src/view/unitView.js +345 -0
- package/dist/src/view/view.d.ts +291 -0
- package/dist/src/view/view.d.ts.map +1 -0
- package/dist/src/view/view.js +691 -0
- package/dist/src/view/view.test.js +214 -0
- package/dist/src/view/viewFactory.d.ts +76 -0
- package/dist/src/view/viewFactory.d.ts.map +1 -0
- package/dist/src/view/viewFactory.js +178 -0
- package/dist/src/view/viewFactory.test.js +17 -0
- package/dist/src/view/viewUtils.d.ts +90 -0
- package/dist/src/view/viewUtils.d.ts.map +1 -0
- package/dist/src/view/viewUtils.js +326 -0
- package/dist/src/view/zoom.d.ts +23 -0
- package/dist/src/view/zoom.d.ts.map +1 -0
- package/dist/src/view/zoom.js +89 -0
- package/package.json +15 -12
- package/dist/style.css +0 -1
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/**
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{"version":3,"file":"axisGenomeSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/dynamic/axisGenomeSource.js"],"names":[],"mappings":"AAEA;;;GAGG;AACH;IACI;;;OAGG;IACH,oBAHW,OAAO,oBAAoB,EAAE,cAAc,QAC3C,OAAO,oBAAoB,EAAE,OAAO,EAI9C;CAKJ;iCAlBgC,wBAAwB"}
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constructor(params: import("../../../spec/data").AxisTicksData, view: import("../../../view/view").default);
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}
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{"version":3,"file":"axisTickSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/dynamic/axisTickSource.js"],"names":[],"mappings":"AAYA;;GAEG;AACH;IAMI;;;OAGG;IACH,oBAHW,OAAO,oBAAoB,EAAE,aAAa,QAC1C,OAAO,oBAAoB,EAAE,OAAO,EAY9C;IAnBD;;OAEG;IACH,OAFU,OAAO,uBAAuB,EAAE,MAAM,EAAE,CAEvC;IAeP,mDAAoB;IAGxB,iCAkCC;CACJ;iCA9DgC,wBAAwB"}
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import {
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validTicks,
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tickValues,
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tickFormat,
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tickCount,
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} from "../../../scale/ticks";
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/**
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*
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export default class AxisTickSource extends SingleAxisLazySource {
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/**
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ticks = [];
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/**
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*/
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constructor(params, view) {
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/** @type {import("../../../spec/data").AxisTicksData} params */
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const paramsWithDefaults = {
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axis: {},
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...params,
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};
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super(view, paramsWithDefaults.channel);
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|
+
|
|
35
|
+
this.params = params;
|
|
36
|
+
}
|
|
37
|
+
|
|
38
|
+
async onDomainChanged() {
|
|
39
|
+
// Note, although this function is async, it is not awaited. Data are updated
|
|
40
|
+
// synchronously to ensure that the new ticks are available before the next frame is drawn.
|
|
41
|
+
|
|
42
|
+
const scale = this.scaleResolution.getScale();
|
|
43
|
+
const axisParams = this.params.axis;
|
|
44
|
+
const axisLength = this.getAxisLength();
|
|
45
|
+
|
|
46
|
+
/**
|
|
47
|
+
* Make ticks more dense in small plots.
|
|
48
|
+
* TODO: Make configurable
|
|
49
|
+
*
|
|
50
|
+
* @param {number} length
|
|
51
|
+
*/
|
|
52
|
+
const tickSpacing = (length) => 25 + 60 * smoothstep(100, 700, length);
|
|
53
|
+
|
|
54
|
+
const requestedCount = isNumber(axisParams.tickCount)
|
|
55
|
+
? axisParams.tickCount
|
|
56
|
+
: Math.round(axisLength / tickSpacing(axisLength));
|
|
57
|
+
|
|
58
|
+
const count = tickCount(scale, requestedCount, axisParams.tickMinStep);
|
|
59
|
+
|
|
60
|
+
const ticks = axisParams.values
|
|
61
|
+
? validTicks(scale, axisParams.values, count)
|
|
62
|
+
: tickValues(scale, count);
|
|
63
|
+
|
|
64
|
+
if (!shallowArrayEquals(ticks, this.ticks)) {
|
|
65
|
+
this.ticks = ticks;
|
|
66
|
+
|
|
67
|
+
const format = tickFormat(scale, requestedCount, axisParams.format);
|
|
68
|
+
this.publishData(
|
|
69
|
+
ticks.map((tick) => ({ value: tick, label: format(tick) }))
|
|
70
|
+
);
|
|
71
|
+
}
|
|
72
|
+
}
|
|
73
|
+
}
|
|
@@ -0,0 +1,46 @@
|
|
|
1
|
+
declare const BamSource_base: {
|
|
2
|
+
new (...args: any[]): {
|
|
3
|
+
[x: string]: any;
|
|
4
|
+
lastQuantizedInterval: number[];
|
|
5
|
+
quantizeInterval(interval: number[], windowSize: number): number[];
|
|
6
|
+
checkAndUpdateLastInterval(interval: number[]): boolean;
|
|
7
|
+
};
|
|
8
|
+
} & typeof SingleAxisLazySource;
|
|
9
|
+
export default class BamSource extends BamSource_base {
|
|
10
|
+
/**
|
|
11
|
+
* @param {import("../../../spec/data").BamData} params
|
|
12
|
+
* @param {import("../../../view/view").default} view
|
|
13
|
+
*/
|
|
14
|
+
constructor(params: import("../../../spec/data").BamData, view: import("../../../view/view").default);
|
|
15
|
+
/** Keep track of the order of the requests */
|
|
16
|
+
lastRequestId: number;
|
|
17
|
+
/**
|
|
18
|
+
* Some BAM files lack the "chr" prefix on their reference names. For example:
|
|
19
|
+
* http://genome.ucsc.edu/goldenPath/help/examples/bamExample.bam
|
|
20
|
+
*
|
|
21
|
+
* N.B. @SN AN records in SAM header may have alternative names for chromosomes.
|
|
22
|
+
* TODO: Explore their usage
|
|
23
|
+
*
|
|
24
|
+
* @type {(chr: string) => string}
|
|
25
|
+
*/
|
|
26
|
+
chrPrefixFixer: (chr: string) => string;
|
|
27
|
+
params: import("../../../spec/data").BamData;
|
|
28
|
+
bam: BamFile;
|
|
29
|
+
headerPromise: Promise<{
|
|
30
|
+
tag: string;
|
|
31
|
+
data: {
|
|
32
|
+
tag: string;
|
|
33
|
+
value: string;
|
|
34
|
+
}[];
|
|
35
|
+
}[]>;
|
|
36
|
+
/**
|
|
37
|
+
* Listen to the domain change event and update data when the covered windows change.
|
|
38
|
+
*
|
|
39
|
+
* @param {number[]} domain Linearized domain
|
|
40
|
+
*/
|
|
41
|
+
onDomainChanged(domain: number[]): Promise<void>;
|
|
42
|
+
}
|
|
43
|
+
import SingleAxisLazySource from "./singleAxisLazySource";
|
|
44
|
+
import { BamFile } from "@gmod/bam";
|
|
45
|
+
export {};
|
|
46
|
+
//# sourceMappingURL=bamSource.d.ts.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"bamSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/dynamic/bamSource.js"],"names":[],"mappings":";;;;;;;;AAOA;IAeI;;;OAGG;IACH,oBAHW,OAAO,oBAAoB,EAAE,OAAO,QACpC,OAAO,oBAAoB,EAAE,OAAO,EAuC9C;IAvDD,8CAA8C;IAC9C,sBAAkB;IAElB;;;;;;;;OAQG;IACH,sBAFgB,MAAM,KAAK,MAAM,CAEH;IAgB1B,6CAAgC;IAShC,aAKE;IAEF;;;;;;SAAyC;IAa7C;;;;OAIG;IACH,wBAFW,MAAM,EAAE,iBA6ClB;CACJ;iCA/GgC,wBAAwB;wBAFjC,WAAW"}
|
|
@@ -0,0 +1,115 @@
|
|
|
1
|
+
import { RemoteFile } from "generic-filehandle";
|
|
2
|
+
import { BamFile } from "@gmod/bam";
|
|
3
|
+
|
|
4
|
+
import SingleAxisLazySource from "./singleAxisLazySource";
|
|
5
|
+
import windowedMixin from "./windowedMixin";
|
|
6
|
+
import addBaseUrl from "@genome-spy/core/utils/addBaseUrl";
|
|
7
|
+
|
|
8
|
+
export default class BamSource extends windowedMixin(SingleAxisLazySource) {
|
|
9
|
+
/** Keep track of the order of the requests */
|
|
10
|
+
lastRequestId = 0;
|
|
11
|
+
|
|
12
|
+
/**
|
|
13
|
+
* Some BAM files lack the "chr" prefix on their reference names. For example:
|
|
14
|
+
* http://genome.ucsc.edu/goldenPath/help/examples/bamExample.bam
|
|
15
|
+
*
|
|
16
|
+
* N.B. @SN AN records in SAM header may have alternative names for chromosomes.
|
|
17
|
+
* TODO: Explore their usage
|
|
18
|
+
*
|
|
19
|
+
* @type {(chr: string) => string}
|
|
20
|
+
*/
|
|
21
|
+
chrPrefixFixer = (chr) => chr;
|
|
22
|
+
|
|
23
|
+
/**
|
|
24
|
+
* @param {import("../../../spec/data").BamData} params
|
|
25
|
+
* @param {import("../../../view/view").default} view
|
|
26
|
+
*/
|
|
27
|
+
constructor(params, view) {
|
|
28
|
+
/** @type {import("../../../spec/data").BamData} */
|
|
29
|
+
const paramsWithDefaults = {
|
|
30
|
+
channel: "x",
|
|
31
|
+
windowSize: 20000,
|
|
32
|
+
...params,
|
|
33
|
+
};
|
|
34
|
+
|
|
35
|
+
super(view, paramsWithDefaults.channel);
|
|
36
|
+
|
|
37
|
+
this.params = paramsWithDefaults;
|
|
38
|
+
|
|
39
|
+
if (!this.params.url) {
|
|
40
|
+
throw new Error("No URL provided for BamSource");
|
|
41
|
+
}
|
|
42
|
+
|
|
43
|
+
const withBase = (/** @type {string} */ uri) =>
|
|
44
|
+
new RemoteFile(addBaseUrl(uri, this.view.getBaseUrl()));
|
|
45
|
+
|
|
46
|
+
this.bam = new BamFile({
|
|
47
|
+
bamFilehandle: withBase(this.params.url),
|
|
48
|
+
baiFilehandle: withBase(
|
|
49
|
+
this.params.indexUrl ?? this.params.url + ".bai"
|
|
50
|
+
),
|
|
51
|
+
});
|
|
52
|
+
|
|
53
|
+
this.headerPromise = this.bam.getHeader();
|
|
54
|
+
this.headerPromise.then((_header) => {
|
|
55
|
+
const g = this.genome.hasChrPrefix();
|
|
56
|
+
// @ts-expect-error protected property
|
|
57
|
+
const b = this.bam.indexToChr?.[0]?.refName.startsWith("chr");
|
|
58
|
+
if (g && !b) {
|
|
59
|
+
this.chrPrefixFixer = (chr) => chr.replace("chr", "");
|
|
60
|
+
} else if (!g && b) {
|
|
61
|
+
this.chrPrefixFixer = (chr) => "chr" + chr;
|
|
62
|
+
}
|
|
63
|
+
});
|
|
64
|
+
}
|
|
65
|
+
|
|
66
|
+
/**
|
|
67
|
+
* Listen to the domain change event and update data when the covered windows change.
|
|
68
|
+
*
|
|
69
|
+
* @param {number[]} domain Linearized domain
|
|
70
|
+
*/
|
|
71
|
+
async onDomainChanged(domain) {
|
|
72
|
+
const windowSize = this.params.windowSize;
|
|
73
|
+
|
|
74
|
+
if (domain[1] - domain[0] > windowSize) {
|
|
75
|
+
return;
|
|
76
|
+
}
|
|
77
|
+
|
|
78
|
+
await this.headerPromise;
|
|
79
|
+
|
|
80
|
+
const quantizedInterval = this.quantizeInterval(domain, windowSize);
|
|
81
|
+
|
|
82
|
+
if (this.checkAndUpdateLastInterval(quantizedInterval)) {
|
|
83
|
+
const discreteChromosomeIntervals =
|
|
84
|
+
this.genome.continuousToDiscreteChromosomeIntervals(
|
|
85
|
+
quantizedInterval
|
|
86
|
+
);
|
|
87
|
+
|
|
88
|
+
// TODO: Error handling
|
|
89
|
+
const sequencesWithChrom = await Promise.all(
|
|
90
|
+
discreteChromosomeIntervals.map((d) =>
|
|
91
|
+
this.bam
|
|
92
|
+
.getRecordsForRange(
|
|
93
|
+
this.chrPrefixFixer(d.chrom),
|
|
94
|
+
d.startPos,
|
|
95
|
+
d.endPos
|
|
96
|
+
)
|
|
97
|
+
.then((records) =>
|
|
98
|
+
records.map((record) => ({
|
|
99
|
+
chrom: d.chrom,
|
|
100
|
+
start: record.get("start"),
|
|
101
|
+
end: record.get("end"),
|
|
102
|
+
name: record.get("name"),
|
|
103
|
+
MD: record.get("MD"),
|
|
104
|
+
cigar: record.get("cigar"),
|
|
105
|
+
mapq: record.get("mq"),
|
|
106
|
+
strand: record.get("strand") === 1 ? "+" : "-",
|
|
107
|
+
}))
|
|
108
|
+
)
|
|
109
|
+
)
|
|
110
|
+
);
|
|
111
|
+
|
|
112
|
+
this.publishData(sequencesWithChrom.flat());
|
|
113
|
+
}
|
|
114
|
+
}
|
|
115
|
+
}
|
|
@@ -0,0 +1,51 @@
|
|
|
1
|
+
declare const BigBedSource_base: {
|
|
2
|
+
new (...args: any[]): {
|
|
3
|
+
[x: string]: any;
|
|
4
|
+
lastQuantizedInterval: number[];
|
|
5
|
+
quantizeInterval(interval: number[], windowSize: number): number[];
|
|
6
|
+
checkAndUpdateLastInterval(interval: number[]): boolean;
|
|
7
|
+
};
|
|
8
|
+
} & typeof SingleAxisLazySource;
|
|
9
|
+
export default class BigBedSource extends BigBedSource_base {
|
|
10
|
+
/**
|
|
11
|
+
* @param {import("../../../spec/data").BigBedData} params
|
|
12
|
+
* @param {import("../../../view/view").default} view
|
|
13
|
+
*/
|
|
14
|
+
constructor(params: import("../../../spec/data").BigBedData, view: import("../../../view/view").default);
|
|
15
|
+
/** Keep track of the order of the requests */
|
|
16
|
+
lastRequestId: number;
|
|
17
|
+
/** @type {BED} */
|
|
18
|
+
parser: BED;
|
|
19
|
+
params: import("../../../spec/data").BigBedData;
|
|
20
|
+
bbi: BigBed;
|
|
21
|
+
doDebouncedRequest: (...args: any[]) => Promise<any>;
|
|
22
|
+
headerPromise: Promise<import("@gmod/bbi").Header>;
|
|
23
|
+
/**
|
|
24
|
+
* Listen to the domain change event and update data when the covered windows change.
|
|
25
|
+
*
|
|
26
|
+
* @param {number[]} domain Linearized domain
|
|
27
|
+
*/
|
|
28
|
+
onDomainChanged(domain: number[]): Promise<void>;
|
|
29
|
+
/**
|
|
30
|
+
* Listen to the domain change event and update data when the covered windows change.
|
|
31
|
+
*
|
|
32
|
+
* @param {number[]} interval linearized domain
|
|
33
|
+
*/
|
|
34
|
+
doRequest(interval: number[]): Promise<void>;
|
|
35
|
+
/**
|
|
36
|
+
*
|
|
37
|
+
* @param {number[]} interval
|
|
38
|
+
*/
|
|
39
|
+
getFeatures(interval: number[]): Promise<{
|
|
40
|
+
requestId: number;
|
|
41
|
+
abort: () => void;
|
|
42
|
+
features: {
|
|
43
|
+
[key: string]: any;
|
|
44
|
+
}[];
|
|
45
|
+
}>;
|
|
46
|
+
}
|
|
47
|
+
import SingleAxisLazySource from "./singleAxisLazySource";
|
|
48
|
+
import BED from "@gmod/bed";
|
|
49
|
+
import { BigBed } from "@gmod/bbi";
|
|
50
|
+
export {};
|
|
51
|
+
//# sourceMappingURL=bigBedSource.d.ts.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"bigBedSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/dynamic/bigBedSource.js"],"names":[],"mappings":";;;;;;;;AASA;IAOI;;;OAGG;IACH,oBAHW,OAAO,oBAAoB,EAAE,UAAU,QACvC,OAAO,oBAAoB,EAAE,OAAO,EAmC9C;IA3CD,8CAA8C;IAC9C,sBAAkB;IAElB,kBAAkB;IAClB,QADW,GAAG,CACP;IAgBH,gDAAgC;IAMhC,YAIE;IAEF,qDAIC;IAED,mDAAyC;IAO7C;;;;OAIG;IACH,wBAFW,MAAM,EAAE,iBAclB;IAED;;;;OAIG;IACH,oBAFW,MAAM,EAAE,iBAWlB;IAED;;;OAGG;IACH,sBAFW,MAAM,EAAE;;;;;;OAkClB;CACJ;iCA3HgC,wBAAwB;gBAFzC,WAAW;uBAFJ,WAAW"}
|
|
@@ -0,0 +1,128 @@
|
|
|
1
|
+
import { BigBed } from "@gmod/bbi";
|
|
2
|
+
import { RemoteFile } from "generic-filehandle";
|
|
3
|
+
import BED from "@gmod/bed";
|
|
4
|
+
|
|
5
|
+
import SingleAxisLazySource from "./singleAxisLazySource";
|
|
6
|
+
import windowedMixin from "./windowedMixin";
|
|
7
|
+
import { debounce } from "../../../utils/debounce";
|
|
8
|
+
import addBaseUrl from "@genome-spy/core/utils/addBaseUrl";
|
|
9
|
+
|
|
10
|
+
export default class BigBedSource extends windowedMixin(SingleAxisLazySource) {
|
|
11
|
+
/** Keep track of the order of the requests */
|
|
12
|
+
lastRequestId = 0;
|
|
13
|
+
|
|
14
|
+
/** @type {BED} */
|
|
15
|
+
parser;
|
|
16
|
+
|
|
17
|
+
/**
|
|
18
|
+
* @param {import("../../../spec/data").BigBedData} params
|
|
19
|
+
* @param {import("../../../view/view").default} view
|
|
20
|
+
*/
|
|
21
|
+
constructor(params, view) {
|
|
22
|
+
/** @type {import("../../../spec/data").BigBedData} */
|
|
23
|
+
const paramsWithDefaults = {
|
|
24
|
+
channel: "x",
|
|
25
|
+
windowSize: 1000000,
|
|
26
|
+
...params,
|
|
27
|
+
};
|
|
28
|
+
|
|
29
|
+
super(view, paramsWithDefaults.channel);
|
|
30
|
+
|
|
31
|
+
this.params = paramsWithDefaults;
|
|
32
|
+
|
|
33
|
+
if (!this.params.url) {
|
|
34
|
+
throw new Error("No URL provided for BigBedSource");
|
|
35
|
+
}
|
|
36
|
+
|
|
37
|
+
this.bbi = new BigBed({
|
|
38
|
+
filehandle: new RemoteFile(
|
|
39
|
+
addBaseUrl(this.params.url, this.view.getBaseUrl())
|
|
40
|
+
),
|
|
41
|
+
});
|
|
42
|
+
|
|
43
|
+
this.doDebouncedRequest = debounce(
|
|
44
|
+
this.doRequest.bind(this),
|
|
45
|
+
200,
|
|
46
|
+
false
|
|
47
|
+
);
|
|
48
|
+
|
|
49
|
+
this.headerPromise = this.bbi.getHeader();
|
|
50
|
+
|
|
51
|
+
this.headerPromise.then((header) => {
|
|
52
|
+
this.parser = new BED({ autoSql: header.autoSql });
|
|
53
|
+
});
|
|
54
|
+
}
|
|
55
|
+
|
|
56
|
+
/**
|
|
57
|
+
* Listen to the domain change event and update data when the covered windows change.
|
|
58
|
+
*
|
|
59
|
+
* @param {number[]} domain Linearized domain
|
|
60
|
+
*/
|
|
61
|
+
async onDomainChanged(domain) {
|
|
62
|
+
const windowSize = this.params.windowSize;
|
|
63
|
+
|
|
64
|
+
if (domain[1] - domain[0] > windowSize) {
|
|
65
|
+
return;
|
|
66
|
+
}
|
|
67
|
+
|
|
68
|
+
const quantizedInterval = this.quantizeInterval(domain, windowSize);
|
|
69
|
+
|
|
70
|
+
if (this.checkAndUpdateLastInterval(quantizedInterval)) {
|
|
71
|
+
this.doDebouncedRequest(quantizedInterval);
|
|
72
|
+
}
|
|
73
|
+
}
|
|
74
|
+
|
|
75
|
+
/**
|
|
76
|
+
* Listen to the domain change event and update data when the covered windows change.
|
|
77
|
+
*
|
|
78
|
+
* @param {number[]} interval linearized domain
|
|
79
|
+
*/
|
|
80
|
+
async doRequest(interval) {
|
|
81
|
+
const featureResponse = await this.getFeatures(interval);
|
|
82
|
+
|
|
83
|
+
// Discard late responses
|
|
84
|
+
if (featureResponse.requestId < this.lastRequestId) {
|
|
85
|
+
return;
|
|
86
|
+
}
|
|
87
|
+
|
|
88
|
+
this.publishData(featureResponse.features);
|
|
89
|
+
}
|
|
90
|
+
|
|
91
|
+
/**
|
|
92
|
+
*
|
|
93
|
+
* @param {number[]} interval
|
|
94
|
+
*/
|
|
95
|
+
async getFeatures(interval) {
|
|
96
|
+
let requestId = ++this.lastRequestId;
|
|
97
|
+
|
|
98
|
+
// TODO: Abort previous requests
|
|
99
|
+
const abortController = new AbortController();
|
|
100
|
+
|
|
101
|
+
const discreteChromosomeIntervals =
|
|
102
|
+
this.genome.continuousToDiscreteChromosomeIntervals(interval);
|
|
103
|
+
|
|
104
|
+
// TODO: Error handling
|
|
105
|
+
const featuresWithChrom = await Promise.all(
|
|
106
|
+
discreteChromosomeIntervals.map((d) =>
|
|
107
|
+
this.bbi
|
|
108
|
+
.getFeatures(d.chrom, d.startPos, d.endPos, {
|
|
109
|
+
signal: abortController.signal,
|
|
110
|
+
})
|
|
111
|
+
.then((features) =>
|
|
112
|
+
features.map((f) =>
|
|
113
|
+
this.parser.parseLine(
|
|
114
|
+
`${d.chrom}\t${f.start}\t${f.end}\t${f.rest}`,
|
|
115
|
+
{ uniqueId: f.uniqueId }
|
|
116
|
+
)
|
|
117
|
+
)
|
|
118
|
+
)
|
|
119
|
+
)
|
|
120
|
+
);
|
|
121
|
+
|
|
122
|
+
return {
|
|
123
|
+
requestId,
|
|
124
|
+
abort: () => abortController.abort(),
|
|
125
|
+
features: featuresWithChrom.flat(), // TODO: Use batches, not flat
|
|
126
|
+
};
|
|
127
|
+
}
|
|
128
|
+
}
|
|
@@ -0,0 +1,58 @@
|
|
|
1
|
+
declare const BigWigSource_base: {
|
|
2
|
+
new (...args: any[]): {
|
|
3
|
+
[x: string]: any;
|
|
4
|
+
lastQuantizedInterval: number[];
|
|
5
|
+
quantizeInterval(interval: number[], windowSize: number): number[];
|
|
6
|
+
checkAndUpdateLastInterval(interval: number[]): boolean;
|
|
7
|
+
};
|
|
8
|
+
} & typeof SingleAxisLazySource;
|
|
9
|
+
/**
|
|
10
|
+
*
|
|
11
|
+
*/
|
|
12
|
+
export default class BigWigSource extends BigWigSource_base {
|
|
13
|
+
/**
|
|
14
|
+
* @param {import("../../../spec/data").BigWigData} params
|
|
15
|
+
* @param {import("../../../view/view").default} view
|
|
16
|
+
*/
|
|
17
|
+
constructor(params: import("../../../spec/data").BigWigData, view: import("../../../view/view").default);
|
|
18
|
+
/** @type {number[]} */
|
|
19
|
+
reductionLevels: number[];
|
|
20
|
+
/** Keep track of the order of the requests */
|
|
21
|
+
lastRequestId: number;
|
|
22
|
+
params: import("../../../spec/data").BigWigData;
|
|
23
|
+
bbi: BigWig;
|
|
24
|
+
doDebouncedRequest: (...args: any[]) => Promise<any>;
|
|
25
|
+
headerPromise: Promise<import("@gmod/bbi").Header>;
|
|
26
|
+
/**
|
|
27
|
+
* Listen to the domain change event and update data when the covered windows change.
|
|
28
|
+
*
|
|
29
|
+
* @param {number[]} domain Linearized domain
|
|
30
|
+
*/
|
|
31
|
+
onDomainChanged(domain: number[]): Promise<void>;
|
|
32
|
+
/**
|
|
33
|
+
* Listen to the domain change event and update data when the covered windows change.
|
|
34
|
+
*
|
|
35
|
+
* @param {number[]} interval linearized domain
|
|
36
|
+
* @param {number} reductionLevel
|
|
37
|
+
*/
|
|
38
|
+
doRequest(interval: number[], reductionLevel: number): Promise<void>;
|
|
39
|
+
/**
|
|
40
|
+
*
|
|
41
|
+
* @param {number[]} interval
|
|
42
|
+
* @param {number} scale
|
|
43
|
+
*/
|
|
44
|
+
getFeatures(interval: number[], scale: number): Promise<{
|
|
45
|
+
requestId: number;
|
|
46
|
+
abort: () => void;
|
|
47
|
+
features: {
|
|
48
|
+
chrom: string;
|
|
49
|
+
start: number;
|
|
50
|
+
end: number;
|
|
51
|
+
score: number;
|
|
52
|
+
}[];
|
|
53
|
+
}>;
|
|
54
|
+
}
|
|
55
|
+
import SingleAxisLazySource from "./singleAxisLazySource";
|
|
56
|
+
import { BigWig } from "@gmod/bbi";
|
|
57
|
+
export {};
|
|
58
|
+
//# sourceMappingURL=bigWigSource.d.ts.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"bigWigSource.d.ts","sourceRoot":"","sources":["../../../../../src/data/sources/dynamic/bigWigSource.js"],"names":[],"mappings":";;;;;;;;AAQA;;GAEG;AACH;IAOI;;;OAGG;IACH,oBAHW,OAAO,oBAAoB,EAAE,UAAU,QACvC,OAAO,oBAAoB,EAAE,OAAO,EA2C9C;IAnDD,uBAAuB;IACvB,iBADW,MAAM,EAAE,CACE;IAErB,8CAA8C;IAC9C,sBAAkB;IAgBd,gDAAgC;IAMhC,YAIE;IAEF,qDAIC;IAED,mDAAyC;IAe7C;;;;OAIG;IACH,wBAFW,MAAM,EAAE,iBAwBlB;IAED;;;;;OAKG;IACH,oBAHW,MAAM,EAAE,kBACR,MAAM,iBAchB;IAED;;;;OAIG;IACH,sBAHW,MAAM,EAAE,SACR,MAAM;;;;;;;;;OAmChB;CACJ;iCArJgC,wBAAwB;uBAJlC,WAAW"}
|