jbrowse-plugin-graphgenomeviewer 7.1.0 → 7.1.2
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 +17 -8
- package/dist/chunks/AddTrackWorkflow-RPH4ZFSX.js +2 -0
- package/dist/chunks/{AddTrackWorkflow-Q6RY23LF.js.map → AddTrackWorkflow-RPH4ZFSX.js.map} +2 -2
- package/dist/chunks/{ChooseSamplesDialog-BNVYBGJQ.js → ChooseSamplesDialog-JRN4YLBY.js} +2 -2
- package/dist/chunks/{ChooseWalksDialog-EN3C6AQA.js → ChooseWalksDialog-UXLFZTZJ.js} +2 -2
- package/dist/chunks/GbzBaseSyntenyAdapter-LRECKL74.js +2 -0
- package/dist/chunks/GbzBaseSyntenyAdapter-LRECKL74.js.map +7 -0
- package/dist/chunks/{GraphGenomeView-Z2WZKEEO.js → GraphGenomeView-NJ5XCREB.js} +2 -2
- package/dist/chunks/GraphTrackSettingsDialog-47PQ6LM7.js +6 -0
- package/dist/chunks/GraphTrackSettingsDialog-47PQ6LM7.js.map +7 -0
- package/dist/chunks/{HighlightColorDialog-EYBKFSJU.js → HighlightColorDialog-UK5VDDV6.js} +2 -2
- package/dist/chunks/{LinearGraphDisplay-WIBVWRQE.js → LinearGraphDisplay-TXTKAACH.js} +2 -2
- package/dist/chunks/MinigraphBubbleAdapter-HW7XQMAI.js +2 -0
- package/dist/chunks/MinigraphBubbleAdapter-HW7XQMAI.js.map +7 -0
- package/dist/chunks/RgfaTabixAdapter-PSKYWD2X.js +3 -0
- package/dist/chunks/RgfaTabixAdapter-PSKYWD2X.js.map +7 -0
- package/dist/chunks/{TrackWarningsDialog-QT4YEXGD.js → TrackWarningsDialog-TRYBOIHX.js} +2 -2
- package/dist/chunks/WalkTabixSyntenyAdapter-U53JLYVU.js +2 -0
- package/dist/chunks/WalkTabixSyntenyAdapter-U53JLYVU.js.map +7 -0
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- package/dist/chunks/renderSvg-KSQI5DH6.js +2 -0
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- package/dist/jbrowse-plugin-graphgenomeviewer.esm.js +4 -4
- package/dist/jbrowse-plugin-graphgenomeviewer.esm.js.map +4 -4
- package/package.json +8 -9
- package/src/GbzBaseSyntenyAdapter/GbzBaseSyntenyAdapter.test.ts +12 -10
- package/src/GbzBaseSyntenyAdapter/GbzBaseSyntenyAdapter.ts +31 -39
- package/src/GbzBaseSyntenyAdapter/configSchema.ts +5 -29
- package/src/GetGraphHaplotypes.ts +6 -15
- package/src/GetGraphReads.ts +7 -14
- package/src/GetSubgraph.ts +11 -20
- package/src/GraphAddTrackWorkflow/AddTrackWorkflow.test.tsx +73 -0
- package/src/GraphAddTrackWorkflow/AddTrackWorkflow.tsx +1 -0
- package/src/GraphAddTrackWorkflow/buildTrackConfig.test.ts +3 -2
- package/src/GraphAddTrackWorkflow/buildTrackConfig.ts +2 -11
- package/src/GraphAddTrackWorkflow/graphManifest.ts +15 -3
- package/src/GraphGenomeView/components/BubbleHalos.tsx +5 -24
- package/src/GraphGenomeView/components/ElTree.tsx +6 -1
- package/src/GraphGenomeView/components/FacetPanels.test.tsx +65 -0
- package/src/GraphGenomeView/components/FacetPanels.tsx +17 -12
- package/src/GraphGenomeView/components/GenePins.tsx +5 -22
- package/src/GraphGenomeView/components/GraphCanvas.tsx +40 -234
- package/src/GraphGenomeView/components/GraphSettingsDialog.tsx +102 -108
- package/src/GraphGenomeView/components/GraphToolbar.tsx +5 -6
- package/src/GraphGenomeView/components/HoverLayer.tsx +3 -7
- package/src/GraphGenomeView/components/HoverTooltip.test.tsx +39 -0
- package/src/GraphGenomeView/components/HoverTooltip.tsx +122 -0
- package/src/GraphGenomeView/components/LabelChip.tsx +3 -5
- package/src/GraphGenomeView/components/LabelLayer.tsx +4 -17
- package/src/GraphGenomeView/components/LabelledSelect.tsx +1 -1
- package/src/GraphGenomeView/components/Legend.tsx +14 -23
- package/src/GraphGenomeView/components/PaneContextMenu.test.tsx +48 -0
- package/src/GraphGenomeView/components/PaneContextMenu.tsx +144 -0
- package/src/GraphGenomeView/components/PaneLayer.tsx +91 -0
- package/src/GraphGenomeView/components/PaneSvg.tsx +32 -50
- package/src/GraphGenomeView/components/ReferenceStripOverlay.test.tsx +48 -0
- package/src/GraphGenomeView/components/ReferenceStripOverlay.tsx +13 -42
- package/src/GraphGenomeView/components/SettingsMenu.test.tsx +29 -0
- package/src/GraphGenomeView/components/SettingsMenu.tsx +56 -65
- package/src/GraphGenomeView/components/TubeMapOverlay.tsx +15 -46
- package/src/GraphGenomeView/components/WalkRowsOverlay.tsx +58 -132
- package/src/GraphGenomeView/components/WalkStrip.tsx +17 -20
- package/src/GraphGenomeView/components/WalkStripLocator.tsx +8 -15
- package/src/GraphGenomeView/components/usePaneGestures.test.tsx +35 -0
- package/src/GraphGenomeView/components/usePaneGestures.ts +88 -91
- package/src/GraphGenomeView/genes/geneFeatures.ts +27 -45
- package/src/GraphGenomeView/graphLayers.ts +4 -4
- package/src/GraphGenomeView/host.ts +1 -1
- package/src/GraphGenomeView/legendSections.test.ts +23 -1
- package/src/GraphGenomeView/legendSections.ts +68 -74
- package/src/GraphGenomeView/model.test.ts +373 -39
- package/src/GraphGenomeView/model.ts +67 -11
- package/src/GraphGenomeView/pane/fitViews.ts +57 -514
- package/src/GraphGenomeView/pane/graphViews.ts +219 -160
- package/src/GraphGenomeView/pane/hostViews.ts +2 -10
- package/src/GraphGenomeView/pane/keepInView.ts +5 -4
- package/src/GraphGenomeView/pane/launchActions.ts +117 -139
- package/src/GraphGenomeView/pane/launchViews.ts +8 -27
- package/src/GraphGenomeView/pane/loadActions.ts +208 -187
- package/src/GraphGenomeView/pane/morph.ts +3 -9
- package/src/GraphGenomeView/pane/paneBase.ts +22 -11
- package/src/GraphGenomeView/pane/renderingActions.ts +65 -11
- package/src/GraphGenomeView/pane/settingActions.ts +17 -42
- package/src/GraphGenomeView/pane/tubeMapViews.ts +445 -0
- package/src/GraphGenomeView/pane/walkRowViews.ts +29 -37
- package/src/GraphGenomeView/renderPipeline.test.ts +1 -1
- package/src/GraphGenomeView/repeats/repeatFeatures.test.ts +23 -0
- package/src/GraphGenomeView/repeats/repeatFeatures.ts +16 -23
- package/src/GraphGenomeView/repeats/walkCalls.test.ts +18 -0
- package/src/GraphGenomeView/repeats/walkCalls.ts +46 -38
- package/src/GraphGenomeView/subgraphLoad.test.ts +67 -3
- package/src/GraphGenomeView/trackFeatures.ts +24 -0
- package/src/GraphGenomeView/tubeMapPanels.ts +28 -36
- package/src/GraphGenomeView/viewModel.ts +8 -56
- package/src/GraphGenomeView/walkRowGroups.ts +104 -30
- package/src/GraphGenomeView/walkRowSpans.test.ts +6 -0
- package/src/GraphGenomeView/walkRowSpans.ts +22 -31
- package/src/GraphGenomeView/walkRowsCut.ts +8 -17
- package/src/LinearGraphDisplay/LinearGraphDisplay.test.ts +173 -26
- package/src/LinearGraphDisplay/components/SubgraphContextSelect.test.tsx +1 -1
- package/src/LinearGraphDisplay/components/SubgraphContextSelect.tsx +3 -3
- package/src/LinearGraphDisplay/components/SubgraphHaplotypesField.test.tsx +3 -3
- package/src/LinearGraphDisplay/components/SubgraphHaplotypesField.tsx +7 -10
- package/src/LinearGraphDisplay/configSchema.ts +0 -3
- package/src/LinearGraphDisplay/denseWindow.ts +8 -11
- package/src/LinearGraphDisplay/model.ts +89 -82
- package/src/MinigraphBubbleAdapter/MinigraphBubbleAdapter.test.ts +21 -0
- package/src/MinigraphBubbleAdapter/MinigraphBubbleAdapter.ts +6 -14
- package/src/MinigraphBubbleAdapter/configSchema.ts +3 -9
- package/src/MinigraphBubbleAdapter/index.ts +1 -2
- package/src/RgfaTabixAdapter/RgfaTabixAdapter.test.ts +45 -1
- package/src/RgfaTabixAdapter/RgfaTabixAdapter.ts +111 -276
- package/src/RgfaTabixAdapter/configSchema.ts +15 -49
- package/src/RgfaTabixAdapter/index.ts +1 -2
- package/src/RgfaTabixAdapter/rgfaBed.ts +25 -15
- package/src/RgfaTabixAdapter/rgfaCut.ts +139 -0
- package/src/RgfaTabixAdapter/test_data/walks2_twopart.GRCh38.walks.bed.gz +0 -0
- package/src/RgfaTabixAdapter/test_data/walks2_twopart.GRCh38.walks.bed.gz.tbi +0 -0
- package/src/RgfaTabixAdapter/walkFiles.test.ts +33 -0
- package/src/RgfaTabixAdapter/walkReader.ts +103 -27
- package/src/RgfaTabixAdapter/walkRowRuns.test.ts +53 -0
- package/src/RgfaTabixAdapter/walkRowRuns.ts +42 -24
- package/src/WalkTabixSyntenyAdapter/WalkTabixSyntenyAdapter.test.ts +37 -6
- package/src/WalkTabixSyntenyAdapter/WalkTabixSyntenyAdapter.ts +23 -45
- package/src/WalkTabixSyntenyAdapter/configSchema.ts +11 -24
- package/src/WalkTabixSyntenyAdapter/index.ts +1 -2
- package/src/WalkTabixSyntenyAdapter/walkLanes.ts +35 -43
- package/src/adapterImplementing.ts +27 -0
- package/src/graphTrackDefaults/index.ts +14 -20
- package/src/hoverSync/lgvHover.ts +2 -4
- package/src/launchFromGraph/contributors.ts +1 -5
- package/src/launchFromGraph/graphMenuItems.ts +3 -4
- package/src/launchFromGraph/launchFromGraph.test.ts +0 -1
- package/src/launchFromGraph/launchFromGraph.ts +8 -13
- package/src/panSNTabix.test.ts +1 -26
- package/src/panSNTabix.ts +54 -51
- package/src/synteny/lanePairs.ts +8 -0
- package/src/synteny/matchFeature.ts +52 -0
- package/src/tabixRange.ts +13 -10
- package/src/version.ts +1 -1
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