react-msaview 9.0.0 → 9.1.1
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 +19 -10
- package/bundle/index.js +111 -115
- package/bundle/index.js.map +4 -4
- package/dist/blosum62.d.ts +3 -0
- package/dist/blosum62.js +43 -0
- package/dist/blosum62.js.map +1 -0
- package/dist/colorSchemes.js +2 -3
- package/dist/colorSchemes.js.map +1 -1
- package/dist/columnCounts.d.ts +0 -1
- package/dist/columnCounts.js +1 -1
- package/dist/columnCounts.js.map +1 -1
- package/dist/components/Loading.d.ts +3 -2
- package/dist/components/Loading.js +7 -7
- package/dist/components/Loading.js.map +1 -1
- package/dist/components/MSAView.d.ts +3 -2
- package/dist/components/MSAView.js +7 -4
- package/dist/components/MSAView.js.map +1 -1
- package/dist/components/MSAViewer.d.ts +1941 -4
- package/dist/components/MSAViewer.js +144 -201
- package/dist/components/MSAViewer.js.map +1 -1
- package/dist/components/MetadataTable.d.ts +4 -1
- package/dist/components/MetadataTable.js +55 -16
- package/dist/components/MetadataTable.js.map +1 -1
- package/dist/components/ResizeHandles.js +3 -2
- package/dist/components/ResizeHandles.js.map +1 -1
- package/dist/components/Track.js +8 -1
- package/dist/components/Track.js.map +1 -1
- package/dist/components/controls.d.ts +11 -0
- package/dist/components/controls.js +49 -0
- package/dist/components/controls.js.map +1 -0
- package/dist/components/dialogs/AnnotationFileDialog.js +12 -18
- package/dist/components/dialogs/AnnotationFileDialog.js.map +1 -1
- package/dist/components/dialogs/ExportSVGDialog.js +5 -7
- package/dist/components/dialogs/ExportSVGDialog.js.map +1 -1
- package/dist/components/dialogs/FeatureDialog.js +2 -2
- package/dist/components/dialogs/FeatureDialog.js.map +1 -1
- package/dist/components/{header/TreeSettingsMenu.d.ts → dialogs/GapThresholdDialog.d.ts} +3 -2
- package/dist/components/dialogs/GapThresholdDialog.js +15 -0
- package/dist/components/dialogs/GapThresholdDialog.js.map +1 -0
- package/dist/components/{header → dialogs}/GappynessSlider.d.ts +1 -1
- package/dist/components/{header → dialogs}/GappynessSlider.js +3 -10
- package/dist/components/dialogs/GappynessSlider.js.map +1 -0
- package/dist/components/{header → dialogs}/GoToBox.d.ts +4 -2
- package/dist/components/dialogs/GoToBox.js +48 -0
- package/dist/components/dialogs/GoToBox.js.map +1 -0
- package/dist/components/dialogs/GoToDialog.d.ts +6 -0
- package/dist/components/dialogs/GoToDialog.js +10 -0
- package/dist/components/dialogs/GoToDialog.js.map +1 -0
- package/dist/components/dialogs/HelpDialog.d.ts +6 -0
- package/dist/components/dialogs/HelpDialog.js +30 -0
- package/dist/components/dialogs/HelpDialog.js.map +1 -0
- package/dist/components/dialogs/MetadataDialog.js +11 -3
- package/dist/components/dialogs/MetadataDialog.js.map +1 -1
- package/dist/components/dialogs/goTo.d.ts +5 -0
- package/dist/components/{header → dialogs}/goTo.js +1 -1
- package/dist/components/dialogs/goTo.js.map +1 -0
- package/dist/components/dialogs/metadataLabels.d.ts +4 -0
- package/dist/components/dialogs/metadataLabels.js +52 -0
- package/dist/components/dialogs/metadataLabels.js.map +1 -0
- package/dist/components/dialogs/metadataRecord.d.ts +1 -0
- package/dist/components/dialogs/metadataRecord.js +38 -0
- package/dist/components/dialogs/metadataRecord.js.map +1 -0
- package/dist/components/header/Header.d.ts +6 -2
- package/dist/components/header/Header.js +30 -34
- package/dist/components/header/Header.js.map +1 -1
- package/dist/components/header/HiddenColumnsChip.d.ts +6 -0
- package/dist/components/header/HiddenColumnsChip.js +15 -0
- package/dist/components/header/HiddenColumnsChip.js.map +1 -0
- package/dist/components/header/{FileMenu.d.ts → MenuBar.d.ts} +3 -3
- package/dist/components/header/MenuBar.js +33 -0
- package/dist/components/header/MenuBar.js.map +1 -0
- package/dist/components/header/ScrollZoomCheckbox.d.ts +7 -0
- package/dist/components/header/ScrollZoomCheckbox.js +19 -0
- package/dist/components/header/ScrollZoomCheckbox.js.map +1 -0
- package/dist/components/header/ZoomControls.js +12 -48
- package/dist/components/header/ZoomControls.js.map +1 -1
- package/dist/components/header/colorSchemeMenuItems.d.ts +4 -0
- package/dist/components/header/colorSchemeMenuItems.js +106 -0
- package/dist/components/header/colorSchemeMenuItems.js.map +1 -0
- package/dist/components/header/getAnnotationsMenu.d.ts +3 -30
- package/dist/components/header/getAnnotationsMenu.js +48 -54
- package/dist/components/header/getAnnotationsMenu.js.map +1 -1
- package/dist/components/header/menuBarItems.d.ts +11 -0
- package/dist/components/header/menuBarItems.js +277 -0
- package/dist/components/header/menuBarItems.js.map +1 -0
- package/dist/components/import/ImportForm.js +12 -6
- package/dist/components/import/ImportForm.js.map +1 -1
- package/dist/components/import/data/seq2.d.ts +0 -1
- package/dist/components/import/data/seq2.js +0 -17
- package/dist/components/import/data/seq2.js.map +1 -1
- package/dist/components/minimap/Minimap.js +7 -3
- package/dist/components/minimap/Minimap.js.map +1 -1
- package/dist/components/minimap/MinimapSVG.js +2 -1
- package/dist/components/minimap/MinimapSVG.js.map +1 -1
- package/dist/components/minimap/minimapLayout.d.ts +12 -0
- package/dist/components/minimap/minimapLayout.js +20 -0
- package/dist/components/minimap/minimapLayout.js.map +1 -1
- package/dist/components/msa/MSACanvas.js +28 -10
- package/dist/components/msa/MSACanvas.js.map +1 -1
- package/dist/components/msa/MSACanvasBlock.js +17 -16
- package/dist/components/msa/MSACanvasBlock.js.map +1 -1
- package/dist/components/msa/MSAMouseoverCanvas.js +2 -2
- package/dist/components/msa/MSAMouseoverCanvas.js.map +1 -1
- package/dist/components/msa/WheelZoomHint.d.ts +7 -0
- package/dist/components/msa/WheelZoomHint.js +38 -0
- package/dist/components/msa/WheelZoomHint.js.map +1 -0
- package/dist/components/msa/drawFeatureSpans.d.ts +50 -11
- package/dist/components/msa/drawFeatureSpans.js +99 -56
- package/dist/components/msa/drawFeatureSpans.js.map +1 -1
- package/dist/components/msa/msaKeys.js +3 -0
- package/dist/components/msa/msaKeys.js.map +1 -1
- package/dist/components/msa/msaRaster.d.ts +14 -2
- package/dist/components/msa/msaRaster.js +20 -10
- package/dist/components/msa/msaRaster.js.map +1 -1
- package/dist/components/msa/renderBoxFeatureCanvasBlock.d.ts +9 -0
- package/dist/components/msa/renderBoxFeatureCanvasBlock.js +39 -8
- package/dist/components/msa/renderBoxFeatureCanvasBlock.js.map +1 -1
- package/dist/components/msa/renderHighlights.d.ts +2 -5
- package/dist/components/msa/renderHighlights.js +5 -6
- package/dist/components/msa/renderHighlights.js.map +1 -1
- package/dist/components/msa/renderMSABlock.d.ts +6 -1
- package/dist/components/msa/renderMSABlock.js +44 -17
- package/dist/components/msa/renderMSABlock.js.map +1 -1
- package/dist/components/msa/renderMSAMouseover.js +2 -1
- package/dist/components/msa/renderMSAMouseover.js.map +1 -1
- package/dist/components/msa/tileColor.js +7 -0
- package/dist/components/msa/tileColor.js.map +1 -1
- package/dist/components/renderCtx.d.ts +1 -1
- package/dist/components/rowpanels/RowPanelBlock.js +2 -2
- package/dist/components/rowpanels/RowPanelBlock.js.map +1 -1
- package/dist/components/rowpanels/renderFeaturePanel.d.ts +5 -1
- package/dist/components/rowpanels/renderFeaturePanel.js +12 -5
- package/dist/components/rowpanels/renderFeaturePanel.js.map +1 -1
- package/dist/components/settings/MenuItemsForm.d.ts +10 -0
- package/dist/components/settings/MenuItemsForm.js +80 -0
- package/dist/components/settings/MenuItemsForm.js.map +1 -0
- package/dist/components/settings/SettingsPanel.d.ts +12 -0
- package/dist/components/settings/SettingsPanel.js +92 -0
- package/dist/components/settings/SettingsPanel.js.map +1 -0
- package/dist/components/{header/ZoomMenu.d.ts → settings/TrackList.d.ts} +2 -2
- package/dist/components/settings/TrackList.js +55 -0
- package/dist/components/settings/TrackList.js.map +1 -0
- package/dist/components/tracks/TrackBlocks.js +2 -2
- package/dist/components/tracks/TrackBlocks.js.map +1 -1
- package/dist/components/tracks/drawTracks.d.ts +1 -53
- package/dist/components/tracks/drawTracks.js +5 -5
- package/dist/components/tracks/drawTracks.js.map +1 -1
- package/dist/components/tree/CladeLabels.d.ts +1 -1
- package/dist/components/tree/CladeLabels.js +22 -34
- package/dist/components/tree/CladeLabels.js.map +1 -1
- package/dist/components/tree/TreeCanvasBlock.js +2 -2
- package/dist/components/tree/TreeCanvasBlock.js.map +1 -1
- package/dist/components/tree/TreeMenu.js +4 -6
- package/dist/components/tree/TreeMenu.js.map +1 -1
- package/dist/components/tree/TreeOverview.js +2 -2
- package/dist/components/tree/TreeOverview.js.map +1 -1
- package/dist/components/tree/cladeBrackets.d.ts +17 -10
- package/dist/components/tree/cladeBrackets.js +33 -3
- package/dist/components/tree/cladeBrackets.js.map +1 -1
- package/dist/components/tree/renderTreeCanvas.js +2 -8
- package/dist/components/tree/renderTreeCanvas.js.map +1 -1
- package/dist/components/tree/renderTreeOverview.js +4 -11
- package/dist/components/tree/renderTreeOverview.js.map +1 -1
- package/dist/constants.d.ts +4 -1
- package/dist/constants.js +7 -1
- package/dist/constants.js.map +1 -1
- package/dist/darkReader.d.ts +7 -0
- package/dist/darkReader.js +42 -0
- package/dist/darkReader.js.map +1 -0
- package/dist/element.js +25 -53
- package/dist/element.js.map +1 -1
- package/dist/exportLayout.d.ts +39 -0
- package/dist/exportLayout.js +78 -0
- package/dist/exportLayout.js.map +1 -0
- package/dist/featurePanels.d.ts +37 -0
- package/dist/featurePanels.js +187 -0
- package/dist/featurePanels.js.map +1 -0
- package/dist/filehandleLoader.d.ts +41 -0
- package/dist/filehandleLoader.js +99 -0
- package/dist/filehandleLoader.js.map +1 -0
- package/dist/headlessRenderEnv.d.ts +12 -39
- package/dist/headlessRenderEnv.js +18 -12
- package/dist/headlessRenderEnv.js.map +1 -1
- package/dist/hierarchy.d.ts +5 -8
- package/dist/hierarchy.js +5 -79
- package/dist/hierarchy.js.map +1 -1
- package/dist/index.d.ts +6 -1
- package/dist/index.js +6 -1
- package/dist/index.js.map +1 -1
- package/dist/measureTextCanvas.d.ts +7 -0
- package/dist/measureTextCanvas.js +8 -6
- package/dist/measureTextCanvas.js.map +1 -1
- package/dist/model/treeModel.d.ts +6 -2
- package/dist/model/treeModel.js +8 -4
- package/dist/model/treeModel.js.map +1 -1
- package/dist/model.d.ts +180 -76
- package/dist/model.js +358 -618
- package/dist/model.js.map +1 -1
- package/dist/neighborJoining.js +1 -40
- package/dist/neighborJoining.js.map +1 -1
- package/dist/renderToSvg.d.ts +2 -7
- package/dist/renderToSvg.js +33 -133
- package/dist/renderToSvg.js.map +1 -1
- package/dist/rerootTree.d.ts +1 -0
- package/dist/rerootTree.js +7 -6
- package/dist/rerootTree.js.map +1 -1
- package/dist/schemeResidueColor.d.ts +12 -0
- package/dist/schemeResidueColor.js +33 -0
- package/dist/schemeResidueColor.js.map +1 -0
- package/dist/similarityColors.d.ts +11 -0
- package/dist/similarityColors.js +90 -0
- package/dist/similarityColors.js.map +1 -0
- package/dist/svgTestUtil.d.ts +74 -32
- package/dist/treeDisplay.d.ts +37 -0
- package/dist/treeDisplay.js +209 -0
- package/dist/treeDisplay.js.map +1 -0
- package/dist/types.d.ts +6 -3
- package/dist/useWheelScroll.d.ts +3 -1
- package/dist/useWheelScroll.js +36 -17
- package/dist/useWheelScroll.js.map +1 -1
- package/dist/util.d.ts +2 -0
- package/dist/util.js +2 -0
- package/dist/util.js.map +1 -1
- package/dist/version.d.ts +1 -1
- package/dist/version.js +1 -1
- package/dist/viewerSnapshot.d.ts +169 -0
- package/dist/viewerSnapshot.js +100 -0
- package/dist/viewerSnapshot.js.map +1 -0
- package/dist/wheelZoom.d.ts +8 -3
- package/dist/wheelZoom.js +44 -32
- package/dist/wheelZoom.js.map +1 -1
- package/dist/zoomSnapshot.d.ts +29 -0
- package/dist/zoomSnapshot.js +47 -0
- package/dist/zoomSnapshot.js.map +1 -0
- package/package.json +11 -11
- package/src/blosum62.ts +45 -0
- package/src/colorSchemes.ts +2 -4
- package/src/columnCounts.ts +1 -1
- package/src/components/Loading.tsx +25 -14
- package/src/components/MSAView.tsx +22 -5
- package/src/components/MSAViewer.tsx +275 -251
- package/src/components/MetadataTable.tsx +83 -26
- package/src/components/ResizeHandles.tsx +9 -2
- package/src/components/Track.tsx +15 -1
- package/src/components/controls.ts +62 -0
- package/src/components/dialogs/AnnotationFileDialog.tsx +16 -21
- package/src/components/dialogs/ExportSVGDialog.tsx +8 -19
- package/src/components/dialogs/FeatureDialog.tsx +2 -5
- package/src/components/dialogs/GapThresholdDialog.tsx +36 -0
- package/src/components/{header → dialogs}/GappynessSlider.tsx +3 -10
- package/src/components/{header → dialogs}/GoToBox.tsx +36 -10
- package/src/components/dialogs/GoToDialog.tsx +30 -0
- package/src/components/dialogs/HelpDialog.tsx +79 -0
- package/src/components/dialogs/MetadataDialog.tsx +32 -4
- package/src/components/{header → dialogs}/goTo.ts +1 -1
- package/src/components/dialogs/metadataLabels.ts +54 -0
- package/src/components/dialogs/metadataRecord.tsx +61 -0
- package/src/components/header/Header.tsx +75 -44
- package/src/components/header/HiddenColumnsChip.tsx +39 -0
- package/src/components/header/MenuBar.tsx +64 -0
- package/src/components/header/ScrollZoomCheckbox.tsx +46 -0
- package/src/components/header/ZoomControls.tsx +23 -74
- package/src/components/header/colorSchemeMenuItems.ts +121 -0
- package/src/components/header/getAnnotationsMenu.ts +52 -56
- package/src/components/header/menuBarItems.ts +357 -0
- package/src/components/import/ImportForm.tsx +19 -7
- package/src/components/import/data/seq2.ts +0 -18
- package/src/components/minimap/Minimap.tsx +11 -3
- package/src/components/minimap/MinimapSVG.tsx +17 -1
- package/src/components/minimap/minimapLayout.ts +27 -0
- package/src/components/msa/MSACanvas.tsx +24 -4
- package/src/components/msa/MSACanvasBlock.tsx +20 -17
- package/src/components/msa/MSAMouseoverCanvas.tsx +2 -2
- package/src/components/msa/WheelZoomHint.tsx +56 -0
- package/src/components/msa/drawFeatureSpans.ts +160 -79
- package/src/components/msa/msaKeys.ts +3 -0
- package/src/components/msa/msaRaster.ts +26 -10
- package/src/components/msa/renderBoxFeatureCanvasBlock.ts +62 -24
- package/src/components/msa/renderHighlights.ts +5 -6
- package/src/components/msa/renderMSABlock.ts +51 -15
- package/src/components/msa/renderMSAMouseover.ts +5 -1
- package/src/components/msa/tileColor.ts +7 -0
- package/src/components/renderCtx.ts +0 -1
- package/src/components/rowpanels/RowPanelBlock.tsx +2 -2
- package/src/components/rowpanels/renderFeaturePanel.ts +26 -7
- package/src/components/settings/MenuItemsForm.tsx +225 -0
- package/src/components/settings/SettingsPanel.tsx +156 -0
- package/src/components/settings/TrackList.tsx +119 -0
- package/src/components/tracks/TrackBlocks.tsx +2 -2
- package/src/components/tracks/drawTracks.ts +5 -5
- package/src/components/tree/CladeLabels.tsx +30 -54
- package/src/components/tree/TreeCanvasBlock.tsx +2 -2
- package/src/components/tree/TreeMenu.tsx +4 -6
- package/src/components/tree/TreeOverview.tsx +2 -2
- package/src/components/tree/cladeBrackets.ts +50 -3
- package/src/components/tree/renderTreeCanvas.ts +2 -13
- package/src/components/tree/renderTreeOverview.ts +7 -14
- package/src/constants.ts +9 -1
- package/src/darkReader.ts +57 -0
- package/src/element.ts +37 -64
- package/src/exportLayout.ts +134 -0
- package/src/featurePanels.ts +269 -0
- package/src/filehandleLoader.ts +136 -0
- package/src/headlessRenderEnv.ts +24 -11
- package/src/hierarchy.ts +5 -88
- package/src/index.ts +9 -5
- package/src/measureTextCanvas.ts +8 -6
- package/src/model/treeModel.ts +9 -3
- package/src/model.ts +452 -807
- package/src/neighborJoining.ts +1 -42
- package/src/renderToSvg.tsx +56 -207
- package/src/rerootTree.ts +7 -6
- package/src/schemeResidueColor.ts +37 -0
- package/src/similarityColors.ts +112 -0
- package/src/treeDisplay.ts +278 -0
- package/src/types.ts +6 -4
- package/src/useWheelScroll.ts +43 -22
- package/src/util.ts +3 -0
- package/src/version.ts +1 -1
- package/src/viewerSnapshot.ts +147 -0
- package/src/wheelZoom.ts +55 -33
- package/src/zoomSnapshot.ts +80 -0
- package/dist/components/header/ColorSchemeMenu.d.ts +0 -12
- package/dist/components/header/ColorSchemeMenu.js +0 -37
- package/dist/components/header/ColorSchemeMenu.js.map +0 -1
- package/dist/components/header/FileMenu.js +0 -66
- package/dist/components/header/FileMenu.js.map +0 -1
- package/dist/components/header/GappynessSlider.js.map +0 -1
- package/dist/components/header/GoToBox.js +0 -31
- package/dist/components/header/GoToBox.js.map +0 -1
- package/dist/components/header/MSASettingsMenu.d.ts +0 -6
- package/dist/components/header/MSASettingsMenu.js +0 -11
- package/dist/components/header/MSASettingsMenu.js.map +0 -1
- package/dist/components/header/ScrollZoomIcons.d.ts +0 -6
- package/dist/components/header/ScrollZoomIcons.js +0 -35
- package/dist/components/header/ScrollZoomIcons.js.map +0 -1
- package/dist/components/header/TreeSettingsMenu.js +0 -42
- package/dist/components/header/TreeSettingsMenu.js.map +0 -1
- package/dist/components/header/ZoomMenu.js +0 -37
- package/dist/components/header/ZoomMenu.js.map +0 -1
- package/dist/components/header/goTo.d.ts +0 -20
- package/dist/components/header/goTo.js.map +0 -1
- package/dist/components/header/settingsMenuItems.d.ts +0 -4
- package/dist/components/header/settingsMenuItems.js +0 -127
- package/dist/components/header/settingsMenuItems.js.map +0 -1
- package/src/components/header/ColorSchemeMenu.tsx +0 -56
- package/src/components/header/FileMenu.tsx +0 -81
- package/src/components/header/MSASettingsMenu.tsx +0 -26
- package/src/components/header/ScrollZoomIcons.tsx +0 -52
- package/src/components/header/TreeSettingsMenu.tsx +0 -60
- package/src/components/header/ZoomMenu.tsx +0 -48
- package/src/components/header/settingsMenuItems.ts +0 -157
package/dist/blosum62.js
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// BLOSUM62 (Henikoff & Henikoff 1992), shared by the neighbor-joining tree and
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// the blosum62_dynamic color scheme
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// prettier-ignore
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const BLOSUM62_KEYS = 'ARNDCQEGHILKMFPSTWYVBZX*';
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// prettier-ignore
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const BLOSUM62_DATA = [
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[4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3, -2, 0, -2, -1, 0, -4],
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[-1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2, -3, -1, 0, -1, -4],
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[-2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3, 3, 0, -1, -4],
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[-2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4, -3, -3, 4, 1, -1, -4],
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[0, -3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2, -2, -1, -3, -3, -2, -4],
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[-1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1, -2, 0, 3, -1, -4],
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[-1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1, -4],
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[0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2, -3, -3, -1, -2, -1, -4],
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[-2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2, -3, 0, 0, -1, -4],
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[-1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3, -1, 3, -3, -3, -1, -4],
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|
+
[-1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2, -1, 1, -4, -3, -1, -4],
|
|
18
|
+
[-1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2, -2, 0, 1, -1, -4],
|
|
19
|
+
[-1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1, -1, 1, -3, -1, -1, -4],
|
|
20
|
+
[-2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3, -1, -3, -3, -1, -4],
|
|
21
|
+
[-1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1, -4, -3, -2, -2, -1, -2, -4],
|
|
22
|
+
[1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2, -2, 0, 0, 0, -4],
|
|
23
|
+
[0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2, -2, 0, -1, -1, 0, -4],
|
|
24
|
+
[-3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2, 11, 2, -3, -4, -3, -2, -4],
|
|
25
|
+
[-2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2, 7, -1, -3, -2, -1, -4],
|
|
26
|
+
[0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3, -1, 4, -3, -2, -1, -4],
|
|
27
|
+
[-2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4, -3, -3, 4, 1, -1, -4],
|
|
28
|
+
[-1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1, -4],
|
|
29
|
+
[0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2, -1, -1, -1, -1, -1, -4],
|
|
30
|
+
[-4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, 1],
|
|
31
|
+
];
|
|
32
|
+
export const NUM_SYMBOLS = BLOSUM62_KEYS.length;
|
|
33
|
+
export const BLOSUM62 = Int8Array.from(BLOSUM62_DATA.flat());
|
|
34
|
+
// charCode -> row/column in BLOSUM62, -1 for anything the matrix does not name.
|
|
35
|
+
// On a 120x800 alignment a Map keyed by upper-cased character took 2.6s to
|
|
36
|
+
// build a tree, against 0.34s for this table.
|
|
37
|
+
export const symbolOfCode = new Int8Array(128).fill(-1);
|
|
38
|
+
for (let i = 0; i < NUM_SYMBOLS; i++) {
|
|
39
|
+
const key = BLOSUM62_KEYS[i];
|
|
40
|
+
symbolOfCode[key.charCodeAt(0)] = i;
|
|
41
|
+
symbolOfCode[key.toLowerCase().charCodeAt(0)] = i;
|
|
42
|
+
}
|
|
43
|
+
//# sourceMappingURL=blosum62.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"blosum62.js","sourceRoot":"","sources":["../src/blosum62.ts"],"names":[],"mappings":"AAAA,+EAA+E;AAC/E,oCAAoC;AAEpC,kBAAkB;AAClB,MAAM,aAAa,GAAG,0BAA0B,CAAA;AAChD,kBAAkB;AAClB,MAAM,aAAa,GAAG;IACpB,CAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,EAAE,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,CAAC;CAC1E,CAAA;AAED,MAAM,CAAC,MAAM,WAAW,GAAG,aAAa,CAAC,MAAM,CAAA;AAC/C,MAAM,CAAC,MAAM,QAAQ,GAAG,SAAS,CAAC,IAAI,CAAC,aAAa,CAAC,IAAI,EAAE,CAAC,CAAA;AAE5D,gFAAgF;AAChF,2EAA2E;AAC3E,8CAA8C;AAC9C,MAAM,CAAC,MAAM,YAAY,GAAG,IAAI,SAAS,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAA;AACvD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE,CAAC;IACrC,MAAM,GAAG,GAAG,aAAa,CAAC,CAAC,CAAE,CAAA;IAC7B,YAAY,CAAC,GAAG,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;IACnC,YAAY,CAAC,GAAG,CAAC,WAAW,EAAE,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;AACnD,CAAC"}
|
package/dist/colorSchemes.js
CHANGED
|
@@ -1,8 +1,6 @@
|
|
|
1
1
|
import { blue, green, orange, red } from '@mui/material/colors';
|
|
2
|
-
import { colord
|
|
3
|
-
import namesPlugin from 'colord/plugins/names';
|
|
2
|
+
import { colord } from 'colord';
|
|
4
3
|
import { transform } from './util.js';
|
|
5
|
-
extend([namesPlugin]);
|
|
6
4
|
// standard A/C/G/T(/U) coloring, shared by the `jbrowse_dna` and `nucleotide`
|
|
7
5
|
// scheme names
|
|
8
6
|
const dna = {
|
|
@@ -77,6 +75,7 @@ const colorSchemes = {
|
|
|
77
75
|
T: 'red',
|
|
78
76
|
},
|
|
79
77
|
percent_identity_dynamic: {},
|
|
78
|
+
blosum62_dynamic: {},
|
|
80
79
|
// https://github.com/biotite-dev/biotite/blob/8c460972f8ab904312f130dfb80f3efc8c9bd7c5/src/biotite/sequence/graphics/color_schemes/flower.json
|
|
81
80
|
flower: {
|
|
82
81
|
A: '#b18a51',
|
package/dist/colorSchemes.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"colorSchemes.js","sourceRoot":"","sources":["../src/colorSchemes.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,EAAE,MAAM,sBAAsB,CAAA;AAC/D,OAAO,EAAE,MAAM,EAAE,MAAM,
|
|
1
|
+
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package/dist/columnCounts.d.ts
CHANGED
package/dist/columnCounts.js
CHANGED
package/dist/columnCounts.js.map
CHANGED
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@@ -1 +1 @@
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1
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+
{"version":3,"file":"columnCounts.js","sourceRoot":"","sources":["../src/columnCounts.ts"],"names":[],"mappings":"AAAA,2EAA2E;AAC3E,gFAAgF;AAChF,gFAAgF;AAChF,gFAAgF;AAChF,+EAA+E;AAC/E,kDAAkD;AAClD,EAAE;AACF,6EAA6E;AAC7E,gFAAgF;AAEhF,MAAM,KAAK,GAAG,EAAE,CAAA;AAChB,MAAM,IAAI,GAAG,EAAE,CAAA;AACf,MAAM,GAAG,GAAG,EAAE,CAAA;AACd,MAAM,IAAI,GAAG,EAAE,CAAA;AACf,MAAM,KAAK,GAAG,EAAE,CAAA;AAEhB,MAAM,CAAC,GAAG,GAAG,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;AAC3B,MAAM,CAAC,GAAG,GAAG,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;AAC3B,MAAM,CAAC,GAAG,GAAG,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;AAC3B,MAAM,CAAC,GAAG,GAAG,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;AAE3B,+EAA+E;AAC/E,oEAAoE;AACpE,MAAM,UAAU,GAAG,IAAI,UAAU,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;AAClD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;IAC5B,UAAU,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;AAC3B,CAAC;AACD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;IAC5B,UAAU,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;AAC3B,CAAC;AACD,UAAU,CAAC,GAAG,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,CAAA;AACpC,UAAU,CAAC,GAAG,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,CAAA;AACnC,UAAU,CAAC,GAAG,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,CAAA;AAEpC,MAAM,YAAY,GAAG,KAAK,CAAC,IAAI,CAAC,EAAE,MAAM,EAAE,KAAK,EAAE,EAAE,CAAC,CAAC,EAAE,IAAI,EAAE,EAAE,CAC7D,IAAI,IAAI,CAAC,IAAI,IAAI,IAAI,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,CAAC,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CACjE,CAAA;AACD,YAAY,CAAC,IAAI,CAAC,GAAG,GAAG,CAAA;AACxB,YAAY,CAAC,GAAG,CAAC,GAAG,GAAG,CAAA;AACvB,YAAY,CAAC,IAAI,CAAC,GAAG,GAAG,CAAA;AACxB,YAAY,CAAC,KAAK,CAAC,GAAG,GAAG,CAAA;AAEzB,SAAS,MAAM,CAAC,IAAY;IAC1B,OAAO,IAAI,GAAG,GAAG,CAAC,CAAC,CAAC,UAAU,CAAC,IAAI,CAAE,CAAC,CAAC,CAAC,KAAK,CAAA;AAC/C,CAAC;AAED,SAAS,SAAS,CAAC,IAAY;IAC7B,OAAO,IAAI,KAAK,IAAI,IAAI,IAAI,KAAK,GAAG,CAAA;AACtC,CAAC;AAED,MAAM,OAAO,YAAY;IACd,UAAU,CAAQ;IACV,MAAM,CAAa;IACpC,gCAAgC;IACvB,MAAM,CAAa;IAC5B,2EAA2E;IAC3E,oDAAoD;IACnC,UAAU,GAAG,IAAI,WAAW,CAAC,KAAK,CAAC,CAAA;IAEpD,YAAY,UAAkB;QAC5B,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,MAAM,GAAG,IAAI,WAAW,CAAC,UAAU,GAAG,KAAK,CAAC,CAAA;QACjD,IAAI,CAAC,MAAM,GAAG,IAAI,WAAW,CAAC,UAAU,CAAC,CAAA;IAC3C,CAAC;IAED,yEAAyE;IACzE,MAAM,CAAC,GAAW;QAChB,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,GAAG,IAAI,CAAA;QACvD,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,MAAM,EAAE,UAAU,CAAC,CAAA;QAC1C,KAAK,IAAI,GAAG,GAAG,CAAC,EAAE,GAAG,GAAG,CAAC,EAAE,GAAG,EAAE,EAAE,CAAC;YACjC,MAAM,IAAI,GAAG,MAAM,CAAC,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC,CAAA;YACxC,MAAM,CAAC,GAAG,GAAG,KAAK,GAAG,IAAI,CAAE,EAAE,CAAA;YAC7B,MAAM,CAAC,GAAG,CAAE,EAAE,CAAA;YACd,UAAU,CAAC,IAAI,CAAE,EAAE,CAAA;QACrB,CAAC;QACD,KAAK,IAAI,GAAG,GAAG,CAAC,EAAE,GAAG,GAAG,UAAU,EAAE,GAAG,EAAE,EAAE,CAAC;YAC1C,MAAM,CAAC,GAAG,GAAG,KAAK,GAAG,IAAI,CAAE,EAAE,CAAA;YAC7B,MAAM,CAAC,GAAG,CAAE,EAAE,CAAA;QAChB,CAAC;QACD,UAAU,CAAC,IAAI,CAAE,IAAI,UAAU,GAAG,CAAC,CAAA;IACrC,CAAC;IAED,GAAG,CAAC,GAAW,EAAE,MAAc;QAC7B,MAAM,IAAI,GAAG,MAAM,CAAC,MAAM,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAA;QACzC,IAAI,CAAC,MAAM,CAAC,GAAG,GAAG,KAAK,GAAG,IAAI,CAAE,EAAE,CAAA;QAClC,IAAI,CAAC,MAAM,CAAC,GAAG,CAAE,EAAE,CAAA;QACnB,IAAI,CAAC,UAAU,CAAC,IAAI,CAAE,EAAE,CAAA;IAC1B,CAAC;IAED,KAAK,CAAC,GAAW;QACf,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,CAAA;IAC9B,CAAC;IAED,KAAK,CAAC,GAAW,EAAE,MAAc;QAC/B,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,GAAG,KAAK,GAAG,MAAM,CAAC,MAAM,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;IACrE,CAAC;IAED,QAAQ,CAAC,GAAW;QAClB,MAAM,IAAI,GAAG,GAAG,GAAG,KAAK,CAAA;QACxB,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,GAAG,IAAI,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,GAAG,GAAG,CAAC,IAAI,CAAC,CAAC,CAAA;IACzE,CAAC;IAED;;;OAGG;IACH,cAAc,CAAC,GAAW,EAAE,EAAyC;QACnE,MAAM,EAAE,MAAM,EAAE,GAAG,IAAI,CAAA;QACvB,MAAM,IAAI,GAAG,GAAG,GAAG,KAAK,CAAA;QACxB,KAAK,IAAI,IAAI,GAAG,CAAC,EAAE,IAAI,GAAG,KAAK,EAAE,IAAI,EAAE,EAAE,CAAC;YACxC,MAAM,KAAK,GAAG,MAAM,CAAC,IAAI,GAAG,IAAI,CAAE,CAAA;YAClC,IAAI,KAAK,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,EAAE,CAAC;gBAClC,EAAE,CAAC,IAAI,EAAE,KAAK,CAAC,CAAA;YACjB,CAAC;QACH,CAAC;IACH,CAAC;IAED;;;;;OAKG;IACH,OAAO,CAAC,GAAW;QACjB,MAAM,WAAW,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAA;QACxD,IAAI,WAAW,KAAK,CAAC,EAAE,CAAC;YACtB,OAAO,CAAC,CAAA;QACV,CAAC;QACD,IAAI,OAAO,GAAG,CAAC,CAAA;QACf,IAAI,CAAC,cAAc,CAAC,GAAG,EAAE,CAAC,KAAK,EAAE,KAAK,EAAE,EAAE;YACxC,MAAM,IAAI,GAAG,KAAK,GAAG,WAAW,CAAA;YAChC,OAAO,IAAI,IAAI,GAAG,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QACnC,CAAC,CAAC,CAAA;QACF,OAAO,OAAO,CAAA;IAChB,CAAC;IAED,gEAAgE;IAChE,cAAc,CAAC,GAAW;QACxB,MAAM,OAAO,GAAuB,EAAE,CAAA;QACtC,IAAI,CAAC,cAAc,CAAC,GAAG,EAAE,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE;YACvC,OAAO,CAAC,IAAI,CAAC,CAAC,YAAY,CAAC,IAAI,CAAE,EAAE,KAAK,CAAC,CAAC,CAAA;QAC5C,CAAC,CAAC,CAAA;QACF,OAAO,OAAO,CAAA;IAChB,CAAC;IAED,uEAAuE;IACvE,IAAI,cAAc;QAChB,MAAM,OAAO,GAAG,IAAI,GAAG,EAAU,CAAA;QACjC,KAAK,IAAI,IAAI,GAAG,CAAC,EAAE,IAAI,GAAG,KAAK,EAAE,IAAI,EAAE,EAAE,CAAC;YACxC,IAAI,IAAI,CAAC,UAAU,CAAC,IAAI,CAAE,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,EAAE,CAAC;gBACnD,OAAO,CAAC,GAAG,CAAC,YAAY,CAAC,IAAI,CAAE,CAAC,CAAA;YAClC,CAAC;QACH,CAAC;QACD,OAAO,OAAO,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@@ -1,6 +1,7 @@
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1
1
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import React from 'react';
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2
2
|
import type { MsaViewModel } from '../model.ts';
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3
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-
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3
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+
import type { ToolbarSlots } from './header/Header.tsx';
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+
declare const Loading: ({ model, ...slots }: {
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model: MsaViewModel;
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-
}) => React.JSX.Element;
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+
} & ToolbarSlots) => React.JSX.Element;
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export default Loading;
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@@ -9,19 +9,19 @@ import ImportForm from './import/ImportForm.js';
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9
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const Reset = observer(function ({ model, error, }) {
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return (React.createElement("div", null,
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React.createElement(ErrorMessage, { error: error }),
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React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
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model.importForm ? (React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
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model.reset();
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} }, "Return to import form")));
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} }, "Return to import form")) : null));
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});
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const Loading = observer(function ({ model }) {
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const { isLoading, dataInitialized, data, error, resetCount, msaFilehandle, treeFilehandle, } = model;
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const Loading = observer(function ({ model, ...slots }) {
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const { isLoading, dataInitialized, data, error, resetCount, msaFilehandle, treeFilehandle, importForm, } = model;
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const hasData = !!(data.msa || data.tree);
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// a failed load keeps its filehandle, so the error outranks the spinner
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const loading = !error && !!(msaFilehandle || treeFilehandle || isLoading);
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-
return (React.createElement("div", null, React.createElement(ErrorBoundary, { key: resetCount, FallbackComponent: e => React.createElement(Reset, { model: model, error: e.error }) }, dataInitialized ? (isLoading ? (React.createElement(StatusMessage, { model: model, variant: "page" })) : (React.createElement(MSAView, { model: model }))) : hasData ? (React.createElement(Reset, { model: model, error: error })) : (React.createElement(React.Fragment, null,
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+
return (React.createElement("div", null, React.createElement(ErrorBoundary, { key: resetCount, FallbackComponent: e => React.createElement(Reset, { model: model, error: e.error }) }, dataInitialized ? (isLoading ? (React.createElement(StatusMessage, { model: model, variant: "page" })) : (React.createElement(MSAView, { model: model, ...slots }))) : hasData ? (React.createElement(Reset, { model: model, error: error })) : (React.createElement(React.Fragment, null,
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loading ? React.createElement(StatusMessage, { model: model, variant: "page" }) : null,
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React.createElement("div", { style: { display: loading ? 'none' : undefined } },
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24
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-
React.createElement(ImportForm, { model: model })))))));
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+
importForm ? (React.createElement("div", { style: { display: loading ? 'none' : undefined } },
|
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+
React.createElement(ImportForm, { model: model }))) : error ? (React.createElement(ErrorMessage, { error: error })) : null)))));
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});
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export default Loading;
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//# sourceMappingURL=Loading.js.map
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@@ -1 +1 @@
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1
|
-
{"version":3,"file":"Loading.js","sourceRoot":"","sources":["../../src/components/Loading.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC/C,OAAO,EAAE,aAAa,EAAE,MAAM,gCAAgC,CAAA;AAC9D,OAAO,EAAE,MAAM,EAAE,MAAM,eAAe,CAAA;AACtC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,OAAO,MAAM,cAAe,CAAA;AACnC,OAAO,aAAa,MAAM,oBAAqB,CAAA;AAC/C,OAAO,UAAU,MAAM,wBAAyB,CAAA;
|
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1
|
+
{"version":3,"file":"Loading.js","sourceRoot":"","sources":["../../src/components/Loading.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC/C,OAAO,EAAE,aAAa,EAAE,MAAM,gCAAgC,CAAA;AAC9D,OAAO,EAAE,MAAM,EAAE,MAAM,eAAe,CAAA;AACtC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,OAAO,MAAM,cAAe,CAAA;AACnC,OAAO,aAAa,MAAM,oBAAqB,CAAA;AAC/C,OAAO,UAAU,MAAM,wBAAyB,CAAA;AAKhD,MAAM,KAAK,GAAG,QAAQ,CAAC,UAAU,EAC/B,KAAK,EACL,KAAK,GAIN;IACC,OAAO,CACL;QACE,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI;QAC7B,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,CAClB,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,KAAK,EAAE,CAAA;YACf,CAAC,4BAGM,CACV,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,OAAO,GAAG,QAAQ,CAAC,UAAU,EACjC,KAAK,EACL,GAAG,KAAK,EAC+B;IACvC,MAAM,EACJ,SAAS,EACT,eAAe,EACf,IAAI,EACJ,KAAK,EACL,UAAU,EACV,aAAa,EACb,cAAc,EACd,UAAU,GACX,GAAG,KAAK,CAAA;IACT,MAAM,OAAO,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,IAAI,IAAI,CAAC,IAAI,CAAC,CAAA;IACzC,wEAAwE;IACxE,MAAM,OAAO,GAAG,CAAC,KAAK,IAAI,CAAC,CAAC,CAAC,aAAa,IAAI,cAAc,IAAI,SAAS,CAAC,CAAA;IAE1E,OAAO,CACL,iCAIE,oBAAC,aAAa,IACZ,GAAG,EAAE,UAAU,EACf,iBAAiB,EAAE,CAAC,CAAC,EAAE,CAAC,oBAAC,KAAK,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,GAAI,IAE9D,eAAe,CAAC,CAAC,CAAC,CACjB,SAAS,CAAC,CAAC,CAAC,CACV,oBAAC,aAAa,IAAC,KAAK,EAAE,KAAK,EAAE,OAAO,EAAC,MAAM,GAAG,CAC/C,CAAC,CAAC,CAAC,CACF,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,KAAM,KAAK,GAAI,CACrC,CACF,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CACZ,oBAAC,KAAK,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,GAAI,CACtC,CAAC,CAAC,CAAC,CACF;QACG,OAAO,CAAC,CAAC,CAAC,oBAAC,aAAa,IAAC,KAAK,EAAE,KAAK,EAAE,OAAO,EAAC,MAAM,GAAG,CAAC,CAAC,CAAC,IAAI;QAC/D,UAAU,CAAC,CAAC,CAAC,CACZ,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,EAAE;YACnD,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,GAAI,CACxB,CACP,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CACV,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAC/B,CAAC,CAAC,CAAC,IAAI,CACP,CACJ,CACa,CACZ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,OAAO,CAAA"}
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@@ -1,6 +1,7 @@
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1
1
|
import React from 'react';
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2
2
|
import type { MsaViewModel } from '../model.ts';
|
|
3
|
-
|
|
3
|
+
import type { ToolbarSlots } from './header/Header.tsx';
|
|
4
|
+
declare const MSAView: ({ model, ...slots }: {
|
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4
5
|
model: MsaViewModel;
|
|
5
|
-
}) => React.JSX.Element;
|
|
6
|
+
} & ToolbarSlots) => React.JSX.Element;
|
|
6
7
|
export default MSAView;
|
|
@@ -9,6 +9,7 @@ import MSAPanel from './msa/MSAPanel.js';
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9
9
|
import { clickColor, hoverColor, selectionFill } from './overlayColors.js';
|
|
10
10
|
import RowPanelHeaders from './rowpanels/RowPanelHeaders.js';
|
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11
11
|
import RowPanels from './rowpanels/RowPanels.js';
|
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12
|
+
import SettingsPanel from './settings/SettingsPanel.js';
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12
13
|
import TreeOverview from './tree/TreeOverview.js';
|
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13
14
|
import TreePanel from './tree/TreePanel.js';
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14
15
|
import TreeRuler from './tree/TreeRuler.js';
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@@ -80,12 +81,14 @@ const View = observer(function ({ model }) {
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80
81
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React.createElement(TrackArea, { model: model }),
|
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81
82
|
React.createElement(MainArea, { model: model })));
|
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82
83
|
});
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83
|
-
const MSAView = observer(function ({ model }) {
|
|
84
|
-
const { height, hideHeader, viewInitialized, DialogComponent, DialogProps } = model;
|
|
84
|
+
const MSAView = observer(function ({ model, ...slots }) {
|
|
85
|
+
const { height, headerHeight, hideHeader, settingsOpen, viewInitialized, DialogComponent, DialogProps, } = model;
|
|
85
86
|
return (React.createElement("div", null, viewInitialized ? (React.createElement(React.Fragment, null,
|
|
86
87
|
React.createElement("div", { style: { height, overflow: 'clip' } },
|
|
87
|
-
hideHeader ? null : React.createElement(Header, { model: model }),
|
|
88
|
-
React.createElement(
|
|
88
|
+
hideHeader ? null : React.createElement(Header, { model: model, ...slots }),
|
|
89
|
+
React.createElement("div", { style: { display: 'flex' } },
|
|
90
|
+
React.createElement(View, { model: model }),
|
|
91
|
+
settingsOpen ? (React.createElement(SettingsPanel, { model: model, height: height - headerHeight })) : null)),
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React.createElement(HorizontalResizeHandle, { model: model }),
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DialogComponent ? (React.createElement(Suspense, { fallback: null },
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React.createElement(DialogComponent, { ...DialogProps }))) : null)) : null));
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1
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+
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