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/src/model/treeModel.ts
CHANGED
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defaultShowBranchLen,
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defaultTreeOrder,
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defaultShowTreeOverview,
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defaultShowTreeScaleBar,
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treeOrders,
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} from '../constants.ts'
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import { stripDefault } from '../stripDefault.ts'
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@@ -93,6 +94,12 @@ export function TreeModelF() {
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*/
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showTreeOverview: stripDefault(types.boolean, defaultShowTreeOverview),
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/**
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* #property
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* draw the branch-length scale bar above the tree of a phylogram
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*/
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showTreeScaleBar: stripDefault(types.boolean, defaultShowTreeScaleBar),
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/**
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* #property
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* height of the tree overview band, px
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},
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/**
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* #action
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* set the height of the tree overview band (px)
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*/
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self.
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setShowTreeScaleBar(arg: boolean) {
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self.showTreeScaleBar = arg
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},
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/**
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* #action
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