@jbrowse/plugin-linear-genome-view 2.4.2 → 2.6.1
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/dist/BaseLinearDisplay/components/BaseLinearDisplay.d.ts +1 -1
- package/dist/BaseLinearDisplay/components/Block.d.ts +3 -3
- package/dist/BaseLinearDisplay/components/BlockMsg.d.ts +1 -1
- package/dist/BaseLinearDisplay/components/LinearBlocks.d.ts +3 -3
- package/dist/BaseLinearDisplay/components/TooLargeMessage.d.ts +5 -5
- package/dist/BaseLinearDisplay/components/TooLargeMessage.js +7 -3
- package/dist/BaseLinearDisplay/components/TooLargeMessage.js.map +1 -1
- package/dist/BaseLinearDisplay/components/Tooltip.d.ts +2 -2
- package/dist/BaseLinearDisplay/index.d.ts +5 -2
- package/dist/BaseLinearDisplay/index.js +7 -1
- package/dist/BaseLinearDisplay/index.js.map +1 -1
- package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts +107 -126
- package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.js +37 -352
- package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.js.map +1 -1
- package/dist/BaseLinearDisplay/models/FeatureDensityMixin.d.ts +99 -0
- package/dist/BaseLinearDisplay/models/FeatureDensityMixin.js +190 -0
- package/dist/BaseLinearDisplay/models/FeatureDensityMixin.js.map +1 -0
- package/dist/BaseLinearDisplay/models/TrackHeightMixin.d.ts +30 -0
- package/dist/BaseLinearDisplay/models/TrackHeightMixin.js +56 -0
- package/dist/BaseLinearDisplay/models/TrackHeightMixin.js.map +1 -0
- package/dist/BaseLinearDisplay/models/autorunFeatureDensityStats.d.ts +2 -0
- package/dist/BaseLinearDisplay/models/autorunFeatureDensityStats.js +42 -0
- package/dist/BaseLinearDisplay/models/autorunFeatureDensityStats.js.map +1 -0
- package/dist/BaseLinearDisplay/models/configSchema.d.ts +35 -1
- package/dist/BaseLinearDisplay/models/configSchema.js +10 -0
- package/dist/BaseLinearDisplay/models/configSchema.js.map +1 -1
- package/dist/BaseLinearDisplay/models/renderSvg.d.ts +8 -0
- package/dist/BaseLinearDisplay/models/renderSvg.js +83 -0
- package/dist/BaseLinearDisplay/models/renderSvg.js.map +1 -0
- package/dist/BaseLinearDisplay/models/serverSideRenderedBlock.js +30 -22
- package/dist/BaseLinearDisplay/models/serverSideRenderedBlock.js.map +1 -1
- package/dist/BaseLinearDisplay/models/util.d.ts +6 -2
- package/dist/BaseLinearDisplay/models/util.js +4 -4
- package/dist/BaseLinearDisplay/models/util.js.map +1 -1
- package/dist/BasicTrack/configSchema.d.ts +73 -1
- package/dist/BasicTrack/configSchema.js +1 -0
- package/dist/BasicTrack/configSchema.js.map +1 -1
- package/dist/FeatureTrack/configSchema.d.ts +73 -1
- package/dist/FeatureTrack/configSchema.js +1 -0
- package/dist/FeatureTrack/configSchema.js.map +1 -1
- package/dist/LinearBareDisplay/configSchema.d.ts +29 -1
- package/dist/LinearBareDisplay/configSchema.js +1 -0
- package/dist/LinearBareDisplay/configSchema.js.map +1 -1
- package/dist/LinearBareDisplay/model.d.ts +106 -42
- package/dist/LinearBareDisplay/model.js +3 -2
- package/dist/LinearBareDisplay/model.js.map +1 -1
- package/dist/LinearBasicDisplay/components/SetMaxHeight.d.ts +2 -2
- package/dist/LinearBasicDisplay/configSchema.d.ts +29 -1
- package/dist/LinearBasicDisplay/configSchema.js +1 -9
- package/dist/LinearBasicDisplay/configSchema.js.map +1 -1
- package/dist/LinearBasicDisplay/model.d.ts +124 -62
- package/dist/LinearBasicDisplay/model.js +1 -0
- package/dist/LinearBasicDisplay/model.js.map +1 -1
- package/dist/LinearGenomeView/components/CenterLine.d.ts +2 -2
- package/dist/LinearGenomeView/components/Cytobands.d.ts +24 -24
- package/dist/LinearGenomeView/components/ExportSvgDialog.d.ts +2 -2
- package/dist/LinearGenomeView/components/GetSequenceDialog.d.ts +2 -2
- package/dist/LinearGenomeView/components/GetSequenceDialog.js +14 -16
- package/dist/LinearGenomeView/components/GetSequenceDialog.js.map +1 -1
- package/dist/LinearGenomeView/components/Gridlines.d.ts +2 -2
- package/dist/LinearGenomeView/components/Header.d.ts +2 -2
- package/dist/LinearGenomeView/components/ImportForm.d.ts +2 -2
- package/dist/LinearGenomeView/components/ImportForm.js +4 -7
- package/dist/LinearGenomeView/components/ImportForm.js.map +1 -1
- package/dist/LinearGenomeView/components/LinearGenomeView.d.ts +2 -2
- package/dist/LinearGenomeView/components/LinearGenomeView.js +28 -8
- package/dist/LinearGenomeView/components/LinearGenomeView.js.map +1 -1
- package/dist/LinearGenomeView/components/MiniControls.d.ts +3 -3
- package/dist/LinearGenomeView/components/MiniControls.js +20 -40
- package/dist/LinearGenomeView/components/MiniControls.js.map +1 -1
- package/dist/LinearGenomeView/components/OverviewRubberband.d.ts +1 -1
- package/dist/LinearGenomeView/components/OverviewScalebar.d.ts +2 -2
- package/dist/LinearGenomeView/components/OverviewScalebar.js +12 -5
- package/dist/LinearGenomeView/components/OverviewScalebar.js.map +1 -1
- package/dist/LinearGenomeView/components/RefNameAutocomplete/AutocompleteTextField.d.ts +10 -0
- package/dist/LinearGenomeView/components/RefNameAutocomplete/AutocompleteTextField.js +22 -0
- package/dist/LinearGenomeView/components/RefNameAutocomplete/AutocompleteTextField.js.map +1 -0
- package/dist/LinearGenomeView/components/RefNameAutocomplete/EndAdornment.d.ts +5 -0
- package/dist/LinearGenomeView/components/RefNameAutocomplete/EndAdornment.js +52 -0
- package/dist/LinearGenomeView/components/RefNameAutocomplete/EndAdornment.js.map +1 -0
- package/dist/LinearGenomeView/components/{HelpDialog.d.ts → RefNameAutocomplete/HelpDialog.d.ts} +2 -2
- package/dist/LinearGenomeView/components/RefNameAutocomplete/HelpDialog.js.map +1 -0
- package/dist/LinearGenomeView/components/RefNameAutocomplete/index.d.ts +18 -0
- package/dist/LinearGenomeView/components/RefNameAutocomplete/index.js +111 -0
- package/dist/LinearGenomeView/components/RefNameAutocomplete/index.js.map +1 -0
- package/dist/LinearGenomeView/components/RefNameAutocomplete/util.d.ts +12 -0
- package/dist/LinearGenomeView/components/RefNameAutocomplete/util.js +59 -0
- package/dist/LinearGenomeView/components/RefNameAutocomplete/util.js.map +1 -0
- package/dist/LinearGenomeView/components/Rubberband.d.ts +1 -1
- package/dist/LinearGenomeView/components/RubberbandSpan.d.ts +2 -2
- package/dist/LinearGenomeView/components/SearchBox.d.ts +2 -2
- package/dist/LinearGenomeView/components/SearchResultsDialog.d.ts +7 -4
- package/dist/LinearGenomeView/components/SearchResultsDialog.js +6 -82
- package/dist/LinearGenomeView/components/SearchResultsDialog.js.map +1 -1
- package/dist/LinearGenomeView/components/SearchResultsTable.d.ts +9 -0
- package/dist/LinearGenomeView/components/SearchResultsTable.js +83 -0
- package/dist/LinearGenomeView/components/SearchResultsTable.js.map +1 -0
- package/dist/LinearGenomeView/components/SequenceSearchDialog.d.ts +2 -2
- package/dist/LinearGenomeView/components/TrackContainer.d.ts +3 -4
- package/dist/LinearGenomeView/components/TrackContainer.js +17 -67
- package/dist/LinearGenomeView/components/TrackContainer.js.map +1 -1
- package/dist/LinearGenomeView/components/TrackLabel.js +6 -10
- package/dist/LinearGenomeView/components/TrackLabel.js.map +1 -1
- package/dist/LinearGenomeView/components/TrackLabelContainer.d.ts +9 -0
- package/dist/LinearGenomeView/components/TrackLabelContainer.js +32 -0
- package/dist/LinearGenomeView/components/TrackLabelContainer.js.map +1 -0
- package/dist/LinearGenomeView/components/TrackRenderingContainer.d.ts +10 -0
- package/dist/LinearGenomeView/components/TrackRenderingContainer.js +74 -0
- package/dist/LinearGenomeView/components/TrackRenderingContainer.js.map +1 -0
- package/dist/LinearGenomeView/components/TracksContainer.d.ts +1 -1
- package/dist/LinearGenomeView/components/TracksContainer.js +5 -7
- package/dist/LinearGenomeView/components/TracksContainer.js.map +1 -1
- package/dist/LinearGenomeView/components/VerticalGuide.d.ts +2 -2
- package/dist/LinearGenomeView/components/ZoomControls.d.ts +2 -2
- package/dist/LinearGenomeView/components/util.js +1 -1
- package/dist/LinearGenomeView/components/util.js.map +1 -1
- package/dist/LinearGenomeView/model.d.ts +51 -37
- package/dist/LinearGenomeView/model.js +132 -209
- package/dist/LinearGenomeView/model.js.map +1 -1
- package/dist/LinearGenomeView/svgcomponents/SVGBackground.d.ts +2 -2
- package/dist/LinearGenomeView/svgcomponents/SVGHeader.d.ts +3 -5
- package/dist/LinearGenomeView/svgcomponents/SVGHeader.js +7 -2
- package/dist/LinearGenomeView/svgcomponents/SVGHeader.js.map +1 -1
- package/dist/LinearGenomeView/svgcomponents/SVGLinearGenomeView.js +1 -1
- package/dist/LinearGenomeView/svgcomponents/SVGLinearGenomeView.js.map +1 -1
- package/dist/LinearGenomeView/svgcomponents/SVGRegionSeparators.d.ts +2 -2
- package/dist/LinearGenomeView/svgcomponents/SVGRuler.d.ts +2 -2
- package/dist/LinearGenomeView/svgcomponents/SVGScalebar.d.ts +2 -2
- package/dist/LinearGenomeView/svgcomponents/SVGTrackLabel.d.ts +2 -2
- package/dist/LinearGenomeView/svgcomponents/SVGTracks.d.ts +2 -2
- package/dist/LinearGenomeView/util.d.ts +29 -0
- package/dist/LinearGenomeView/util.js +79 -1
- package/dist/LinearGenomeView/util.js.map +1 -1
- package/dist/index.d.ts +325 -180
- package/dist/index.js +6 -3
- package/dist/index.js.map +1 -1
- package/esm/BaseLinearDisplay/components/BaseLinearDisplay.d.ts +1 -1
- package/esm/BaseLinearDisplay/components/Block.d.ts +3 -3
- package/esm/BaseLinearDisplay/components/BlockMsg.d.ts +1 -1
- package/esm/BaseLinearDisplay/components/LinearBlocks.d.ts +3 -3
- package/esm/BaseLinearDisplay/components/TooLargeMessage.d.ts +5 -5
- package/esm/BaseLinearDisplay/components/TooLargeMessage.js +7 -3
- package/esm/BaseLinearDisplay/components/TooLargeMessage.js.map +1 -1
- package/esm/BaseLinearDisplay/components/Tooltip.d.ts +2 -2
- package/esm/BaseLinearDisplay/index.d.ts +5 -2
- package/esm/BaseLinearDisplay/index.js +3 -0
- package/esm/BaseLinearDisplay/index.js.map +1 -1
- package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts +107 -126
- package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.js +39 -331
- package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.js.map +1 -1
- package/esm/BaseLinearDisplay/models/FeatureDensityMixin.d.ts +99 -0
- package/esm/BaseLinearDisplay/models/FeatureDensityMixin.js +184 -0
- package/esm/BaseLinearDisplay/models/FeatureDensityMixin.js.map +1 -0
- package/esm/BaseLinearDisplay/models/TrackHeightMixin.d.ts +30 -0
- package/esm/BaseLinearDisplay/models/TrackHeightMixin.js +53 -0
- package/esm/BaseLinearDisplay/models/TrackHeightMixin.js.map +1 -0
- package/esm/BaseLinearDisplay/models/autorunFeatureDensityStats.d.ts +2 -0
- package/esm/BaseLinearDisplay/models/autorunFeatureDensityStats.js +39 -0
- package/esm/BaseLinearDisplay/models/autorunFeatureDensityStats.js.map +1 -0
- package/esm/BaseLinearDisplay/models/configSchema.d.ts +35 -1
- package/esm/BaseLinearDisplay/models/configSchema.js +10 -0
- package/esm/BaseLinearDisplay/models/configSchema.js.map +1 -1
- package/esm/BaseLinearDisplay/models/renderSvg.d.ts +8 -0
- package/esm/BaseLinearDisplay/models/renderSvg.js +54 -0
- package/esm/BaseLinearDisplay/models/renderSvg.js.map +1 -0
- package/esm/BaseLinearDisplay/models/serverSideRenderedBlock.js +30 -22
- package/esm/BaseLinearDisplay/models/serverSideRenderedBlock.js.map +1 -1
- package/esm/BaseLinearDisplay/models/util.d.ts +6 -2
- package/esm/BaseLinearDisplay/models/util.js +2 -2
- package/esm/BaseLinearDisplay/models/util.js.map +1 -1
- package/esm/BasicTrack/configSchema.d.ts +73 -1
- package/esm/BasicTrack/configSchema.js +1 -0
- package/esm/BasicTrack/configSchema.js.map +1 -1
- package/esm/FeatureTrack/configSchema.d.ts +73 -1
- package/esm/FeatureTrack/configSchema.js +1 -0
- package/esm/FeatureTrack/configSchema.js.map +1 -1
- package/esm/LinearBareDisplay/configSchema.d.ts +29 -1
- package/esm/LinearBareDisplay/configSchema.js +1 -0
- package/esm/LinearBareDisplay/configSchema.js.map +1 -1
- package/esm/LinearBareDisplay/model.d.ts +106 -42
- package/esm/LinearBareDisplay/model.js +2 -1
- package/esm/LinearBareDisplay/model.js.map +1 -1
- package/esm/LinearBasicDisplay/components/SetMaxHeight.d.ts +2 -2
- package/esm/LinearBasicDisplay/configSchema.d.ts +29 -1
- package/esm/LinearBasicDisplay/configSchema.js +1 -9
- package/esm/LinearBasicDisplay/configSchema.js.map +1 -1
- package/esm/LinearBasicDisplay/model.d.ts +124 -62
- package/esm/LinearBasicDisplay/model.js +1 -0
- package/esm/LinearBasicDisplay/model.js.map +1 -1
- package/esm/LinearGenomeView/components/CenterLine.d.ts +2 -2
- package/esm/LinearGenomeView/components/Cytobands.d.ts +24 -24
- package/esm/LinearGenomeView/components/ExportSvgDialog.d.ts +2 -2
- package/esm/LinearGenomeView/components/GetSequenceDialog.d.ts +2 -2
- package/esm/LinearGenomeView/components/GetSequenceDialog.js +15 -17
- package/esm/LinearGenomeView/components/GetSequenceDialog.js.map +1 -1
- package/esm/LinearGenomeView/components/Gridlines.d.ts +2 -2
- package/esm/LinearGenomeView/components/Header.d.ts +2 -2
- package/esm/LinearGenomeView/components/ImportForm.d.ts +2 -2
- package/esm/LinearGenomeView/components/ImportForm.js +5 -8
- package/esm/LinearGenomeView/components/ImportForm.js.map +1 -1
- package/esm/LinearGenomeView/components/LinearGenomeView.d.ts +2 -2
- package/esm/LinearGenomeView/components/LinearGenomeView.js +4 -7
- package/esm/LinearGenomeView/components/LinearGenomeView.js.map +1 -1
- package/esm/LinearGenomeView/components/MiniControls.d.ts +3 -3
- package/esm/LinearGenomeView/components/MiniControls.js +20 -17
- package/esm/LinearGenomeView/components/MiniControls.js.map +1 -1
- package/esm/LinearGenomeView/components/OverviewRubberband.d.ts +1 -1
- package/esm/LinearGenomeView/components/OverviewScalebar.d.ts +2 -2
- package/esm/LinearGenomeView/components/OverviewScalebar.js +12 -5
- package/esm/LinearGenomeView/components/OverviewScalebar.js.map +1 -1
- package/esm/LinearGenomeView/components/RefNameAutocomplete/AutocompleteTextField.d.ts +10 -0
- package/esm/LinearGenomeView/components/RefNameAutocomplete/AutocompleteTextField.js +16 -0
- package/esm/LinearGenomeView/components/RefNameAutocomplete/AutocompleteTextField.js.map +1 -0
- package/esm/LinearGenomeView/components/RefNameAutocomplete/EndAdornment.d.ts +5 -0
- package/esm/LinearGenomeView/components/RefNameAutocomplete/EndAdornment.js +23 -0
- package/esm/LinearGenomeView/components/RefNameAutocomplete/EndAdornment.js.map +1 -0
- package/esm/LinearGenomeView/components/{HelpDialog.d.ts → RefNameAutocomplete/HelpDialog.d.ts} +2 -2
- package/esm/LinearGenomeView/components/RefNameAutocomplete/HelpDialog.js.map +1 -0
- package/esm/LinearGenomeView/components/RefNameAutocomplete/index.d.ts +18 -0
- package/esm/LinearGenomeView/components/RefNameAutocomplete/index.js +83 -0
- package/esm/LinearGenomeView/components/RefNameAutocomplete/index.js.map +1 -0
- package/esm/LinearGenomeView/components/RefNameAutocomplete/util.d.ts +12 -0
- package/esm/LinearGenomeView/components/RefNameAutocomplete/util.js +50 -0
- package/esm/LinearGenomeView/components/RefNameAutocomplete/util.js.map +1 -0
- package/esm/LinearGenomeView/components/Rubberband.d.ts +1 -1
- package/esm/LinearGenomeView/components/RubberbandSpan.d.ts +2 -2
- package/esm/LinearGenomeView/components/SearchBox.d.ts +2 -2
- package/esm/LinearGenomeView/components/SearchResultsDialog.d.ts +7 -4
- package/esm/LinearGenomeView/components/SearchResultsDialog.js +7 -83
- package/esm/LinearGenomeView/components/SearchResultsDialog.js.map +1 -1
- package/esm/LinearGenomeView/components/SearchResultsTable.d.ts +9 -0
- package/esm/LinearGenomeView/components/SearchResultsTable.js +77 -0
- package/esm/LinearGenomeView/components/SearchResultsTable.js.map +1 -0
- package/esm/LinearGenomeView/components/SequenceSearchDialog.d.ts +2 -2
- package/esm/LinearGenomeView/components/TrackContainer.d.ts +3 -4
- package/esm/LinearGenomeView/components/TrackContainer.js +18 -68
- package/esm/LinearGenomeView/components/TrackContainer.js.map +1 -1
- package/esm/LinearGenomeView/components/TrackLabel.js +6 -10
- package/esm/LinearGenomeView/components/TrackLabel.js.map +1 -1
- package/esm/LinearGenomeView/components/TrackLabelContainer.d.ts +9 -0
- package/esm/LinearGenomeView/components/TrackLabelContainer.js +27 -0
- package/esm/LinearGenomeView/components/TrackLabelContainer.js.map +1 -0
- package/esm/LinearGenomeView/components/TrackRenderingContainer.d.ts +10 -0
- package/esm/LinearGenomeView/components/TrackRenderingContainer.js +49 -0
- package/esm/LinearGenomeView/components/TrackRenderingContainer.js.map +1 -0
- package/esm/LinearGenomeView/components/TracksContainer.d.ts +1 -1
- package/esm/LinearGenomeView/components/TracksContainer.js +5 -7
- package/esm/LinearGenomeView/components/TracksContainer.js.map +1 -1
- package/esm/LinearGenomeView/components/VerticalGuide.d.ts +2 -2
- package/esm/LinearGenomeView/components/ZoomControls.d.ts +2 -2
- package/esm/LinearGenomeView/components/util.js +1 -1
- package/esm/LinearGenomeView/components/util.js.map +1 -1
- package/esm/LinearGenomeView/model.d.ts +51 -37
- package/esm/LinearGenomeView/model.js +129 -206
- package/esm/LinearGenomeView/model.js.map +1 -1
- package/esm/LinearGenomeView/svgcomponents/SVGBackground.d.ts +2 -2
- package/esm/LinearGenomeView/svgcomponents/SVGHeader.d.ts +3 -5
- package/esm/LinearGenomeView/svgcomponents/SVGHeader.js +7 -2
- package/esm/LinearGenomeView/svgcomponents/SVGHeader.js.map +1 -1
- package/esm/LinearGenomeView/svgcomponents/SVGLinearGenomeView.js +1 -1
- package/esm/LinearGenomeView/svgcomponents/SVGLinearGenomeView.js.map +1 -1
- package/esm/LinearGenomeView/svgcomponents/SVGRegionSeparators.d.ts +2 -2
- package/esm/LinearGenomeView/svgcomponents/SVGRuler.d.ts +2 -2
- package/esm/LinearGenomeView/svgcomponents/SVGScalebar.d.ts +2 -2
- package/esm/LinearGenomeView/svgcomponents/SVGTrackLabel.d.ts +2 -2
- package/esm/LinearGenomeView/svgcomponents/SVGTracks.d.ts +2 -2
- package/esm/LinearGenomeView/util.d.ts +29 -0
- package/esm/LinearGenomeView/util.js +76 -0
- package/esm/LinearGenomeView/util.js.map +1 -1
- package/esm/index.d.ts +325 -180
- package/esm/index.js +1 -1
- package/esm/index.js.map +1 -1
- package/package.json +3 -3
- package/src/BaseLinearDisplay/components/TooLargeMessage.tsx +10 -6
- package/src/BaseLinearDisplay/index.ts +5 -1
- package/src/BaseLinearDisplay/models/BaseLinearDisplayModel.tsx +50 -401
- package/src/BaseLinearDisplay/models/FeatureDensityMixin.tsx +213 -0
- package/src/BaseLinearDisplay/models/TrackHeightMixin.tsx +59 -0
- package/src/BaseLinearDisplay/models/autorunFeatureDensityStats.ts +46 -0
- package/src/BaseLinearDisplay/models/configSchema.ts +11 -0
- package/src/BaseLinearDisplay/models/renderSvg.tsx +101 -0
- package/src/BaseLinearDisplay/models/serverSideRenderedBlock.ts +40 -32
- package/src/BaseLinearDisplay/models/util.ts +10 -4
- package/src/BasicTrack/configSchema.ts +1 -0
- package/src/FeatureTrack/configSchema.ts +1 -0
- package/src/LinearBareDisplay/configSchema.ts +1 -0
- package/src/LinearBareDisplay/model.ts +2 -1
- package/src/LinearBasicDisplay/configSchema.ts +1 -10
- package/src/LinearBasicDisplay/model.ts +1 -0
- package/src/LinearGenomeView/components/GetSequenceDialog.tsx +15 -25
- package/src/LinearGenomeView/components/ImportForm.tsx +4 -14
- package/src/LinearGenomeView/components/LinearGenomeView.test.tsx +3 -3
- package/src/LinearGenomeView/components/LinearGenomeView.tsx +6 -17
- package/src/LinearGenomeView/components/MiniControls.tsx +37 -38
- package/src/LinearGenomeView/components/OverviewScalebar.tsx +13 -6
- package/src/LinearGenomeView/components/RefNameAutocomplete/AutocompleteTextField.tsx +53 -0
- package/src/LinearGenomeView/components/RefNameAutocomplete/EndAdornment.tsx +44 -0
- package/src/LinearGenomeView/components/RefNameAutocomplete/index.tsx +160 -0
- package/src/LinearGenomeView/components/RefNameAutocomplete/util.ts +65 -0
- package/src/LinearGenomeView/components/SearchResultsDialog.tsx +17 -112
- package/src/LinearGenomeView/components/SearchResultsTable.tsx +121 -0
- package/src/LinearGenomeView/components/TrackContainer.tsx +25 -104
- package/src/LinearGenomeView/components/TrackLabel.tsx +7 -27
- package/src/LinearGenomeView/components/TrackLabelContainer.tsx +48 -0
- package/src/LinearGenomeView/components/TrackRenderingContainer.tsx +96 -0
- package/src/LinearGenomeView/components/TracksContainer.tsx +9 -6
- package/src/LinearGenomeView/components/__snapshots__/LinearGenomeView.test.tsx.snap +14 -14
- package/src/LinearGenomeView/components/util.ts +2 -1
- package/src/LinearGenomeView/index.test.ts +10 -12
- package/src/LinearGenomeView/model.ts +175 -247
- package/src/LinearGenomeView/svgcomponents/SVGHeader.tsx +8 -6
- package/src/LinearGenomeView/svgcomponents/SVGLinearGenomeView.tsx +1 -1
- package/src/LinearGenomeView/util.ts +98 -0
- package/src/index.ts +11 -5
- package/dist/LinearGenomeView/components/HelpDialog.js.map +0 -1
- package/dist/LinearGenomeView/components/RefNameAutocomplete.d.ts +0 -23
- package/dist/LinearGenomeView/components/RefNameAutocomplete.js +0 -182
- package/dist/LinearGenomeView/components/RefNameAutocomplete.js.map +0 -1
- package/esm/LinearGenomeView/components/HelpDialog.js.map +0 -1
- package/esm/LinearGenomeView/components/RefNameAutocomplete.d.ts +0 -23
- package/esm/LinearGenomeView/components/RefNameAutocomplete.js +0 -154
- package/esm/LinearGenomeView/components/RefNameAutocomplete.js.map +0 -1
- package/src/LinearGenomeView/components/RefNameAutocomplete.tsx +0 -279
- /package/dist/LinearGenomeView/components/{HelpDialog.js → RefNameAutocomplete/HelpDialog.js} +0 -0
- /package/esm/LinearGenomeView/components/{HelpDialog.js → RefNameAutocomplete/HelpDialog.js} +0 -0
- /package/src/LinearGenomeView/components/{HelpDialog.tsx → RefNameAutocomplete/HelpDialog.tsx} +0 -0
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* Given a scale ( bp/px ) and minimum distances (px) between major and minor
|
|
3
9
|
* gridlines, return an object like `{ majorPitch: bp, minorPitch: bp }` giving
|
|
@@ -82,3 +88,95 @@ export function makeTicks(
|
|
|
82
88
|
}
|
|
83
89
|
return ticks
|
|
84
90
|
}
|
|
91
|
+
|
|
92
|
+
/**
|
|
93
|
+
* Generate location objects for a set of parsed locstrings, which includes
|
|
94
|
+
* translating the refNames to assembly-canonical refNames and adding the
|
|
95
|
+
* 'parentRegion'
|
|
96
|
+
*
|
|
97
|
+
* Used by navToLocations and navToLocString
|
|
98
|
+
*/
|
|
99
|
+
export async function generateLocations(
|
|
100
|
+
regions: ParsedLocString[] = [],
|
|
101
|
+
assemblyManager: AssemblyManager,
|
|
102
|
+
assemblyName?: string,
|
|
103
|
+
) {
|
|
104
|
+
return Promise.all(
|
|
105
|
+
regions.map(async region => {
|
|
106
|
+
const asmName = region.assemblyName || assemblyName
|
|
107
|
+
if (!asmName) {
|
|
108
|
+
throw new Error('no assembly provided')
|
|
109
|
+
}
|
|
110
|
+
const asm = await assemblyManager.waitForAssembly(asmName)
|
|
111
|
+
const { refName } = region
|
|
112
|
+
if (!asm) {
|
|
113
|
+
throw new Error(`assembly ${asmName} not found`)
|
|
114
|
+
}
|
|
115
|
+
const { regions } = asm
|
|
116
|
+
if (!regions) {
|
|
117
|
+
throw new Error(`regions not loaded yet for ${asmName}`)
|
|
118
|
+
}
|
|
119
|
+
const canonicalRefName = asm.getCanonicalRefName(region.refName)
|
|
120
|
+
if (!canonicalRefName) {
|
|
121
|
+
throw new Error(`Could not find refName ${refName} in ${asm.name}`)
|
|
122
|
+
}
|
|
123
|
+
const parentRegion = regions.find(r => r.refName === canonicalRefName)
|
|
124
|
+
if (!parentRegion) {
|
|
125
|
+
throw new Error(`Could not find refName ${refName} in ${asmName}`)
|
|
126
|
+
}
|
|
127
|
+
|
|
128
|
+
return {
|
|
129
|
+
...(region as Omit<typeof region, symbol>),
|
|
130
|
+
assemblyName: asmName,
|
|
131
|
+
parentRegion,
|
|
132
|
+
}
|
|
133
|
+
}),
|
|
134
|
+
)
|
|
135
|
+
}
|
|
136
|
+
|
|
137
|
+
/**
|
|
138
|
+
* Parses locString or space separated set of locStrings into location objects
|
|
139
|
+
* Example inputs:
|
|
140
|
+
* "chr1"
|
|
141
|
+
* "chr1:1-100"
|
|
142
|
+
* "chr1:1..100"
|
|
143
|
+
* "chr1 chr2"
|
|
144
|
+
* "chr1:1-100 chr2:1-100"
|
|
145
|
+
* "chr1 100 200" equivalent to "chr1:1-100"
|
|
146
|
+
*
|
|
147
|
+
* Used by navToLocString
|
|
148
|
+
*/
|
|
149
|
+
export function parseLocStrings(
|
|
150
|
+
input: string,
|
|
151
|
+
assemblyName: string,
|
|
152
|
+
isValidRefName: (str: string, assemblyName: string) => boolean,
|
|
153
|
+
) {
|
|
154
|
+
const inputs = input
|
|
155
|
+
.split(/(\s+)/)
|
|
156
|
+
.map(f => f.trim())
|
|
157
|
+
.filter(f => !!f)
|
|
158
|
+
// first try interpreting as a whitespace-separated sequence of
|
|
159
|
+
// multiple locstrings
|
|
160
|
+
try {
|
|
161
|
+
return inputs.map(loc =>
|
|
162
|
+
parseLocString(loc, ref => isValidRefName(ref, assemblyName)),
|
|
163
|
+
)
|
|
164
|
+
} catch (e) {
|
|
165
|
+
// if this fails, try interpreting as a whitespace-separated refname,
|
|
166
|
+
// start, end if start and end are integer inputs
|
|
167
|
+
const [refName, start, end] = inputs
|
|
168
|
+
if (
|
|
169
|
+
`${e}`.match(/Unknown reference sequence/) &&
|
|
170
|
+
Number.isInteger(+start) &&
|
|
171
|
+
Number.isInteger(+end)
|
|
172
|
+
) {
|
|
173
|
+
return [
|
|
174
|
+
parseLocString(refName + ':' + start + '..' + end, ref =>
|
|
175
|
+
isValidRefName(ref, assemblyName),
|
|
176
|
+
),
|
|
177
|
+
]
|
|
178
|
+
} else {
|
|
179
|
+
throw e
|
|
180
|
+
}
|
|
181
|
+
}
|
|
182
|
+
}
|
package/src/index.ts
CHANGED
|
@@ -19,7 +19,6 @@ import LinearGenomeViewF, {
|
|
|
19
19
|
} from './LinearGenomeView'
|
|
20
20
|
|
|
21
21
|
import LinearBasicDisplayF from './LinearBasicDisplay'
|
|
22
|
-
|
|
23
22
|
import FeatureTrackF from './FeatureTrack'
|
|
24
23
|
import BasicTrackF from './BasicTrack'
|
|
25
24
|
import LaunchLinearGenomeViewF from './LaunchLinearGenomeView'
|
|
@@ -58,19 +57,26 @@ export default class LinearGenomeViewPlugin extends Plugin {
|
|
|
58
57
|
}
|
|
59
58
|
}
|
|
60
59
|
|
|
61
|
-
export type {
|
|
60
|
+
export type {
|
|
61
|
+
ExportSvgDisplayOptions,
|
|
62
|
+
BaseLinearDisplayModel,
|
|
63
|
+
BlockModel,
|
|
64
|
+
} from './BaseLinearDisplay'
|
|
62
65
|
|
|
63
66
|
export { configSchemaFactory as linearBareDisplayConfigSchemaFactory } from './LinearBareDisplay'
|
|
64
67
|
export {
|
|
65
|
-
BlockMsg,
|
|
66
68
|
baseLinearDisplayConfigSchema,
|
|
67
|
-
BaseLinearDisplayComponent,
|
|
68
69
|
BaseLinearDisplay,
|
|
70
|
+
BlockMsg,
|
|
71
|
+
BaseLinearDisplayComponent,
|
|
72
|
+
TrackHeightMixin,
|
|
73
|
+
FeatureDensityMixin,
|
|
74
|
+
TooLargeMessage,
|
|
69
75
|
} from './BaseLinearDisplay'
|
|
70
76
|
export {
|
|
71
77
|
type LinearGenomeViewModel,
|
|
72
|
-
RefNameAutocomplete,
|
|
73
78
|
type LinearGenomeViewStateModel,
|
|
79
|
+
RefNameAutocomplete,
|
|
74
80
|
SearchBox,
|
|
75
81
|
} from './LinearGenomeView'
|
|
76
82
|
export {
|
|
@@ -1 +0,0 @@
|
|
|
1
|
-
{"version":3,"file":"HelpDialog.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/HelpDialog.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,4CAA6E;AAC7E,yCAAyC;AAEzC,SAAwB,UAAU,CAAC,EACjC,WAAW,GAGZ;IACC,OAAO,CACL,8BAAC,WAAM,IACL,IAAI,QACJ,QAAQ,EAAC,IAAI,EACb,OAAO,EAAE,WAAW,EACpB,KAAK,EAAC,sBAAsB;QAE5B,8BAAC,wBAAa;YACZ,sDAAkB;YAClB;gBACE,+IAGK;gBACL;;oBAEM,6DAA2B;;oBAAI,4DAA0B;wKAI1D,CACF;YACL,6DAAyB;YACzB;gBACE;oBACE,mDAAiB;6DACd;gBACL;oBACE,mDAAiB;+CACd;gBACL;oBACE,0EAAwC;mFAErC;gBACL;oBACE,oEAAkC;0EAE/B;gBACL;oBACE,6DAA2B;8DACxB;gBACL;oBACE,yEAAuC;0FAEpC;gBACL;oBACE,2DAAyB;sEAEtB,CACF,CACS;QAChB,8BAAC,kBAAO,OAAG;QACX,8BAAC,wBAAa;YACZ,8BAAC,iBAAM,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,EAAE,KAAK,EAAC,SAAS,YAE5C,CACK,CACT,CACV,CAAA;AACH,CAAC;AAhED,6BAgEC"}
|
|
@@ -1,23 +0,0 @@
|
|
|
1
|
-
import React from 'react';
|
|
2
|
-
import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
|
|
3
|
-
import { TextFieldProps as TFP } from '@mui/material';
|
|
4
|
-
import { LinearGenomeViewModel } from '..';
|
|
5
|
-
export interface Option {
|
|
6
|
-
group?: string;
|
|
7
|
-
result: BaseResult;
|
|
8
|
-
}
|
|
9
|
-
declare function RefNameAutocomplete({ model, onSelect, assemblyName, style, fetchResults, onChange, value, showHelp, minWidth, maxWidth, TextFieldProps, }: {
|
|
10
|
-
model: LinearGenomeViewModel;
|
|
11
|
-
onSelect?: (region: BaseResult) => void;
|
|
12
|
-
onChange?: (val: string) => void;
|
|
13
|
-
assemblyName?: string;
|
|
14
|
-
value?: string;
|
|
15
|
-
fetchResults: (query: string) => Promise<BaseResult[]>;
|
|
16
|
-
style?: React.CSSProperties;
|
|
17
|
-
minWidth?: number;
|
|
18
|
-
maxWidth?: number;
|
|
19
|
-
showHelp?: boolean;
|
|
20
|
-
TextFieldProps?: TFP;
|
|
21
|
-
}): JSX.Element;
|
|
22
|
-
declare const _default: typeof RefNameAutocomplete;
|
|
23
|
-
export default _default;
|
|
@@ -1,182 +0,0 @@
|
|
|
1
|
-
"use strict";
|
|
2
|
-
var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
|
|
3
|
-
if (k2 === undefined) k2 = k;
|
|
4
|
-
var desc = Object.getOwnPropertyDescriptor(m, k);
|
|
5
|
-
if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
|
|
6
|
-
desc = { enumerable: true, get: function() { return m[k]; } };
|
|
7
|
-
}
|
|
8
|
-
Object.defineProperty(o, k2, desc);
|
|
9
|
-
}) : (function(o, m, k, k2) {
|
|
10
|
-
if (k2 === undefined) k2 = k;
|
|
11
|
-
o[k2] = m[k];
|
|
12
|
-
}));
|
|
13
|
-
var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
|
|
14
|
-
Object.defineProperty(o, "default", { enumerable: true, value: v });
|
|
15
|
-
}) : function(o, v) {
|
|
16
|
-
o["default"] = v;
|
|
17
|
-
});
|
|
18
|
-
var __importStar = (this && this.__importStar) || function (mod) {
|
|
19
|
-
if (mod && mod.__esModule) return mod;
|
|
20
|
-
var result = {};
|
|
21
|
-
if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
|
|
22
|
-
__setModuleDefault(result, mod);
|
|
23
|
-
return result;
|
|
24
|
-
};
|
|
25
|
-
var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
26
|
-
return (mod && mod.__esModule) ? mod : { "default": mod };
|
|
27
|
-
};
|
|
28
|
-
Object.defineProperty(exports, "__esModule", { value: true });
|
|
29
|
-
const react_1 = __importStar(require("react"));
|
|
30
|
-
const mobx_react_1 = require("mobx-react");
|
|
31
|
-
const util_1 = require("@jbrowse/core/util");
|
|
32
|
-
const BaseResults_1 = __importStar(require("@jbrowse/core/TextSearch/BaseResults"));
|
|
33
|
-
const material_1 = require("@mui/material");
|
|
34
|
-
// icons
|
|
35
|
-
const Search_1 = __importDefault(require("@mui/icons-material/Search"));
|
|
36
|
-
const Help_1 = __importDefault(require("@mui/icons-material/Help"));
|
|
37
|
-
// lazy
|
|
38
|
-
const HelpDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./HelpDialog'))));
|
|
39
|
-
function aggregateResults(results) {
|
|
40
|
-
const m = {};
|
|
41
|
-
for (const result of results) {
|
|
42
|
-
const displayString = result.getDisplayString();
|
|
43
|
-
if (!m[displayString]) {
|
|
44
|
-
m[displayString] = [];
|
|
45
|
-
}
|
|
46
|
-
m[displayString].push(result);
|
|
47
|
-
}
|
|
48
|
-
return m;
|
|
49
|
-
}
|
|
50
|
-
function getDeduplicatedResult(results) {
|
|
51
|
-
return Object.entries(aggregateResults(results)).map(([displayString, results]) => results.length === 1
|
|
52
|
-
? {
|
|
53
|
-
result: results[0],
|
|
54
|
-
}
|
|
55
|
-
: {
|
|
56
|
-
// deduplicate a "multi-result"
|
|
57
|
-
result: new BaseResults_1.default({
|
|
58
|
-
displayString,
|
|
59
|
-
results,
|
|
60
|
-
label: displayString,
|
|
61
|
-
}),
|
|
62
|
-
});
|
|
63
|
-
}
|
|
64
|
-
// the logic of this method is to only apply a filter to RefSequenceResults
|
|
65
|
-
// because they do not have a matchedObject. the trix search results already
|
|
66
|
-
// filter so don't need re-filtering
|
|
67
|
-
function filterOptions(options, searchQuery) {
|
|
68
|
-
return options.filter(({ result }) => result.getLabel().toLowerCase().includes(searchQuery) ||
|
|
69
|
-
result.matchedObject);
|
|
70
|
-
}
|
|
71
|
-
function RefNameAutocomplete({ model, onSelect, assemblyName, style, fetchResults, onChange, value, showHelp = true, minWidth = 200, maxWidth = 550, TextFieldProps = {}, }) {
|
|
72
|
-
const session = (0, util_1.getSession)(model);
|
|
73
|
-
const { assemblyManager } = session;
|
|
74
|
-
const [open, setOpen] = (0, react_1.useState)(false);
|
|
75
|
-
const [loaded, setLoaded] = (0, react_1.useState)(true);
|
|
76
|
-
const [isHelpDialogDisplayed, setHelpDialogDisplayed] = (0, react_1.useState)(false);
|
|
77
|
-
const [currentSearch, setCurrentSearch] = (0, react_1.useState)('');
|
|
78
|
-
const [inputValue, setInputValue] = (0, react_1.useState)('');
|
|
79
|
-
const [searchOptions, setSearchOptions] = (0, react_1.useState)();
|
|
80
|
-
const debouncedSearch = (0, util_1.useDebounce)(currentSearch, 300);
|
|
81
|
-
const assembly = assemblyName ? assemblyManager.get(assemblyName) : undefined;
|
|
82
|
-
const { coarseVisibleLocStrings, hasDisplayedRegions } = model;
|
|
83
|
-
const regions = assembly === null || assembly === void 0 ? void 0 : assembly.regions;
|
|
84
|
-
const options = (0, react_1.useMemo)(() => (regions === null || regions === void 0 ? void 0 : regions.map(option => ({
|
|
85
|
-
result: new BaseResults_1.RefSequenceResult({
|
|
86
|
-
refName: option.refName,
|
|
87
|
-
label: option.refName,
|
|
88
|
-
matchedAttribute: 'refName',
|
|
89
|
-
}),
|
|
90
|
-
}))) || [], [regions]);
|
|
91
|
-
(0, react_1.useEffect)(() => {
|
|
92
|
-
let active = true;
|
|
93
|
-
(async () => {
|
|
94
|
-
try {
|
|
95
|
-
if (debouncedSearch === '' || !assemblyName) {
|
|
96
|
-
return;
|
|
97
|
-
}
|
|
98
|
-
setLoaded(false);
|
|
99
|
-
const results = await fetchResults(debouncedSearch);
|
|
100
|
-
if (active) {
|
|
101
|
-
setLoaded(true);
|
|
102
|
-
setSearchOptions(getDeduplicatedResult(results));
|
|
103
|
-
}
|
|
104
|
-
}
|
|
105
|
-
catch (e) {
|
|
106
|
-
console.error(e);
|
|
107
|
-
if (active) {
|
|
108
|
-
session.notify(`${e}`, 'error');
|
|
109
|
-
}
|
|
110
|
-
}
|
|
111
|
-
})();
|
|
112
|
-
return () => {
|
|
113
|
-
active = false;
|
|
114
|
-
};
|
|
115
|
-
}, [assemblyName, fetchResults, debouncedSearch, session, model]);
|
|
116
|
-
const inputBoxVal = coarseVisibleLocStrings || value || '';
|
|
117
|
-
// heuristic, text width + icon width + 50 accommodates help icon and search
|
|
118
|
-
// icon
|
|
119
|
-
const width = Math.min(Math.max((0, util_1.measureText)(inputBoxVal, 16) + 50, minWidth), maxWidth);
|
|
120
|
-
// notes on implementation:
|
|
121
|
-
// The selectOnFocus setting helps highlight the field when clicked
|
|
122
|
-
return (react_1.default.createElement(react_1.default.Fragment, null,
|
|
123
|
-
react_1.default.createElement(material_1.Autocomplete, { "data-testid": "autocomplete", disableListWrap: true, disableClearable: true, disabled: !assemblyName, freeSolo: true, includeInputInList: true, selectOnFocus: true, style: { ...style, width }, value: inputBoxVal, loading: !loaded, inputValue: inputValue, onInputChange: (_event, newInputValue) => {
|
|
124
|
-
setInputValue(newInputValue);
|
|
125
|
-
onChange === null || onChange === void 0 ? void 0 : onChange(newInputValue);
|
|
126
|
-
}, loadingText: "loading results", open: open, onOpen: () => setOpen(true), onClose: () => {
|
|
127
|
-
setOpen(false);
|
|
128
|
-
setLoaded(true);
|
|
129
|
-
if (hasDisplayedRegions) {
|
|
130
|
-
setCurrentSearch('');
|
|
131
|
-
setSearchOptions(undefined);
|
|
132
|
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setInputValue(inputBoxVal);
|
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}, options: !(searchOptions === null || searchOptions === void 0 ? void 0 : searchOptions.length) ? options : searchOptions, getOptionDisabled: option => (option === null || option === void 0 ? void 0 : option.group) === 'limitOption', filterOptions: (options, params) => {
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{
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: []),
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return (react_1.default.createElement(material_1.TextField, { onBlur: () =>
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setInputValue(inputBoxVal), ...params, ...TextFieldProps, helperText: helperText, InputProps: {
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react_1.default.createElement(Search_1.default, { fontSize: "small" }),
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react_1.default.createElement(Help_1.default, { fontSize: "small" }))) : null),
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params.InputProps.endAdornment)),
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}, placeholder: "Search for location", onChange: e => setCurrentSearch(e.target.value) }));
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}, getOptionLabel: option => (typeof option === 'string'
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? option
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: option.result.getDisplayString()) || '' }),
|
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|
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react_1.default.createElement(HelpDialog, { handleClose: () => setHelpDialogDisplayed(false) }))) : null));
|
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}
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|
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exports.default = (0, mobx_react_1.observer)(RefNameAutocomplete);
|
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//# sourceMappingURL=RefNameAutocomplete.js.map
|
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{"version":3,"file":"RefNameAutocomplete.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/RefNameAutocomplete.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAA2E;AAC3E,2CAAqC;AACrC,6CAAyE;AACzE,oFAE6C;AAC7C,4CAMsB;AAEtB,QAAQ;AACR,wEAAmD;AACnD,oEAA+C;AAK/C,OAAO;AACP,MAAM,UAAU,GAAG,IAAA,YAAI,EAAC,GAAG,EAAE,mDAAQ,cAAc,GAAC,CAAC,CAAA;AAOrD,SAAS,gBAAgB,CAAC,OAAqB;IAC7C,MAAM,CAAC,GAAoC,EAAE,CAAA;IAE7C,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE;QAC5B,MAAM,aAAa,GAAG,MAAM,CAAC,gBAAgB,EAAE,CAAA;QAC/C,IAAI,CAAC,CAAC,CAAC,aAAa,CAAC,EAAE;YACrB,CAAC,CAAC,aAAa,CAAC,GAAG,EAAE,CAAA;SACtB;QACD,CAAC,CAAC,aAAa,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;KAC9B;IACD,OAAO,CAAC,CAAA;AACV,CAAC;AAED,SAAS,qBAAqB,CAAC,OAAqB;IAClD,OAAO,MAAM,CAAC,OAAO,CAAC,gBAAgB,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,CAClD,CAAC,CAAC,aAAa,EAAE,OAAO,CAAC,EAAE,EAAE,CAC3B,OAAO,CAAC,MAAM,KAAK,CAAC;QAClB,CAAC,CAAC;YACE,MAAM,EAAE,OAAO,CAAC,CAAC,CAAC;SACnB;QACH,CAAC,CAAC;YACE,+BAA+B;YAC/B,MAAM,EAAE,IAAI,qBAAU,CAAC;gBACrB,aAAa;gBACb,OAAO;gBACP,KAAK,EAAE,aAAa;aACrB,CAAC;SACH,CACR,CAAA;AACH,CAAC;AAED,2EAA2E;AAC3E,4EAA4E;AAC5E,oCAAoC;AACpC,SAAS,aAAa,CAAC,OAAiB,EAAE,WAAmB;IAC3D,OAAO,OAAO,CAAC,MAAM,CACnB,CAAC,EAAE,MAAM,EAAE,EAAE,EAAE,CACb,MAAM,CAAC,QAAQ,EAAE,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,WAAW,CAAC;QACrD,MAAM,CAAC,aAAa,CACvB,CAAA;AACH,CAAC;AAED,SAAS,mBAAmB,CAAC,EAC3B,KAAK,EACL,QAAQ,EACR,YAAY,EACZ,KAAK,EACL,YAAY,EACZ,QAAQ,EACR,KAAK,EACL,QAAQ,GAAG,IAAI,EACf,QAAQ,GAAG,GAAG,EACd,QAAQ,GAAG,GAAG,EACd,cAAc,GAAG,EAAE,GAapB;IACC,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,KAAK,CAAC,CAAA;IACjC,MAAM,EAAE,eAAe,EAAE,GAAG,OAAO,CAAA;IACnC,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,GAAG,IAAA,gBAAQ,EAAC,KAAK,CAAC,CAAA;IACvC,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,IAAA,gBAAQ,EAAC,IAAI,CAAC,CAAA;IAC1C,MAAM,CAAC,qBAAqB,EAAE,sBAAsB,CAAC,GAAG,IAAA,gBAAQ,EAAC,KAAK,CAAC,CAAA;IACvE,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC,GAAG,IAAA,gBAAQ,EAAC,EAAE,CAAC,CAAA;IACtD,MAAM,CAAC,UAAU,EAAE,aAAa,CAAC,GAAG,IAAA,gBAAQ,EAAC,EAAE,CAAC,CAAA;IAChD,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC,GAAG,IAAA,gBAAQ,GAAY,CAAA;IAC9D,MAAM,eAAe,GAAG,IAAA,kBAAW,EAAC,aAAa,EAAE,GAAG,CAAC,CAAA;IACvD,MAAM,QAAQ,GAAG,YAAY,CAAC,CAAC,CAAC,eAAe,CAAC,GAAG,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IAC7E,MAAM,EAAE,uBAAuB,EAAE,mBAAmB,EAAE,GAAG,KAAK,CAAA;IAE9D,MAAM,OAAO,GAAG,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,OAAO,CAAA;IAEjC,MAAM,OAAO,GAAG,IAAA,eAAO,EACrB,GAAG,EAAE,CACH,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC;QACtB,MAAM,EAAE,IAAI,+BAAiB,CAAC;YAC5B,OAAO,EAAE,MAAM,CAAC,OAAO;YACvB,KAAK,EAAE,MAAM,CAAC,OAAO;YACrB,gBAAgB,EAAE,SAAS;SAC5B,CAAC;KACH,CAAC,CAAC,KAAI,EAAE,EACX,CAAC,OAAO,CAAC,CACV,CAAA;IAED,IAAA,iBAAS,EAAC,GAAG,EAAE;QACb,IAAI,MAAM,GAAG,IAAI,CAGhB;QAAA,CAAC,KAAK,IAAI,EAAE;YACX,IAAI;gBACF,IAAI,eAAe,KAAK,EAAE,IAAI,CAAC,YAAY,EAAE;oBAC3C,OAAM;iBACP;gBAED,SAAS,CAAC,KAAK,CAAC,CAAA;gBAChB,MAAM,OAAO,GAAG,MAAM,YAAY,CAAC,eAAe,CAAC,CAAA;gBACnD,IAAI,MAAM,EAAE;oBACV,SAAS,CAAC,IAAI,CAAC,CAAA;oBACf,gBAAgB,CAAC,qBAAqB,CAAC,OAAO,CAAC,CAAC,CAAA;iBACjD;aACF;YAAC,OAAO,CAAC,EAAE;gBACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;gBAChB,IAAI,MAAM,EAAE;oBACV,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,EAAE,OAAO,CAAC,CAAA;iBAChC;aACF;QACH,CAAC,CAAC,EAAE,CAAA;QAEJ,OAAO,GAAG,EAAE;YACV,MAAM,GAAG,KAAK,CAAA;QAChB,CAAC,CAAA;IACH,CAAC,EAAE,CAAC,YAAY,EAAE,YAAY,EAAE,eAAe,EAAE,OAAO,EAAE,KAAK,CAAC,CAAC,CAAA;IAEjE,MAAM,WAAW,GAAG,uBAAuB,IAAI,KAAK,IAAI,EAAE,CAAA;IAE1D,4EAA4E;IAC5E,OAAO;IACP,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CACpB,IAAI,CAAC,GAAG,CAAC,IAAA,kBAAW,EAAC,WAAW,EAAE,EAAE,CAAC,GAAG,EAAE,EAAE,QAAQ,CAAC,EACrD,QAAQ,CACT,CAAA;IAED,2BAA2B;IAC3B,mEAAmE;IACnE,OAAO,CACL;QACE,8BAAC,uBAAY,mBACC,cAAc,EAC1B,eAAe,QACf,gBAAgB,QAChB,QAAQ,EAAE,CAAC,YAAY,EACvB,QAAQ,QACR,kBAAkB,QAClB,aAAa,QACb,KAAK,EAAE,EAAE,GAAG,KAAK,EAAE,KAAK,EAAE,EAC1B,KAAK,EAAE,WAAW,EAClB,OAAO,EAAE,CAAC,MAAM,EAChB,UAAU,EAAE,UAAU,EACtB,aAAa,EAAE,CAAC,MAAM,EAAE,aAAa,EAAE,EAAE;gBACvC,aAAa,CAAC,aAAa,CAAC,CAAA;gBAC5B,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAG,aAAa,CAAC,CAAA;YAC3B,CAAC,EACD,WAAW,EAAC,iBAAiB,EAC7B,IAAI,EAAE,IAAI,EACV,MAAM,EAAE,GAAG,EAAE,CAAC,OAAO,CAAC,IAAI,CAAC,EAC3B,OAAO,EAAE,GAAG,EAAE;gBACZ,OAAO,CAAC,KAAK,CAAC,CAAA;gBACd,SAAS,CAAC,IAAI,CAAC,CAAA;gBACf,IAAI,mBAAmB,EAAE;oBACvB,gBAAgB,CAAC,EAAE,CAAC,CAAA;oBACpB,gBAAgB,CAAC,SAAS,CAAC,CAAA;iBAC5B;YACH,CAAC,EACD,QAAQ,EAAE,CAAC,MAAM,EAAE,cAAc,EAAE,EAAE;gBACnC,IAAI,CAAC,cAAc,IAAI,CAAC,YAAY,EAAE;oBACpC,OAAM;iBACP;gBAED,IAAI,OAAO,cAAc,KAAK,QAAQ,EAAE;oBACtC,0CAA0C;oBAC1C,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAG,IAAI,qBAAU,CAAC,EAAE,KAAK,EAAE,cAAc,EAAE,CAAC,CAAC,CAAA;iBACtD;qBAAM;oBACL,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAG,cAAc,CAAC,MAAM,CAAC,CAAA;iBAClC;gBACD,aAAa,CAAC,WAAW,CAAC,CAAA;YAC5B,CAAC,EACD,OAAO,EAAE,CAAC,CAAA,aAAa,aAAb,aAAa,uBAAb,aAAa,CAAE,MAAM,CAAA,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,aAAa,EACzD,iBAAiB,EAAE,MAAM,CAAC,EAAE,CAAC,CAAA,MAAM,aAAN,MAAM,uBAAN,MAAM,CAAE,KAAK,MAAK,aAAa,EAC5D,aAAa,EAAE,CAAC,OAAO,EAAE,MAAM,EAAE,EAAE;gBACjC,MAAM,QAAQ,GAAG,aAAa,CAC5B,OAAO,EACP,MAAM,CAAC,UAAU,CAAC,iBAAiB,EAAE,CACtC,CAAA;gBACD,OAAO;oBACL,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC;oBACzB,GAAG,CAAC,QAAQ,CAAC,MAAM,GAAG,GAAG;wBACv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|
|
@@ -1 +0,0 @@
|
|
|
1
|
-
{"version":3,"file":"HelpDialog.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/HelpDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,MAAM,EAAE,aAAa,EAAE,aAAa,EAAE,OAAO,EAAE,MAAM,eAAe,CAAA;AAC7E,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AAEzC,MAAM,CAAC,OAAO,UAAU,UAAU,CAAC,EACjC,WAAW,GAGZ;IACC,OAAO,CACL,oBAAC,MAAM,IACL,IAAI,QACJ,QAAQ,EAAC,IAAI,EACb,OAAO,EAAE,WAAW,EACpB,KAAK,EAAC,sBAAsB;QAE5B,oBAAC,aAAa;YACZ,4CAAkB;YAClB;gBACE,qIAGK;gBACL;;oBAEM,mDAA2B;;oBAAI,kDAA0B;wKAI1D,CACF;YACL,mDAAyB;YACzB;gBACE;oBACE,yCAAiB;6DACd;gBACL;oBACE,yCAAiB;+CACd;gBACL;oBACE,gEAAwC;mFAErC;gBACL;oBACE,0DAAkC;0EAE/B;gBACL;oBACE,mDAA2B;8DACxB;gBACL;oBACE,+DAAuC;0FAEpC;gBACL;oBACE,iDAAyB;sEAEtB,CACF,CACS;QAChB,oBAAC,OAAO,OAAG;QACX,oBAAC,aAAa;YACZ,oBAAC,MAAM,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,EAAE,KAAK,EAAC,SAAS,YAE5C,CACK,CACT,CACV,CAAA;AACH,CAAC"}
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@@ -1,23 +0,0 @@
|
|
|
1
|
-
import React from 'react';
|
|
2
|
-
import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
|
|
3
|
-
import { TextFieldProps as TFP } from '@mui/material';
|
|
4
|
-
import { LinearGenomeViewModel } from '..';
|
|
5
|
-
export interface Option {
|
|
6
|
-
group?: string;
|
|
7
|
-
result: BaseResult;
|
|
8
|
-
}
|
|
9
|
-
declare function RefNameAutocomplete({ model, onSelect, assemblyName, style, fetchResults, onChange, value, showHelp, minWidth, maxWidth, TextFieldProps, }: {
|
|
10
|
-
model: LinearGenomeViewModel;
|
|
11
|
-
onSelect?: (region: BaseResult) => void;
|
|
12
|
-
onChange?: (val: string) => void;
|
|
13
|
-
assemblyName?: string;
|
|
14
|
-
value?: string;
|
|
15
|
-
fetchResults: (query: string) => Promise<BaseResult[]>;
|
|
16
|
-
style?: React.CSSProperties;
|
|
17
|
-
minWidth?: number;
|
|
18
|
-
maxWidth?: number;
|
|
19
|
-
showHelp?: boolean;
|
|
20
|
-
TextFieldProps?: TFP;
|
|
21
|
-
}): JSX.Element;
|
|
22
|
-
declare const _default: typeof RefNameAutocomplete;
|
|
23
|
-
export default _default;
|
|
@@ -1,154 +0,0 @@
|
|
|
1
|
-
import React, { Suspense, lazy, useMemo, useEffect, useState } from 'react';
|
|
2
|
-
import { observer } from 'mobx-react';
|
|
3
|
-
import { getSession, useDebounce, measureText } from '@jbrowse/core/util';
|
|
4
|
-
import BaseResult, { RefSequenceResult, } from '@jbrowse/core/TextSearch/BaseResults';
|
|
5
|
-
import { Autocomplete, IconButton, InputAdornment, TextField, } from '@mui/material';
|
|
6
|
-
// icons
|
|
7
|
-
import SearchIcon from '@mui/icons-material/Search';
|
|
8
|
-
import HelpIcon from '@mui/icons-material/Help';
|
|
9
|
-
// lazy
|
|
10
|
-
const HelpDialog = lazy(() => import('./HelpDialog'));
|
|
11
|
-
function aggregateResults(results) {
|
|
12
|
-
const m = {};
|
|
13
|
-
for (const result of results) {
|
|
14
|
-
const displayString = result.getDisplayString();
|
|
15
|
-
if (!m[displayString]) {
|
|
16
|
-
m[displayString] = [];
|
|
17
|
-
}
|
|
18
|
-
m[displayString].push(result);
|
|
19
|
-
}
|
|
20
|
-
return m;
|
|
21
|
-
}
|
|
22
|
-
function getDeduplicatedResult(results) {
|
|
23
|
-
return Object.entries(aggregateResults(results)).map(([displayString, results]) => results.length === 1
|
|
24
|
-
? {
|
|
25
|
-
result: results[0],
|
|
26
|
-
}
|
|
27
|
-
: {
|
|
28
|
-
// deduplicate a "multi-result"
|
|
29
|
-
result: new BaseResult({
|
|
30
|
-
displayString,
|
|
31
|
-
results,
|
|
32
|
-
label: displayString,
|
|
33
|
-
}),
|
|
34
|
-
});
|
|
35
|
-
}
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|
36
|
-
// the logic of this method is to only apply a filter to RefSequenceResults
|
|
37
|
-
// because they do not have a matchedObject. the trix search results already
|
|
38
|
-
// filter so don't need re-filtering
|
|
39
|
-
function filterOptions(options, searchQuery) {
|
|
40
|
-
return options.filter(({ result }) => result.getLabel().toLowerCase().includes(searchQuery) ||
|
|
41
|
-
result.matchedObject);
|
|
42
|
-
}
|
|
43
|
-
function RefNameAutocomplete({ model, onSelect, assemblyName, style, fetchResults, onChange, value, showHelp = true, minWidth = 200, maxWidth = 550, TextFieldProps = {}, }) {
|
|
44
|
-
const session = getSession(model);
|
|
45
|
-
const { assemblyManager } = session;
|
|
46
|
-
const [open, setOpen] = useState(false);
|
|
47
|
-
const [loaded, setLoaded] = useState(true);
|
|
48
|
-
const [isHelpDialogDisplayed, setHelpDialogDisplayed] = useState(false);
|
|
49
|
-
const [currentSearch, setCurrentSearch] = useState('');
|
|
50
|
-
const [inputValue, setInputValue] = useState('');
|
|
51
|
-
const [searchOptions, setSearchOptions] = useState();
|
|
52
|
-
const debouncedSearch = useDebounce(currentSearch, 300);
|
|
53
|
-
const assembly = assemblyName ? assemblyManager.get(assemblyName) : undefined;
|
|
54
|
-
const { coarseVisibleLocStrings, hasDisplayedRegions } = model;
|
|
55
|
-
const regions = assembly === null || assembly === void 0 ? void 0 : assembly.regions;
|
|
56
|
-
const options = useMemo(() => (regions === null || regions === void 0 ? void 0 : regions.map(option => ({
|
|
57
|
-
result: new RefSequenceResult({
|
|
58
|
-
refName: option.refName,
|
|
59
|
-
label: option.refName,
|
|
60
|
-
matchedAttribute: 'refName',
|
|
61
|
-
}),
|
|
62
|
-
}))) || [], [regions]);
|
|
63
|
-
useEffect(() => {
|
|
64
|
-
let active = true;
|
|
65
|
-
(async () => {
|
|
66
|
-
try {
|
|
67
|
-
if (debouncedSearch === '' || !assemblyName) {
|
|
68
|
-
return;
|
|
69
|
-
}
|
|
70
|
-
setLoaded(false);
|
|
71
|
-
const results = await fetchResults(debouncedSearch);
|
|
72
|
-
if (active) {
|
|
73
|
-
setLoaded(true);
|
|
74
|
-
setSearchOptions(getDeduplicatedResult(results));
|
|
75
|
-
}
|
|
76
|
-
}
|
|
77
|
-
catch (e) {
|
|
78
|
-
console.error(e);
|
|
79
|
-
if (active) {
|
|
80
|
-
session.notify(`${e}`, 'error');
|
|
81
|
-
}
|
|
82
|
-
}
|
|
83
|
-
})();
|
|
84
|
-
return () => {
|
|
85
|
-
active = false;
|
|
86
|
-
};
|
|
87
|
-
}, [assemblyName, fetchResults, debouncedSearch, session, model]);
|
|
88
|
-
const inputBoxVal = coarseVisibleLocStrings || value || '';
|
|
89
|
-
// heuristic, text width + icon width + 50 accommodates help icon and search
|
|
90
|
-
// icon
|
|
91
|
-
const width = Math.min(Math.max(measureText(inputBoxVal, 16) + 50, minWidth), maxWidth);
|
|
92
|
-
// notes on implementation:
|
|
93
|
-
// The selectOnFocus setting helps highlight the field when clicked
|
|
94
|
-
return (React.createElement(React.Fragment, null,
|
|
95
|
-
React.createElement(Autocomplete, { "data-testid": "autocomplete", disableListWrap: true, disableClearable: true, disabled: !assemblyName, freeSolo: true, includeInputInList: true, selectOnFocus: true, style: { ...style, width }, value: inputBoxVal, loading: !loaded, inputValue: inputValue, onInputChange: (_event, newInputValue) => {
|
|
96
|
-
setInputValue(newInputValue);
|
|
97
|
-
onChange === null || onChange === void 0 ? void 0 : onChange(newInputValue);
|
|
98
|
-
}, loadingText: "loading results", open: open, onOpen: () => setOpen(true), onClose: () => {
|
|
99
|
-
setOpen(false);
|
|
100
|
-
setLoaded(true);
|
|
101
|
-
if (hasDisplayedRegions) {
|
|
102
|
-
setCurrentSearch('');
|
|
103
|
-
setSearchOptions(undefined);
|
|
104
|
-
}
|
|
105
|
-
}, onChange: (_event, selectedOption) => {
|
|
106
|
-
if (!selectedOption || !assemblyName) {
|
|
107
|
-
return;
|
|
108
|
-
}
|
|
109
|
-
if (typeof selectedOption === 'string') {
|
|
110
|
-
// handles string inputs on keyPress enter
|
|
111
|
-
onSelect === null || onSelect === void 0 ? void 0 : onSelect(new BaseResult({ label: selectedOption }));
|
|
112
|
-
}
|
|
113
|
-
else {
|
|
114
|
-
onSelect === null || onSelect === void 0 ? void 0 : onSelect(selectedOption.result);
|
|
115
|
-
}
|
|
116
|
-
setInputValue(inputBoxVal);
|
|
117
|
-
}, options: !(searchOptions === null || searchOptions === void 0 ? void 0 : searchOptions.length) ? options : searchOptions, getOptionDisabled: option => (option === null || option === void 0 ? void 0 : option.group) === 'limitOption', filterOptions: (options, params) => {
|
|
118
|
-
const filtered = filterOptions(options, params.inputValue.toLocaleLowerCase());
|
|
119
|
-
return [
|
|
120
|
-
...filtered.slice(0, 100),
|
|
121
|
-
...(filtered.length > 100
|
|
122
|
-
? [
|
|
123
|
-
{
|
|
124
|
-
group: 'limitOption',
|
|
125
|
-
result: new BaseResult({
|
|
126
|
-
label: 'keep typing for more results',
|
|
127
|
-
}),
|
|
128
|
-
},
|
|
129
|
-
]
|
|
130
|
-
: []),
|
|
131
|
-
];
|
|
132
|
-
}, renderInput: params => {
|
|
133
|
-
const { helperText, InputProps = {} } = TextFieldProps;
|
|
134
|
-
return (React.createElement(TextField, { onBlur: () =>
|
|
135
|
-
// this is used to restore a refName or the non-user-typed input
|
|
136
|
-
// to the box on blurring
|
|
137
|
-
setInputValue(inputBoxVal), ...params, ...TextFieldProps, helperText: helperText, InputProps: {
|
|
138
|
-
...params.InputProps,
|
|
139
|
-
...InputProps,
|
|
140
|
-
endAdornment: (React.createElement(React.Fragment, null,
|
|
141
|
-
React.createElement(InputAdornment, { position: "end", style: { marginRight: 7 } },
|
|
142
|
-
React.createElement(SearchIcon, { fontSize: "small" }),
|
|
143
|
-
showHelp ? (React.createElement(IconButton, { onClick: () => setHelpDialogDisplayed(true), size: "small" },
|
|
144
|
-
React.createElement(HelpIcon, { fontSize: "small" }))) : null),
|
|
145
|
-
params.InputProps.endAdornment)),
|
|
146
|
-
}, placeholder: "Search for location", onChange: e => setCurrentSearch(e.target.value) }));
|
|
147
|
-
}, getOptionLabel: option => (typeof option === 'string'
|
|
148
|
-
? option
|
|
149
|
-
: option.result.getDisplayString()) || '' }),
|
|
150
|
-
isHelpDialogDisplayed ? (React.createElement(Suspense, { fallback: React.createElement("div", null) },
|
|
151
|
-
React.createElement(HelpDialog, { handleClose: () => setHelpDialogDisplayed(false) }))) : null));
|
|
152
|
-
}
|
|
153
|
-
export default observer(RefNameAutocomplete);
|
|
154
|
-
//# sourceMappingURL=RefNameAutocomplete.js.map
|
|
@@ -1 +0,0 @@
|
|
|
1
|
-
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|