@jbrowse/plugin-wiggle 3.6.5 → 4.0.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/esm/BigWigAdapter/BigWigAdapter.d.ts +14 -1
- package/esm/BigWigAdapter/BigWigAdapter.js +118 -22
- package/esm/BigWigAdapter/configSchema.d.ts +2 -2
- package/esm/BigWigAdapter/configSchema.js +1 -1
- package/esm/BigWigAdapter/index.js +2 -2
- package/esm/CreateMultiWiggleExtension/ConfirmDialog.js +1 -1
- package/esm/CreateMultiWiggleExtension/index.js +2 -2
- package/esm/DensityRenderer/DensityRenderer.d.ts +5 -6
- package/esm/DensityRenderer/DensityRenderer.js +6 -5
- package/esm/DensityRenderer/configSchema.d.ts +3 -3
- package/esm/DensityRenderer/configSchema.js +1 -1
- package/esm/DensityRenderer/index.js +11 -9
- package/esm/DensityRenderer/makeImageData.d.ts +3 -0
- package/esm/DensityRenderer/makeImageData.js +13 -0
- package/esm/DensityRenderer/renderDensity.d.ts +3 -0
- package/esm/DensityRenderer/renderDensity.js +18 -0
- package/esm/LinePlotRenderer/LinePlotRenderer.d.ts +5 -7
- package/esm/LinePlotRenderer/LinePlotRenderer.js +6 -15
- package/esm/LinePlotRenderer/configSchema.d.ts +4 -4
- package/esm/LinePlotRenderer/configSchema.js +1 -1
- package/esm/LinePlotRenderer/index.js +4 -4
- package/esm/LinePlotRenderer/makeImageData.d.ts +3 -0
- package/esm/LinePlotRenderer/makeImageData.js +13 -0
- package/esm/LinePlotRenderer/renderLinePlot.d.ts +3 -0
- package/esm/LinePlotRenderer/renderLinePlot.js +23 -0
- package/esm/LinearWiggleDisplay/components/Tooltip.d.ts +2 -2
- package/esm/LinearWiggleDisplay/components/Tooltip.js +10 -6
- package/esm/LinearWiggleDisplay/components/WiggleDisplayComponent.d.ts +1 -1
- package/esm/LinearWiggleDisplay/components/WiggleDisplayComponent.js +2 -2
- package/esm/LinearWiggleDisplay/configSchema.d.ts +9 -9
- package/esm/LinearWiggleDisplay/configSchema.js +2 -2
- package/esm/LinearWiggleDisplay/index.d.ts +3 -3
- package/esm/LinearWiggleDisplay/index.js +6 -6
- package/esm/LinearWiggleDisplay/model.d.ts +1130 -92
- package/esm/LinearWiggleDisplay/model.js +58 -18
- package/esm/LinearWiggleDisplay/renderSvg.d.ts +1 -1
- package/esm/LinearWiggleDisplay/renderSvg.js +3 -2
- package/esm/MultiDensityRenderer/MultiDensityRenderer.d.ts +5 -7
- package/esm/MultiDensityRenderer/MultiDensityRenderer.js +6 -24
- package/esm/MultiDensityRenderer/configSchema.d.ts +3 -3
- package/esm/MultiDensityRenderer/configSchema.js +1 -1
- package/esm/MultiDensityRenderer/index.js +4 -4
- package/esm/MultiDensityRenderer/makeImageData.d.ts +3 -0
- package/esm/MultiDensityRenderer/makeImageData.js +7 -0
- package/esm/MultiDensityRenderer/renderMultiDensity.d.ts +3 -0
- package/esm/MultiDensityRenderer/renderMultiDensity.js +37 -0
- package/esm/MultiLineRenderer/MultiLineRenderer.d.ts +5 -7
- package/esm/MultiLineRenderer/MultiLineRenderer.js +6 -17
- package/esm/MultiLineRenderer/configSchema.d.ts +5 -5
- package/esm/MultiLineRenderer/configSchema.js +2 -2
- package/esm/MultiLineRenderer/index.js +4 -4
- package/esm/MultiLineRenderer/makeImageData.d.ts +3 -0
- package/esm/MultiLineRenderer/makeImageData.js +7 -0
- package/esm/MultiLineRenderer/renderMultiLine.d.ts +3 -0
- package/esm/MultiLineRenderer/renderMultiLine.js +34 -0
- package/esm/MultiLinearWiggleDisplay/components/ColorLegend.d.ts +2 -2
- package/esm/MultiLinearWiggleDisplay/components/ColorLegend.js +11 -5
- package/esm/MultiLinearWiggleDisplay/components/FullHeightScaleBar.d.ts +1 -1
- package/esm/MultiLinearWiggleDisplay/components/FullHeightScaleBar.js +4 -4
- package/esm/MultiLinearWiggleDisplay/components/IndividualScaleBars.d.ts +1 -1
- package/esm/MultiLinearWiggleDisplay/components/IndividualScaleBars.js +5 -5
- package/esm/MultiLinearWiggleDisplay/components/LegendItem.d.ts +3 -3
- package/esm/MultiLinearWiggleDisplay/components/LegendItem.js +2 -4
- package/esm/MultiLinearWiggleDisplay/components/LegendItemText.d.ts +12 -0
- package/esm/MultiLinearWiggleDisplay/components/LegendItemText.js +11 -0
- package/esm/MultiLinearWiggleDisplay/components/RectBg.d.ts +1 -1
- package/esm/MultiLinearWiggleDisplay/components/RectBg.js +4 -3
- package/esm/MultiLinearWiggleDisplay/components/ScoreLegend.d.ts +2 -2
- package/esm/MultiLinearWiggleDisplay/components/ScoreLegend.js +3 -3
- package/esm/MultiLinearWiggleDisplay/components/SetColorDialog.d.ts +1 -1
- package/esm/MultiLinearWiggleDisplay/components/SetColorDialog.js +4 -34
- package/esm/MultiLinearWiggleDisplay/components/SourcesGrid.d.ts +1 -1
- package/esm/MultiLinearWiggleDisplay/components/SourcesGrid.js +3 -3
- package/esm/MultiLinearWiggleDisplay/components/Tooltip.d.ts +2 -4
- package/esm/MultiLinearWiggleDisplay/components/Tooltip.js +15 -12
- package/esm/MultiLinearWiggleDisplay/components/WiggleClusterDialog/WiggleClusterDialog.d.ts +1 -1
- package/esm/MultiLinearWiggleDisplay/components/WiggleClusterDialog/WiggleClusterDialog.js +3 -3
- package/esm/MultiLinearWiggleDisplay/components/WiggleClusterDialog/WiggleClusterDialogAuto.d.ts +1 -1
- package/esm/MultiLinearWiggleDisplay/components/WiggleClusterDialog/WiggleClusterDialogAuto.js +13 -6
- package/esm/MultiLinearWiggleDisplay/components/WiggleClusterDialog/WiggleClusterDialogManual.d.ts +1 -1
- package/esm/MultiLinearWiggleDisplay/components/WiggleClusterDialog/WiggleClusterDialogManual.js +24 -21
- package/esm/MultiLinearWiggleDisplay/components/WiggleClusterDialog/types.d.ts +2 -1
- package/esm/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.d.ts +1 -1
- package/esm/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.js +2 -2
- package/esm/MultiLinearWiggleDisplay/components/YScaleBars.d.ts +2 -2
- package/esm/MultiLinearWiggleDisplay/components/YScaleBars.js +5 -16
- package/esm/MultiLinearWiggleDisplay/components/YScaleBarsWrapper.d.ts +7 -0
- package/esm/MultiLinearWiggleDisplay/components/YScaleBarsWrapper.js +15 -0
- package/esm/MultiLinearWiggleDisplay/components/types.d.ts +10 -0
- package/esm/MultiLinearWiggleDisplay/components/types.js +1 -0
- package/esm/MultiLinearWiggleDisplay/components/ui/SetColorDialog.d.ts +31 -0
- package/esm/MultiLinearWiggleDisplay/components/ui/SetColorDialog.js +45 -0
- package/esm/MultiLinearWiggleDisplay/components/ui/SetColorDialogBulkEditPanel.d.ts +10 -0
- package/esm/MultiLinearWiggleDisplay/components/ui/SetColorDialogBulkEditPanel.js +81 -0
- package/esm/MultiLinearWiggleDisplay/components/ui/SetColorDialogHelpfulTips.d.ts +1 -0
- package/esm/MultiLinearWiggleDisplay/components/ui/SetColorDialogHelpfulTips.js +4 -0
- package/esm/MultiLinearWiggleDisplay/components/ui/SetColorDialogRowPalettizer.d.ts +10 -0
- package/esm/MultiLinearWiggleDisplay/components/ui/SetColorDialogRowPalettizer.js +39 -0
- package/esm/MultiLinearWiggleDisplay/components/util.d.ts +5 -9
- package/esm/MultiLinearWiggleDisplay/configSchema.d.ts +9 -9
- package/esm/MultiLinearWiggleDisplay/configSchema.js +2 -2
- package/esm/MultiLinearWiggleDisplay/index.js +3 -3
- package/esm/MultiLinearWiggleDisplay/model.d.ts +3628 -93
- package/esm/MultiLinearWiggleDisplay/model.js +80 -50
- package/esm/MultiLinearWiggleDisplay/renderSvg.d.ts +1 -1
- package/esm/MultiLinearWiggleDisplay/renderSvg.js +3 -2
- package/esm/MultiLinearWiggleDisplay/types.d.ts +1 -0
- package/esm/MultiLinearWiggleDisplay/util.d.ts +0 -1
- package/esm/MultiLinearWiggleDisplay/util.js +1 -7
- package/esm/MultiQuantitativeTrack/configSchema.d.ts +16 -11
- package/esm/MultiQuantitativeTrack/index.js +13 -2
- package/esm/MultiRowLineRenderer/MultiRowLineRenderer.d.ts +5 -7
- package/esm/MultiRowLineRenderer/MultiRowLineRenderer.js +6 -29
- package/esm/MultiRowLineRenderer/configSchema.d.ts +5 -5
- package/esm/MultiRowLineRenderer/configSchema.js +2 -2
- package/esm/MultiRowLineRenderer/index.js +4 -4
- package/esm/MultiRowLineRenderer/makeImageData.d.ts +3 -0
- package/esm/MultiRowLineRenderer/makeImageData.js +7 -0
- package/esm/MultiRowLineRenderer/renderMultiRowLine.d.ts +3 -0
- package/esm/MultiRowLineRenderer/renderMultiRowLine.js +44 -0
- package/esm/MultiRowXYPlotRenderer/MultiRowXYPlotRenderer.d.ts +5 -7
- package/esm/MultiRowXYPlotRenderer/MultiRowXYPlotRenderer.js +6 -29
- package/esm/MultiRowXYPlotRenderer/configSchema.d.ts +5 -5
- package/esm/MultiRowXYPlotRenderer/configSchema.js +2 -2
- package/esm/MultiRowXYPlotRenderer/index.js +4 -4
- package/esm/MultiRowXYPlotRenderer/makeImageData.d.ts +3 -0
- package/esm/MultiRowXYPlotRenderer/makeImageData.js +7 -0
- package/esm/MultiRowXYPlotRenderer/renderMultiRowXYPlot.d.ts +3 -0
- package/esm/MultiRowXYPlotRenderer/renderMultiRowXYPlot.js +42 -0
- package/esm/MultiWiggleAdapter/MultiWiggleAdapter.d.ts +7 -1
- package/esm/MultiWiggleAdapter/MultiWiggleAdapter.js +81 -26
- package/esm/MultiWiggleAdapter/configSchema.d.ts +2 -2
- package/esm/MultiWiggleAdapter/index.js +2 -2
- package/esm/MultiWiggleAddTrackWorkflow/AddTrackWorkflow.d.ts +1 -1
- package/esm/MultiWiggleAddTrackWorkflow/AddTrackWorkflow.js +4 -5
- package/esm/MultiWiggleAddTrackWorkflow/index.js +2 -2
- package/esm/MultiWiggleRendering.d.ts +7 -7
- package/esm/MultiWiggleRendering.js +9 -7
- package/esm/MultiXYPlotRenderer/MultiXYPlotRenderer.d.ts +5 -7
- package/esm/MultiXYPlotRenderer/MultiXYPlotRenderer.js +6 -20
- package/esm/MultiXYPlotRenderer/configSchema.d.ts +5 -5
- package/esm/MultiXYPlotRenderer/configSchema.js +2 -2
- package/esm/MultiXYPlotRenderer/index.js +4 -4
- package/esm/MultiXYPlotRenderer/makeImageData.d.ts +3 -0
- package/esm/MultiXYPlotRenderer/makeImageData.js +7 -0
- package/esm/MultiXYPlotRenderer/renderMultiXYPlot.d.ts +3 -0
- package/esm/MultiXYPlotRenderer/renderMultiXYPlot.js +35 -0
- package/esm/QuantitativeTrack/configSchema.d.ts +16 -11
- package/esm/QuantitativeTrack/index.js +13 -2
- package/esm/SVGErrorBox.d.ts +5 -0
- package/esm/SVGErrorBox.js +4 -0
- package/esm/Tooltip.d.ts +1 -3
- package/esm/Tooltip.js +7 -7
- package/esm/WiggleRPC/MultiWiggleClusterScoreMatrix.d.ts +2 -10
- package/esm/WiggleRPC/MultiWiggleClusterScoreMatrix.js +3 -15
- package/esm/WiggleRPC/MultiWiggleGetScoreMatrix.d.ts +1 -1
- package/esm/WiggleRPC/MultiWiggleGetScoreMatrix.js +2 -5
- package/esm/WiggleRPC/MultiWiggleGetSources.js +1 -4
- package/esm/WiggleRPC/WiggleGetGlobalQuantitativeStats.js +1 -4
- package/esm/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.d.ts +10 -0
- package/esm/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.js +26 -5
- package/esm/WiggleRPC/executeClusterScoreMatrix.d.ts +6 -0
- package/esm/WiggleRPC/executeClusterScoreMatrix.js +15 -0
- package/esm/WiggleRPC/getScoreMatrix.d.ts +1 -1
- package/esm/WiggleRPC/getScoreMatrix.js +9 -6
- package/esm/WiggleRPC/rpcMethods.d.ts +5 -5
- package/esm/WiggleRPC/rpcMethods.js +5 -5
- package/esm/WiggleRPC/types.d.ts +1 -1
- package/esm/WiggleRendering.d.ts +2 -3
- package/esm/WiggleRendering.js +16 -3
- package/esm/XYPlotRenderer/XYPlotRenderer.d.ts +5 -6
- package/esm/XYPlotRenderer/XYPlotRenderer.js +6 -20
- package/esm/XYPlotRenderer/configSchema.d.ts +5 -5
- package/esm/XYPlotRenderer/configSchema.js +2 -2
- package/esm/XYPlotRenderer/index.d.ts +3 -3
- package/esm/XYPlotRenderer/index.js +14 -12
- package/esm/XYPlotRenderer/makeImageData.d.ts +3 -0
- package/esm/XYPlotRenderer/makeImageData.js +13 -0
- package/esm/XYPlotRenderer/renderXYPlot.d.ts +3 -0
- package/esm/XYPlotRenderer/renderXYPlot.js +23 -0
- package/esm/configSchema.d.ts +3 -3
- package/esm/configSchema.js +1 -1
- package/esm/drawDensity.d.ts +4 -2
- package/esm/drawDensity.js +25 -15
- package/esm/drawLine.d.ts +5 -3
- package/esm/drawLine.js +118 -41
- package/esm/drawXY.d.ts +4 -2
- package/esm/drawXY.js +75 -36
- package/esm/getMultiWiggleSourcesAutorun.d.ts +4 -2
- package/esm/getMultiWiggleSourcesAutorun.js +7 -2
- package/esm/getQuantitativeStats.d.ts +4 -2
- package/esm/getQuantitativeStats.js +18 -7
- package/esm/getQuantitativeStatsAutorun.d.ts +3 -2
- package/esm/getQuantitativeStatsAutorun.js +3 -3
- package/esm/index.d.ts +15 -19
- package/esm/index.js +31 -37
- package/esm/multiRendererHelper.d.ts +7 -0
- package/esm/multiRendererHelper.js +12 -0
- package/esm/saveTrackFormats/bedGraph.d.ts +4 -0
- package/esm/saveTrackFormats/bedGraph.js +11 -0
- package/esm/shared/SharedWiggleConfigSchema.d.ts +5 -5
- package/esm/shared/SharedWiggleConfigSchema.js +1 -1
- package/esm/shared/SharedWiggleMixin.d.ts +1083 -120
- package/esm/shared/SharedWiggleMixin.js +48 -26
- package/esm/shared/YScaleBar.d.ts +1 -1
- package/esm/shared/YScaleBar.js +16 -4
- package/esm/shared/axisPropsFromTickScale.d.ts +7 -0
- package/esm/shared/axisPropsFromTickScale.js +12 -0
- package/esm/svgExportUtil.d.ts +9 -0
- package/esm/svgExportUtil.js +6 -0
- package/esm/types.d.ts +24 -0
- package/esm/types.js +1 -0
- package/esm/util.d.ts +35 -1
- package/esm/util.js +61 -2
- package/package.json +35 -38
- package/dist/BigWigAdapter/BigWigAdapter.d.ts +0 -25
- package/dist/BigWigAdapter/BigWigAdapter.js +0 -81
- package/dist/BigWigAdapter/configSchema.d.ts +0 -20
- package/dist/BigWigAdapter/configSchema.js +0 -37
- package/dist/BigWigAdapter/index.d.ts +0 -2
- package/dist/BigWigAdapter/index.js +0 -54
- package/dist/CreateMultiWiggleExtension/ConfirmDialog.d.ts +0 -8
- package/dist/CreateMultiWiggleExtension/ConfirmDialog.js +0 -26
- package/dist/CreateMultiWiggleExtension/index.d.ts +0 -2
- package/dist/CreateMultiWiggleExtension/index.js +0 -95
- package/dist/DensityRenderer/DensityRenderer.d.ts +0 -7
- package/dist/DensityRenderer/DensityRenderer.js +0 -46
- package/dist/DensityRenderer/configSchema.d.ts +0 -37
- package/dist/DensityRenderer/configSchema.js +0 -13
- package/dist/DensityRenderer/index.d.ts +0 -2
- package/dist/DensityRenderer/index.js +0 -17
- package/dist/GuessAdapter/index.d.ts +0 -2
- package/dist/GuessAdapter/index.js +0 -25
- package/dist/LinePlotRenderer/LinePlotRenderer.d.ts +0 -8
- package/dist/LinePlotRenderer/LinePlotRenderer.js +0 -56
- package/dist/LinePlotRenderer/configSchema.d.ts +0 -43
- package/dist/LinePlotRenderer/configSchema.js +0 -19
- package/dist/LinePlotRenderer/index.d.ts +0 -2
- package/dist/LinePlotRenderer/index.js +0 -17
- package/dist/LinearWiggleDisplay/components/SetColorDialog.d.ts +0 -12
- package/dist/LinearWiggleDisplay/components/SetColorDialog.js +0 -31
- package/dist/LinearWiggleDisplay/components/Tooltip.d.ts +0 -15
- package/dist/LinearWiggleDisplay/components/Tooltip.js +0 -32
- package/dist/LinearWiggleDisplay/components/WiggleDisplayComponent.d.ts +0 -5
- package/dist/LinearWiggleDisplay/components/WiggleDisplayComponent.js +0 -28
- package/dist/LinearWiggleDisplay/configSchema.d.ts +0 -78
- package/dist/LinearWiggleDisplay/configSchema.js +0 -29
- package/dist/LinearWiggleDisplay/index.d.ts +0 -5
- package/dist/LinearWiggleDisplay/index.js +0 -65
- package/dist/LinearWiggleDisplay/model.d.ts +0 -419
- package/dist/LinearWiggleDisplay/model.js +0 -262
- package/dist/LinearWiggleDisplay/renderSvg.d.ts +0 -3
- package/dist/LinearWiggleDisplay/renderSvg.js +0 -16
- package/dist/MultiDensityRenderer/MultiDensityRenderer.d.ts +0 -8
- package/dist/MultiDensityRenderer/MultiDensityRenderer.js +0 -65
- package/dist/MultiDensityRenderer/configSchema.d.ts +0 -37
- package/dist/MultiDensityRenderer/configSchema.js +0 -13
- package/dist/MultiDensityRenderer/index.d.ts +0 -2
- package/dist/MultiDensityRenderer/index.js +0 -17
- package/dist/MultiLineRenderer/MultiLineRenderer.d.ts +0 -8
- package/dist/MultiLineRenderer/MultiLineRenderer.js +0 -58
- package/dist/MultiLineRenderer/configSchema.d.ts +0 -49
- package/dist/MultiLineRenderer/configSchema.js +0 -26
- package/dist/MultiLineRenderer/index.d.ts +0 -2
- package/dist/MultiLineRenderer/index.js +0 -17
- package/dist/MultiLinearWiggleDisplay/components/ColorLegend.d.ts +0 -7
- package/dist/MultiLinearWiggleDisplay/components/ColorLegend.js +0 -18
- package/dist/MultiLinearWiggleDisplay/components/FullHeightScaleBar.d.ts +0 -7
- package/dist/MultiLinearWiggleDisplay/components/FullHeightScaleBar.js +0 -17
- package/dist/MultiLinearWiggleDisplay/components/IndividualScaleBars.d.ts +0 -7
- package/dist/MultiLinearWiggleDisplay/components/IndividualScaleBars.js +0 -15
- package/dist/MultiLinearWiggleDisplay/components/LegendItem.d.ts +0 -11
- package/dist/MultiLinearWiggleDisplay/components/LegendItem.js +0 -19
- package/dist/MultiLinearWiggleDisplay/components/RectBg.d.ts +0 -8
- package/dist/MultiLinearWiggleDisplay/components/RectBg.js +0 -9
- package/dist/MultiLinearWiggleDisplay/components/ScoreLegend.d.ts +0 -5
- package/dist/MultiLinearWiggleDisplay/components/ScoreLegend.js +0 -19
- package/dist/MultiLinearWiggleDisplay/components/SetColorDialog.d.ts +0 -9
- package/dist/MultiLinearWiggleDisplay/components/SetColorDialog.js +0 -42
- package/dist/MultiLinearWiggleDisplay/components/SourcesGrid.d.ts +0 -7
- package/dist/MultiLinearWiggleDisplay/components/SourcesGrid.js +0 -130
- package/dist/MultiLinearWiggleDisplay/components/Tooltip.d.ts +0 -18
- package/dist/MultiLinearWiggleDisplay/components/Tooltip.js +0 -35
- package/dist/MultiLinearWiggleDisplay/components/WiggleClusterDialog/WiggleClusterDialog.d.ts +0 -6
- package/dist/MultiLinearWiggleDisplay/components/WiggleClusterDialog/WiggleClusterDialog.js +0 -29
- package/dist/MultiLinearWiggleDisplay/components/WiggleClusterDialog/WiggleClusterDialogAuto.d.ts +0 -7
- package/dist/MultiLinearWiggleDisplay/components/WiggleClusterDialog/WiggleClusterDialogAuto.js +0 -79
- package/dist/MultiLinearWiggleDisplay/components/WiggleClusterDialog/WiggleClusterDialogManual.d.ts +0 -7
- package/dist/MultiLinearWiggleDisplay/components/WiggleClusterDialog/WiggleClusterDialogManual.js +0 -145
- package/dist/MultiLinearWiggleDisplay/components/WiggleClusterDialog/types.d.ts +0 -7
- package/dist/MultiLinearWiggleDisplay/components/WiggleClusterDialog/types.js +0 -2
- package/dist/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.d.ts +0 -5
- package/dist/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.js +0 -14
- package/dist/MultiLinearWiggleDisplay/components/YScaleBars.d.ts +0 -7
- package/dist/MultiLinearWiggleDisplay/components/YScaleBars.js +0 -28
- package/dist/MultiLinearWiggleDisplay/components/util.d.ts +0 -13
- package/dist/MultiLinearWiggleDisplay/components/util.js +0 -45
- package/dist/MultiLinearWiggleDisplay/configSchema.d.ts +0 -84
- package/dist/MultiLinearWiggleDisplay/configSchema.js +0 -44
- package/dist/MultiLinearWiggleDisplay/index.d.ts +0 -2
- package/dist/MultiLinearWiggleDisplay/index.js +0 -57
- package/dist/MultiLinearWiggleDisplay/model.d.ts +0 -436
- package/dist/MultiLinearWiggleDisplay/model.js +0 -413
- package/dist/MultiLinearWiggleDisplay/renderSvg.d.ts +0 -3
- package/dist/MultiLinearWiggleDisplay/renderSvg.js +0 -15
- package/dist/MultiLinearWiggleDisplay/types.d.ts +0 -14
- package/dist/MultiLinearWiggleDisplay/types.js +0 -2
- package/dist/MultiLinearWiggleDisplay/util.d.ts +0 -1
- package/dist/MultiLinearWiggleDisplay/util.js +0 -10
- package/dist/MultiQuantitativeTrack/configSchema.d.ts +0 -80
- package/dist/MultiQuantitativeTrack/configSchema.js +0 -11
- package/dist/MultiQuantitativeTrack/index.d.ts +0 -2
- package/dist/MultiQuantitativeTrack/index.js +0 -20
- package/dist/MultiRowLineRenderer/MultiRowLineRenderer.d.ts +0 -8
- package/dist/MultiRowLineRenderer/MultiRowLineRenderer.js +0 -70
- package/dist/MultiRowLineRenderer/configSchema.d.ts +0 -49
- package/dist/MultiRowLineRenderer/configSchema.js +0 -26
- package/dist/MultiRowLineRenderer/index.d.ts +0 -2
- package/dist/MultiRowLineRenderer/index.js +0 -17
- package/dist/MultiRowXYPlotRenderer/MultiRowXYPlotRenderer.d.ts +0 -8
- package/dist/MultiRowXYPlotRenderer/MultiRowXYPlotRenderer.js +0 -70
- package/dist/MultiRowXYPlotRenderer/configSchema.d.ts +0 -57
- package/dist/MultiRowXYPlotRenderer/configSchema.js +0 -34
- package/dist/MultiRowXYPlotRenderer/index.d.ts +0 -2
- package/dist/MultiRowXYPlotRenderer/index.js +0 -17
- package/dist/MultiWiggleAdapter/MultiWiggleAdapter.d.ts +0 -30
- package/dist/MultiWiggleAdapter/MultiWiggleAdapter.js +0 -85
- package/dist/MultiWiggleAdapter/configSchema.d.ts +0 -13
- package/dist/MultiWiggleAdapter/configSchema.js +0 -17
- package/dist/MultiWiggleAdapter/index.d.ts +0 -2
- package/dist/MultiWiggleAdapter/index.js +0 -57
- package/dist/MultiWiggleAddTrackWorkflow/AddTrackWorkflow.d.ts +0 -5
- package/dist/MultiWiggleAddTrackWorkflow/AddTrackWorkflow.js +0 -89
- package/dist/MultiWiggleAddTrackWorkflow/index.d.ts +0 -2
- package/dist/MultiWiggleAddTrackWorkflow/index.js +0 -46
- package/dist/MultiWiggleRendering.d.ts +0 -19
- package/dist/MultiWiggleRendering.js +0 -81
- package/dist/MultiXYPlotRenderer/MultiXYPlotRenderer.d.ts +0 -8
- package/dist/MultiXYPlotRenderer/MultiXYPlotRenderer.js +0 -61
- package/dist/MultiXYPlotRenderer/configSchema.d.ts +0 -57
- package/dist/MultiXYPlotRenderer/configSchema.js +0 -34
- package/dist/MultiXYPlotRenderer/index.d.ts +0 -2
- package/dist/MultiXYPlotRenderer/index.js +0 -17
- package/dist/QuantitativeTrack/configSchema.d.ts +0 -80
- package/dist/QuantitativeTrack/configSchema.js +0 -11
- package/dist/QuantitativeTrack/index.d.ts +0 -2
- package/dist/QuantitativeTrack/index.js +0 -20
- package/dist/Tooltip.d.ts +0 -18
- package/dist/Tooltip.js +0 -34
- package/dist/WiggleBaseRenderer.d.ts +0 -57
- package/dist/WiggleBaseRenderer.js +0 -42
- package/dist/WiggleRPC/MultiWiggleClusterScoreMatrix.d.ts +0 -14
- package/dist/WiggleRPC/MultiWiggleClusterScoreMatrix.js +0 -31
- package/dist/WiggleRPC/MultiWiggleGetScoreMatrix.d.ts +0 -6
- package/dist/WiggleRPC/MultiWiggleGetScoreMatrix.js +0 -22
- package/dist/WiggleRPC/MultiWiggleGetSources.d.ts +0 -14
- package/dist/WiggleRPC/MultiWiggleGetSources.js +0 -22
- package/dist/WiggleRPC/WiggleGetGlobalQuantitativeStats.d.ts +0 -12
- package/dist/WiggleRPC/WiggleGetGlobalQuantitativeStats.js +0 -22
- package/dist/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.d.ts +0 -13
- package/dist/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.js +0 -22
- package/dist/WiggleRPC/getScoreMatrix.d.ts +0 -6
- package/dist/WiggleRPC/getScoreMatrix.js +0 -35
- package/dist/WiggleRPC/rpcMethods.d.ts +0 -5
- package/dist/WiggleRPC/rpcMethods.js +0 -21
- package/dist/WiggleRPC/type.d.ts +0 -0
- package/dist/WiggleRPC/type.js +0 -1
- package/dist/WiggleRPC/types.d.ts +0 -13
- package/dist/WiggleRPC/types.js +0 -2
- package/dist/WiggleRendering.d.ts +0 -14
- package/dist/WiggleRendering.js +0 -35
- package/dist/XYPlotRenderer/XYPlotRenderer.d.ts +0 -7
- package/dist/XYPlotRenderer/XYPlotRenderer.js +0 -61
- package/dist/XYPlotRenderer/configSchema.d.ts +0 -57
- package/dist/XYPlotRenderer/configSchema.js +0 -34
- package/dist/XYPlotRenderer/index.d.ts +0 -5
- package/dist/XYPlotRenderer/index.js +0 -24
- package/dist/configSchema.d.ts +0 -37
- package/dist/configSchema.js +0 -47
- package/dist/drawDensity.d.ts +0 -18
- package/dist/drawDensity.js +0 -81
- package/dist/drawLine.d.ts +0 -20
- package/dist/drawLine.js +0 -77
- package/dist/drawXY.d.ts +0 -21
- package/dist/drawXY.js +0 -191
- package/dist/getMultiWiggleSourcesAutorun.d.ts +0 -17
- package/dist/getMultiWiggleSourcesAutorun.js +0 -38
- package/dist/getQuantitativeStats.d.ts +0 -13
- package/dist/getQuantitativeStats.js +0 -70
- package/dist/getQuantitativeStatsAutorun.d.ts +0 -13
- package/dist/getQuantitativeStatsAutorun.js +0 -35
- package/dist/index.d.ts +0 -91
- package/dist/index.js +0 -112
- package/dist/shared/SetMinMaxDialog.d.ts +0 -10
- package/dist/shared/SetMinMaxDialog.js +0 -26
- package/dist/shared/SharedWiggleConfigSchema.d.ts +0 -66
- package/dist/shared/SharedWiggleConfigSchema.js +0 -56
- package/dist/shared/SharedWiggleMixin.d.ts +0 -405
- package/dist/shared/SharedWiggleMixin.js +0 -343
- package/dist/shared/YScaleBar.d.ts +0 -9
- package/dist/shared/YScaleBar.js +0 -12
- package/dist/util.d.ts +0 -24
- package/dist/util.js +0 -105
- package/esm/WiggleBaseRenderer.d.ts +0 -57
- package/esm/WiggleBaseRenderer.js +0 -36
- package/esm/WiggleRPC/type.d.ts +0 -0
- package/esm/WiggleRPC/type.js +0 -1
package/dist/drawLine.js
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exports.drawLine = drawLine;
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const configuration_1 = require("@jbrowse/core/configuration");
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const util_1 = require("@jbrowse/core/util");
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const stopToken_1 = require("@jbrowse/core/util/stopToken");
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const util_2 = require("./util");
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const fudgeFactor = 0.3;
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const clipHeight = 2;
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function drawLine(ctx, props) {
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const { features, regions, bpPerPx, scaleOpts, height: unadjustedHeight, ticks: { values }, displayCrossHatches, colorCallback, config, offset = 0, stopToken, } = props;
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const region = regions[0];
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const width = (region.end - region.start) / bpPerPx;
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const height = unadjustedHeight - offset * 2;
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const clipColor = (0, configuration_1.readConfObject)(config, 'clipColor');
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const scale = (0, util_2.getScale)({ ...scaleOpts, range: [0, height] });
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const niceMin = domain[0];
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const niceMax = domain[1];
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const toY = (n) => (0, util_1.clamp)(height - (scale(n) || 0), 0, height) + offset;
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let lastVal;
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let prevLeftPx = Number.NEGATIVE_INFINITY;
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const reducedFeatures = [];
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let start = performance.now();
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for (const feature of features.values()) {
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start = performance.now();
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}
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const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
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if (Math.floor(leftPx) !== Math.floor(prevLeftPx) || rightPx - leftPx > 1) {
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prevLeftPx = leftPx;
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}
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const score = feature.get('score');
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const lowClipping = score < niceMin;
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const highClipping = score > niceMax;
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const w = rightPx - leftPx + fudgeFactor;
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const c = colorCallback(feature, score);
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ctx.beginPath();
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ctx.strokeStyle = c;
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const startPos = lastVal !== undefined ? lastVal : score;
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if (!region.reversed) {
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ctx.moveTo(leftPx, toY(startPos));
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ctx.lineTo(leftPx, toY(score));
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ctx.lineTo(rightPx, toY(score));
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}
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else {
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ctx.moveTo(rightPx, toY(startPos));
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ctx.lineTo(rightPx, toY(score));
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ctx.lineTo(leftPx, toY(score));
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}
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ctx.stroke();
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lastVal = score;
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if (highClipping) {
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ctx.fillStyle = clipColor;
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ctx.fillRect(leftPx, offset, w, clipHeight);
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}
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else if (lowClipping && scaleOpts.scaleType !== 'log') {
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ctx.fillStyle = clipColor;
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ctx.fillRect(leftPx, height - clipHeight, w, height);
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}
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}
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if (displayCrossHatches) {
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ctx.lineWidth = 1;
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ctx.strokeStyle = 'rgba(200,200,200,0.5)';
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for (const tick of values) {
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ctx.beginPath();
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ctx.moveTo(0, Math.round(toY(tick)));
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ctx.lineTo(width, Math.round(toY(tick)));
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}
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return {
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};
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}
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import type { ScaleOpts } from './util';
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import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
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import type { Feature, Region } from '@jbrowse/core/util';
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export declare function drawXY(ctx: CanvasRenderingContext2D, props: {
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stopToken?: string;
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features: Map<string, Feature> | Feature[];
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bpPerPx: number;
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regions: Region[];
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scaleOpts: ScaleOpts;
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height: number;
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ticks: {
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values: number[];
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};
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config: AnyConfigurationModel;
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displayCrossHatches: boolean;
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inverted: boolean;
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offset?: number;
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colorCallback: (f: Feature, score: number) => string;
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}): {
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reducedFeatures: Feature[];
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};
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.drawXY = drawXY;
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const configuration_1 = require("@jbrowse/core/configuration");
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const util_1 = require("@jbrowse/core/util");
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const colord_1 = require("@jbrowse/core/util/colord");
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const stopToken_1 = require("@jbrowse/core/util/stopToken");
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const util_2 = require("./util");
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function lighten(color, amount) {
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...hslColor,
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l: (0, util_1.clamp)(l, 0, 100),
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});
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}
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function darken(color, amount) {
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return (0, colord_1.colord)({
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...hslColor,
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});
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}
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const fudgeFactor = 0.3;
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const clipHeight = 2;
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function drawXY(ctx, props) {
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const { features, bpPerPx, regions, scaleOpts, height: unadjustedHeight, config, ticks, displayCrossHatches, offset = 0, colorCallback, inverted, stopToken, } = props;
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const region = regions[0];
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const width = (region.end - region.start) / bpPerPx;
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const height = unadjustedHeight - offset * 2;
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const filled = (0, configuration_1.readConfObject)(config, 'filled');
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const clipColor = (0, configuration_1.readConfObject)(config, 'clipColor');
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const summaryScoreMode = (0, configuration_1.readConfObject)(config, 'summaryScoreMode');
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const pivotValue = (0, configuration_1.readConfObject)(config, 'bicolorPivotValue');
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const minSize = (0, configuration_1.readConfObject)(config, 'minSize');
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const originY = (0, util_2.getOrigin)(scaleOpts.scaleType);
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const domain = scale.domain();
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const niceMin = domain[0];
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const niceMax = domain[1];
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const toY = (n) => (0, util_1.clamp)(height - (scale(n) || 0), 0, height) + offset;
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const toOrigin = (n) => toY(originY) - toY(n);
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const getHeight = (n) => (filled ? toOrigin(n) : Math.max(minSize, 1));
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let hasClipping = false;
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let prevLeftPx = Number.NEGATIVE_INFINITY;
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const reducedFeatures = [];
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const crossingOrigin = niceMin < pivotValue && niceMax > pivotValue;
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let start = performance.now();
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if (summaryScoreMode === 'whiskers') {
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let lastCol;
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let lastMix;
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start = performance.now();
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for (const feature of features.values()) {
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if (performance.now() - start > 400) {
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(0, stopToken_1.checkStopToken)(stopToken);
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start = performance.now();
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}
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const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
|
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if (feature.get('summary')) {
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const w = Math.max(rightPx - leftPx + fudgeFactor, minSize);
|
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const max = feature.get('maxScore');
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const c = colorCallback(feature, max);
|
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const effectiveC = crossingOrigin
|
|
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|
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? c
|
|
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|
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: c === lastCol
|
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67
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? lastMix
|
|
68
|
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: (lastMix = lighten((0, colord_1.colord)(c), 0.4).toHex());
|
|
69
|
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(0, util_2.fillRectCtx)(leftPx, toY(max), w, getHeight(max), ctx, effectiveC);
|
|
70
|
-
lastCol = c;
|
|
71
|
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}
|
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72
|
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}
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lastMix = undefined;
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lastCol = undefined;
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|
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start = performance.now();
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for (const feature of features.values()) {
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if (performance.now() - start > 400) {
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(0, stopToken_1.checkStopToken)(stopToken);
|
|
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|
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start = performance.now();
|
|
80
|
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}
|
|
81
|
-
const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
|
|
82
|
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const score = feature.get('score');
|
|
83
|
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const max = feature.get('maxScore');
|
|
84
|
-
const min = feature.get('minScore');
|
|
85
|
-
const summary = feature.get('summary');
|
|
86
|
-
const c = colorCallback(feature, score);
|
|
87
|
-
const effectiveC = crossingOrigin && summary
|
|
88
|
-
? c === lastCol
|
|
89
|
-
? lastMix
|
|
90
|
-
: (lastMix = (0, colord_1.colord)(colorCallback(feature, max))
|
|
91
|
-
.mix((0, colord_1.colord)(colorCallback(feature, min)))
|
|
92
|
-
.toString())
|
|
93
|
-
: c;
|
|
94
|
-
const w = Math.max(rightPx - leftPx + fudgeFactor, minSize);
|
|
95
|
-
if (Math.floor(leftPx) !== Math.floor(prevLeftPx) ||
|
|
96
|
-
rightPx - leftPx > 1) {
|
|
97
|
-
reducedFeatures.push(feature);
|
|
98
|
-
prevLeftPx = leftPx;
|
|
99
|
-
}
|
|
100
|
-
hasClipping = hasClipping || score < niceMin || score > niceMax;
|
|
101
|
-
(0, util_2.fillRectCtx)(leftPx, toY(score), w, getHeight(score), ctx, effectiveC);
|
|
102
|
-
lastCol = c;
|
|
103
|
-
}
|
|
104
|
-
lastMix = undefined;
|
|
105
|
-
lastCol = undefined;
|
|
106
|
-
start = performance.now();
|
|
107
|
-
for (const feature of features.values()) {
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|
108
|
-
if (performance.now() - start > 400) {
|
|
109
|
-
(0, stopToken_1.checkStopToken)(stopToken);
|
|
110
|
-
start = performance.now();
|
|
111
|
-
}
|
|
112
|
-
const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
|
|
113
|
-
if (feature.get('summary')) {
|
|
114
|
-
const min = feature.get('minScore');
|
|
115
|
-
const c = colorCallback(feature, min);
|
|
116
|
-
const w = Math.max(rightPx - leftPx + fudgeFactor, minSize);
|
|
117
|
-
const effectiveC = crossingOrigin
|
|
118
|
-
? c
|
|
119
|
-
: c === lastCol
|
|
120
|
-
? lastMix
|
|
121
|
-
: (lastMix = darken((0, colord_1.colord)(c), 0.4).toHex());
|
|
122
|
-
(0, util_2.fillRectCtx)(leftPx, toY(min), w, getHeight(min), ctx, effectiveC);
|
|
123
|
-
lastCol = c;
|
|
124
|
-
}
|
|
125
|
-
}
|
|
126
|
-
}
|
|
127
|
-
else {
|
|
128
|
-
start = performance.now();
|
|
129
|
-
for (const feature of features.values()) {
|
|
130
|
-
if (performance.now() - start > 400) {
|
|
131
|
-
(0, stopToken_1.checkStopToken)(stopToken);
|
|
132
|
-
start = performance.now();
|
|
133
|
-
}
|
|
134
|
-
const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
|
|
135
|
-
if (Math.floor(leftPx) !== Math.floor(prevLeftPx) ||
|
|
136
|
-
rightPx - leftPx > 1) {
|
|
137
|
-
reducedFeatures.push(feature);
|
|
138
|
-
prevLeftPx = leftPx;
|
|
139
|
-
}
|
|
140
|
-
const score = feature.get('score');
|
|
141
|
-
const c = colorCallback(feature, score);
|
|
142
|
-
hasClipping = hasClipping || score < niceMin || score > niceMax;
|
|
143
|
-
const w = Math.max(rightPx - leftPx + fudgeFactor, minSize);
|
|
144
|
-
if (summaryScoreMode === 'max') {
|
|
145
|
-
const s = feature.get('summary') ? feature.get('maxScore') : score;
|
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(0, util_2.fillRectCtx)(leftPx, toY(s), w, getHeight(s), ctx, c);
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else if (summaryScoreMode === 'min') {
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(0, util_2.fillRectCtx)(leftPx, toY(s), w, getHeight(s), ctx, c);
|
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else {
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}
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start = performance.now();
|
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}
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|
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const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
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const w = rightPx - leftPx + fudgeFactor;
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const score = feature.get('score');
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}
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else if (score < niceMin && scaleOpts.scaleType !== 'log') {
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}
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}
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ctx.lineWidth = 1;
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ctx.strokeStyle = 'rgba(200,200,200,0.5)';
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ctx.beginPath();
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ctx.moveTo(0, Math.round(toY(tick)));
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}
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}
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return {
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reducedFeatures,
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};
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}
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@@ -1,17 +0,0 @@
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import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
|
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export interface Source {
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name: string;
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color?: string;
|
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|
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group?: string;
|
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|
-
}
|
|
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|
-
export declare function getMultiWiggleSourcesAutorun(self: {
|
|
8
|
-
quantitativeStatsReady: boolean;
|
|
9
|
-
configuration: AnyConfigurationModel;
|
|
10
|
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adapterConfig: AnyConfigurationModel;
|
|
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|
-
autoscaleType: string;
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|
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adapterProps: () => Record<string, unknown>;
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setSourcesLoading: (aborter: string) => void;
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|
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setError: (error: unknown) => void;
|
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|
-
setMessage: (str: string) => void;
|
|
16
|
-
setSources: (sources: Source[]) => void;
|
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|
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}): void;
|
|
@@ -1,38 +0,0 @@
|
|
|
1
|
-
"use strict";
|
|
2
|
-
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
-
exports.getMultiWiggleSourcesAutorun = getMultiWiggleSourcesAutorun;
|
|
4
|
-
const util_1 = require("@jbrowse/core/util");
|
|
5
|
-
const aborting_1 = require("@jbrowse/core/util/aborting");
|
|
6
|
-
const stopToken_1 = require("@jbrowse/core/util/stopToken");
|
|
7
|
-
const tracks_1 = require("@jbrowse/core/util/tracks");
|
|
8
|
-
const mobx_1 = require("mobx");
|
|
9
|
-
const mobx_state_tree_1 = require("mobx-state-tree");
|
|
10
|
-
function getMultiWiggleSourcesAutorun(self) {
|
|
11
|
-
(0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
|
|
12
|
-
try {
|
|
13
|
-
const view = (0, util_1.getContainingView)(self);
|
|
14
|
-
if (!view.initialized) {
|
|
15
|
-
return;
|
|
16
|
-
}
|
|
17
|
-
const { rpcManager } = (0, util_1.getSession)(self);
|
|
18
|
-
const { adapterConfig } = self;
|
|
19
|
-
const token = (0, stopToken_1.createStopToken)();
|
|
20
|
-
self.setSourcesLoading(token);
|
|
21
|
-
const sessionId = (0, tracks_1.getRpcSessionId)(self);
|
|
22
|
-
const sources = (await rpcManager.call(sessionId, 'MultiWiggleGetSources', {
|
|
23
|
-
regions: view.staticBlocks.contentBlocks,
|
|
24
|
-
sessionId,
|
|
25
|
-
adapterConfig,
|
|
26
|
-
}));
|
|
27
|
-
if ((0, mobx_state_tree_1.isAlive)(self)) {
|
|
28
|
-
self.setSources(sources);
|
|
29
|
-
}
|
|
30
|
-
}
|
|
31
|
-
catch (e) {
|
|
32
|
-
if (!(0, aborting_1.isAbortException)(e) && (0, mobx_state_tree_1.isAlive)(self)) {
|
|
33
|
-
console.error(e);
|
|
34
|
-
(0, util_1.getSession)(self).notifyError(`${e}`, e);
|
|
35
|
-
}
|
|
36
|
-
}
|
|
37
|
-
}));
|
|
38
|
-
}
|
|
@@ -1,13 +0,0 @@
|
|
|
1
|
-
import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
|
|
2
|
-
import type { QuantitativeStats } from '@jbrowse/core/util/stats';
|
|
3
|
-
export declare function getQuantitativeStats(self: {
|
|
4
|
-
adapterConfig: AnyConfigurationModel;
|
|
5
|
-
configuration: AnyConfigurationModel;
|
|
6
|
-
autoscaleType: string;
|
|
7
|
-
setMessage: (str: string) => void;
|
|
8
|
-
}, opts: {
|
|
9
|
-
headers?: Record<string, string>;
|
|
10
|
-
stopToken?: string;
|
|
11
|
-
filters: string[];
|
|
12
|
-
currStatsBpPerPx: number;
|
|
13
|
-
}): Promise<QuantitativeStats>;
|
|
@@ -1,70 +0,0 @@
|
|
|
1
|
-
"use strict";
|
|
2
|
-
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
-
exports.getQuantitativeStats = getQuantitativeStats;
|
|
4
|
-
const configuration_1 = require("@jbrowse/core/configuration");
|
|
5
|
-
const util_1 = require("@jbrowse/core/util");
|
|
6
|
-
const tracks_1 = require("@jbrowse/core/util/tracks");
|
|
7
|
-
const mobx_state_tree_1 = require("mobx-state-tree");
|
|
8
|
-
async function getQuantitativeStats(self, opts) {
|
|
9
|
-
const { rpcManager } = (0, util_1.getSession)(self);
|
|
10
|
-
const numStdDev = (0, configuration_1.getConf)(self, 'numStdDev') || 3;
|
|
11
|
-
const { adapterConfig, autoscaleType } = self;
|
|
12
|
-
const sessionId = (0, tracks_1.getRpcSessionId)(self);
|
|
13
|
-
const { currStatsBpPerPx } = opts;
|
|
14
|
-
const params = {
|
|
15
|
-
sessionId,
|
|
16
|
-
adapterConfig,
|
|
17
|
-
statusCallback: (message) => {
|
|
18
|
-
if ((0, mobx_state_tree_1.isAlive)(self)) {
|
|
19
|
-
self.setMessage(message);
|
|
20
|
-
}
|
|
21
|
-
},
|
|
22
|
-
...opts,
|
|
23
|
-
};
|
|
24
|
-
if (autoscaleType === 'global' || autoscaleType === 'globalsd') {
|
|
25
|
-
const results = (await rpcManager.call(sessionId, 'WiggleGetGlobalQuantitativeStats', params));
|
|
26
|
-
const { scoreMin, scoreMean, scoreStdDev } = results;
|
|
27
|
-
return autoscaleType === 'globalsd'
|
|
28
|
-
? {
|
|
29
|
-
...results,
|
|
30
|
-
scoreMin: scoreMin >= 0 ? 0 : scoreMean - numStdDev * scoreStdDev,
|
|
31
|
-
scoreMax: scoreMean + numStdDev * scoreStdDev,
|
|
32
|
-
currStatsBpPerPx,
|
|
33
|
-
}
|
|
34
|
-
: {
|
|
35
|
-
...results,
|
|
36
|
-
currStatsBpPerPx,
|
|
37
|
-
};
|
|
38
|
-
}
|
|
39
|
-
if (autoscaleType === 'local' || autoscaleType === 'localsd') {
|
|
40
|
-
const { dynamicBlocks, bpPerPx } = (0, util_1.getContainingView)(self);
|
|
41
|
-
const results = (await rpcManager.call(sessionId, 'WiggleGetMultiRegionQuantitativeStats', {
|
|
42
|
-
...params,
|
|
43
|
-
regions: dynamicBlocks.contentBlocks.map(region => {
|
|
44
|
-
const { start, end } = region;
|
|
45
|
-
return {
|
|
46
|
-
...JSON.parse(JSON.stringify(region)),
|
|
47
|
-
start: Math.floor(start),
|
|
48
|
-
end: Math.ceil(end),
|
|
49
|
-
};
|
|
50
|
-
}),
|
|
51
|
-
bpPerPx,
|
|
52
|
-
}));
|
|
53
|
-
const { scoreMin, scoreMean, scoreStdDev } = results;
|
|
54
|
-
return autoscaleType === 'localsd'
|
|
55
|
-
? {
|
|
56
|
-
...results,
|
|
57
|
-
scoreMin: scoreMin >= 0 ? 0 : scoreMean - numStdDev * scoreStdDev,
|
|
58
|
-
scoreMax: scoreMean + numStdDev * scoreStdDev,
|
|
59
|
-
currStatsBpPerPx,
|
|
60
|
-
}
|
|
61
|
-
: {
|
|
62
|
-
...results,
|
|
63
|
-
currStatsBpPerPx,
|
|
64
|
-
};
|
|
65
|
-
}
|
|
66
|
-
if (autoscaleType === 'zscale') {
|
|
67
|
-
return rpcManager.call(sessionId, 'WiggleGetGlobalQuantitativeStats', params);
|
|
68
|
-
}
|
|
69
|
-
throw new Error(`invalid autoscaleType '${autoscaleType}'`);
|
|
70
|
-
}
|
|
@@ -1,13 +0,0 @@
|
|
|
1
|
-
import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
|
|
2
|
-
import type { QuantitativeStats } from '@jbrowse/core/util/stats';
|
|
3
|
-
export declare function getQuantitativeStatsAutorun(self: {
|
|
4
|
-
quantitativeStatsReady: boolean;
|
|
5
|
-
configuration: AnyConfigurationModel;
|
|
6
|
-
adapterConfig: AnyConfigurationModel;
|
|
7
|
-
autoscaleType: string;
|
|
8
|
-
adapterProps: () => Record<string, unknown>;
|
|
9
|
-
setStatsLoading: (token: string) => void;
|
|
10
|
-
setError: (error: unknown) => void;
|
|
11
|
-
setMessage: (str: string) => void;
|
|
12
|
-
updateQuantitativeStats: (stats: QuantitativeStats, region: string) => void;
|
|
13
|
-
}): void;
|
|
@@ -1,35 +0,0 @@
|
|
|
1
|
-
"use strict";
|
|
2
|
-
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
-
exports.getQuantitativeStatsAutorun = getQuantitativeStatsAutorun;
|
|
4
|
-
const util_1 = require("@jbrowse/core/util");
|
|
5
|
-
const stopToken_1 = require("@jbrowse/core/util/stopToken");
|
|
6
|
-
const mobx_1 = require("mobx");
|
|
7
|
-
const mobx_state_tree_1 = require("mobx-state-tree");
|
|
8
|
-
const getQuantitativeStats_1 = require("./getQuantitativeStats");
|
|
9
|
-
function getQuantitativeStatsAutorun(self) {
|
|
10
|
-
(0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
|
|
11
|
-
try {
|
|
12
|
-
if (self.quantitativeStatsReady) {
|
|
13
|
-
const view = (0, util_1.getContainingView)(self);
|
|
14
|
-
const stopToken = (0, stopToken_1.createStopToken)();
|
|
15
|
-
self.setStatsLoading(stopToken);
|
|
16
|
-
const statsRegion = JSON.stringify(view.dynamicBlocks);
|
|
17
|
-
const wiggleStats = await (0, getQuantitativeStats_1.getQuantitativeStats)(self, {
|
|
18
|
-
stopToken,
|
|
19
|
-
filters: [],
|
|
20
|
-
currStatsBpPerPx: view.bpPerPx,
|
|
21
|
-
...self.adapterProps(),
|
|
22
|
-
});
|
|
23
|
-
if ((0, mobx_state_tree_1.isAlive)(self)) {
|
|
24
|
-
self.updateQuantitativeStats(wiggleStats, statsRegion);
|
|
25
|
-
}
|
|
26
|
-
}
|
|
27
|
-
}
|
|
28
|
-
catch (e) {
|
|
29
|
-
if ((0, mobx_state_tree_1.isAlive)(self) && !(0, util_1.isAbortException)(e)) {
|
|
30
|
-
console.error(e);
|
|
31
|
-
self.setError(e);
|
|
32
|
-
}
|
|
33
|
-
}
|
|
34
|
-
}, { delay: 1000 }));
|
|
35
|
-
}
|
package/dist/index.d.ts
DELETED
|
@@ -1,91 +0,0 @@
|
|
|
1
|
-
import Plugin from '@jbrowse/core/Plugin';
|
|
2
|
-
import { modelFactory as linearWiggleDisplayModelFactory } from './LinearWiggleDisplay';
|
|
3
|
-
import WiggleBaseRenderer from './WiggleBaseRenderer';
|
|
4
|
-
import { XYPlotRenderer } from './XYPlotRenderer';
|
|
5
|
-
import * as utils from './util';
|
|
6
|
-
import type PluginManager from '@jbrowse/core/PluginManager';
|
|
7
|
-
export default class WigglePlugin extends Plugin {
|
|
8
|
-
name: string;
|
|
9
|
-
install(pm: PluginManager): void;
|
|
10
|
-
exports: {
|
|
11
|
-
LinearWiggleDisplayReactComponent: (props: {
|
|
12
|
-
model: import("./LinearWiggleDisplay/model").WiggleDisplayModel;
|
|
13
|
-
}) => import("react/jsx-runtime").JSX.Element;
|
|
14
|
-
XYPlotRendererReactComponent: (props: {
|
|
15
|
-
regions: import("@jbrowse/core/util").Region[];
|
|
16
|
-
features: Map<string, import("@jbrowse/core/util").Feature>;
|
|
17
|
-
bpPerPx: number;
|
|
18
|
-
width: number;
|
|
19
|
-
height: number;
|
|
20
|
-
blockKey: string;
|
|
21
|
-
onMouseLeave?: (event: React.MouseEvent) => void;
|
|
22
|
-
onMouseMove?: (event: React.MouseEvent, arg?: string) => void;
|
|
23
|
-
onFeatureClick?: (event: React.MouseEvent, arg?: string) => void;
|
|
24
|
-
}) => import("react/jsx-runtime").JSX.Element;
|
|
25
|
-
XYPlotRenderer: typeof XYPlotRenderer;
|
|
26
|
-
WiggleBaseRenderer: typeof WiggleBaseRenderer;
|
|
27
|
-
linearWiggleDisplayModelFactory: typeof linearWiggleDisplayModelFactory;
|
|
28
|
-
xyPlotRendererConfigSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
|
|
29
|
-
filled: {
|
|
30
|
-
type: string;
|
|
31
|
-
defaultValue: boolean;
|
|
32
|
-
};
|
|
33
|
-
displayCrossHatches: {
|
|
34
|
-
type: string;
|
|
35
|
-
description: string;
|
|
36
|
-
defaultValue: boolean;
|
|
37
|
-
};
|
|
38
|
-
summaryScoreMode: {
|
|
39
|
-
type: string;
|
|
40
|
-
model: import("mobx-state-tree").ISimpleType<string>;
|
|
41
|
-
description: string;
|
|
42
|
-
defaultValue: string;
|
|
43
|
-
};
|
|
44
|
-
minSize: {
|
|
45
|
-
type: string;
|
|
46
|
-
defaultValue: number;
|
|
47
|
-
};
|
|
48
|
-
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
|
|
49
|
-
color: {
|
|
50
|
-
type: string;
|
|
51
|
-
description: string;
|
|
52
|
-
defaultValue: string;
|
|
53
|
-
contextVariable: string[];
|
|
54
|
-
};
|
|
55
|
-
posColor: {
|
|
56
|
-
type: string;
|
|
57
|
-
description: string;
|
|
58
|
-
defaultValue: string;
|
|
59
|
-
contextVariable: string[];
|
|
60
|
-
};
|
|
61
|
-
negColor: {
|
|
62
|
-
type: string;
|
|
63
|
-
description: string;
|
|
64
|
-
defaultValue: string;
|
|
65
|
-
contextVariable: string[];
|
|
66
|
-
};
|
|
67
|
-
clipColor: {
|
|
68
|
-
type: string;
|
|
69
|
-
description: string;
|
|
70
|
-
defaultValue: string;
|
|
71
|
-
};
|
|
72
|
-
bicolorPivot: {
|
|
73
|
-
type: string;
|
|
74
|
-
model: import("mobx-state-tree").ISimpleType<string>;
|
|
75
|
-
description: string;
|
|
76
|
-
defaultValue: string;
|
|
77
|
-
};
|
|
78
|
-
bicolorPivotValue: {
|
|
79
|
-
type: string;
|
|
80
|
-
defaultValue: number;
|
|
81
|
-
description: string;
|
|
82
|
-
};
|
|
83
|
-
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>, undefined>>;
|
|
84
|
-
utils: typeof utils;
|
|
85
|
-
};
|
|
86
|
-
}
|
|
87
|
-
export * from './util';
|
|
88
|
-
export { default as WiggleRendering } from './WiggleRendering';
|
|
89
|
-
export { ReactComponent as LinearWiggleDisplayReactComponent, Tooltip, modelFactory as linearWiggleDisplayModelFactory, } from './LinearWiggleDisplay';
|
|
90
|
-
export type { TooltipContentsComponent } from './Tooltip';
|
|
91
|
-
export { default as WiggleBaseRenderer } from './WiggleBaseRenderer';
|