@jbrowse/plugin-wiggle 2.17.0 → 3.0.0
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/dist/BigWigAdapter/BigWigAdapter.d.ts +4 -3
- package/dist/BigWigAdapter/BigWigAdapter.js +3 -8
- package/dist/BigWigAdapter/configSchema.d.ts +0 -9
- package/dist/BigWigAdapter/configSchema.js +1 -13
- package/dist/BigWigAdapter/index.d.ts +1 -1
- package/dist/BigWigAdapter/index.js +17 -7
- package/dist/CreateMultiWiggleExtension/ConfirmDialog.d.ts +2 -3
- package/dist/CreateMultiWiggleExtension/ConfirmDialog.js +14 -49
- package/dist/CreateMultiWiggleExtension/index.d.ts +1 -1
- package/dist/CreateMultiWiggleExtension/index.js +43 -33
- package/dist/DensityRenderer/DensityRenderer.d.ts +2 -1
- package/dist/DensityRenderer/DensityRenderer.js +35 -2
- package/dist/DensityRenderer/configSchema.js +1 -7
- package/dist/DensityRenderer/index.d.ts +1 -1
- package/dist/DensityRenderer/index.js +1 -1
- package/dist/GuessAdapter/index.d.ts +2 -0
- package/dist/GuessAdapter/index.js +25 -0
- package/dist/LinePlotRenderer/LinePlotRenderer.d.ts +3 -2
- package/dist/LinePlotRenderer/LinePlotRenderer.js +35 -2
- package/dist/LinePlotRenderer/configSchema.d.ts +0 -3
- package/dist/LinePlotRenderer/configSchema.js +1 -10
- package/dist/LinePlotRenderer/index.d.ts +1 -1
- package/dist/LinearWiggleDisplay/components/SetColorDialog.d.ts +1 -2
- package/dist/LinearWiggleDisplay/components/SetColorDialog.js +23 -59
- package/dist/LinearWiggleDisplay/components/Tooltip.d.ts +3 -4
- package/dist/LinearWiggleDisplay/components/Tooltip.js +5 -18
- package/dist/LinearWiggleDisplay/components/WiggleDisplayComponent.d.ts +2 -3
- package/dist/LinearWiggleDisplay/components/WiggleDisplayComponent.js +11 -14
- package/dist/LinearWiggleDisplay/configSchema.d.ts +1 -12
- package/dist/LinearWiggleDisplay/configSchema.js +0 -15
- package/dist/LinearWiggleDisplay/index.d.ts +1 -1
- package/dist/LinearWiggleDisplay/index.js +18 -8
- package/dist/LinearWiggleDisplay/model.d.ts +44 -79
- package/dist/LinearWiggleDisplay/model.js +39 -71
- package/dist/LinearWiggleDisplay/renderSvg.d.ts +3 -4
- package/dist/LinearWiggleDisplay/renderSvg.js +2 -6
- package/dist/MultiDensityRenderer/MultiDensityRenderer.d.ts +4 -3
- package/dist/MultiDensityRenderer/MultiDensityRenderer.js +40 -6
- package/dist/MultiDensityRenderer/configSchema.js +1 -7
- package/dist/MultiDensityRenderer/index.d.ts +1 -1
- package/dist/MultiLineRenderer/MultiLineRenderer.d.ts +3 -2
- package/dist/MultiLineRenderer/MultiLineRenderer.js +35 -3
- package/dist/MultiLineRenderer/configSchema.d.ts +0 -6
- package/dist/MultiLineRenderer/configSchema.js +1 -13
- package/dist/MultiLineRenderer/index.d.ts +1 -1
- package/dist/MultiLinearWiggleDisplay/components/ColorLegend.d.ts +3 -5
- package/dist/MultiLinearWiggleDisplay/components/ColorLegend.js +5 -15
- package/dist/MultiLinearWiggleDisplay/components/FullHeightScaleBar.d.ts +7 -0
- package/dist/MultiLinearWiggleDisplay/components/FullHeightScaleBar.js +17 -0
- package/dist/MultiLinearWiggleDisplay/components/IndividualScaleBars.d.ts +7 -0
- package/dist/MultiLinearWiggleDisplay/components/IndividualScaleBars.js +15 -0
- package/dist/MultiLinearWiggleDisplay/components/LegendItem.d.ts +11 -0
- package/dist/MultiLinearWiggleDisplay/components/LegendItem.js +19 -0
- package/dist/MultiLinearWiggleDisplay/components/RectBg.d.ts +1 -2
- package/dist/MultiLinearWiggleDisplay/components/RectBg.js +2 -5
- package/dist/MultiLinearWiggleDisplay/components/ScoreLegend.d.ts +2 -3
- package/dist/MultiLinearWiggleDisplay/components/ScoreLegend.js +2 -4
- package/dist/MultiLinearWiggleDisplay/components/SetColorDialog.d.ts +2 -3
- package/dist/MultiLinearWiggleDisplay/components/SetColorDialog.js +21 -60
- package/dist/MultiLinearWiggleDisplay/components/SourcesGrid.d.ts +2 -3
- package/dist/MultiLinearWiggleDisplay/components/SourcesGrid.js +80 -97
- package/dist/MultiLinearWiggleDisplay/components/Tooltip.d.ts +4 -5
- package/dist/MultiLinearWiggleDisplay/components/Tooltip.js +8 -23
- package/dist/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.d.ts +2 -3
- package/dist/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.js +2 -4
- package/dist/MultiLinearWiggleDisplay/components/YScaleBars.d.ts +2 -3
- package/dist/MultiLinearWiggleDisplay/components/YScaleBars.js +7 -27
- package/dist/MultiLinearWiggleDisplay/components/util.d.ts +1 -1
- package/dist/MultiLinearWiggleDisplay/components/util.js +1 -1
- package/dist/MultiLinearWiggleDisplay/configSchema.d.ts +1 -10
- package/dist/MultiLinearWiggleDisplay/configSchema.js +1 -19
- package/dist/MultiLinearWiggleDisplay/index.d.ts +1 -1
- package/dist/MultiLinearWiggleDisplay/index.js +18 -8
- package/dist/MultiLinearWiggleDisplay/model.d.ts +27 -146
- package/dist/MultiLinearWiggleDisplay/model.js +44 -128
- package/dist/MultiLinearWiggleDisplay/renderSvg.d.ts +3 -4
- package/dist/MultiLinearWiggleDisplay/renderSvg.js +2 -5
- package/dist/MultiLinearWiggleDisplay/util.d.ts +1 -0
- package/dist/MultiLinearWiggleDisplay/util.js +10 -0
- package/dist/MultiQuantitativeTrack/configSchema.d.ts +1 -1
- package/dist/MultiQuantitativeTrack/configSchema.js +1 -7
- package/dist/MultiQuantitativeTrack/index.d.ts +1 -1
- package/dist/MultiQuantitativeTrack/index.js +1 -1
- package/dist/MultiRowLineRenderer/MultiRowLineRenderer.d.ts +3 -2
- package/dist/MultiRowLineRenderer/MultiRowLineRenderer.js +35 -3
- package/dist/MultiRowLineRenderer/configSchema.d.ts +0 -6
- package/dist/MultiRowLineRenderer/configSchema.js +2 -14
- package/dist/MultiRowLineRenderer/index.d.ts +1 -1
- package/dist/MultiRowXYPlotRenderer/MultiRowXYPlotRenderer.d.ts +3 -2
- package/dist/MultiRowXYPlotRenderer/MultiRowXYPlotRenderer.js +35 -3
- package/dist/MultiRowXYPlotRenderer/configSchema.d.ts +0 -12
- package/dist/MultiRowXYPlotRenderer/configSchema.js +2 -20
- package/dist/MultiRowXYPlotRenderer/index.d.ts +1 -1
- package/dist/MultiWiggleAdapter/MultiWiggleAdapter.d.ts +4 -3
- package/dist/MultiWiggleAdapter/MultiWiggleAdapter.js +8 -13
- package/dist/MultiWiggleAdapter/configSchema.d.ts +0 -6
- package/dist/MultiWiggleAdapter/configSchema.js +1 -10
- package/dist/MultiWiggleAdapter/index.d.ts +1 -1
- package/dist/MultiWiggleAdapter/index.js +18 -8
- package/dist/MultiWiggleAddTrackWorkflow/AddTrackWorkflow.d.ts +4 -4
- package/dist/MultiWiggleAddTrackWorkflow/AddTrackWorkflow.js +63 -104
- package/dist/MultiWiggleAddTrackWorkflow/index.d.ts +1 -1
- package/dist/MultiWiggleAddTrackWorkflow/index.js +18 -9
- package/dist/MultiWiggleRendering.d.ts +4 -5
- package/dist/MultiWiggleRendering.js +6 -29
- package/dist/MultiXYPlotRenderer/MultiXYPlotRenderer.d.ts +3 -2
- package/dist/MultiXYPlotRenderer/MultiXYPlotRenderer.js +36 -4
- package/dist/MultiXYPlotRenderer/configSchema.d.ts +0 -12
- package/dist/MultiXYPlotRenderer/configSchema.js +1 -19
- package/dist/MultiXYPlotRenderer/index.d.ts +1 -1
- package/dist/QuantitativeTrack/configSchema.d.ts +1 -1
- package/dist/QuantitativeTrack/configSchema.js +1 -7
- package/dist/QuantitativeTrack/index.d.ts +1 -1
- package/dist/QuantitativeTrack/index.js +1 -1
- package/dist/Tooltip.d.ts +2 -3
- package/dist/Tooltip.js +7 -34
- package/dist/WiggleBaseRenderer.d.ts +8 -11
- package/dist/WiggleBaseRenderer.js +0 -1
- package/dist/WiggleRPC/MultiWiggleGetSources.d.ts +5 -12
- package/dist/WiggleRPC/MultiWiggleGetSources.js +2 -29
- package/dist/WiggleRPC/WiggleGetGlobalQuantitativeStats.d.ts +5 -7
- package/dist/WiggleRPC/WiggleGetGlobalQuantitativeStats.js +2 -15
- package/dist/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.d.ts +4 -11
- package/dist/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.js +2 -29
- package/dist/WiggleRendering.d.ts +3 -4
- package/dist/WiggleRendering.js +5 -30
- package/dist/XYPlotRenderer/XYPlotRenderer.d.ts +3 -2
- package/dist/XYPlotRenderer/XYPlotRenderer.js +37 -6
- package/dist/XYPlotRenderer/configSchema.d.ts +0 -12
- package/dist/XYPlotRenderer/configSchema.js +2 -20
- package/dist/XYPlotRenderer/index.d.ts +1 -1
- package/dist/configSchema.d.ts +0 -18
- package/dist/configSchema.js +1 -23
- package/dist/drawDensity.d.ts +3 -3
- package/dist/drawDensity.js +0 -4
- package/dist/drawLine.d.ts +3 -3
- package/dist/drawLine.js +0 -5
- package/dist/drawXY.d.ts +4 -3
- package/dist/drawXY.js +28 -12
- package/dist/getMultiWiggleSourcesAutorun.d.ts +2 -2
- package/dist/getMultiWiggleSourcesAutorun.js +10 -7
- package/dist/getQuantitativeStats.d.ts +3 -3
- package/dist/getQuantitativeStats.js +2 -10
- package/dist/getQuantitativeStatsAutorun.d.ts +3 -3
- package/dist/getQuantitativeStatsAutorun.js +18 -20
- package/dist/index.d.ts +7 -7
- package/dist/index.js +40 -58
- package/dist/shared/SetMinMaxDialog.d.ts +1 -2
- package/dist/shared/SetMinMaxDialog.js +12 -42
- package/dist/shared/SharedWiggleConfigSchema.d.ts +0 -26
- package/dist/shared/SharedWiggleConfigSchema.js +1 -30
- package/dist/shared/SharedWiggleMixin.d.ts +26 -231
- package/dist/shared/SharedWiggleMixin.js +24 -184
- package/dist/shared/YScaleBar.d.ts +1 -2
- package/dist/shared/YScaleBar.js +2 -5
- package/dist/util.d.ts +0 -28
- package/dist/util.js +1 -45
- package/esm/BigWigAdapter/BigWigAdapter.d.ts +4 -3
- package/esm/BigWigAdapter/BigWigAdapter.js +5 -10
- package/esm/BigWigAdapter/configSchema.d.ts +0 -9
- package/esm/BigWigAdapter/configSchema.js +1 -13
- package/esm/BigWigAdapter/index.d.ts +1 -1
- package/esm/CreateMultiWiggleExtension/ConfirmDialog.d.ts +2 -3
- package/esm/CreateMultiWiggleExtension/ConfirmDialog.js +14 -26
- package/esm/CreateMultiWiggleExtension/index.d.ts +1 -1
- package/esm/CreateMultiWiggleExtension/index.js +26 -26
- package/esm/DensityRenderer/DensityRenderer.d.ts +2 -1
- package/esm/DensityRenderer/DensityRenderer.js +1 -1
- package/esm/DensityRenderer/configSchema.js +1 -7
- package/esm/DensityRenderer/index.d.ts +1 -1
- package/esm/DensityRenderer/index.js +1 -1
- package/esm/GuessAdapter/index.d.ts +2 -0
- package/esm/GuessAdapter/index.js +22 -0
- package/esm/LinePlotRenderer/LinePlotRenderer.d.ts +3 -2
- package/esm/LinePlotRenderer/LinePlotRenderer.js +1 -1
- package/esm/LinePlotRenderer/configSchema.d.ts +0 -3
- package/esm/LinePlotRenderer/configSchema.js +1 -10
- package/esm/LinePlotRenderer/index.d.ts +1 -1
- package/esm/LinearWiggleDisplay/components/SetColorDialog.d.ts +1 -2
- package/esm/LinearWiggleDisplay/components/SetColorDialog.js +23 -36
- package/esm/LinearWiggleDisplay/components/Tooltip.d.ts +3 -4
- package/esm/LinearWiggleDisplay/components/Tooltip.js +5 -18
- package/esm/LinearWiggleDisplay/components/WiggleDisplayComponent.d.ts +2 -3
- package/esm/LinearWiggleDisplay/components/WiggleDisplayComponent.js +12 -15
- package/esm/LinearWiggleDisplay/configSchema.d.ts +1 -12
- package/esm/LinearWiggleDisplay/configSchema.js +0 -15
- package/esm/LinearWiggleDisplay/index.d.ts +1 -1
- package/esm/LinearWiggleDisplay/index.js +1 -1
- package/esm/LinearWiggleDisplay/model.d.ts +44 -79
- package/esm/LinearWiggleDisplay/model.js +24 -66
- package/esm/LinearWiggleDisplay/renderSvg.d.ts +3 -4
- package/esm/LinearWiggleDisplay/renderSvg.js +2 -6
- package/esm/MultiDensityRenderer/MultiDensityRenderer.d.ts +4 -3
- package/esm/MultiDensityRenderer/MultiDensityRenderer.js +5 -4
- package/esm/MultiDensityRenderer/configSchema.js +1 -7
- package/esm/MultiDensityRenderer/index.d.ts +1 -1
- package/esm/MultiLineRenderer/MultiLineRenderer.d.ts +3 -2
- package/esm/MultiLineRenderer/MultiLineRenderer.js +1 -2
- package/esm/MultiLineRenderer/configSchema.d.ts +0 -6
- package/esm/MultiLineRenderer/configSchema.js +1 -13
- package/esm/MultiLineRenderer/index.d.ts +1 -1
- package/esm/MultiLinearWiggleDisplay/components/ColorLegend.d.ts +3 -5
- package/esm/MultiLinearWiggleDisplay/components/ColorLegend.js +5 -15
- package/esm/MultiLinearWiggleDisplay/components/FullHeightScaleBar.d.ts +7 -0
- package/esm/MultiLinearWiggleDisplay/components/FullHeightScaleBar.js +12 -0
- package/esm/MultiLinearWiggleDisplay/components/IndividualScaleBars.d.ts +7 -0
- package/esm/MultiLinearWiggleDisplay/components/IndividualScaleBars.js +10 -0
- package/esm/MultiLinearWiggleDisplay/components/LegendItem.d.ts +11 -0
- package/esm/MultiLinearWiggleDisplay/components/LegendItem.js +14 -0
- package/esm/MultiLinearWiggleDisplay/components/RectBg.d.ts +1 -2
- package/esm/MultiLinearWiggleDisplay/components/RectBg.js +2 -2
- package/esm/MultiLinearWiggleDisplay/components/ScoreLegend.d.ts +2 -3
- package/esm/MultiLinearWiggleDisplay/components/ScoreLegend.js +3 -5
- package/esm/MultiLinearWiggleDisplay/components/SetColorDialog.d.ts +2 -3
- package/esm/MultiLinearWiggleDisplay/components/SetColorDialog.js +22 -38
- package/esm/MultiLinearWiggleDisplay/components/SourcesGrid.d.ts +2 -3
- package/esm/MultiLinearWiggleDisplay/components/SourcesGrid.js +64 -91
- package/esm/MultiLinearWiggleDisplay/components/Tooltip.d.ts +4 -5
- package/esm/MultiLinearWiggleDisplay/components/Tooltip.js +8 -23
- package/esm/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.d.ts +2 -3
- package/esm/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.js +2 -4
- package/esm/MultiLinearWiggleDisplay/components/YScaleBars.d.ts +2 -3
- package/esm/MultiLinearWiggleDisplay/components/YScaleBars.js +8 -28
- package/esm/MultiLinearWiggleDisplay/components/util.d.ts +1 -1
- package/esm/MultiLinearWiggleDisplay/components/util.js +1 -1
- package/esm/MultiLinearWiggleDisplay/configSchema.d.ts +1 -10
- package/esm/MultiLinearWiggleDisplay/configSchema.js +1 -19
- package/esm/MultiLinearWiggleDisplay/index.d.ts +1 -1
- package/esm/MultiLinearWiggleDisplay/index.js +1 -1
- package/esm/MultiLinearWiggleDisplay/model.d.ts +27 -146
- package/esm/MultiLinearWiggleDisplay/model.js +27 -121
- package/esm/MultiLinearWiggleDisplay/renderSvg.d.ts +3 -4
- package/esm/MultiLinearWiggleDisplay/renderSvg.js +2 -5
- package/esm/MultiLinearWiggleDisplay/util.d.ts +1 -0
- package/esm/MultiLinearWiggleDisplay/util.js +7 -0
- package/esm/MultiQuantitativeTrack/configSchema.d.ts +1 -1
- package/esm/MultiQuantitativeTrack/configSchema.js +1 -7
- package/esm/MultiQuantitativeTrack/index.d.ts +1 -1
- package/esm/MultiQuantitativeTrack/index.js +1 -1
- package/esm/MultiRowLineRenderer/MultiRowLineRenderer.d.ts +3 -2
- package/esm/MultiRowLineRenderer/MultiRowLineRenderer.js +1 -2
- package/esm/MultiRowLineRenderer/configSchema.d.ts +0 -6
- package/esm/MultiRowLineRenderer/configSchema.js +2 -14
- package/esm/MultiRowLineRenderer/index.d.ts +1 -1
- package/esm/MultiRowXYPlotRenderer/MultiRowXYPlotRenderer.d.ts +3 -2
- package/esm/MultiRowXYPlotRenderer/MultiRowXYPlotRenderer.js +1 -2
- package/esm/MultiRowXYPlotRenderer/configSchema.d.ts +0 -12
- package/esm/MultiRowXYPlotRenderer/configSchema.js +2 -20
- package/esm/MultiRowXYPlotRenderer/index.d.ts +1 -1
- package/esm/MultiWiggleAdapter/MultiWiggleAdapter.d.ts +4 -3
- package/esm/MultiWiggleAdapter/MultiWiggleAdapter.js +9 -14
- package/esm/MultiWiggleAdapter/configSchema.d.ts +0 -6
- package/esm/MultiWiggleAdapter/configSchema.js +1 -10
- package/esm/MultiWiggleAdapter/index.d.ts +1 -1
- package/esm/MultiWiggleAdapter/index.js +1 -1
- package/esm/MultiWiggleAddTrackWorkflow/AddTrackWorkflow.d.ts +4 -4
- package/esm/MultiWiggleAddTrackWorkflow/AddTrackWorkflow.js +63 -80
- package/esm/MultiWiggleAddTrackWorkflow/index.d.ts +1 -1
- package/esm/MultiWiggleAddTrackWorkflow/index.js +1 -2
- package/esm/MultiWiggleRendering.d.ts +4 -5
- package/esm/MultiWiggleRendering.js +6 -6
- package/esm/MultiXYPlotRenderer/MultiXYPlotRenderer.d.ts +3 -2
- package/esm/MultiXYPlotRenderer/MultiXYPlotRenderer.js +2 -3
- package/esm/MultiXYPlotRenderer/configSchema.d.ts +0 -12
- package/esm/MultiXYPlotRenderer/configSchema.js +1 -19
- package/esm/MultiXYPlotRenderer/index.d.ts +1 -1
- package/esm/QuantitativeTrack/configSchema.d.ts +1 -1
- package/esm/QuantitativeTrack/configSchema.js +1 -7
- package/esm/QuantitativeTrack/index.d.ts +1 -1
- package/esm/QuantitativeTrack/index.js +1 -1
- package/esm/Tooltip.d.ts +2 -3
- package/esm/Tooltip.js +7 -11
- package/esm/WiggleBaseRenderer.d.ts +8 -11
- package/esm/WiggleBaseRenderer.js +0 -1
- package/esm/WiggleRPC/MultiWiggleGetSources.d.ts +5 -12
- package/esm/WiggleRPC/MultiWiggleGetSources.js +2 -29
- package/esm/WiggleRPC/WiggleGetGlobalQuantitativeStats.d.ts +5 -7
- package/esm/WiggleRPC/WiggleGetGlobalQuantitativeStats.js +2 -15
- package/esm/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.d.ts +4 -11
- package/esm/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.js +2 -29
- package/esm/WiggleRendering.d.ts +3 -4
- package/esm/WiggleRendering.js +5 -7
- package/esm/XYPlotRenderer/XYPlotRenderer.d.ts +3 -2
- package/esm/XYPlotRenderer/XYPlotRenderer.js +3 -5
- package/esm/XYPlotRenderer/configSchema.d.ts +0 -12
- package/esm/XYPlotRenderer/configSchema.js +2 -20
- package/esm/XYPlotRenderer/index.d.ts +1 -1
- package/esm/configSchema.d.ts +0 -18
- package/esm/configSchema.js +1 -23
- package/esm/drawDensity.d.ts +3 -3
- package/esm/drawDensity.js +1 -5
- package/esm/drawLine.d.ts +3 -3
- package/esm/drawLine.js +1 -6
- package/esm/drawXY.d.ts +4 -3
- package/esm/drawXY.js +29 -13
- package/esm/getMultiWiggleSourcesAutorun.d.ts +2 -2
- package/esm/getMultiWiggleSourcesAutorun.js +9 -6
- package/esm/getQuantitativeStats.d.ts +3 -3
- package/esm/getQuantitativeStats.js +3 -11
- package/esm/getQuantitativeStatsAutorun.d.ts +3 -3
- package/esm/getQuantitativeStatsAutorun.js +18 -20
- package/esm/index.d.ts +7 -7
- package/esm/index.js +14 -42
- package/esm/shared/SetMinMaxDialog.d.ts +1 -2
- package/esm/shared/SetMinMaxDialog.js +12 -19
- package/esm/shared/SharedWiggleConfigSchema.d.ts +0 -26
- package/esm/shared/SharedWiggleConfigSchema.js +1 -30
- package/esm/shared/SharedWiggleMixin.d.ts +26 -231
- package/esm/shared/SharedWiggleMixin.js +8 -178
- package/esm/shared/YScaleBar.d.ts +1 -2
- package/esm/shared/YScaleBar.js +2 -2
- package/esm/util.d.ts +0 -28
- package/esm/util.js +1 -45
- package/package.json +3 -6
- package/dist/MultiLinearWiggleDisplay/components/DraggableDialog.d.ts +0 -6
- package/dist/MultiLinearWiggleDisplay/components/DraggableDialog.js +0 -66
- package/esm/MultiLinearWiggleDisplay/components/DraggableDialog.d.ts +0 -6
- package/esm/MultiLinearWiggleDisplay/components/DraggableDialog.js +0 -38
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-
*/
|
|
41
26
|
minSize: {
|
|
42
27
|
type: 'number',
|
|
43
28
|
defaultValue: 0.7,
|
|
44
29
|
},
|
|
45
30
|
}, {
|
|
46
|
-
/**
|
|
47
|
-
* #baseConfiguration
|
|
48
|
-
*/
|
|
49
31
|
baseConfiguration: configSchema_1.default,
|
|
50
32
|
explicitlyTyped: true,
|
|
51
33
|
});
|
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
import PluginManager from '@jbrowse/core/PluginManager';
|
|
1
|
+
import type PluginManager from '@jbrowse/core/PluginManager';
|
|
2
2
|
export default function XYPlotRendererF(pluginManager: PluginManager): void;
|
|
3
3
|
export { default as XYPlotRenderer } from './XYPlotRenderer';
|
|
4
4
|
export { default as ReactComponent } from '../WiggleRendering';
|
package/dist/configSchema.d.ts
CHANGED
|
@@ -1,48 +1,30 @@
|
|
|
1
1
|
declare const WiggleRenderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
|
|
2
|
-
/**
|
|
3
|
-
* #slot
|
|
4
|
-
*/
|
|
5
2
|
color: {
|
|
6
3
|
type: string;
|
|
7
4
|
description: string;
|
|
8
5
|
defaultValue: string;
|
|
9
6
|
};
|
|
10
|
-
/**
|
|
11
|
-
* #slot
|
|
12
|
-
*/
|
|
13
7
|
posColor: {
|
|
14
8
|
type: string;
|
|
15
9
|
description: string;
|
|
16
10
|
defaultValue: string;
|
|
17
11
|
};
|
|
18
|
-
/**
|
|
19
|
-
* #slot
|
|
20
|
-
*/
|
|
21
12
|
negColor: {
|
|
22
13
|
type: string;
|
|
23
14
|
description: string;
|
|
24
15
|
defaultValue: string;
|
|
25
16
|
};
|
|
26
|
-
/**
|
|
27
|
-
* #slot
|
|
28
|
-
*/
|
|
29
17
|
clipColor: {
|
|
30
18
|
type: string;
|
|
31
19
|
description: string;
|
|
32
20
|
defaultValue: string;
|
|
33
21
|
};
|
|
34
|
-
/**
|
|
35
|
-
* #slot
|
|
36
|
-
*/
|
|
37
22
|
bicolorPivot: {
|
|
38
23
|
type: string;
|
|
39
24
|
model: import("mobx-state-tree").ISimpleType<string>;
|
|
40
25
|
description: string;
|
|
41
26
|
defaultValue: string;
|
|
42
27
|
};
|
|
43
|
-
/**
|
|
44
|
-
* #slot
|
|
45
|
-
*/
|
|
46
28
|
bicolorPivotValue: {
|
|
47
29
|
type: string;
|
|
48
30
|
defaultValue: number;
|
package/dist/configSchema.js
CHANGED
|
@@ -2,47 +2,28 @@
|
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
3
|
const configuration_1 = require("@jbrowse/core/configuration");
|
|
4
4
|
const mobx_state_tree_1 = require("mobx-state-tree");
|
|
5
|
-
|
|
6
|
-
* #config WiggleRenderer
|
|
7
|
-
* this is the "base wiggle renderer config schema"
|
|
8
|
-
*/
|
|
9
|
-
function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
|
|
5
|
+
function x() { }
|
|
10
6
|
const WiggleRenderer = (0, configuration_1.ConfigurationSchema)('WiggleRenderer', {
|
|
11
|
-
/**
|
|
12
|
-
* #slot
|
|
13
|
-
*/
|
|
14
7
|
color: {
|
|
15
8
|
type: 'color',
|
|
16
9
|
description: 'the color of track, overrides posColor and negColor',
|
|
17
10
|
defaultValue: '#f0f',
|
|
18
11
|
},
|
|
19
|
-
/**
|
|
20
|
-
* #slot
|
|
21
|
-
*/
|
|
22
12
|
posColor: {
|
|
23
13
|
type: 'color',
|
|
24
14
|
description: 'the color to use when the score is positive',
|
|
25
15
|
defaultValue: 'blue',
|
|
26
16
|
},
|
|
27
|
-
/**
|
|
28
|
-
* #slot
|
|
29
|
-
*/
|
|
30
17
|
negColor: {
|
|
31
18
|
type: 'color',
|
|
32
19
|
description: 'the color to use when the score is negative',
|
|
33
20
|
defaultValue: 'red',
|
|
34
21
|
},
|
|
35
|
-
/**
|
|
36
|
-
* #slot
|
|
37
|
-
*/
|
|
38
22
|
clipColor: {
|
|
39
23
|
type: 'color',
|
|
40
24
|
description: 'the color of the clipping marker',
|
|
41
25
|
defaultValue: 'red',
|
|
42
26
|
},
|
|
43
|
-
/**
|
|
44
|
-
* #slot
|
|
45
|
-
*/
|
|
46
27
|
bicolorPivot: {
|
|
47
28
|
type: 'stringEnum',
|
|
48
29
|
model: mobx_state_tree_1.types.enumeration('Scale type', [
|
|
@@ -54,9 +35,6 @@ const WiggleRenderer = (0, configuration_1.ConfigurationSchema)('WiggleRenderer'
|
|
|
54
35
|
description: 'type of bicolor pivot',
|
|
55
36
|
defaultValue: 'numeric',
|
|
56
37
|
},
|
|
57
|
-
/**
|
|
58
|
-
* #slot
|
|
59
|
-
*/
|
|
60
38
|
bicolorPivotValue: {
|
|
61
39
|
type: 'number',
|
|
62
40
|
defaultValue: 0,
|
package/dist/drawDensity.d.ts
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
|
-
import {
|
|
2
|
-
import {
|
|
3
|
-
import {
|
|
1
|
+
import type { ScaleOpts } from './util';
|
|
2
|
+
import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
|
|
3
|
+
import type { Feature, Region } from '@jbrowse/core/util';
|
|
4
4
|
export declare function drawDensity(ctx: CanvasRenderingContext2D, props: {
|
|
5
5
|
features: Map<string, Feature> | Feature[];
|
|
6
6
|
regions: Region[];
|
package/dist/drawDensity.js
CHANGED
|
@@ -3,7 +3,6 @@ Object.defineProperty(exports, "__esModule", { value: true });
|
|
|
3
3
|
exports.drawDensity = drawDensity;
|
|
4
4
|
const configuration_1 = require("@jbrowse/core/configuration");
|
|
5
5
|
const util_1 = require("@jbrowse/core/util");
|
|
6
|
-
// locals
|
|
7
6
|
const util_2 = require("./util");
|
|
8
7
|
const fudgeFactor = 0.3;
|
|
9
8
|
const clipHeight = 2;
|
|
@@ -34,7 +33,6 @@ function drawDensity(ctx, props) {
|
|
|
34
33
|
const reducedFeatures = [];
|
|
35
34
|
for (const feature of features.values()) {
|
|
36
35
|
const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
|
|
37
|
-
// create reduced features, avoiding multiple features per px
|
|
38
36
|
if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
|
|
39
37
|
reducedFeatures.push(feature);
|
|
40
38
|
prevLeftPx = leftPx;
|
|
@@ -45,8 +43,6 @@ function drawDensity(ctx, props) {
|
|
|
45
43
|
ctx.fillStyle = cb(feature, score);
|
|
46
44
|
ctx.fillRect(leftPx, 0, w, height);
|
|
47
45
|
}
|
|
48
|
-
// second pass: draw clipping
|
|
49
|
-
// avoid persisting the red fillstyle with save/restore
|
|
50
46
|
ctx.save();
|
|
51
47
|
if (hasClipping) {
|
|
52
48
|
ctx.fillStyle = clipColor;
|
package/dist/drawLine.d.ts
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
|
-
import {
|
|
2
|
-
import {
|
|
3
|
-
import {
|
|
1
|
+
import type { ScaleOpts } from './util';
|
|
2
|
+
import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
|
|
3
|
+
import type { Feature, Region } from '@jbrowse/core/util';
|
|
4
4
|
export declare function drawLine(ctx: CanvasRenderingContext2D, props: {
|
|
5
5
|
features: Map<string, Feature> | Feature[];
|
|
6
6
|
regions: Region[];
|
package/dist/drawLine.js
CHANGED
|
@@ -3,7 +3,6 @@ Object.defineProperty(exports, "__esModule", { value: true });
|
|
|
3
3
|
exports.drawLine = drawLine;
|
|
4
4
|
const configuration_1 = require("@jbrowse/core/configuration");
|
|
5
5
|
const util_1 = require("@jbrowse/core/util");
|
|
6
|
-
// locals
|
|
7
6
|
const util_2 = require("./util");
|
|
8
7
|
const fudgeFactor = 0.3;
|
|
9
8
|
const clipHeight = 2;
|
|
@@ -11,9 +10,6 @@ function drawLine(ctx, props) {
|
|
|
11
10
|
const { features, regions, bpPerPx, scaleOpts, height: unadjustedHeight, ticks: { values }, displayCrossHatches, colorCallback, config, offset = 0, } = props;
|
|
12
11
|
const region = regions[0];
|
|
13
12
|
const width = (region.end - region.start) / bpPerPx;
|
|
14
|
-
// the adjusted height takes into account YSCALEBAR_LABEL_OFFSET from the
|
|
15
|
-
// wiggle display, and makes the height of the actual drawn area add
|
|
16
|
-
// "padding" to the top and bottom of the display
|
|
17
13
|
const height = unadjustedHeight - offset * 2;
|
|
18
14
|
const clipColor = (0, configuration_1.readConfObject)(config, 'clipColor');
|
|
19
15
|
const scale = (0, util_2.getScale)({ ...scaleOpts, range: [0, height] });
|
|
@@ -26,7 +22,6 @@ function drawLine(ctx, props) {
|
|
|
26
22
|
const reducedFeatures = [];
|
|
27
23
|
for (const feature of features.values()) {
|
|
28
24
|
const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
|
|
29
|
-
// create reduced features, avoiding multiple features per px
|
|
30
25
|
if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
|
|
31
26
|
reducedFeatures.push(feature);
|
|
32
27
|
prevLeftPx = leftPx;
|
package/dist/drawXY.d.ts
CHANGED
|
@@ -1,7 +1,8 @@
|
|
|
1
|
-
import {
|
|
2
|
-
import {
|
|
3
|
-
import {
|
|
1
|
+
import type { ScaleOpts } from './util';
|
|
2
|
+
import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
|
|
3
|
+
import type { Feature, Region } from '@jbrowse/core/util';
|
|
4
4
|
export declare function drawXY(ctx: CanvasRenderingContext2D, props: {
|
|
5
|
+
stopToken?: string;
|
|
5
6
|
features: Map<string, Feature> | Feature[];
|
|
6
7
|
bpPerPx: number;
|
|
7
8
|
regions: Region[];
|
package/dist/drawXY.js
CHANGED
|
@@ -2,9 +2,9 @@
|
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
3
|
exports.drawXY = drawXY;
|
|
4
4
|
const configuration_1 = require("@jbrowse/core/configuration");
|
|
5
|
-
const colord_1 = require("@jbrowse/core/util/colord");
|
|
6
5
|
const util_1 = require("@jbrowse/core/util");
|
|
7
|
-
|
|
6
|
+
const colord_1 = require("@jbrowse/core/util/colord");
|
|
7
|
+
const stopToken_1 = require("@jbrowse/core/util/stopToken");
|
|
8
8
|
const util_2 = require("./util");
|
|
9
9
|
function lighten(color, amount) {
|
|
10
10
|
const hslColor = color.toHsl();
|
|
@@ -22,9 +22,6 @@ function drawXY(ctx, props) {
|
|
|
22
22
|
const { features, bpPerPx, regions, scaleOpts, height: unadjustedHeight, config, ticks, displayCrossHatches, offset = 0, colorCallback, } = props;
|
|
23
23
|
const region = regions[0];
|
|
24
24
|
const width = (region.end - region.start) / bpPerPx;
|
|
25
|
-
// the adjusted height takes into account YSCALEBAR_LABEL_OFFSET from the
|
|
26
|
-
// wiggle display, and makes the height of the actual drawn area add
|
|
27
|
-
// "padding" to the top and bottom of the display
|
|
28
25
|
const height = unadjustedHeight - offset * 2;
|
|
29
26
|
const filled = (0, configuration_1.readConfObject)(config, 'filled');
|
|
30
27
|
const clipColor = (0, configuration_1.readConfObject)(config, 'clipColor');
|
|
@@ -43,13 +40,16 @@ function drawXY(ctx, props) {
|
|
|
43
40
|
let prevLeftPx = Number.NEGATIVE_INFINITY;
|
|
44
41
|
const reducedFeatures = [];
|
|
45
42
|
const crossingOrigin = niceMin < pivotValue && niceMax > pivotValue;
|
|
46
|
-
|
|
47
|
-
// passes. this reduces subpixel rendering issues. note: for stylistic
|
|
48
|
-
// reasons, clipping indicator is only drawn for score, not min/max score
|
|
43
|
+
let start = performance.now();
|
|
49
44
|
if (summaryScoreMode === 'whiskers') {
|
|
50
45
|
let lastCol;
|
|
51
46
|
let lastMix;
|
|
47
|
+
start = performance.now();
|
|
52
48
|
for (const feature of features.values()) {
|
|
49
|
+
if (performance.now() - start > 400) {
|
|
50
|
+
(0, stopToken_1.checkStopToken)();
|
|
51
|
+
start = performance.now();
|
|
52
|
+
}
|
|
53
53
|
const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
|
|
54
54
|
if (feature.get('summary')) {
|
|
55
55
|
const w = Math.max(rightPx - leftPx + fudgeFactor, minSize);
|
|
@@ -66,7 +66,12 @@ function drawXY(ctx, props) {
|
|
|
66
66
|
}
|
|
67
67
|
lastMix = undefined;
|
|
68
68
|
lastCol = undefined;
|
|
69
|
+
start = performance.now();
|
|
69
70
|
for (const feature of features.values()) {
|
|
71
|
+
if (performance.now() - start > 400) {
|
|
72
|
+
(0, stopToken_1.checkStopToken)();
|
|
73
|
+
start = performance.now();
|
|
74
|
+
}
|
|
70
75
|
const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
|
|
71
76
|
const score = feature.get('score');
|
|
72
77
|
const max = feature.get('maxScore');
|
|
@@ -81,7 +86,6 @@ function drawXY(ctx, props) {
|
|
|
81
86
|
.toString())
|
|
82
87
|
: c;
|
|
83
88
|
const w = Math.max(rightPx - leftPx + fudgeFactor, minSize);
|
|
84
|
-
// create reduced features, avoiding multiple features per px
|
|
85
89
|
if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
|
|
86
90
|
reducedFeatures.push(feature);
|
|
87
91
|
prevLeftPx = leftPx;
|
|
@@ -92,7 +96,12 @@ function drawXY(ctx, props) {
|
|
|
92
96
|
}
|
|
93
97
|
lastMix = undefined;
|
|
94
98
|
lastCol = undefined;
|
|
99
|
+
start = performance.now();
|
|
95
100
|
for (const feature of features.values()) {
|
|
101
|
+
if (performance.now() - start > 400) {
|
|
102
|
+
(0, stopToken_1.checkStopToken)();
|
|
103
|
+
start = performance.now();
|
|
104
|
+
}
|
|
96
105
|
const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
|
|
97
106
|
if (feature.get('summary')) {
|
|
98
107
|
const min = feature.get('minScore');
|
|
@@ -109,9 +118,13 @@ function drawXY(ctx, props) {
|
|
|
109
118
|
}
|
|
110
119
|
}
|
|
111
120
|
else {
|
|
121
|
+
start = performance.now();
|
|
112
122
|
for (const feature of features.values()) {
|
|
123
|
+
if (performance.now() - start > 400) {
|
|
124
|
+
(0, stopToken_1.checkStopToken)();
|
|
125
|
+
start = performance.now();
|
|
126
|
+
}
|
|
113
127
|
const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
|
|
114
|
-
// create reduced features, avoiding multiple features per px
|
|
115
128
|
if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
|
|
116
129
|
reducedFeatures.push(feature);
|
|
117
130
|
prevLeftPx = leftPx;
|
|
@@ -133,12 +146,15 @@ function drawXY(ctx, props) {
|
|
|
133
146
|
}
|
|
134
147
|
}
|
|
135
148
|
}
|
|
136
|
-
// second pass: draw clipping
|
|
137
|
-
// avoid persisting the red fillstyle with save/restore
|
|
138
149
|
ctx.save();
|
|
139
150
|
if (hasClipping) {
|
|
140
151
|
ctx.fillStyle = clipColor;
|
|
152
|
+
start = performance.now();
|
|
141
153
|
for (const feature of features.values()) {
|
|
154
|
+
if (performance.now() - start > 400) {
|
|
155
|
+
(0, stopToken_1.checkStopToken)();
|
|
156
|
+
start = performance.now();
|
|
157
|
+
}
|
|
142
158
|
const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
|
|
143
159
|
const w = rightPx - leftPx + fudgeFactor;
|
|
144
160
|
const score = feature.get('score');
|
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
import { AnyConfigurationModel } from '@jbrowse/core/configuration';
|
|
1
|
+
import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
|
|
2
2
|
export interface Source {
|
|
3
3
|
name: string;
|
|
4
4
|
color?: string;
|
|
@@ -10,7 +10,7 @@ export declare function getMultiWiggleSourcesAutorun(self: {
|
|
|
10
10
|
adapterConfig: AnyConfigurationModel;
|
|
11
11
|
autoscaleType: string;
|
|
12
12
|
adapterProps: () => Record<string, unknown>;
|
|
13
|
-
|
|
13
|
+
setSourcesLoading: (aborter: string) => void;
|
|
14
14
|
setError: (error: unknown) => void;
|
|
15
15
|
setMessage: (str: string) => void;
|
|
16
16
|
setSources: (sources: Source[]) => void;
|
|
@@ -1,21 +1,24 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
3
|
exports.getMultiWiggleSourcesAutorun = getMultiWiggleSourcesAutorun;
|
|
4
|
-
const mobx_1 = require("mobx");
|
|
5
|
-
const mobx_state_tree_1 = require("mobx-state-tree");
|
|
6
|
-
// jbrowse
|
|
7
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");
|
|
8
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");
|
|
9
10
|
function getMultiWiggleSourcesAutorun(self) {
|
|
10
11
|
(0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
|
|
11
12
|
try {
|
|
12
|
-
const { rpcManager } = (0, util_1.getSession)(self);
|
|
13
|
-
const { adapterConfig } = self;
|
|
14
|
-
const sessionId = (0, tracks_1.getRpcSessionId)(self);
|
|
15
13
|
const view = (0, util_1.getContainingView)(self);
|
|
16
14
|
if (!view.initialized) {
|
|
17
15
|
return;
|
|
18
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);
|
|
19
22
|
const sources = (await rpcManager.call(sessionId, 'MultiWiggleGetSources', {
|
|
20
23
|
regions: view.staticBlocks.contentBlocks,
|
|
21
24
|
sessionId,
|
|
@@ -26,7 +29,7 @@ function getMultiWiggleSourcesAutorun(self) {
|
|
|
26
29
|
}
|
|
27
30
|
}
|
|
28
31
|
catch (e) {
|
|
29
|
-
if (!(0,
|
|
32
|
+
if (!(0, aborting_1.isAbortException)(e) && (0, mobx_state_tree_1.isAlive)(self)) {
|
|
30
33
|
console.error(e);
|
|
31
34
|
(0, util_1.getSession)(self).notifyError(`${e}`, e);
|
|
32
35
|
}
|
|
@@ -1,5 +1,5 @@
|
|
|
1
|
-
import {
|
|
2
|
-
import {
|
|
1
|
+
import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
|
|
2
|
+
import type { QuantitativeStats } from '@jbrowse/core/util/stats';
|
|
3
3
|
export declare function getQuantitativeStats(self: {
|
|
4
4
|
adapterConfig: AnyConfigurationModel;
|
|
5
5
|
configuration: AnyConfigurationModel;
|
|
@@ -7,7 +7,7 @@ export declare function getQuantitativeStats(self: {
|
|
|
7
7
|
setMessage: (str: string) => void;
|
|
8
8
|
}, opts: {
|
|
9
9
|
headers?: Record<string, string>;
|
|
10
|
-
|
|
10
|
+
stopToken?: string;
|
|
11
11
|
filters: string[];
|
|
12
12
|
currStatsBpPerPx: number;
|
|
13
13
|
}): Promise<QuantitativeStats>;
|
|
@@ -1,11 +1,10 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
3
|
exports.getQuantitativeStats = getQuantitativeStats;
|
|
4
|
-
const
|
|
5
|
-
// jbrowse
|
|
4
|
+
const configuration_1 = require("@jbrowse/core/configuration");
|
|
6
5
|
const util_1 = require("@jbrowse/core/util");
|
|
7
6
|
const tracks_1 = require("@jbrowse/core/util/tracks");
|
|
8
|
-
const
|
|
7
|
+
const mobx_state_tree_1 = require("mobx-state-tree");
|
|
9
8
|
async function getQuantitativeStats(self, opts) {
|
|
10
9
|
const { rpcManager } = (0, util_1.getSession)(self);
|
|
11
10
|
const numStdDev = (0, configuration_1.getConf)(self, 'numStdDev') || 3;
|
|
@@ -25,10 +24,6 @@ async function getQuantitativeStats(self, opts) {
|
|
|
25
24
|
if (autoscaleType === 'global' || autoscaleType === 'globalsd') {
|
|
26
25
|
const results = (await rpcManager.call(sessionId, 'WiggleGetGlobalQuantitativeStats', params));
|
|
27
26
|
const { scoreMin, scoreMean, scoreStdDev } = results;
|
|
28
|
-
// globalsd uses heuristic to avoid unnecessary scoreMin<0
|
|
29
|
-
//
|
|
30
|
-
// if the scoreMin is never less than 0 helps with most coverage bigwigs
|
|
31
|
-
// just being >0
|
|
32
27
|
return autoscaleType === 'globalsd'
|
|
33
28
|
? {
|
|
34
29
|
...results,
|
|
@@ -56,9 +51,6 @@ async function getQuantitativeStats(self, opts) {
|
|
|
56
51
|
bpPerPx,
|
|
57
52
|
}));
|
|
58
53
|
const { scoreMin, scoreMean, scoreStdDev } = results;
|
|
59
|
-
// localsd uses heuristic to avoid unnecessary scoreMin<0 if the
|
|
60
|
-
// scoreMin is never less than 0 helps with most coverage bigwigs
|
|
61
|
-
// just being >0
|
|
62
54
|
return autoscaleType === 'localsd'
|
|
63
55
|
? {
|
|
64
56
|
...results,
|
|
@@ -1,12 +1,12 @@
|
|
|
1
|
-
import {
|
|
2
|
-
import {
|
|
1
|
+
import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
|
|
2
|
+
import type { QuantitativeStats } from '@jbrowse/core/util/stats';
|
|
3
3
|
export declare function getQuantitativeStatsAutorun(self: {
|
|
4
4
|
quantitativeStatsReady: boolean;
|
|
5
5
|
configuration: AnyConfigurationModel;
|
|
6
6
|
adapterConfig: AnyConfigurationModel;
|
|
7
7
|
autoscaleType: string;
|
|
8
8
|
adapterProps: () => Record<string, unknown>;
|
|
9
|
-
setStatsLoading: (
|
|
9
|
+
setStatsLoading: (token: string) => void;
|
|
10
10
|
setError: (error: unknown) => void;
|
|
11
11
|
setMessage: (str: string) => void;
|
|
12
12
|
updateQuantitativeStats: (stats: QuantitativeStats, region: string) => void;
|
|
@@ -1,35 +1,33 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
3
|
exports.getQuantitativeStatsAutorun = getQuantitativeStatsAutorun;
|
|
4
|
+
const util_1 = require("@jbrowse/core/util");
|
|
5
|
+
const stopToken_1 = require("@jbrowse/core/util/stopToken");
|
|
4
6
|
const mobx_1 = require("mobx");
|
|
5
7
|
const mobx_state_tree_1 = require("mobx-state-tree");
|
|
6
|
-
// jbrowse
|
|
7
|
-
const util_1 = require("@jbrowse/core/util");
|
|
8
|
-
// locals
|
|
9
8
|
const getQuantitativeStats_1 = require("./getQuantitativeStats");
|
|
10
9
|
function getQuantitativeStatsAutorun(self) {
|
|
11
10
|
(0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
|
|
12
11
|
try {
|
|
13
|
-
|
|
14
|
-
|
|
15
|
-
|
|
16
|
-
|
|
17
|
-
|
|
18
|
-
|
|
19
|
-
|
|
20
|
-
|
|
21
|
-
|
|
22
|
-
|
|
23
|
-
|
|
24
|
-
|
|
25
|
-
|
|
26
|
-
|
|
27
|
-
self.updateQuantitativeStats(wiggleStats, statsRegion);
|
|
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
|
+
}
|
|
28
26
|
}
|
|
29
27
|
}
|
|
30
28
|
catch (e) {
|
|
31
|
-
|
|
32
|
-
|
|
29
|
+
if ((0, mobx_state_tree_1.isAlive)(self) && !(0, util_1.isAbortException)(e)) {
|
|
30
|
+
console.error(e);
|
|
33
31
|
self.setError(e);
|
|
34
32
|
}
|
|
35
33
|
}
|
package/dist/index.d.ts
CHANGED
|
@@ -1,18 +1,18 @@
|
|
|
1
1
|
import Plugin from '@jbrowse/core/Plugin';
|
|
2
|
-
import PluginManager from '@jbrowse/core/PluginManager';
|
|
3
|
-
import WiggleBaseRenderer from './WiggleBaseRenderer';
|
|
4
|
-
import * as utils from './util';
|
|
5
2
|
import { modelFactory as linearWiggleDisplayModelFactory } from './LinearWiggleDisplay';
|
|
3
|
+
import WiggleBaseRenderer from './WiggleBaseRenderer';
|
|
6
4
|
import { XYPlotRenderer } from './XYPlotRenderer';
|
|
5
|
+
import * as utils from './util';
|
|
6
|
+
import type PluginManager from '@jbrowse/core/PluginManager';
|
|
7
7
|
export default class WigglePlugin extends Plugin {
|
|
8
8
|
name: string;
|
|
9
9
|
install(pm: PluginManager): void;
|
|
10
10
|
exports: {
|
|
11
11
|
LinearWiggleDisplayReactComponent: (props: {
|
|
12
12
|
model: import("./LinearWiggleDisplay/model").WiggleDisplayModel;
|
|
13
|
-
}) => import("react").JSX.Element;
|
|
13
|
+
}) => import("react/jsx-runtime").JSX.Element;
|
|
14
14
|
XYPlotRendererReactComponent: (props: {
|
|
15
|
-
regions: import("@jbrowse/core/util
|
|
15
|
+
regions: import("@jbrowse/core/util").Region[];
|
|
16
16
|
features: Map<string, import("@jbrowse/core/util").Feature>;
|
|
17
17
|
bpPerPx: number;
|
|
18
18
|
width: number;
|
|
@@ -21,7 +21,7 @@ export default class WigglePlugin extends Plugin {
|
|
|
21
21
|
onMouseLeave?: (event: React.MouseEvent) => void;
|
|
22
22
|
onMouseMove?: (event: React.MouseEvent, arg?: string) => void;
|
|
23
23
|
onFeatureClick?: (event: React.MouseEvent, arg?: string) => void;
|
|
24
|
-
}) => import("react").JSX.Element;
|
|
24
|
+
}) => import("react/jsx-runtime").JSX.Element;
|
|
25
25
|
XYPlotRenderer: typeof XYPlotRenderer;
|
|
26
26
|
WiggleBaseRenderer: typeof WiggleBaseRenderer;
|
|
27
27
|
linearWiggleDisplayModelFactory: typeof linearWiggleDisplayModelFactory;
|
|
@@ -83,6 +83,6 @@ export default class WigglePlugin extends Plugin {
|
|
|
83
83
|
}
|
|
84
84
|
export * from './util';
|
|
85
85
|
export { default as WiggleRendering } from './WiggleRendering';
|
|
86
|
-
export {
|
|
86
|
+
export { ReactComponent as LinearWiggleDisplayReactComponent, Tooltip, modelFactory as linearWiggleDisplayModelFactory, } from './LinearWiggleDisplay';
|
|
87
87
|
export type { TooltipContentsComponent } from './Tooltip';
|
|
88
88
|
export { default as WiggleBaseRenderer } from './WiggleBaseRenderer';
|