@jbrowse/plugin-linear-comparative-view 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/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.d.ts +6 -5
- package/dist/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.js +36 -60
- package/dist/LGVSyntenyDisplay/components/util.d.ts +9 -6
- package/dist/LGVSyntenyDisplay/components/util.js +6 -13
- package/dist/LGVSyntenyDisplay/configSchemaF.d.ts +19 -10
- package/dist/LGVSyntenyDisplay/configSchemaF.js +12 -9
- package/dist/LGVSyntenyDisplay/index.d.ts +1 -1
- package/dist/LGVSyntenyDisplay/index.js +1 -1
- package/dist/LGVSyntenyDisplay/model.d.ts +122 -69
- package/dist/LGVSyntenyDisplay/model.js +20 -37
- package/dist/LaunchLinearSyntenyView.d.ts +1 -1
- package/dist/LaunchLinearSyntenyView.js +1 -3
- package/dist/LinearComparativeDisplay/configSchemaF.d.ts +0 -3
- package/dist/LinearComparativeDisplay/configSchemaF.js +0 -6
- package/dist/LinearComparativeDisplay/index.d.ts +1 -1
- package/dist/LinearComparativeDisplay/stateModelFactory.d.ts +12 -69
- package/dist/LinearComparativeDisplay/stateModelFactory.js +13 -57
- package/dist/LinearComparativeView/components/Header.d.ts +2 -3
- package/dist/LinearComparativeView/components/Header.js +56 -86
- package/dist/LinearComparativeView/components/HeaderSearchBoxes.d.ts +2 -3
- package/dist/LinearComparativeView/components/HeaderSearchBoxes.js +5 -15
- package/dist/LinearComparativeView/components/LinearComparativeRenderArea.d.ts +2 -3
- package/dist/LinearComparativeView/components/LinearComparativeRenderArea.js +17 -32
- package/dist/LinearComparativeView/components/LinearComparativeView.d.ts +2 -3
- package/dist/LinearComparativeView/components/LinearComparativeView.js +4 -9
- package/dist/LinearComparativeView/components/Rubberband.d.ts +2 -3
- package/dist/LinearComparativeView/components/Rubberband.js +36 -69
- package/dist/LinearComparativeView/components/VerticalGuide.d.ts +2 -3
- package/dist/LinearComparativeView/components/VerticalGuide.js +5 -9
- package/dist/LinearComparativeView/index.d.ts +1 -1
- package/dist/LinearComparativeView/index.js +17 -7
- package/dist/LinearComparativeView/model.d.ts +38 -90
- package/dist/LinearComparativeView/model.js +40 -107
- package/dist/LinearReadVsRef/LinearReadVsRef.d.ts +2 -3
- package/dist/LinearReadVsRef/LinearReadVsRef.js +10 -55
- package/dist/LinearReadVsRef/index.d.ts +1 -1
- package/dist/LinearReadVsRef/index.js +17 -9
- package/dist/LinearSyntenyDisplay/afterAttach.d.ts +1 -1
- package/dist/LinearSyntenyDisplay/afterAttach.js +8 -12
- package/dist/LinearSyntenyDisplay/components/Component.d.ts +2 -3
- package/dist/LinearSyntenyDisplay/components/Component.js +11 -36
- package/dist/LinearSyntenyDisplay/components/LinearSyntenyRendering.d.ts +2 -3
- package/dist/LinearSyntenyDisplay/components/LinearSyntenyRendering.js +95 -106
- package/dist/LinearSyntenyDisplay/components/SyntenyContextMenu.d.ts +3 -4
- package/dist/LinearSyntenyDisplay/components/SyntenyContextMenu.js +3 -6
- package/dist/LinearSyntenyDisplay/components/SyntenyTooltip.d.ts +1 -2
- package/dist/LinearSyntenyDisplay/components/SyntenyTooltip.js +3 -4
- package/dist/LinearSyntenyDisplay/components/util.d.ts +3 -3
- package/dist/LinearSyntenyDisplay/components/util.js +0 -9
- package/dist/LinearSyntenyDisplay/configSchemaF.d.ts +1 -12
- package/dist/LinearSyntenyDisplay/configSchemaF.js +0 -15
- package/dist/LinearSyntenyDisplay/drawSynteny.d.ts +1 -1
- package/dist/LinearSyntenyDisplay/drawSynteny.js +1 -23
- package/dist/LinearSyntenyDisplay/index.d.ts +1 -1
- package/dist/LinearSyntenyDisplay/index.js +18 -9
- package/dist/LinearSyntenyDisplay/model.d.ts +8 -102
- package/dist/LinearSyntenyDisplay/model.js +18 -99
- package/dist/LinearSyntenyView/components/ExportSvgDialog.d.ts +2 -3
- package/dist/LinearSyntenyView/components/ExportSvgDialog.js +35 -76
- package/dist/LinearSyntenyView/components/Icons.d.ts +3 -4
- package/dist/LinearSyntenyView/components/Icons.js +3 -8
- package/dist/LinearSyntenyView/components/ImportForm/ImportSyntenyOpenCustomTrack.d.ts +8 -0
- package/dist/LinearSyntenyView/components/ImportForm/ImportSyntenyOpenCustomTrack.js +130 -0
- package/dist/LinearSyntenyView/components/ImportForm/ImportSyntenyPreConfigured.d.ts +8 -0
- package/dist/LinearSyntenyView/components/ImportForm/ImportSyntenyPreConfigured.js +39 -0
- package/dist/LinearSyntenyView/components/ImportForm/ImportSyntenyTrackSelectorArea.d.ts +7 -0
- package/dist/LinearSyntenyView/components/ImportForm/ImportSyntenyTrackSelectorArea.js +22 -0
- package/dist/LinearSyntenyView/components/ImportForm/LinearSyntenyImportForm.d.ts +2 -3
- package/dist/LinearSyntenyView/components/ImportForm/LinearSyntenyImportForm.js +49 -150
- package/dist/LinearSyntenyView/components/ImportForm/doSubmit.d.ts +5 -0
- package/dist/LinearSyntenyView/components/ImportForm/doSubmit.js +43 -0
- package/dist/LinearSyntenyView/components/ImportForm/getAdapter.d.ts +117 -0
- package/dist/LinearSyntenyView/components/ImportForm/getAdapter.js +68 -0
- package/dist/LinearSyntenyView/components/ImportForm/util.js +1 -3
- package/dist/LinearSyntenyView/components/LinearSyntenyView.d.ts +2 -3
- package/dist/LinearSyntenyView/components/LinearSyntenyView.js +20 -10
- package/dist/LinearSyntenyView/index.d.ts +1 -1
- package/dist/LinearSyntenyView/index.js +17 -7
- package/dist/LinearSyntenyView/model.d.ts +54 -58
- package/dist/LinearSyntenyView/model.js +61 -56
- package/dist/LinearSyntenyView/svgcomponents/SVGBackground.d.ts +1 -2
- package/dist/LinearSyntenyView/svgcomponents/SVGBackground.js +3 -6
- package/dist/LinearSyntenyView/svgcomponents/SVGLinearGenomeView.d.ts +2 -3
- package/dist/LinearSyntenyView/svgcomponents/SVGLinearGenomeView.js +3 -11
- package/dist/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.d.ts +1 -1
- package/dist/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.js +7 -24
- package/dist/LinearSyntenyView/types.d.ts +12 -0
- package/dist/LinearSyntenyView/types.js +2 -0
- package/dist/LinearSyntenyViewHelper/index.d.ts +1 -1
- package/dist/LinearSyntenyViewHelper/index.js +2 -2
- package/dist/LinearSyntenyViewHelper/stateModelFactory.d.ts +2 -14
- package/dist/LinearSyntenyViewHelper/stateModelFactory.js +2 -29
- package/dist/SyntenyFeatureDetail/LinkToSyntenyView.d.ts +5 -0
- package/dist/SyntenyFeatureDetail/LinkToSyntenyView.js +87 -0
- package/dist/SyntenyFeatureDetail/SyntenyFeatureDetail.d.ts +2 -11
- package/dist/SyntenyFeatureDetail/SyntenyFeatureDetail.js +5 -90
- package/dist/SyntenyFeatureDetail/index.d.ts +1 -1
- package/dist/SyntenyFeatureDetail/index.js +18 -14
- package/dist/SyntenyFeatureDetail/types.d.ts +9 -0
- package/dist/SyntenyFeatureDetail/types.js +2 -0
- package/dist/SyntenyTrack/configSchema.d.ts +1 -1
- package/dist/SyntenyTrack/configSchema.js +1 -9
- package/dist/SyntenyTrack/index.d.ts +1 -1
- package/dist/SyntenyTrack/index.js +1 -1
- package/dist/index.d.ts +1 -1
- package/dist/index.js +4 -4
- package/dist/util.d.ts +2 -2
- package/dist/util.js +1 -11
- package/esm/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.d.ts +6 -5
- package/esm/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.js +35 -36
- package/esm/LGVSyntenyDisplay/components/util.d.ts +9 -6
- package/esm/LGVSyntenyDisplay/components/util.js +6 -13
- package/esm/LGVSyntenyDisplay/configSchemaF.d.ts +19 -10
- package/esm/LGVSyntenyDisplay/configSchemaF.js +12 -9
- package/esm/LGVSyntenyDisplay/index.d.ts +1 -1
- package/esm/LGVSyntenyDisplay/index.js +1 -1
- package/esm/LGVSyntenyDisplay/model.d.ts +122 -69
- package/esm/LGVSyntenyDisplay/model.js +4 -31
- package/esm/LaunchLinearSyntenyView.d.ts +1 -1
- package/esm/LaunchLinearSyntenyView.js +1 -3
- package/esm/LinearComparativeDisplay/configSchemaF.d.ts +0 -3
- package/esm/LinearComparativeDisplay/configSchemaF.js +0 -6
- package/esm/LinearComparativeDisplay/index.d.ts +1 -1
- package/esm/LinearComparativeDisplay/stateModelFactory.d.ts +12 -69
- package/esm/LinearComparativeDisplay/stateModelFactory.js +14 -58
- package/esm/LinearComparativeView/components/Header.d.ts +2 -3
- package/esm/LinearComparativeView/components/Header.js +56 -63
- package/esm/LinearComparativeView/components/HeaderSearchBoxes.d.ts +2 -3
- package/esm/LinearComparativeView/components/HeaderSearchBoxes.js +5 -12
- package/esm/LinearComparativeView/components/LinearComparativeRenderArea.d.ts +2 -3
- package/esm/LinearComparativeView/components/LinearComparativeRenderArea.js +17 -29
- package/esm/LinearComparativeView/components/LinearComparativeView.d.ts +2 -3
- package/esm/LinearComparativeView/components/LinearComparativeView.js +4 -9
- package/esm/LinearComparativeView/components/Rubberband.d.ts +2 -3
- package/esm/LinearComparativeView/components/Rubberband.js +36 -46
- package/esm/LinearComparativeView/components/VerticalGuide.d.ts +2 -3
- package/esm/LinearComparativeView/components/VerticalGuide.js +5 -6
- package/esm/LinearComparativeView/index.d.ts +1 -1
- package/esm/LinearComparativeView/model.d.ts +38 -90
- package/esm/LinearComparativeView/model.js +24 -101
- package/esm/LinearReadVsRef/LinearReadVsRef.d.ts +2 -3
- package/esm/LinearReadVsRef/LinearReadVsRef.js +10 -32
- package/esm/LinearReadVsRef/index.d.ts +1 -1
- package/esm/LinearReadVsRef/index.js +1 -3
- package/esm/LinearSyntenyDisplay/afterAttach.d.ts +1 -1
- package/esm/LinearSyntenyDisplay/afterAttach.js +8 -12
- package/esm/LinearSyntenyDisplay/components/Component.d.ts +2 -3
- package/esm/LinearSyntenyDisplay/components/Component.js +11 -13
- package/esm/LinearSyntenyDisplay/components/LinearSyntenyRendering.d.ts +2 -3
- package/esm/LinearSyntenyDisplay/components/LinearSyntenyRendering.js +79 -100
- package/esm/LinearSyntenyDisplay/components/SyntenyContextMenu.d.ts +3 -4
- package/esm/LinearSyntenyDisplay/components/SyntenyContextMenu.js +3 -3
- package/esm/LinearSyntenyDisplay/components/SyntenyTooltip.d.ts +1 -2
- package/esm/LinearSyntenyDisplay/components/SyntenyTooltip.js +3 -4
- package/esm/LinearSyntenyDisplay/components/util.d.ts +3 -3
- package/esm/LinearSyntenyDisplay/components/util.js +2 -11
- package/esm/LinearSyntenyDisplay/configSchemaF.d.ts +1 -12
- package/esm/LinearSyntenyDisplay/configSchemaF.js +0 -15
- package/esm/LinearSyntenyDisplay/drawSynteny.d.ts +1 -1
- package/esm/LinearSyntenyDisplay/drawSynteny.js +1 -23
- package/esm/LinearSyntenyDisplay/index.d.ts +1 -1
- package/esm/LinearSyntenyDisplay/index.js +1 -2
- package/esm/LinearSyntenyDisplay/model.d.ts +8 -102
- package/esm/LinearSyntenyDisplay/model.js +1 -92
- package/esm/LinearSyntenyView/components/ExportSvgDialog.d.ts +2 -3
- package/esm/LinearSyntenyView/components/ExportSvgDialog.js +35 -53
- package/esm/LinearSyntenyView/components/Icons.d.ts +3 -4
- package/esm/LinearSyntenyView/components/Icons.js +3 -5
- package/esm/LinearSyntenyView/components/ImportForm/ImportSyntenyOpenCustomTrack.d.ts +8 -0
- package/esm/LinearSyntenyView/components/ImportForm/ImportSyntenyOpenCustomTrack.js +125 -0
- package/esm/LinearSyntenyView/components/ImportForm/ImportSyntenyPreConfigured.d.ts +8 -0
- package/esm/LinearSyntenyView/components/ImportForm/ImportSyntenyPreConfigured.js +37 -0
- package/esm/LinearSyntenyView/components/ImportForm/ImportSyntenyTrackSelectorArea.d.ts +7 -0
- package/esm/LinearSyntenyView/components/ImportForm/ImportSyntenyTrackSelectorArea.js +16 -0
- package/esm/LinearSyntenyView/components/ImportForm/LinearSyntenyImportForm.d.ts +2 -3
- package/esm/LinearSyntenyView/components/ImportForm/LinearSyntenyImportForm.js +49 -127
- package/esm/LinearSyntenyView/components/ImportForm/doSubmit.d.ts +5 -0
- package/esm/LinearSyntenyView/components/ImportForm/doSubmit.js +40 -0
- package/esm/LinearSyntenyView/components/ImportForm/getAdapter.d.ts +117 -0
- package/esm/LinearSyntenyView/components/ImportForm/getAdapter.js +65 -0
- package/esm/LinearSyntenyView/components/ImportForm/util.js +1 -3
- package/esm/LinearSyntenyView/components/LinearSyntenyView.d.ts +2 -3
- package/esm/LinearSyntenyView/components/LinearSyntenyView.js +3 -3
- package/esm/LinearSyntenyView/index.d.ts +1 -1
- package/esm/LinearSyntenyView/model.d.ts +54 -58
- package/esm/LinearSyntenyView/model.js +44 -49
- package/esm/LinearSyntenyView/svgcomponents/SVGBackground.d.ts +1 -2
- package/esm/LinearSyntenyView/svgcomponents/SVGBackground.js +3 -3
- package/esm/LinearSyntenyView/svgcomponents/SVGLinearGenomeView.d.ts +2 -3
- package/esm/LinearSyntenyView/svgcomponents/SVGLinearGenomeView.js +4 -9
- package/esm/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.d.ts +1 -1
- package/esm/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.js +8 -25
- package/esm/LinearSyntenyView/types.d.ts +12 -0
- package/esm/LinearSyntenyView/types.js +1 -0
- package/esm/LinearSyntenyViewHelper/index.d.ts +1 -1
- package/esm/LinearSyntenyViewHelper/index.js +2 -2
- package/esm/LinearSyntenyViewHelper/stateModelFactory.d.ts +2 -14
- package/esm/LinearSyntenyViewHelper/stateModelFactory.js +2 -29
- package/esm/SyntenyFeatureDetail/LinkToSyntenyView.d.ts +5 -0
- package/esm/SyntenyFeatureDetail/LinkToSyntenyView.js +52 -0
- package/esm/SyntenyFeatureDetail/SyntenyFeatureDetail.d.ts +2 -11
- package/esm/SyntenyFeatureDetail/SyntenyFeatureDetail.js +6 -68
- package/esm/SyntenyFeatureDetail/index.d.ts +1 -1
- package/esm/SyntenyFeatureDetail/index.js +1 -7
- package/esm/SyntenyFeatureDetail/types.d.ts +9 -0
- package/esm/SyntenyFeatureDetail/types.js +1 -0
- package/esm/SyntenyTrack/configSchema.d.ts +1 -1
- package/esm/SyntenyTrack/configSchema.js +1 -9
- package/esm/SyntenyTrack/index.d.ts +1 -1
- package/esm/SyntenyTrack/index.js +1 -1
- package/esm/index.d.ts +1 -1
- package/esm/index.js +4 -4
- package/esm/util.d.ts +2 -2
- package/esm/util.js +1 -11
- package/package.json +2 -4
- package/dist/LinearSyntenyView/components/ImportForm/AddCustomTrack.d.ts +0 -10
- package/dist/LinearSyntenyView/components/ImportForm/AddCustomTrack.js +0 -194
- package/dist/LinearSyntenyView/components/ImportForm/Spacer.d.ts +0 -2
- package/dist/LinearSyntenyView/components/ImportForm/Spacer.js +0 -10
- package/dist/LinearSyntenyView/components/ImportForm/TrackSelector.d.ts +0 -10
- package/dist/LinearSyntenyView/components/ImportForm/TrackSelector.js +0 -59
- package/dist/LinearSyntenyView/components/ImportForm/TrackSelectorUtil.d.ts +0 -14
- package/dist/LinearSyntenyView/components/ImportForm/TrackSelectorUtil.js +0 -52
- package/esm/LinearSyntenyView/components/ImportForm/AddCustomTrack.d.ts +0 -10
- package/esm/LinearSyntenyView/components/ImportForm/AddCustomTrack.js +0 -169
- package/esm/LinearSyntenyView/components/ImportForm/Spacer.d.ts +0 -2
- package/esm/LinearSyntenyView/components/ImportForm/Spacer.js +0 -4
- package/esm/LinearSyntenyView/components/ImportForm/TrackSelector.d.ts +0 -10
- package/esm/LinearSyntenyView/components/ImportForm/TrackSelector.js +0 -34
- package/esm/LinearSyntenyView/components/ImportForm/TrackSelectorUtil.d.ts +0 -14
- package/esm/LinearSyntenyView/components/ImportForm/TrackSelectorUtil.js +0 -23
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@@ -1,46 +1,27 @@
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-
import {
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import {
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+
import { ConfigurationReference, readConfObject, } from '@jbrowse/core/configuration';
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+
import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes/models';
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import { dedupe, getContainingView, getSession, makeAbortableReaction, } from '@jbrowse/core/util';
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+
import { stopStopToken } from '@jbrowse/core/util/stopToken';
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import { getRpcSessionId } from '@jbrowse/core/util/tracks';
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import {
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/**
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* #stateModel LinearComparativeDisplay
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* extends
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* - [BaseDisplay](../basedisplay)
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*/
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+
import { getParent, getSnapshot, types } from 'mobx-state-tree';
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function stateModelFactory(configSchema) {
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return types
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.compose('LinearComparativeDisplay', BaseDisplay, types.model({
|
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/**
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|
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*/
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type: types.literal('LinearComparativeDisplay'),
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/**
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*/
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configuration: ConfigurationReference(configSchema),
|
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}))
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.volatile((
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+
.volatile(() => ({
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|
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}))
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/**
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*/
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return getParent(self, 4).level;
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|
},
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/**
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* #getter
|
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*/
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get height() {
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|
return getParent(self, 4).height;
|
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|
},
|
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|
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/**
|
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* #getter
|
|
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|
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*/
|
|
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25
|
renderProps() {
|
|
45
26
|
return {
|
|
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27
|
rpcDriverName: self.rpcDriverName,
|
|
@@ -50,33 +31,18 @@ function stateModelFactory(configSchema) {
|
|
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31
|
},
|
|
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32
|
}))
|
|
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33
|
.actions(self => {
|
|
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|
-
let
|
|
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|
+
let stopToken;
|
|
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35
|
return {
|
|
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|
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|
|
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|
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* #action
|
|
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|
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* controlled by a reaction
|
|
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|
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*/
|
|
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|
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setLoading(abortController) {
|
|
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|
+
setLoading(newStopToken) {
|
|
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37
|
self.message = undefined;
|
|
61
38
|
self.error = undefined;
|
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|
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|
|
39
|
+
stopToken = newStopToken;
|
|
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40
|
},
|
|
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|
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/**
|
|
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|
-
* #action
|
|
66
|
-
* controlled by a reaction
|
|
67
|
-
*/
|
|
68
41
|
setMessage(messageText) {
|
|
69
|
-
if (renderInProgress && !renderInProgress.signal.aborted) {
|
|
70
|
-
renderInProgress.abort();
|
|
71
|
-
}
|
|
72
42
|
self.message = messageText;
|
|
73
43
|
self.error = undefined;
|
|
74
|
-
|
|
44
|
+
stopToken = undefined;
|
|
75
45
|
},
|
|
76
|
-
/**
|
|
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|
-
* #action
|
|
78
|
-
* controlled by a reaction
|
|
79
|
-
*/
|
|
80
46
|
setRendered(args) {
|
|
81
47
|
if (!args) {
|
|
82
48
|
return;
|
|
@@ -101,34 +67,27 @@ function stateModelFactory(configSchema) {
|
|
|
101
67
|
}
|
|
102
68
|
self.message = undefined;
|
|
103
69
|
self.error = undefined;
|
|
104
|
-
|
|
70
|
+
stopToken = undefined;
|
|
105
71
|
if (foundNewFeatureNotInExistingMap ||
|
|
106
72
|
foundExistingFeatureNotInNewMap ||
|
|
107
73
|
!self.features) {
|
|
108
74
|
self.features = features;
|
|
109
75
|
}
|
|
110
76
|
},
|
|
111
|
-
/**
|
|
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|
-
* #action
|
|
113
|
-
* controlled by a reaction
|
|
114
|
-
*/
|
|
115
77
|
setError(error) {
|
|
116
78
|
console.error(error);
|
|
117
|
-
if (
|
|
118
|
-
|
|
79
|
+
if (stopToken !== undefined) {
|
|
80
|
+
stopStopToken(stopToken);
|
|
119
81
|
}
|
|
120
|
-
// the rendering failed for some reason
|
|
121
82
|
self.message = undefined;
|
|
122
83
|
self.error = error;
|
|
123
|
-
|
|
84
|
+
stopToken = undefined;
|
|
124
85
|
},
|
|
125
86
|
};
|
|
126
87
|
})
|
|
127
88
|
.actions(self => ({
|
|
128
89
|
afterAttach() {
|
|
129
|
-
makeAbortableReaction(
|
|
130
|
-
// @ts-expect-error
|
|
131
|
-
self, renderBlockData, renderBlockEffect, {
|
|
90
|
+
makeAbortableReaction(self, renderBlockData, renderBlockEffect, {
|
|
132
91
|
name: `${self.type} ${self.id} rendering`,
|
|
133
92
|
delay: 1000,
|
|
134
93
|
fireImmediately: true,
|
|
@@ -139,9 +98,6 @@ function stateModelFactory(configSchema) {
|
|
|
139
98
|
function renderBlockData(self) {
|
|
140
99
|
const { rpcManager } = getSession(self);
|
|
141
100
|
const display = self;
|
|
142
|
-
// Alternative to readConfObject(config) is below used because
|
|
143
|
-
// renderProps is something under our control. Compare to
|
|
144
|
-
// serverSideRenderedBlock
|
|
145
101
|
readConfObject(self.configuration);
|
|
146
102
|
const { level, adapterConfig } = self;
|
|
147
103
|
const parent = getContainingView(self);
|
|
@@ -1,6 +1,5 @@
|
|
|
1
|
-
import
|
|
2
|
-
import { LinearComparativeViewModel } from '../model';
|
|
1
|
+
import type { LinearComparativeViewModel } from '../model';
|
|
3
2
|
declare const Header: ({ model, }: {
|
|
4
3
|
model: LinearComparativeViewModel;
|
|
5
|
-
}) =>
|
|
4
|
+
}) => import("react/jsx-runtime").JSX.Element;
|
|
6
5
|
export default Header;
|
|
@@ -1,12 +1,12 @@
|
|
|
1
|
-
import
|
|
2
|
-
import {
|
|
3
|
-
import { FormGroup } from '@mui/material';
|
|
4
|
-
import { makeStyles } from 'tss-react/mui';
|
|
1
|
+
import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
|
|
2
|
+
import { useState } from 'react';
|
|
5
3
|
import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
|
|
6
|
-
|
|
4
|
+
import { TrackSelector as TrackSelectorIcon } from '@jbrowse/core/ui/Icons';
|
|
7
5
|
import MoreVertIcon from '@mui/icons-material/MoreVert';
|
|
8
6
|
import SearchIcon from '@mui/icons-material/Search';
|
|
9
|
-
import {
|
|
7
|
+
import { FormGroup } from '@mui/material';
|
|
8
|
+
import { observer } from 'mobx-react';
|
|
9
|
+
import { makeStyles } from 'tss-react/mui';
|
|
10
10
|
import HeaderSearchBoxes from './HeaderSearchBoxes';
|
|
11
11
|
const useStyles = makeStyles()({
|
|
12
12
|
inline: {
|
|
@@ -18,67 +18,60 @@ const Header = observer(function ({ model, }) {
|
|
|
18
18
|
const { views } = model;
|
|
19
19
|
const [showSearchBoxes, setShowSearchBoxes] = useState(views.length <= 3);
|
|
20
20
|
const [sideBySide, setSideBySide] = useState(views.length <= 3);
|
|
21
|
-
return (
|
|
22
|
-
|
|
23
|
-
|
|
24
|
-
|
|
25
|
-
|
|
26
|
-
|
|
27
|
-
|
|
21
|
+
return (_jsxs(FormGroup, { row: true, children: [_jsx(CascadingMenuButton, { menuItems: [
|
|
22
|
+
{
|
|
23
|
+
label: 'Synteny track selectors',
|
|
24
|
+
type: 'subMenu',
|
|
25
|
+
subMenu: views.slice(0, -1).map((_, idx) => ({
|
|
26
|
+
label: `Row ${idx + 1}->${idx + 2} (${views[idx].assemblyNames.join(',')}->${views[idx + 1].assemblyNames.join(',')})`,
|
|
27
|
+
onClick: () => {
|
|
28
|
+
model.activateTrackSelector(idx);
|
|
29
|
+
},
|
|
30
|
+
})),
|
|
31
|
+
},
|
|
32
|
+
{
|
|
33
|
+
label: 'Row track selectors',
|
|
34
|
+
type: 'subMenu',
|
|
35
|
+
subMenu: views.map((view, idx) => ({
|
|
36
|
+
label: `Row ${idx + 1} track selector (${view.assemblyNames.join(',')})`,
|
|
37
|
+
onClick: () => view.activateTrackSelector(),
|
|
38
|
+
})),
|
|
39
|
+
},
|
|
40
|
+
], children: _jsx(TrackSelectorIcon, {}) }), _jsx(CascadingMenuButton, { menuItems: [
|
|
41
|
+
{
|
|
42
|
+
label: 'Row view menus',
|
|
43
|
+
type: 'subMenu',
|
|
44
|
+
subMenu: views.map((view, idx) => ({
|
|
45
|
+
label: `View ${idx + 1} Menu`,
|
|
46
|
+
subMenu: view.menuItems(),
|
|
47
|
+
})),
|
|
48
|
+
},
|
|
49
|
+
...model.headerMenuItems(),
|
|
50
|
+
], children: _jsx(MoreVertIcon, {}) }), _jsx(CascadingMenuButton, { menuItems: [
|
|
51
|
+
{
|
|
52
|
+
label: 'Show search boxes',
|
|
53
|
+
type: 'checkbox',
|
|
54
|
+
checked: showSearchBoxes,
|
|
28
55
|
onClick: () => {
|
|
29
|
-
|
|
56
|
+
setShowSearchBoxes(!showSearchBoxes);
|
|
30
57
|
},
|
|
31
|
-
})),
|
|
32
|
-
},
|
|
33
|
-
{
|
|
34
|
-
label: 'Row track selectors',
|
|
35
|
-
type: 'subMenu',
|
|
36
|
-
subMenu: views.map((view, idx) => ({
|
|
37
|
-
label: `Row ${idx + 1} track selector (${view.assemblyNames.join(',')})`,
|
|
38
|
-
onClick: () => view.activateTrackSelector(),
|
|
39
|
-
})),
|
|
40
|
-
},
|
|
41
|
-
] },
|
|
42
|
-
React.createElement(TrackSelectorIcon, null)),
|
|
43
|
-
React.createElement(CascadingMenuButton, { menuItems: [
|
|
44
|
-
{
|
|
45
|
-
label: 'Row view menus',
|
|
46
|
-
type: 'subMenu',
|
|
47
|
-
subMenu: views.map((view, idx) => ({
|
|
48
|
-
label: `View ${idx + 1} Menu`,
|
|
49
|
-
subMenu: view.menuItems(),
|
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})),
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},
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...model.headerMenuItems(),
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] },
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React.createElement(MoreVertIcon, null)),
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React.createElement(CascadingMenuButton, { menuItems: [
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{
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label: 'Show search boxes',
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type: 'checkbox',
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checked: showSearchBoxes,
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onClick: () => {
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setShowSearchBoxes(!showSearchBoxes);
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},
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{
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label: 'Orientation - Side-by-side',
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type: 'radio',
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checked: sideBySide,
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onClick: () => {
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setSideBySide(!sideBySide);
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},
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},
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{
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label: 'Orientation - Vertical',
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type: 'radio',
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checked: !sideBySide,
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onClick: () => {
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setSideBySide(!sideBySide);
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},
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},
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},
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] },
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React.createElement(SearchIcon, null)),
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showSearchBoxes ? (React.createElement("span", { className: sideBySide ? classes.inline : undefined }, views.map(view => (React.createElement(HeaderSearchBoxes, { key: view.id, view: view }))))) : null));
|
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|
+
], children: _jsx(SearchIcon, {}) }), showSearchBoxes ? (_jsx("span", { className: sideBySide ? classes.inline : undefined, children: views.map(view => (_jsx(HeaderSearchBoxes, { view: view }, view.id))) })) : null] }));
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});
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export default Header;
|
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@@ -1,6 +1,5 @@
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1
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-
import
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2
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-
import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
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1
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+
import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
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declare const HeaderSearchBoxes: ({ view, }: {
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3
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view: LinearGenomeViewModel;
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5
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-
}) =>
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4
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+
}) => import("react/jsx-runtime").JSX.Element;
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5
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export default HeaderSearchBoxes;
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@@ -1,10 +1,9 @@
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1
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-
import
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2
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-
import {
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1
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+
import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
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2
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+
import { toLocale } from '@jbrowse/core/util';
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3
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+
import { SearchBox } from '@jbrowse/plugin-linear-genome-view';
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3
4
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import { Typography } from '@mui/material';
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5
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+
import { observer } from 'mobx-react';
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4
6
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import { makeStyles } from 'tss-react/mui';
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5
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-
// jbrowse
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import { SearchBox, } from '@jbrowse/plugin-linear-genome-view';
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-
import { toLocale } from '@jbrowse/core/util';
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7
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const useStyles = makeStyles()(() => ({
|
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9
8
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bp: {
|
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display: 'flex',
|
|
@@ -18,12 +17,6 @@ const useStyles = makeStyles()(() => ({
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|
const HeaderSearchBoxes = observer(function ({ view, }) {
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const { classes } = useStyles();
|
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19
|
const { assemblyNames, coarseTotalBp } = view;
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return (
|
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React.createElement(SearchBox, { model: view, showHelp: false }),
|
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|
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React.createElement(Typography, { variant: "body2", color: "textSecondary", className: classes.bp },
|
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|
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assemblyNames.join(','),
|
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25
|
-
" ",
|
|
26
|
-
toLocale(Math.round(coarseTotalBp)),
|
|
27
|
-
" bp")));
|
|
20
|
+
return (_jsxs("span", { className: classes.searchBox, children: [_jsx(SearchBox, { model: view, showHelp: false }), _jsxs(Typography, { variant: "body2", color: "textSecondary", className: classes.bp, children: [assemblyNames.join(','), " ", toLocale(Math.round(coarseTotalBp)), " bp"] })] }));
|
|
28
21
|
});
|
|
29
22
|
export default HeaderSearchBoxes;
|
|
@@ -1,6 +1,5 @@
|
|
|
1
|
-
import
|
|
2
|
-
import { LinearComparativeViewModel } from '../model';
|
|
1
|
+
import type { LinearComparativeViewModel } from '../model';
|
|
3
2
|
declare const LinearComparativeRenderArea: ({ model, }: {
|
|
4
3
|
model: LinearComparativeViewModel;
|
|
5
|
-
}) =>
|
|
4
|
+
}) => import("react/jsx-runtime").JSX.Element;
|
|
6
5
|
export default LinearComparativeRenderArea;
|
|
@@ -1,9 +1,10 @@
|
|
|
1
|
-
import
|
|
2
|
-
import { makeStyles } from 'tss-react/mui';
|
|
3
|
-
import { observer } from 'mobx-react';
|
|
4
|
-
import { getEnv } from '@jbrowse/core/util';
|
|
5
|
-
import { ResizeHandle } from '@jbrowse/core/ui';
|
|
1
|
+
import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
|
|
6
2
|
import { getConf } from '@jbrowse/core/configuration';
|
|
3
|
+
import { ResizeHandle } from '@jbrowse/core/ui';
|
|
4
|
+
import { getEnv } from '@jbrowse/core/util';
|
|
5
|
+
import { observer } from 'mobx-react';
|
|
6
|
+
import { Fragment } from 'react/jsx-runtime';
|
|
7
|
+
import { makeStyles } from 'tss-react/mui';
|
|
7
8
|
const useStyles = makeStyles()({
|
|
8
9
|
container: {
|
|
9
10
|
display: 'grid',
|
|
@@ -20,37 +21,24 @@ const useStyles = makeStyles()({
|
|
|
20
21
|
function View({ view }) {
|
|
21
22
|
const { pluginManager } = getEnv(view);
|
|
22
23
|
const { ReactComponent } = pluginManager.getViewType(view.type);
|
|
23
|
-
return
|
|
24
|
+
return _jsx(ReactComponent, { model: view });
|
|
24
25
|
}
|
|
25
26
|
const LinearComparativeRenderArea = observer(function ({ model, }) {
|
|
26
27
|
const { classes } = useStyles();
|
|
27
28
|
const { views, levels } = model;
|
|
28
|
-
|
|
29
|
-
React.createElement(View, { key: views[0].id, view: views[0] }),
|
|
30
|
-
];
|
|
31
|
-
for (let i = 1; i < views.length; i++) {
|
|
32
|
-
const view = views[i];
|
|
33
|
-
const level = levels[i - 1];
|
|
34
|
-
RenderList.push(React.createElement(React.Fragment, { key: view.id },
|
|
35
|
-
React.createElement("div", { className: classes.container },
|
|
36
|
-
React.createElement(Overlays, { model: model, level: i - 1 })),
|
|
37
|
-
React.createElement(ResizeHandle, { onDrag: n => level === null || level === void 0 ? void 0 : level.setHeight(level.height + n), className: classes.resizeHandle }),
|
|
38
|
-
React.createElement(View, { view: view })));
|
|
39
|
-
}
|
|
40
|
-
return React.createElement("div", { className: classes.container }, RenderList);
|
|
29
|
+
return (_jsx("div", { className: classes.container, children: views.map((view, i) => (_jsxs(Fragment, { children: [i > 0 ? (_jsxs(_Fragment, { children: [_jsx("div", { className: classes.container, children: _jsx(Overlays, { model: model, level: i - 1 }) }), _jsx(ResizeHandle, { onDrag: n => { var _a, _b; return (_a = levels[i - 1]) === null || _a === void 0 ? void 0 : _a.setHeight((((_b = levels[i - 1]) === null || _b === void 0 ? void 0 : _b.height) || 0) + n); }, className: classes.resizeHandle })] })) : null, _jsx(View, { view: view })] }, view.id))) }));
|
|
41
30
|
});
|
|
42
31
|
const Overlays = observer(function ({ model, level, }) {
|
|
43
32
|
var _a;
|
|
44
33
|
const { classes } = useStyles();
|
|
45
|
-
return (
|
|
46
|
-
|
|
47
|
-
|
|
48
|
-
|
|
49
|
-
|
|
50
|
-
|
|
51
|
-
|
|
52
|
-
|
|
53
|
-
|
|
54
|
-
})));
|
|
34
|
+
return (_jsx(_Fragment, { children: (_a = model.levels[level]) === null || _a === void 0 ? void 0 : _a.tracks.map(track => {
|
|
35
|
+
const [display] = track.displays;
|
|
36
|
+
const { RenderingComponent } = display;
|
|
37
|
+
const trackId = getConf(track, 'trackId');
|
|
38
|
+
return RenderingComponent ? (_jsx("div", { className: classes.overlay, style: {
|
|
39
|
+
height: display.height,
|
|
40
|
+
overflow: 'hidden',
|
|
41
|
+
}, children: _jsx(RenderingComponent, { model: display }) }, trackId)) : null;
|
|
42
|
+
}) }));
|
|
55
43
|
});
|
|
56
44
|
export default LinearComparativeRenderArea;
|
|
@@ -1,6 +1,5 @@
|
|
|
1
|
-
import
|
|
2
|
-
import { LinearComparativeViewModel } from '../model';
|
|
1
|
+
import type { LinearComparativeViewModel } from '../model';
|
|
3
2
|
declare const LinearComparativeView: ({ model, }: {
|
|
4
3
|
model: LinearComparativeViewModel;
|
|
5
|
-
}) =>
|
|
4
|
+
}) => import("react/jsx-runtime").JSX.Element;
|
|
6
5
|
export default LinearComparativeView;
|
|
@@ -1,12 +1,10 @@
|
|
|
1
|
-
import
|
|
2
|
-
import { makeStyles } from 'tss-react/mui';
|
|
1
|
+
import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
|
|
3
2
|
import { observer } from 'mobx-react';
|
|
4
|
-
import
|
|
3
|
+
import { makeStyles } from 'tss-react/mui';
|
|
5
4
|
import Header from './Header';
|
|
6
5
|
import LinearComparativeRenderArea from './LinearComparativeRenderArea';
|
|
6
|
+
import Rubberband from './Rubberband';
|
|
7
7
|
const useStyles = makeStyles()(theme => ({
|
|
8
|
-
// this helps keep the vertical guide inside the parent view container,
|
|
9
|
-
// similar style exists in the single LGV's trackscontainer
|
|
10
8
|
rubberbandContainer: {
|
|
11
9
|
position: 'relative',
|
|
12
10
|
overflow: 'hidden',
|
|
@@ -22,9 +20,6 @@ const useStyles = makeStyles()(theme => ({
|
|
|
22
20
|
}));
|
|
23
21
|
const LinearComparativeView = observer(function ({ model, }) {
|
|
24
22
|
const { classes } = useStyles();
|
|
25
|
-
return (
|
|
26
|
-
React.createElement(Header, { model: model }),
|
|
27
|
-
React.createElement(Rubberband, { model: model, ControlComponent: React.createElement("div", { className: classes.rubberbandDiv }) }),
|
|
28
|
-
React.createElement(LinearComparativeRenderArea, { model: model })));
|
|
23
|
+
return (_jsxs("div", { className: classes.rubberbandContainer, children: [_jsx(Header, { model: model }), _jsx(Rubberband, { model: model, ControlComponent: _jsx("div", { className: classes.rubberbandDiv }) }), _jsx(LinearComparativeRenderArea, { model: model })] }));
|
|
29
24
|
});
|
|
30
25
|
export default LinearComparativeView;
|
|
@@ -1,8 +1,7 @@
|
|
|
1
|
-
import
|
|
2
|
-
import { LinearComparativeViewModel } from '../model';
|
|
1
|
+
import type { LinearComparativeViewModel } from '../model';
|
|
3
2
|
type LCV = LinearComparativeViewModel;
|
|
4
3
|
declare const LinearComparativeRubberband: ({ model, ControlComponent, }: {
|
|
5
4
|
model: LCV;
|
|
6
5
|
ControlComponent?: React.ReactElement;
|
|
7
|
-
}) =>
|
|
6
|
+
}) => import("react/jsx-runtime").JSX.Element;
|
|
8
7
|
export default LinearComparativeRubberband;
|