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Add BEDPE add track workflow, avoid showing "Add track" when disabled #3631

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merged 2 commits into from May 18, 2023
Merged

Add BEDPE add track workflow, avoid showing "Add track" when disabled #3631

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2743d46
boost bedpe support with better track guessing and not failing on nul…
carolinebridge Apr 6, 2023
82563e9
Clarify the undefined case in typescript
cmdcolin May 18, 2023
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12 changes: 8 additions & 4 deletions plugins/bed/src/BedpeAdapter/BedpeAdapter.ts
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Expand Up @@ -168,12 +168,16 @@ export default class BedpeAdapter extends BaseFeatureDataAdapter {
return featureData(f, uniqueId, true, names)
})

for (const obj of ret1) {
intervalTree.insert([obj.get('start'), obj.get('end')], obj)
if (ret1) {
for (const obj of ret1) {
intervalTree.insert([obj.get('start'), obj.get('end')], obj)
}
}

for (const obj of ret2) {
intervalTree.insert([obj.get('start'), obj.get('end')], obj)
if (ret2) {
for (const obj of ret2) {
intervalTree.insert([obj.get('start'), obj.get('end')], obj)
}
}

return intervalTree
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13 changes: 13 additions & 0 deletions plugins/bed/src/index.ts
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Expand Up @@ -10,6 +10,7 @@ import {
makeIndex,
makeIndexType,
AdapterGuesser,
TrackTypeGuesser,
} from '@jbrowse/core/util/tracks'

export default class BedPlugin extends Plugin {
Expand Down Expand Up @@ -116,5 +117,17 @@ export default class BedPlugin extends Plugin {
}
},
)

pluginManager.addToExtensionPoint(
'Core-guessTrackTypeForLocation',
(trackTypeGuesser: TrackTypeGuesser) => {
return (adapterName: string) => {
if (adapterName === 'BedpeAdapter') {
return 'VariantTrack'
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the choice to make it use VariantTrack may make it unable to use the linear arc display, which may be useful for BEDPE (arc connects the two regions). at one point you mentioned trying to add arc rendering for VariantTrack but that it was tricky. could revisit that perhaps...

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more tangential but multi-region arc may be useful too. the LinearAlignmentsArcDisplay ended up becoming multi-region capable recently, and similar concept could apply to the regular LinearArcDisplay

}
return trackTypeGuesser(adapterName)
}
},
)
}
}
30 changes: 18 additions & 12 deletions ...ins/data-management/src/HierarchicalTrackSelectorWidget/components/tree/HamburgerMenu.tsx
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Expand Up @@ -6,6 +6,7 @@ import JBrowseMenu from '@jbrowse/core/ui/Menu'
import {
getSession,
isSessionModelWithWidgets,
isSessionWithAddTracks,
isSessionModelWithConnections,
} from '@jbrowse/core/util'
import {
Expand Down Expand Up @@ -116,6 +117,22 @@ export default observer(function HamburgerMenu({
onClick: () => setConnectionManagerOpen(true),
})
}

const trackMenuItems = [
{
label: 'Add track...',
onClick: () => {
if (isSessionModelWithWidgets(session)) {
session.showWidget(
session.addWidget('AddTrackWidget', 'addTrackWidget', {
view: model.view.id,
}),
)
}
},
},
]

return (
<>
<IconButton
Expand All @@ -134,18 +151,7 @@ export default observer(function HamburgerMenu({
}}
onClose={() => setMenuEl(undefined)}
menuItems={[
{
label: 'Add track...',
onClick: () => {
if (isSessionModelWithWidgets(session)) {
session.showWidget(
session.addWidget('AddTrackWidget', 'addTrackWidget', {
view: model.view.id,
}),
)
}
},
},
...(isSessionWithAddTracks(session) ? trackMenuItems : []),
...(session.makeConnection ? connectionMenuItems : []),

...(assemblyNames.length > 1
Expand Down