Misc

GMOD · Jan 24, 2025 · 45588a2 · 45588a2
1 parent 6abb9a5
commit 45588a2
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Showing 30 changed files with 1,415 additions and 701 deletions.
diff --git a/plugins/alignments/src/GuessAlignmentsTypes/index.ts b/plugins/alignments/src/GuessAlignmentsTypes/index.ts
@@ -1,3 +1,4 @@
+import { testAdapter } from '@jbrowse/core/util'
 import {
   getFileName,
   makeIndex,
@@ -9,8 +10,6 @@ import type {
   AdapterGuesser,
   TrackTypeGuesser,
 } from '@jbrowse/core/util/tracks'
-import { testAdapter } from '@jbrowse/core/util'
-
 import type { FileLocation } from '@jbrowse/core/util/types'
 
 export default function GuessAlignmentsTypesF(pluginManager: PluginManager) {

diff --git a/plugins/bed/src/GuessAdapter/index.ts b/plugins/bed/src/GuessAdapter/index.ts
@@ -1,9 +1,9 @@
+import { testAdapter } from '@jbrowse/core/util'
 import {
   getFileName,
   makeIndex,
   makeIndexType,
 } from '@jbrowse/core/util/tracks'
-import { testAdapter } from '@jbrowse/core/util'
 
 import type PluginManager from '@jbrowse/core/PluginManager'
 import type {
@@ -28,7 +28,7 @@ export default function GuessAdapterF(pluginManager: PluginManager) {
         ) {
           return {
             type: 'BedpeAdapter',
-            bedpeAdapter: file,
+            bedpeLocation: file,
           }
         } else if (
           testAdapter(fileName, /\.bb$/i, adapterHint, 'BigBedAdapter') ||

diff --git a/plugins/comparative-adapters/src/BlastTabularAdapter/index.ts b/plugins/comparative-adapters/src/BlastTabularAdapter/index.ts
@@ -12,7 +12,7 @@ export default function BlastTabularAdapterF(pluginManager: PluginManager) {
         displayName: 'Tabular BLAST output adapter',
         configSchema,
         adapterMetadata: {
-          hiddenFromGUI: true,
+          category: 'Synteny adapters',
         },
         getAdapterClass: () =>
           import('./BlastTabularAdapter').then(r => r.default),

diff --git a/plugins/comparative-adapters/src/ChainAdapter/index.ts b/plugins/comparative-adapters/src/ChainAdapter/index.ts
@@ -12,7 +12,7 @@ export default function ChainAdapterF(pluginManager: PluginManager) {
         displayName: 'Liftover chain adapter',
         configSchema,
         adapterMetadata: {
-          hiddenFromGUI: true,
+          category: 'Synteny adapters',
         },
         getAdapterClass: () => import('./ChainAdapter').then(r => r.default),
       }),

diff --git a/...ns/comparative-adapters/src/ComparativeAddTrackComponent/ComparativeAddTrackComponent.tsx b/...ns/comparative-adapters/src/ComparativeAddTrackComponent/ComparativeAddTrackComponent.tsx
@@ -0,0 +1,49 @@
+import { useEffect, useState } from 'react'
+
+import { AssemblySelector } from '@jbrowse/core/ui'
+import { getSession } from '@jbrowse/core/util'
+import { observer } from 'mobx-react'
+
+const ComparativeAddTrackComponent = observer(function ({ model }: any) {
+  const session = getSession(model)
+  const [r0, setR0] = useState(session.assemblies[0]?.name)
+  const [r1, setR1] = useState(session.assemblies[0]?.name)
+  useEffect(() => {
+    model.setMixinData({
+      adapter: {
+        queryAssembly: r0,
+        targetAssembly: r1,
+      },
+    })
+  }, [model, r0, r1])
+  return (
+    <>
+      <AssemblySelector
+        session={session}
+        label="Query assembly"
+        helperText=""
+        selected={r0}
+        onChange={asm => {
+          setR0(asm)
+        }}
+        TextFieldProps={{
+          fullWidth: true,
+        }}
+      />
+      <AssemblySelector
+        session={session}
+        label="Target assembly"
+        helperText=""
+        selected={r1}
+        onChange={asm => {
+          setR1(asm)
+        }}
+        TextFieldProps={{
+          fullWidth: true,
+        }}
+      />
+    </>
+  )
+})
+
+export default ComparativeAddTrackComponent
diff --git a/plugins/comparative-adapters/src/ComparativeAddTrackComponent/index.tsx b/plugins/comparative-adapters/src/ComparativeAddTrackComponent/index.tsx
@@ -1,52 +1,13 @@
-import { useEffect, useState } from 'react'
+import { lazy } from 'react'
 
-import { AssemblySelector } from '@jbrowse/core/ui'
-import { getSession } from '@jbrowse/core/util'
-import { observer } from 'mobx-react'
+import { pairwiseTypes } from '../syntenyTypes'
 
 import type PluginManager from '@jbrowse/core/PluginManager'
 
-const ComparativeAddTrackComponent = observer(function ({ model }: any) {
-  const session = getSession(model)
-  const [r0, setR0] = useState(session.assemblies[0]?.name)
-  const [r1, setR1] = useState(session.assemblies[0]?.name)
-  useEffect(() => {
-    model.setMixinData({
-      adapter: {
-        queryAssembly: r0,
-        targetAssembly: r1,
-      },
-    })
-  }, [model, r0, r1])
-  return (
-    <>
-      <AssemblySelector
-        session={session}
-        label="Query assembly"
-        helperText=""
-        selected={r0}
-        onChange={asm => {
-          setR0(asm)
-        }}
-        TextFieldProps={{
-          fullWidth: true,
-        }}
-      />
-      <AssemblySelector
-        session={session}
-        label="Target assembly"
-        helperText=""
-        selected={r1}
-        onChange={asm => {
-          setR1(asm)
-        }}
-        TextFieldProps={{
-          fullWidth: true,
-        }}
-      />
-    </>
-  )
-})
+// lazies
+const ComparativeAddTrackComponent = lazy(
+  () => import('./ComparativeAddTrackComponent'),
+)
 
 export default function ComparativeAddTrackComponentF(
   pluginManager: PluginManager,
@@ -55,7 +16,7 @@ export default function ComparativeAddTrackComponentF(
     'Core-addTrackComponent',
     // @ts-expect-error
     (comp, { model }: { trackAdapterType: string }) => {
-      return model.trackAdapterType === 'PAFAdapter'
+      return pairwiseTypes.includes(model.trackAdapterType)
         ? ComparativeAddTrackComponent
         : comp
     },

diff --git a/plugins/comparative-adapters/src/DeltaAdapter/index.ts b/plugins/comparative-adapters/src/DeltaAdapter/index.ts
@@ -12,7 +12,7 @@ export default function DeltaAdapterF(pluginManager: PluginManager) {
         displayName: 'MUMmer delta adapter',
         configSchema,
         adapterMetadata: {
-          hiddenFromGUI: true,
+          category: 'Synteny adapters',
         },
         getAdapterClass: () => import('./DeltaAdapter').then(r => r.default),
       }),

diff --git a/plugins/comparative-adapters/src/GuessAdapter/index.ts b/plugins/comparative-adapters/src/GuessAdapter/index.ts
@@ -1,9 +1,11 @@
+import { testAdapter } from '@jbrowse/core/util'
 import {
   getFileName,
   makeIndex,
   makeIndexType,
 } from '@jbrowse/core/util/tracks'
-import { testAdapter } from '@jbrowse/core/util'
+
+import { syntenyTypes } from '../syntenyTypes'
 
 import type PluginManager from '@jbrowse/core/PluginManager'
 import type {
@@ -28,19 +30,48 @@ export default function GuessAdapterF(pluginManager: PluginManager) {
             type: 'PAFAdapter',
             pafLocation: file,
           }
+        } else if (adapterHint === 'BlastTabularAdapter') {
+          return {
+            type: 'BlastTabularAdapter',
+            blastTableLocation: file,
+          }
+        } else if (
+          testAdapter(
+            fileName,
+            /\.anchors.simple(.gz)?/i,
+            adapterHint,
+            'MCScanSimpleAnchorsAdapter',
+          )
+        ) {
+          return {
+            type: 'MCScanSimpleAnchorsAdapter',
+            mcscanSimpleAnchorsLocation: file,
+          }
+        } else if (
+          testAdapter(
+            fileName,
+            /\.anchors(.gz)?/i,
+            adapterHint,
+            'MCScanAnchorsAdapter',
+          )
+        ) {
+          return {
+            type: 'MCScanAnchorsAdapter',
+            mcscanAnchorsLocation: file,
+          }
         } else if (
           testAdapter(fileName, /\.delta(.gz)?/i, adapterHint, 'DeltaAdapter')
         ) {
           return {
             type: 'DeltaAdapter',
-            deltaAdapter: file,
+            deltaLocation: file,
           }
         } else if (
           testAdapter(fileName, /\.chain(.gz)?/i, adapterHint, 'ChainAdapter')
         ) {
           return {
             type: 'ChainAdapter',
-            chainAdapter: file,
+            chainLocation: file,
           }
         } else if (
           testAdapter(fileName, /\.out(.gz)?/i, adapterHint, 'MashMapAdapter')
@@ -75,15 +106,7 @@ export default function GuessAdapterF(pluginManager: PluginManager) {
     'Core-guessTrackTypeForLocation',
     (trackTypeGuesser: TrackTypeGuesser) => {
       return (adapterName: string) =>
-        [
-          'PAFAdapter',
-          'ChainAdapter',
-          'DeltaAdapter',
-          'MashMapAdapter',
-          'MCScanAnchorsAdapter',
-          'MCScanSimpleAnchorsAdapter',
-          'PairwiseIndexedPAFAdapter',
-        ].includes(adapterName)
+        syntenyTypes.includes(adapterName)
           ? 'SyntenyTrack'
           : trackTypeGuesser(adapterName)
     },

diff --git a/plugins/comparative-adapters/src/MCScanAddTrackComponent/MCScanAddTrackComponent.tsx b/plugins/comparative-adapters/src/MCScanAddTrackComponent/MCScanAddTrackComponent.tsx
@@ -0,0 +1,77 @@
+import { useEffect, useState } from 'react'
+
+import { AssemblySelector, FileSelector } from '@jbrowse/core/ui'
+import { getSession } from '@jbrowse/core/util'
+import { Typography } from '@mui/material'
+import { observer } from 'mobx-react'
+
+import type { FileLocation } from '@jbrowse/core/util'
+
+const MCScanAddTrackComponent = observer(function ({ model }: any) {
+  const session = getSession(model)
+  const [r0, setR0] = useState(session.assemblies[0]?.name)
+  const [r1, setR1] = useState(session.assemblies[0]?.name)
+  const [bed1Location, setBed1Location] = useState<FileLocation>()
+  const [bed2Location, setBed2Location] = useState<FileLocation>()
+  useEffect(() => {
+    model.setMixinData({
+      adapter: {
+        assemblyNamees: [r0, r1],
+        bed1Location,
+        bed2Location,
+      },
+    })
+  }, [model, bed1Location, bed2Location, r0, r1])
+  return (
+    <div style={{ marginTop: 20 }}>
+      <Typography>
+        JBrowse requires the two BED files that specify the genomic locations of
+        the genes in the .anchors files
+      </Typography>
+      <AssemblySelector
+        session={session}
+        label="BED1 assembly"
+        helperText=""
+        selected={r0}
+        onChange={asm => {
+          setR0(asm)
+        }}
+        TextFieldProps={{
+          fullWidth: true,
+        }}
+      />
+      <AssemblySelector
+        session={session}
+        label="BED2 assembly"
+        helperText=""
+        selected={r1}
+        onChange={asm => {
+          setR1(asm)
+        }}
+        TextFieldProps={{
+          fullWidth: true,
+        }}
+      />
+      <FileSelector
+        name="BED1"
+        inline
+        description=""
+        location={bed1Location}
+        setLocation={loc => {
+          setBed1Location(loc)
+        }}
+      />
+      <FileSelector
+        name="BED2"
+        inline
+        description=""
+        location={bed2Location}
+        setLocation={loc => {
+          setBed2Location(loc)
+        }}
+      />
+    </div>
+  )
+})
+
+export default MCScanAddTrackComponent
diff --git a/plugins/comparative-adapters/src/MCScanAddTrackComponent/index.tsx b/plugins/comparative-adapters/src/MCScanAddTrackComponent/index.tsx
@@ -0,0 +1,20 @@
+import { lazy } from 'react'
+
+import { mcscanTypes } from '../syntenyTypes'
+
+import type PluginManager from '@jbrowse/core/PluginManager'
+
+// lazies
+const MCScanAddTrackComponent = lazy(() => import('./MCScanAddTrackComponent'))
+
+export default function MCScanAddTrackComponentF(pluginManager: PluginManager) {
+  pluginManager.addToExtensionPoint(
+    'Core-addTrackComponent',
+    // @ts-expect-error
+    (comp, { model }: { trackAdapterType: string }) => {
+      return mcscanTypes.includes(model.trackAdapterType)
+        ? MCScanAddTrackComponent
+        : comp
+    },
+  )
+}
diff --git a/plugins/comparative-adapters/src/MCScanAnchorsAdapter/index.ts b/plugins/comparative-adapters/src/MCScanAnchorsAdapter/index.ts
@@ -12,7 +12,7 @@ export default function MCScanAnchorsAdapterF(pluginManager: PluginManager) {
         displayName: 'MCScan anchors adapter',
         configSchema,
         adapterMetadata: {
-          hiddenFromGUI: true,
+          category: 'Synteny adapters',
         },
 
         getAdapterClass: () =>

diff --git a/plugins/comparative-adapters/src/MCScanSimpleAnchorsAdapter/index.ts b/plugins/comparative-adapters/src/MCScanSimpleAnchorsAdapter/index.ts
@@ -14,7 +14,7 @@ export default function MCScanSimpleAnchorsAdapterF(
         displayName: 'MCScan anchors.simple adapter',
         configSchema,
         adapterMetadata: {
-          hiddenFromGUI: true,
+          category: 'Synteny adapters',
         },
         getAdapterClass: () =>
           import('./MCScanSimpleAnchorsAdapter').then(r => r.default),

diff --git a/plugins/comparative-adapters/src/MashMapAdapter/index.ts b/plugins/comparative-adapters/src/MashMapAdapter/index.ts
@@ -12,7 +12,7 @@ export default function MashMapAdapterF(pluginManager: PluginManager) {
         displayName: 'MashMap adapter',
         configSchema,
         adapterMetadata: {
-          hiddenFromGUI: true,
+          category: 'Synteny adapters',
         },
         getAdapterClass: () => import('./MashMapAdapter').then(r => r.default),
       }),

diff --git a/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/index.ts b/plugins/comparative-adapters/src/PairwiseIndexedPAFAdapter/index.ts
@@ -14,7 +14,7 @@ export default function PairwiseIndexedPAFAdapterF(
         displayName: 'Pairwise indexed PAF adapter',
         configSchema,
         adapterMetadata: {
-          hiddenFromGUI: true,
+          category: 'Synteny adapters',
         },
         getAdapterClass: () =>
           import('./PairwiseIndexedPAFAdapter').then(r => r.default),