jbrowse-plugin-protein3d 0.0.3 → 0.0.5

package/src/LaunchProteinView/components/AlphaFoldDBSearch.tsx

@@ -7,6 +7,7 @@ import {
   Feature,
   getContainingView,
   getSession,
+  isSessionWithAddTracks,
 } from '@jbrowse/core/util'
 import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui'
 import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
@@ -78,13 +79,14 @@ const AlphaFoldDBSearch = observer(function ({
     ? `https://alphafold.ebi.ac.uk/files/AF-${uniprotId}-F1-model_v4.cif`
     : undefined
   const {
-    seq: structureSequence,
+    sequences: structureSequences,
     isLoading: isRemoteStructureSequenceLoading,
     error: remoteStructureSequenceError,
   } = useRemoteStructureFileSequence({ url })
   const e =
     myGeneError || isoformProteinSequencesError || remoteStructureSequenceError
 
+  const structureSequence = structureSequences?.[0]
   useEffect(() => {
     if (isoformSequences !== undefined) {
       const ret =
@@ -102,8 +104,8 @@ const AlphaFoldDBSearch = observer(function ({
       <DialogContent className={classes.dialogContent}>
         {e ? <ErrorMessage error={e} /> : null}
         <Typography>
-          Automatically find AlphaFoldDB entry for given transcript{' '}
-          <HelpButton />
+          Automatically find AlphaFoldDB entry for given transcript via gene ID
+          lookup <HelpButton />
         </Typography>
         {isRemoteStructureSequenceLoading ? (
           <LoadingEllipses
@@ -116,7 +118,7 @@ const AlphaFoldDBSearch = observer(function ({
             variant="h6"
             message="Looking up UniProt ID from mygene.info"
           />
-        ) : !uniprotId ? (
+        ) : uniprotId ? null : (
           <div>
             UniProt ID not found. Search sequence on AlphaFoldDB{' '}
             <a
@@ -130,7 +132,7 @@ const AlphaFoldDBSearch = observer(function ({
             After visiting the above link, then paste the structure URL into the
             Manual tab
           </div>
-        ) : null}
+        )}
         {isIsoformProteinSequencesLoading ? (
           <LoadingEllipses
             variant="h6"
@@ -160,7 +162,9 @@ const AlphaFoldDBSearch = observer(function ({
         <Button
           variant="contained"
           color="secondary"
-          onClick={() => handleClose()}
+          onClick={() => {
+            handleClose()
+          }}
         >
           Cancel
         </Button>
@@ -173,16 +177,173 @@ const AlphaFoldDBSearch = observer(function ({
           onClick={() => {
             session.addView('ProteinView', {
               type: 'ProteinView',
-              url,
-              seq2: userSelectedProteinSequence?.seq,
-              feature: selectedTranscript?.toJSON(),
-              connectedViewId: view.id,
-              displayName: `Protein view ${getGeneDisplayName(feature)} - ${getTranscriptDisplayName(selectedTranscript)}`,
+              isFloating: true,
+              structures: [
+                {
+                  url,
+                  userProvidedTranscriptSequence:
+                    userSelectedProteinSequence?.seq,
+                  feature: selectedTranscript?.toJSON(),
+                  connectedViewId: view.id,
+                },
+              ],
+              displayName: [
+                'Protein view',
+                uniprotId,
+                getGeneDisplayName(feature),
+                getTranscriptDisplayName(selectedTranscript),
+              ].join(' - '),
             })
             handleClose()
           }}
         >
-          Submit
+          Launch 3-D protein structure view
+        </Button>
+        <Button
+          variant="contained"
+          disabled={
+            !uniprotId || !userSelectedProteinSequence || !selectedTranscript
+          }
+          onClick={() => {
+            if (uniprotId && isSessionWithAddTracks(session)) {
+              // eslint-disable-next-line @typescript-eslint/no-floating-promises
+              ;(async () => {
+                try {
+                  session.addTemporaryAssembly?.({
+                    name: uniprotId,
+                    sequence: {
+                      type: 'ReferenceSequenceTrack',
+                      trackId: `${uniprotId}-ReferenceSequenceTrack`,
+                      sequenceType: 'pep',
+                      adapter: {
+                        type: 'UnindexedFastaAdapter',
+                        rewriteRefNames: "jexl:split(refName,'|')[1]",
+                        fastaLocation: {
+                          uri: `https://rest.uniprot.org/uniprotkb/${uniprotId}.fasta`,
+                        },
+                      },
+                    },
+                  })
+                  const url = `https://rest.uniprot.org/uniprotkb/${uniprotId}.gff`
+                  const res = await fetch(url)
+                  if (!res.ok) {
+                    throw new Error(`HTTP ${res.status} fetching ${url}`)
+                  }
+                  const data = await res.text()
+
+                  const types = [
+                    ...new Set(
+                      data
+                        .split('\n')
+                        .filter(f => !f.startsWith('#'))
+                        .map(f => f.trim())
+                        .filter(f => !!f)
+                        .map(f => f.split('\t')[2]),
+                    ),
+                  ]
+                  types.forEach(type => {
+                    const s = `${uniprotId}-${type}`
+                    session.addTrackConf({
+                      type: 'FeatureTrack',
+                      trackId: s,
+                      name: type,
+                      adapter: {
+                        type: 'Gff3Adapter',
+                        gffLocation: {
+                          uri: `https://rest.uniprot.org/uniprotkb/${uniprotId}.gff`,
+                        },
+                      },
+                      assemblyNames: [uniprotId],
+                      displays: [
+                        {
+                          displayId: `${s}-LinearBasicDisplay`,
+                          type: 'LinearBasicDisplay',
+                          jexlFilters: [`get(feature,'type')=='${type}'`],
+                        },
+                      ],
+                    })
+                  })
+                  session.addTrackConf({
+                    type: 'FeatureTrack',
+                    trackId: `${uniprotId}-Antigen`,
+                    name: 'Antigen',
+                    adapter: {
+                      type: 'Gff3Adapter',
+                      gffLocation: {
+                        uri: `https://www.ebi.ac.uk/proteins/api/antigen/${uniprotId}?format=gff`,
+                      },
+                    },
+                    assemblyNames: [uniprotId],
+                  })
+                  session.addTrackConf({
+                    type: 'FeatureTrack',
+                    trackId: `${uniprotId}-Variation`,
+                    name: 'Variation',
+                    adapter: {
+                      type: 'UniProtVariationAdapter',
+                      location: {
+                        uri: `https://www.ebi.ac.uk/proteins/api/variation/${uniprotId}.json`,
+                      },
+                    },
+                    assemblyNames: [uniprotId],
+                  })
+                  session.addTrackConf({
+                    type: 'QuantitativeTrack',
+                    trackId: `${uniprotId}-AlphaFold-confidence`,
+                    name: 'AlphaFold confidence',
+                    adapter: {
+                      type: 'AlphaFoldConfidenceAdapter',
+                      location: {
+                        uri: `https://alphafold.ebi.ac.uk/files/AF-${uniprotId}-F1-confidence_v4.json`,
+                      },
+                    },
+                    assemblyNames: [uniprotId],
+                  })
+                  session.addTrackConf({
+                    type: 'MultiQuantitativeTrack',
+                    trackId: `${uniprotId}-AlphaMissense-scores`,
+                    name: 'AlphaMissense scores',
+                    assemblyNames: [uniprotId],
+                    adapter: {
+                      type: 'AlphaMissensePathogenicityAdapter',
+                      location: {
+                        uri: `https://alphafold.ebi.ac.uk/files/AF-${uniprotId}-F1-aa-substitutions.csv`,
+                      },
+                    },
+                    displays: [
+                      {
+                        type: 'MultiLinearWiggleDisplay',
+                        displayId: `${uniprotId}-AlphaMissense-scores-MultiLinearWiggleDisplay`,
+                        defaultRendering: 'multirowdensity',
+                        renderers: {
+                          MultiDensityRenderer: {
+                            type: 'MultiDensityRenderer',
+                            bicolorPivotValue: 0.5,
+                          },
+                        },
+                      },
+                    ],
+                  })
+                  const view = session.addView('LinearGenomeView', {
+                    type: 'LinearGenomeView',
+                    displayName: [
+                      'Protein view',
+                      uniprotId,
+                      getGeneDisplayName(feature),
+                      getTranscriptDisplayName(selectedTranscript),
+                    ].join(' - '),
+                  }) as LinearGenomeViewModel
+                  await view.navToLocString(uniprotId, uniprotId)
+                } catch (e) {
+                  console.error(e)
+                  session.notifyError(`${e}`, e)
+                }
+              })()
+            }
+            handleClose()
+          }}
+        >
+          Launch linear protein annotation view
         </Button>
       </DialogActions>
     </>

package/src/LaunchProteinView/components/AlphaFoldDBSearchStatus.tsx

@@ -39,11 +39,7 @@ export default function AlphaFoldDBSearchStatus({
     : undefined
   const [showAllProteinSequences, setShowAllProteinSequences] = useState(false)
 
-  return !uniprotId ? (
-    <Typography>
-      Searching {getDisplayName(selectedTranscript)} for UniProt ID
-    </Typography>
-  ) : (
+  return uniprotId ? (
     <>
       <Typography>
         Found Uniprot ID:{' '}
@@ -62,7 +58,9 @@ export default function AlphaFoldDBSearchStatus({
           <Button
             variant="contained"
             color="primary"
-            onClick={() => setShowAllProteinSequences(!showAllProteinSequences)}
+            onClick={() => {
+              setShowAllProteinSequences(!showAllProteinSequences)
+            }}
           >
             {showAllProteinSequences
               ? 'Hide all isoform protein sequences'
@@ -80,5 +78,9 @@ export default function AlphaFoldDBSearchStatus({
         <NotFound uniprotId={uniprotId} />
       )}
     </>
+  ) : (
+    <Typography>
+      Searching {getDisplayName(selectedTranscript)} for UniProt ID
+    </Typography>
   )
 }

package/src/LaunchProteinView/components/HelpButton.tsx

@@ -10,12 +10,20 @@ export default function HelpButton() {
   const [show, setShow] = useState(false)
   return (
     <>
-      <IconButton onClick={() => setShow(true)}>
+      <IconButton
+        onClick={() => {
+          setShow(true)
+        }}
+      >
         <Help />
       </IconButton>
       {show ? (
         <Suspense fallback={null}>
-          <HelpDialog handleClose={() => setShow(false)} />
+          <HelpDialog
+            handleClose={() => {
+              setShow(false)
+            }}
+          />
         </Suspense>
       ) : null}
     </>

package/src/LaunchProteinView/components/HelpDialog.tsx

@@ -62,7 +62,12 @@ export default function HelpDialog({
       </DialogContent>
       <Divider />
       <DialogActions>
-        <Button onClick={() => handleClose()} color="primary">
+        <Button
+          onClick={() => {
+            handleClose()
+          }}
+          color="primary"
+        >
           Close
         </Button>
       </DialogActions>

package/src/LaunchProteinView/components/LaunchProteinViewDialog.tsx

@@ -6,6 +6,7 @@ import { AbstractTrackModel, Feature } from '@jbrowse/core/util'
 // locals
 import AlphaFoldDBSearch from './AlphaFoldDBSearch'
 import UserProvidedStructure from './UserProvidedStructure'
+import ManualUniProtIDEntry from './ManualUniProtIDEntry'
 import TabPanel from './TabPanel'
 
 export default function LaunchProteinViewDialog({
@@ -22,12 +23,20 @@ export default function LaunchProteinViewDialog({
     <Dialog
       maxWidth="xl"
       title="Launch protein view"
-      onClose={() => handleClose()}
       open
+      onClose={() => {
+        handleClose()
+      }}
     >
-      <Tabs value={choice} onChange={(_, val) => setChoice(val)}>
-        <Tab value={0} label="Automatic lookup" />
-        <Tab value={1} label="Manual" />
+      <Tabs
+        value={choice}
+        onChange={(_, val) => {
+          setChoice(val)
+        }}
+      >
+        <Tab value={0} label="Automatic UniProt lookup" />
+        <Tab value={1} label="Manual UniProt entry" />
+        <Tab value={2} label="Open file manually" />
       </Tabs>
       <TabPanel value={choice} index={0}>
         <AlphaFoldDBSearch
@@ -37,6 +46,13 @@ export default function LaunchProteinViewDialog({
         />
       </TabPanel>
       <TabPanel value={choice} index={1}>
+        <ManualUniProtIDEntry
+          model={model}
+          feature={feature}
+          handleClose={handleClose}
+        />
+      </TabPanel>
+      <TabPanel value={choice} index={2}>
         <UserProvidedStructure
           model={model}
           feature={feature}

package/src/LaunchProteinView/components/MSATable.tsx

@@ -71,7 +71,9 @@ export default function MSATable({
         className={classes.margin}
         control={
           <Checkbox
-            onChange={event => setShowInFastaFormat(event.target.checked)}
+            onChange={event => {
+              setShowInFastaFormat(event.target.checked)
+            }}
             checked={showInFastaFormat}
           />
         }