jbrowse-plugin-protein3d 0.0.2 → 0.0.3

package/src/LaunchProteinView/components/UserProvidedStructure.tsx

@@ -3,13 +3,13 @@ import { observer } from 'mobx-react'
 import {
   Button,
   DialogActions,
-  Radio,
-  RadioGroup,
   DialogContent,
-  TextField,
   FormControlLabel,
   FormControl,
   Link,
+  Radio,
+  RadioGroup,
+  TextField,
   Typography,
 } from '@mui/material'
 import { makeStyles } from 'tss-react/mui'
@@ -28,11 +28,17 @@ import {
   getId,
   getTranscriptDisplayName,
   getTranscriptFeatures,
-} from '../util'
+} from './util'
+
+// components
 import TranscriptSelector from './TranscriptSelector'
+import MSATable from './MSATable'
+import HelpButton from './HelpButton'
 
 // hooks
-import useAllSequences from '../useProteinSequences'
+import useIsoformProteinSequences from './useIsoformProteinSequences'
+import useLocalStructureFileSequence from './useLocalStructureFileSequence'
+import useRemoteStructureFileSequence from './useRemoteStructureFileSequence'
 
 const useStyles = makeStyles()(theme => ({
   dialogContent: {
@@ -73,62 +79,58 @@ const UserProvidedStructure = observer(function ({
   const { classes } = useStyles()
   const session = getSession(model)
   const [file, setFile] = useState<File>()
+  const [pdbId, setPdbId] = useState('')
   const [choice, setChoice] = useState('file')
   const [error2, setError] = useState<unknown>()
   const [structureURL, setStructureURL] = useState('')
-  const [selection, setSelection] = useState<string>()
+  const [userSelection, setUserSelection] = useState<string>()
+  const [showAllProteinSequences, setShowAllProteinSequences] = useState(false)
 
   // check if we are looking at a 'two-level' or 'three-level' feature by
   // finding exon/CDS subfeatures. we want to select from transcript names
   const options = getTranscriptFeatures(feature)
   const view = getContainingView(model) as LGV
-  const selectedTranscript = options.find(val => getId(val) === selection)
-  const { seqs, error } = useAllSequences({ feature, view })
-  const protein = seqs?.[selection ?? '']
+  const selectedTranscript = options.find(val => getId(val) === userSelection)
+  const { isoformSequences, error } = useIsoformProteinSequences({
+    feature,
+    view,
+  })
+  const protein = isoformSequences?.[userSelection ?? '']
+  const { seq: structureSequence1, error: error3 } =
+    useLocalStructureFileSequence({ file })
+
+  const { seq: structureSequence2, error: error4 } =
+    useRemoteStructureFileSequence({ url: structureURL })
+  const structureName =
+    file?.name ??
+    structureURL.slice(structureURL.lastIndexOf('/') + 1) ??
+    'structureSequence'
+  const structureSequence = structureSequence1 ?? structureSequence2
+
   useEffect(() => {
-    if (selection === undefined && seqs !== undefined) {
-      setSelection(options.find(f => !!seqs[f.id()])?.id())
+    if (isoformSequences !== undefined) {
+      const ret =
+        options.find(
+          f =>
+            isoformSequences[f.id()]?.seq.replaceAll('*', '') ==
+            structureSequence,
+        ) ?? options.find(f => !!isoformSequences[f.id()])
+      setUserSelection(ret?.id())
     }
-  }, [options, selection, seqs])
+  }, [options, structureSequence, isoformSequences])
 
-  const e = error || error2
+  const e = error || error2 || error3 || error4
   return (
     <>
       <DialogContent className={classes.dialogContent}>
         {e ? <ErrorMessage error={e} /> : null}
         <HelpText />
-        {seqs ? (
-          <>
-            <TranscriptSelector
-              val={selection ?? ''}
-              setVal={setSelection}
-              options={options}
-              feature={feature}
-              seqs={seqs}
-            />
-            {selectedTranscript ? (
-              <TextField
-                variant="outlined"
-                multiline
-                minRows={5}
-                maxRows={10}
-                fullWidth
-                value={`>${selectedTranscript.get('name') || selectedTranscript.get('id')}\n${protein}`}
-                InputProps={{
-                  readOnly: true,
-                  classes: {
-                    input: classes.textAreaFont,
-                  },
-                }}
-              />
-            ) : null}
-          </>
-        ) : (
-          <div style={{ margin: 20 }}>
-            <LoadingEllipses title="Loading protein sequences" variant="h6" />
-          </div>
-        )}
+
         <div style={{ display: 'flex', margin: 30 }}>
+          <Typography>
+            Open your structure file <HelpButton />
+          </Typography>
+
           <FormControl component="fieldset">
             <RadioGroup
               value={choice}
@@ -136,6 +138,11 @@ const UserProvidedStructure = observer(function ({
             >
               <FormControlLabel value="url" control={<Radio />} label="URL" />
               <FormControlLabel value="file" control={<Radio />} label="File" />
+              <FormControlLabel
+                value="pdb"
+                control={<Radio />}
+                label="PDB ID"
+              />
             </RadioGroup>
           </FormControl>
           {choice === 'url' ? (
@@ -170,6 +177,56 @@ const UserProvidedStructure = observer(function ({
               </Button>
             </div>
           ) : null}
+          {choice === 'pdb' ? (
+            <TextField
+              value={pdbId}
+              onChange={event => {
+                const s = event.target.value
+                setPdbId(s)
+                setStructureURL(`https://files.rcsb.org/download/${s}.cif`)
+              }}
+              label="PDB ID"
+            />
+          ) : null}
+        </div>
+        <div style={{ margin: 20 }}>
+          {isoformSequences ? (
+            structureSequence ? (
+              <>
+                <TranscriptSelector
+                  val={userSelection ?? ''}
+                  setVal={setUserSelection}
+                  structureSequence={structureSequence}
+                  isoforms={options}
+                  feature={feature}
+                  isoformSequences={isoformSequences}
+                />
+                <div style={{ margin: 10 }}>
+                  <Button
+                    variant="contained"
+                    color="primary"
+                    onClick={() =>
+                      setShowAllProteinSequences(!showAllProteinSequences)
+                    }
+                  >
+                    {showAllProteinSequences
+                      ? 'Hide all isoform protein sequences'
+                      : 'Show all isoform protein sequences'}
+                  </Button>
+
+                  {showAllProteinSequences ? (
+                    <MSATable
+                      structureSequence={structureSequence}
+                      structureName={structureName}
+                      isoformSequences={isoformSequences}
+                    />
+                  ) : null}
+                </div>
+              </>
+            ) : null
+          ) : (
+            <LoadingEllipses title="Loading protein sequences" variant="h6" />
+          )}
         </div>
       </DialogContent>
       <DialogActions>
@@ -188,26 +245,15 @@ const UserProvidedStructure = observer(function ({
             // eslint-disable-next-line @typescript-eslint/no-floating-promises
             ;(async () => {
               try {
-                if (file) {
-                  const data = await file.text()
-                  session.addView('ProteinView', {
-                    type: 'ProteinView',
-                    data,
-                    seq2: protein,
-                    feature: selectedTranscript?.toJSON(),
-                    connectedViewId: view.id,
-                    displayName: `Protein view ${getGeneDisplayName(feature)} - ${getTranscriptDisplayName(selectedTranscript)}`,
-                  })
-                } else if (structureURL) {
-                  session.addView('ProteinView', {
-                    type: 'ProteinView',
-                    url: structureURL,
-                    seq2: protein,
-                    feature: selectedTranscript?.toJSON(),
-                    connectedViewId: view.id,
-                    displayName: `Protein view ${getGeneDisplayName(feature)} - ${getTranscriptDisplayName(selectedTranscript)}`,
-                  })
-                }
+                session.addView('ProteinView', {
+                  type: 'ProteinView',
+                  seq2: protein,
+                  feature: selectedTranscript?.toJSON(),
+                  connectedViewId: view.id,
+                  displayName: `Protein view ${getGeneDisplayName(feature)} - ${getTranscriptDisplayName(selectedTranscript)}`,
+                  ...(file ? { data: await file.text() } : {}),
+                  ...(structureURL ? { url: structureURL } : {}),
+                })
                 handleClose()
               } catch (e) {
                 console.error(e)

package/src/LaunchProteinView/{useProteinSequences.ts → components/useIsoformProteinSequences.ts}

@@ -5,32 +5,37 @@ import { Feature } from '@jbrowse/core/util'
 import { getTranscriptFeatures } from './util'
 import { fetchProteinSeq } from './calculateProteinSequence'
 
-export default function useAllSequences({
+export default function useIsoformProteinSequences({
   feature,
   view,
 }: {
   feature: Feature
-  view: { assemblyNames?: string[] } | undefined
+  view?: { assemblyNames?: string[] }
 }) {
   const [error, setError] = useState<unknown>()
-  const [seqs, setSeqs] = useState<Record<string, string>>()
+  const [isoformSequences, setIsoformSequences] =
+    useState<Record<string, { feature: Feature; seq: string }>>()
+  const [isLoading, setLoading] = useState(false)
   useEffect(() => {
     // eslint-disable-next-line @typescript-eslint/no-floating-promises
     ;(async () => {
       try {
-        const ret = [] as [string, string][]
+        setLoading(true)
+        const ret = [] as [string, { feature: Feature; seq: string }][]
         for (const f of getTranscriptFeatures(feature)) {
           const seq = await fetchProteinSeq({ view, feature: f })
           if (seq) {
-            ret.push([f.id(), seq])
+            ret.push([f.id(), { feature: f, seq }])
           }
         }
-        setSeqs(Object.fromEntries(ret))
+        setIsoformSequences(Object.fromEntries(ret))
       } catch (e) {
         console.error(e)
         setError(e)
+      } finally {
+        setLoading(false)
       }
     })()
   }, [feature, view])
-  return { seqs, error }
+  return { isLoading, isoformSequences, error }
 }

package/src/LaunchProteinView/components/useLocalStructureFileSequence.ts

@@ -0,0 +1,53 @@
+import { useEffect, useState } from 'react'
+import { createPluginUI } from 'molstar/lib/mol-plugin-ui'
+import { renderReact18 } from 'molstar/lib/mol-plugin-ui/react18'
+import { loadStructureFromData } from '../../ProteinView/loadStructureFromData'
+
+async function structureFileSequenceFetcher(
+  file: File,
+  format: 'pdb' | 'mmcif',
+) {
+  const ret = document.createElement('div')
+  const p = await createPluginUI({
+    target: ret,
+    render: renderReact18,
+  })
+  const data = await file.text()
+  const { seq } = await loadStructureFromData({ data, plugin: p, format })
+  p.unmount()
+  ret.remove()
+  return seq
+}
+
+export default function useLocalStructureFileSequence({
+  file,
+}: {
+  file?: File
+}) {
+  const [error, setError] = useState<unknown>()
+  const [isLoading, setLoading] = useState(false)
+  const [seq, setSeq] = useState<string>()
+  useEffect(() => {
+    // eslint-disable-next-line @typescript-eslint/no-floating-promises
+    ;(async () => {
+      try {
+        if (file) {
+          setLoading(true)
+
+          const ext = file.name.slice(file.name.lastIndexOf('.') + 1) || 'pdb'
+          const seq = await structureFileSequenceFetcher(
+            file,
+            (ext === 'cif' ? 'mmcif' : ext) as 'pdb' | 'mmcif',
+          )
+          setSeq(seq)
+        }
+      } catch (e) {
+        console.error(e)
+        setError(e)
+      } finally {
+        setLoading(false)
+      }
+    })()
+  }, [file])
+  return { error, isLoading, seq }
+}

package/src/LaunchProteinView/{useMyGeneInfo.ts → components/useMyGeneInfoUniprotIdLookup.ts}

@@ -1,5 +1,5 @@
 import { useEffect, useState } from 'react'
-import { jsonfetch } from '../fetchUtils'
+import { jsonfetch } from '../../fetchUtils'
 import { stripTrailingVersion } from './util'
 
 interface MyGeneInfoResults {
@@ -13,25 +13,30 @@ interface MyGeneInfoResults {
 export default function useMyGeneInfo({ id }: { id: string }) {
   const [result, setResult] = useState<MyGeneInfoResults>()
   const [error, setError] = useState<unknown>()
-  const [loading, setLoading] = useState(false)
+  const [isLoading, setLoading] = useState(false)
   useEffect(() => {
     // eslint-disable-next-line @typescript-eslint/no-floating-promises
     ;(async () => {
       try {
-        if (!id) {
-          return
+        if (id) {
+          setLoading(true)
+          const res = await jsonfetch(
+            `https://mygene.info/v3/query?q=${stripTrailingVersion(id)}&fields=uniprot,symbol`,
+          )
+          setResult(res)
         }
-        setLoading(true)
-        const res = await jsonfetch(
-          `https://mygene.info/v3/query?q=${stripTrailingVersion(id)}&fields=uniprot,symbol`,
-        )
-        setLoading(false)
-        setResult(res)
       } catch (e) {
         console.error(e)
         setError(e)
+      } finally {
+        setLoading(false)
       }
     })()
   }, [id])
-  return { loading, result: result?.hits[0]?.uniprot['Swiss-Prot'], error }
+
+  return {
+    isLoading,
+    uniprotId: result?.hits[0]?.uniprot?.['Swiss-Prot'],
+    error,
+  }
 }

package/src/LaunchProteinView/components/useRemoteStructureFileSequence.ts

@@ -0,0 +1,44 @@
+import { useEffect, useState } from 'react'
+import { createPluginUI } from 'molstar/lib/mol-plugin-ui'
+import { renderReact18 } from 'molstar/lib/mol-plugin-ui/react18'
+import { loadStructureFromURL } from '../../ProteinView/loadStructureFromURL'
+
+async function structureFileSequenceFetcher(url: string) {
+  const ret = document.createElement('div')
+  const p = await createPluginUI({
+    target: ret,
+    render: renderReact18,
+  })
+  const { seq } = await loadStructureFromURL({ url, plugin: p })
+  p.unmount()
+  ret.remove()
+  return seq
+}
+
+export default function useRemoteStructureFileSequence({
+  url,
+}: {
+  url?: string
+}) {
+  const [error, setError] = useState<unknown>()
+  const [isLoading, setLoading] = useState(false)
+  const [seq, setSeq] = useState<string>()
+  useEffect(() => {
+    // eslint-disable-next-line @typescript-eslint/no-floating-promises
+    ;(async () => {
+      try {
+        if (url) {
+          setLoading(true)
+          const seq = await structureFileSequenceFetcher(url)
+          setSeq(seq)
+        }
+      } catch (e) {
+        console.error(e)
+        setError(e)
+      } finally {
+        setLoading(false)
+      }
+    })()
+  }, [url])
+  return { error, isLoading, seq }
+}

package/src/LaunchProteinView/{util.ts → components/util.ts}

@@ -1,15 +1,5 @@
 import { Feature } from '@jbrowse/core/util'
 
-export interface Row {
-  gene_id: string
-  gene_id_version: string
-  transcript_id_version: string
-  transcript_id: string
-  pdb_id: string
-  refseq_mrna_predicted_id: string
-  refseq_mrna_id: string
-}
-
 export function getTranscriptFeatures(feature: Feature) {
   // check if we are looking at a 'two-level' or 'three-level' feature by
   // finding exon/CDS subfeatures. we want to select from transcript names
@@ -29,30 +19,8 @@ export function z(n: number) {
   return n.toLocaleString('en-US')
 }
 
-export function createMapFromData(data?: Row[]) {
-  const map = new Map<string, string>()
-  if (data) {
-    for (const d of data) {
-      const { pdb_id, transcript_id, refseq_mrna_id, transcript_id_version } = d
-      if (!pdb_id) {
-        continue
-      }
-      if (transcript_id) {
-        map.set(transcript_id, pdb_id)
-      }
-      if (refseq_mrna_id) {
-        map.set(refseq_mrna_id, pdb_id)
-      }
-      if (transcript_id_version) {
-        map.set(transcript_id_version, pdb_id)
-      }
-    }
-  }
-  return map
-}
-
 export function getDisplayName(f: Feature): string {
-  return f.get('id')
+  return f.get('name') || f.get('id')
 }
 
 export function getId(val?: Feature): string {
@@ -62,13 +30,13 @@ export function getId(val?: Feature): string {
 export function getTranscriptDisplayName(val?: Feature): string {
   return val === undefined
     ? ''
-    : [val.get('name'), val.get('id')].filter(f => !!f).join(' ')
+    : [val.get('name') || val.get('id')].filter(f => !!f).join(' ')
 }
 
 export function getGeneDisplayName(val?: Feature): string {
   return val === undefined
     ? ''
-    : [val.get('gene_name') || val.get('name'), val.get('id')]
+    : [val.get('gene_name') || val.get('name') || val.get('id')]
         .filter(f => !!f)
         .join(' ')
 }

package/src/LaunchProteinView/index.ts

@@ -26,7 +26,7 @@ function extendStateModel(stateModel: IAnyModelType) {
           ...(feature
             ? [
                 {
-                  label: 'Launch protein view',
+                  label: 'Launch 3-D protein view',
                   icon: AddIcon,
                   onClick: () => {
                     getSession(track).queueDialog(handleClose => [

package/src/ProteinView/components/Header.tsx

@@ -20,11 +20,13 @@ const ProteinViewHeader = observer(function ({
   return (
     <div>
       <InformativeHeaderArea model={model} />
-      {showAlignment && alignment ? (
-        <ProteinAlignment model={model} />
-      ) : (
-        <LoadingEllipses message="Loading pairwise alignment" />
-      )}
+      {showAlignment ? (
+        alignment ? (
+          <ProteinAlignment model={model} />
+        ) : (
+          <LoadingEllipses message="Loading pairwise alignment" />
+        )
+      ) : null}
     </div>
   )
 })

package/src/ProteinView/components/SplitString.tsx

@@ -23,7 +23,7 @@ export default function SplitString({
       style={{
         background:
           col !== undefined && i === col
-            ? '#f69'
+            ? '#f698'
             : set?.has(i) && showHighlight
               ? '#33ff19'
               : undefined,

package/src/ProteinView/model.ts

@@ -32,6 +32,7 @@ type MaybeLGV = LGV | undefined
 function stateModelFactory() {
   return types
     .compose(
+      'ProteinView',
       BaseViewModel,
       types.model({
         /**
@@ -92,15 +93,15 @@ function stateModelFactory() {
         /**
          * #property
          */
-        showHighlight: true,
+        showHighlight: false,
         /**
          * #property
          */
-        zoomToBaseLevel: false,
+        zoomToBaseLevel: true,
         /**
          * #property
          */
-        showAlignment: true,
+        showAlignment: false,
       }),
     )
     .volatile(() => ({
@@ -316,25 +317,52 @@ function stateModelFactory() {
       get structureSeqHoverPos(): number | undefined {
         return self.hoverPosition?.structureSeqPos
       },
+
+      get exactMatch() {
+        const r1 = self.seq1?.replaceAll('*', '')
+        const r2 = self.seq2?.replaceAll('*', '')
+        return r1 === r2
+      },
     }))
     .actions(self => ({
       afterAttach() {
-        // pairwise align transcript sequence to structure sequence
+        // pairwise align transcript sequence to structure residues
         addDisposer(
           self,
           autorun(async () => {
             try {
-              const { seq1, seq2 } = self
+              const { seq1, seq2, exactMatch } = self
               if (!!self.alignment || !seq1 || !seq2) {
                 return
               }
-              const alignment = await launchPairwiseAlignment({
-                seq1,
-                seq2,
-                algorithm: 'emboss_needle',
-                onProgress: arg => self.setProgress(arg),
-              })
-              self.setAlignment(alignment.alignment)
+              const r1 = seq1.replaceAll('*', '')
+              const r2 = seq2.replaceAll('*', '')
+              if (!exactMatch) {
+                const alignment = await launchPairwiseAlignment({
+                  seq1: r1,
+                  seq2: r2,
+                  algorithm: 'emboss_needle',
+                  onProgress: arg => self.setProgress(arg),
+                })
+                self.setAlignment(alignment.alignment)
+
+                // showHighlight when we are
+                self.setShowHighlight(true)
+                self.setShowAlignment(true)
+              } else {
+                let consensus = ''
+                // eslint-disable-next-line @typescript-eslint/prefer-for-of
+                for (let i = 0; i < r1.length; i++) {
+                  consensus += '|'
+                }
+                self.setAlignment({
+                  consensus,
+                  alns: [
+                    { id: 'seq1', seq: r1 },
+                    { id: 'seq2', seq: r2 },
+                  ],
+                })
+              }
             } catch (e) {
               console.error(e)
               self.setError(e)

package/src/index.ts

@@ -1,12 +1,11 @@
 import Plugin from '@jbrowse/core/Plugin'
 import PluginManager from '@jbrowse/core/PluginManager'
-import { types } from 'mobx-state-tree'
+
 // locals
 import { version } from '../package.json'
 import ProteinViewF from './ProteinView'
 import LaunchProteinViewF from './LaunchProteinView'
 import AddHighlightModelF from './AddHighlightModel'
-import ProteinModelSessionExtension from './ProteinModelSessionExtension'
 
 export default class ProteinViewer extends Plugin {
   name = 'ProteinViewer'
@@ -16,16 +15,6 @@ export default class ProteinViewer extends Plugin {
     ProteinViewF(pluginManager)
     LaunchProteinViewF(pluginManager)
     AddHighlightModelF(pluginManager)
-
-    pluginManager.addToExtensionPoint('Core-extendSession', session => {
-      return types.compose(
-        types.model({
-          proteinModel: types.optional(ProteinModelSessionExtension, {}),
-        }),
-        // @ts-expect-error
-        session,
-      )
-    })
   }
 
   configure(_pluginManager: PluginManager) {}

package/dist/LaunchProteinView/calculateProteinSequence.js.map

@@ -1 +0,0 @@
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package/dist/LaunchProteinView/components/PreLoadedStructureMapping.d.ts

@@ -1,8 +0,0 @@
-import React from 'react';
-import { AbstractTrackModel, Feature } from '@jbrowse/core/util';
-declare const AutoForm: ({ model, feature, handleClose, }: {
-    model: AbstractTrackModel;
-    feature: Feature;
-    handleClose: () => void;
-}) => React.JSX.Element;
-export default AutoForm;