jbrowse-plugin-protein3d 0.4.9 → 0.4.11

package/dist/LaunchProteinView/components/AlphaFoldDBSearch.d.ts

@@ -1,9 +1,11 @@
 import React from 'react';
 import type { AlignmentAlgorithm } from '../../ProteinView/types';
-import type { AbstractTrackModel, Feature } from '@jbrowse/core/util';
-declare const AlphaFoldDBSearch: ({ feature, model, handleClose, alignmentAlgorithm, onAlignmentAlgorithmChange, }: {
+import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+declare const AlphaFoldDBSearch: ({ feature, session, view, handleClose, alignmentAlgorithm, onAlignmentAlgorithmChange, }: {
     feature: Feature;
-    model: AbstractTrackModel;
+    session: AbstractSessionModel;
+    view: LinearGenomeViewModel;
     handleClose: () => void;
     alignmentAlgorithm: AlignmentAlgorithm;
     onAlignmentAlgorithmChange: (algorithm: AlignmentAlgorithm) => void;

package/dist/LaunchProteinView/components/AlphaFoldDBSearch.js

@@ -1,6 +1,5 @@
 import React from 'react';
 import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui';
-import { getContainingView, getSession } from '@jbrowse/core/util';
 import { DialogActions, DialogContent, Typography } from '@mui/material';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
@@ -30,10 +29,8 @@ const useStyles = makeStyles()({
         alignItems: 'flex-start',
     },
 });
-const AlphaFoldDBSearch = observer(function AlphaFoldDBSearch({ feature, model, handleClose, alignmentAlgorithm, onAlignmentAlgorithmChange, }) {
+const AlphaFoldDBSearch = observer(function AlphaFoldDBSearch({ feature, session, view, handleClose, alignmentAlgorithm, onAlignmentAlgorithmChange, }) {
     const { classes } = useStyles();
-    const session = getSession(model);
-    const view = getContainingView(model);
     const state = useAlphaFoldDBSearch({ feature, view });
     return (React.createElement(React.Fragment, null,
         React.createElement(DialogContent, { className: classes.dialogContent },

package/dist/LaunchProteinView/components/AlphaFoldDBSearchStatus.js

@@ -1,8 +1,8 @@
-import React, { useState } from 'react';
-import { Button, Typography } from '@mui/material';
-import MSATable from './MSATable';
+import React from 'react';
+import { Typography } from '@mui/material';
+import IsoformSequencesToggle from './IsoformSequencesToggle';
 import ExternalLink from '../../components/ExternalLink';
-import { getDisplayName } from '../utils/util';
+import { getTranscriptDisplayName } from '../utils/util';
 function NotFound({ uniprotId }) {
     return (React.createElement(Typography, null,
         "No structure found for this UniProtID in AlphaFoldDB",
@@ -10,7 +10,6 @@ function NotFound({ uniprotId }) {
         React.createElement(ExternalLink, { href: `https://alphafold.ebi.ac.uk/search/text/${uniprotId}` }, "(search for results)")));
 }
 export default function AlphaFoldDBSearchStatus({ uniprotId, selectedTranscript, structureSequence, isoformSequences, url, }) {
-    const [showAllProteinSequences, setShowAllProteinSequences] = useState(false);
     return uniprotId ? (React.createElement(React.Fragment, null,
         React.createElement("div", null,
             React.createElement(Typography, null,
@@ -20,16 +19,12 @@ export default function AlphaFoldDBSearchStatus({ uniprotId, selectedTranscript,
             React.createElement(Typography, null,
                 "AlphaFoldDB link: ",
                 React.createElement(ExternalLink, { href: url }, url))),
-        structureSequence ? (React.createElement("div", { style: { margin: 20 } },
-            React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
-                    setShowAllProteinSequences(!showAllProteinSequences);
-                } }, showAllProteinSequences
-                ? 'Hide all isoform protein sequences'
-                : 'Show all isoform protein sequences'),
-            showAllProteinSequences ? (React.createElement(MSATable, { structureSequence: structureSequence, structureName: uniprotId, isoformSequences: isoformSequences })) : null)) : (React.createElement(NotFound, { uniprotId: uniprotId })))) : (React.createElement(Typography, null,
+        structureSequence ? (React.createElement(IsoformSequencesToggle, { structureSequence: structureSequence, structureName: uniprotId, isoformSequences: isoformSequences })) : (React.createElement(NotFound, { uniprotId: uniprotId })))) : (React.createElement(Typography, null,
         "Searching",
         ' ',
-        selectedTranscript ? getDisplayName(selectedTranscript) : 'transcript',
+        selectedTranscript
+            ? getTranscriptDisplayName(selectedTranscript)
+            : 'transcript',
         ' ',
         "for UniProt ID"));
 }

package/dist/LaunchProteinView/components/FoldseekSearch.d.ts

@@ -1,8 +1,10 @@
 import React from 'react';
-import type { AbstractTrackModel, Feature } from '@jbrowse/core/util';
-declare const FoldseekSearch: ({ feature, model, handleClose, }: {
+import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+declare const FoldseekSearch: ({ feature, session, view, handleClose, }: {
     feature: Feature;
-    model: AbstractTrackModel;
+    session: AbstractSessionModel;
+    view: LinearGenomeViewModel;
     handleClose: () => void;
 }) => React.JSX.Element;
 export default FoldseekSearch;

package/dist/LaunchProteinView/components/FoldseekSearch.js

@@ -1,6 +1,5 @@
 import React, { useState } from 'react';
 import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui';
-import { getContainingView, getSession } from '@jbrowse/core/util';
 import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
@@ -8,10 +7,9 @@ import FoldseekDatabaseSelector from './FoldseekDatabaseSelector';
 import FoldseekResultsTable from './FoldseekResultsTable';
 import TranscriptSelector from './TranscriptSelector';
 import useFoldseekSearch from '../hooks/useFoldseekSearch';
-import useIsoformProteinSequences from '../hooks/useIsoformProteinSequences';
-import useTranscriptSelection from '../hooks/useTranscriptSelection';
+import useTranscriptIsoformSelection from '../hooks/useTranscriptIsoformSelection';
 import { DEFAULT_DATABASES } from '../services/foldseekApi';
-import { getTranscriptFeatures } from '../utils/util';
+import { stripStopCodon } from '../utils/util';
 const useStyles = makeStyles()({
     dialogContent: {
         width: '80em',
@@ -28,21 +26,15 @@ const useStyles = makeStyles()({
         gap: 8,
     },
 });
-const FoldseekSearch = observer(function FoldseekSearch({ feature, model, handleClose, }) {
+const FoldseekSearch = observer(function FoldseekSearch({ feature, session, view, handleClose, }) {
     const { classes } = useStyles();
-    const session = getSession(model);
-    const view = getContainingView(model);
     const [userEditedSequence, setUserEditedSequence] = useState();
     const [selectedDatabases, setSelectedDatabases] = useState(DEFAULT_DATABASES);
     const { results, cleanedAaSequence, di3Sequence, isLoading, isPredicting, error, statusMessage, predictStructure, search, reset, } = useFoldseekSearch();
-    const transcripts = getTranscriptFeatures(feature);
-    const { isoformSequences, isLoading: isLoadingIsoforms, error: isoformError, } = useIsoformProteinSequences({ feature, view });
-    const { userSelection: effectiveSelectedTranscriptId, setUserSelection } = useTranscriptSelection({ options: transcripts, isoformSequences });
-    const selectedTranscript = transcripts.find(t => t.id() === effectiveSelectedTranscriptId);
-    const selectedIsoformData = effectiveSelectedTranscriptId
-        ? isoformSequences?.[effectiveSelectedTranscriptId]
-        : undefined;
-    const cleanedSequence = selectedIsoformData?.seq.replace(/\*/g, '') ?? '';
+    const { transcripts, isoformSequences, isLoading: isLoadingIsoforms, error: isoformError, selectedTranscriptId: effectiveSelectedTranscriptId, setSelectedTranscriptId: setUserSelection, selectedTranscript, selectedIsoform: selectedIsoformData, } = useTranscriptIsoformSelection({ feature, view });
+    const cleanedSequence = selectedIsoformData
+        ? stripStopCodon(selectedIsoformData.seq)
+        : '';
     const sequence = userEditedSequence ?? cleanedSequence;
     const setUserSelectionWithReset = (id) => {
         setUserSelection(id);

package/dist/LaunchProteinView/components/IsoformSequencesToggle.d.ts

@@ -0,0 +1,10 @@
+import React from 'react';
+import type { Feature } from '@jbrowse/core/util';
+export default function IsoformSequencesToggle({ structureSequence, structureName, isoformSequences, }: {
+    structureSequence: string;
+    structureName: string;
+    isoformSequences: Record<string, {
+        feature: Feature;
+        seq: string;
+    }>;
+}): React.JSX.Element;

package/dist/LaunchProteinView/components/IsoformSequencesToggle.js

@@ -0,0 +1,13 @@
+import React, { useState } from 'react';
+import { Button } from '@mui/material';
+import MSATable from './MSATable';
+export default function IsoformSequencesToggle({ structureSequence, structureName, isoformSequences, }) {
+    const [show, setShow] = useState(false);
+    return (React.createElement("div", { style: { margin: 10 } },
+        React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
+                setShow(!show);
+            } }, show
+            ? 'Hide all isoform protein sequences'
+            : 'Show all isoform protein sequences'),
+        show ? (React.createElement(MSATable, { structureSequence: structureSequence, structureName: structureName, isoformSequences: isoformSequences })) : null));
+}

package/dist/LaunchProteinView/components/LaunchProteinViewDialog.js

@@ -1,5 +1,6 @@
 import React, { useState } from 'react';
 import { Dialog } from '@jbrowse/core/ui';
+import { getContainingView, getSession } from '@jbrowse/core/util';
 import { Tab, Tabs } from '@mui/material';
 import AlphaFoldDBSearch from './AlphaFoldDBSearch';
 import FoldseekSearch from './FoldseekSearch';
@@ -11,6 +12,8 @@ import { useLocalStorage } from '../hooks/useLocalStorage';
 export default function LaunchProteinViewDialog({ handleClose, feature, model, }) {
     const [choice, setChoice] = useState(0);
     const [alignmentAlgorithm, setAlignmentAlgorithm] = useLocalStorage('jbrowse-protein3d-alignment-algorithm', DEFAULT_ALIGNMENT_ALGORITHM);
+    const session = getSession(model);
+    const view = getContainingView(model);
     return (React.createElement(Dialog, { maxWidth: "xl", title: "Launch protein view", titleNode: React.createElement(React.Fragment, null,
             "Launch protein view ",
             React.createElement(HelpButton, null)), open: true, onClose: handleClose },
@@ -21,9 +24,9 @@ export default function LaunchProteinViewDialog({ handleClose, feature, model, }
             React.createElement(Tab, { value: 1, label: "Foldseek search" }),
             React.createElement(Tab, { value: 2, label: "Open file manually" })),
         React.createElement(TabPanel, { value: choice, index: 0 },
-            React.createElement(AlphaFoldDBSearch, { model: model, feature: feature, handleClose: handleClose, alignmentAlgorithm: alignmentAlgorithm, onAlignmentAlgorithmChange: setAlignmentAlgorithm })),
+            React.createElement(AlphaFoldDBSearch, { session: session, view: view, feature: feature, handleClose: handleClose, alignmentAlgorithm: alignmentAlgorithm, onAlignmentAlgorithmChange: setAlignmentAlgorithm })),
         React.createElement(TabPanel, { value: choice, index: 1 },
-            React.createElement(FoldseekSearch, { model: model, feature: feature, handleClose: handleClose })),
+            React.createElement(FoldseekSearch, { session: session, view: view, feature: feature, handleClose: handleClose })),
         React.createElement(TabPanel, { value: choice, index: 2 },
-            React.createElement(UserProvidedStructure, { model: model, feature: feature, handleClose: handleClose, alignmentAlgorithm: alignmentAlgorithm, onAlignmentAlgorithmChange: setAlignmentAlgorithm }))));
+            React.createElement(UserProvidedStructure, { session: session, view: view, feature: feature, handleClose: handleClose, alignmentAlgorithm: alignmentAlgorithm, onAlignmentAlgorithmChange: setAlignmentAlgorithm }))));
 }

package/dist/LaunchProteinView/components/StructureSourcePicker.d.ts

@@ -1,10 +1,9 @@
 import React from 'react';
-export default function StructureSourcePicker({ choice, setChoice, structureURL, setStructureURL, file: _file, setFile, pdbId, setPdbId, }: {
+export default function StructureSourcePicker({ choice, setChoice, structureURL, setStructureURL, setFile, pdbId, setPdbId, }: {
     choice: string;
     setChoice: (c: string) => void;
     structureURL: string;
     setStructureURL: (url: string) => void;
-    file: File | undefined;
     setFile: (f: File) => void;
     pdbId: string;
     setPdbId: (id: string) => void;

package/dist/LaunchProteinView/components/StructureSourcePicker.js

@@ -2,7 +2,7 @@ import React from 'react';
 import { Button, FormControl, FormControlLabel, Radio, RadioGroup, TextField, Typography, } from '@mui/material';
 import HelpButton from './HelpButton';
 import { getPdbStructureUrl } from '../utils/launchViewUtils';
-export default function StructureSourcePicker({ choice, setChoice, structureURL, setStructureURL, file: _file, setFile, pdbId, setPdbId, }) {
+export default function StructureSourcePicker({ choice, setChoice, structureURL, setStructureURL, setFile, pdbId, setPdbId, }) {
     return (React.createElement("div", { style: { display: 'flex', margin: 30 } },
         React.createElement(Typography, null,
             "Open your structure file ",

package/dist/LaunchProteinView/components/UserProvidedStructure.d.ts

@@ -1,9 +1,12 @@
 import React from 'react';
 import type { AlignmentAlgorithm } from '../../ProteinView/types';
-import type { AbstractTrackModel, Feature } from '@jbrowse/core/util';
-declare const UserProvidedStructure: ({ feature, model, handleClose, alignmentAlgorithm, onAlignmentAlgorithmChange, }: {
+import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+type LGV = LinearGenomeViewModel;
+declare const UserProvidedStructure: ({ feature, session, view, handleClose, alignmentAlgorithm, onAlignmentAlgorithmChange, }: {
     feature: Feature;
-    model: AbstractTrackModel;
+    session: AbstractSessionModel;
+    view: LGV;
     handleClose: () => void;
     alignmentAlgorithm: AlignmentAlgorithm;
     onAlignmentAlgorithmChange: (algorithm: AlignmentAlgorithm) => void;

package/dist/LaunchProteinView/components/UserProvidedStructure.js

@@ -1,20 +1,17 @@
 import React, { useState } from 'react';
 import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui';
-import { getContainingView, getSession } from '@jbrowse/core/util';
 import { Button, DialogActions, DialogContent } from '@mui/material';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
-import MSATable from './MSATable';
+import IsoformSequencesToggle from './IsoformSequencesToggle';
 import SequenceMismatchNotice from './SequenceMismatchNotice';
 import StructureSourcePicker from './StructureSourcePicker';
 import TranscriptSelector from './TranscriptSelector';
 import ExternalLink from '../../components/ExternalLink';
-import useIsoformProteinSequences from '../hooks/useIsoformProteinSequences';
-import useLocalStructureFileSequence from '../hooks/useLocalStructureFileSequence';
-import useRemoteStructureFileSequence from '../hooks/useRemoteStructureFileSequence';
-import useTranscriptSelection from '../hooks/useTranscriptSelection';
+import useStructureFileSequence from '../hooks/useStructureFileSequence';
+import useTranscriptIsoformSelection from '../hooks/useTranscriptIsoformSelection';
 import { launch3DProteinView } from '../utils/launchViewUtils';
-import { getGeneDisplayName, getId, getTranscriptDisplayName, getTranscriptFeatures, stripStopCodon, } from '../utils/util';
+import { getGeneDisplayName, getTranscriptDisplayName, stripStopCodon, } from '../utils/util';
 const useStyles = makeStyles()(theme => ({
     dialogContent: {
         marginTop: theme.spacing(6),
@@ -31,36 +28,20 @@ function HelpText() {
         React.createElement(ExternalLink, { href: "https://github.com/sokrypton/ColabFold" }, "ColabFold"),
         ". This plugin will align the protein sequence calculated from the genome to the protein sequence embedded in the structure file which allows for slight differences in these two representations."));
 }
-const UserProvidedStructure = observer(function UserProvidedStructure({ feature, model, handleClose, alignmentAlgorithm, onAlignmentAlgorithmChange, }) {
+const UserProvidedStructure = observer(function UserProvidedStructure({ feature, session, view, handleClose, alignmentAlgorithm, onAlignmentAlgorithmChange, }) {
     const { classes } = useStyles();
-    const session = getSession(model);
     const [file, setFile] = useState();
     const [pdbId, setPdbId] = useState('');
     const [choice, setChoice] = useState('file');
     const [submitError, setSubmitError] = useState();
     const [structureURL, setStructureURL] = useState('');
-    const [showAllProteinSequences, setShowAllProteinSequences] = useState(false);
     const activeFile = choice === 'file' ? file : undefined;
     const activeURL = choice === 'file' ? '' : structureURL;
-    const options = getTranscriptFeatures(feature);
-    const view = getContainingView(model);
-    const { isoformSequences, error: isoformError } = useIsoformProteinSequences({
-        feature,
-        view,
-    });
-    const { sequences: localSequences, error: localFileError } = useLocalStructureFileSequence({ file: activeFile });
-    const { sequences: remoteSequences, error: remoteFileError } = useRemoteStructureFileSequence({ url: activeURL });
+    const { sequences: structureSequences, error: fileError } = useStructureFileSequence({ file: activeFile, url: activeURL });
     const structureName = activeFile?.name ?? activeURL.slice(activeURL.lastIndexOf('/') + 1);
-    const structureSequences = activeFile ? localSequences : remoteSequences;
     const structureSequence = structureSequences?.[0];
-    const { userSelection, setUserSelection } = useTranscriptSelection({
-        options,
-        isoformSequences,
-        structureSequence,
-    });
-    const selectedTranscript = options.find(val => getId(val) === userSelection);
-    const protein = userSelection ? isoformSequences?.[userSelection] : undefined;
-    const error = isoformError ?? submitError ?? localFileError ?? remoteFileError;
+    const { transcripts: options, isoformSequences, selectedTranscriptId: userSelection, setSelectedTranscriptId: setUserSelection, selectedTranscript, selectedIsoform: protein, error: isoformError, } = useTranscriptIsoformSelection({ feature, view, structureSequence });
+    const error = isoformError ?? submitError ?? fileError;
     const canLaunch = !!(activeURL || activeFile) && !!protein && !!selectedTranscript;
     const sequencesDiffer = !!protein?.seq &&
         !!structureSequence &&
@@ -94,16 +75,10 @@ const UserProvidedStructure = observer(function UserProvidedStructure({ feature,
         React.createElement(DialogContent, { className: classes.dialogContent },
             error ? React.createElement(ErrorMessage, { error: error }) : null,
             React.createElement(HelpText, null),
-            React.createElement(StructureSourcePicker, { choice: choice, setChoice: setChoice, structureURL: structureURL, setStructureURL: setStructureURL, file: file, setFile: setFile, pdbId: pdbId, setPdbId: setPdbId }),
+            React.createElement(StructureSourcePicker, { choice: choice, setChoice: setChoice, structureURL: structureURL, setStructureURL: setStructureURL, setFile: setFile, pdbId: pdbId, setPdbId: setPdbId }),
             React.createElement("div", { style: { margin: 20 } }, isoformSequences ? (structureSequence ? (React.createElement(React.Fragment, null,
                 React.createElement(TranscriptSelector, { val: userSelection, setVal: setUserSelection, structureSequence: structureSequence, isoforms: options, feature: feature, isoformSequences: isoformSequences }),
-                React.createElement("div", { style: { margin: 10 } },
-                    React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
-                            setShowAllProteinSequences(!showAllProteinSequences);
-                        } }, showAllProteinSequences
-                        ? 'Hide all isoform protein sequences'
-                        : 'Show all isoform protein sequences'),
-                    showAllProteinSequences ? (React.createElement(MSATable, { structureSequence: structureSequence, structureName: structureName, isoformSequences: isoformSequences })) : null))) : null) : (React.createElement(LoadingEllipses, { title: "Loading protein sequences", variant: "h6" })))),
+                React.createElement(IsoformSequencesToggle, { structureSequence: structureSequence, structureName: structureName, isoformSequences: isoformSequences }))) : null) : (React.createElement(LoadingEllipses, { title: "Loading protein sequences", variant: "h6" })))),
         React.createElement(DialogActions, null,
             sequencesDiffer ? (React.createElement(SequenceMismatchNotice, { alignmentAlgorithm: alignmentAlgorithm, onAlignmentAlgorithmChange: onAlignmentAlgorithmChange })) : null,
             React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {

package/dist/LaunchProteinView/hooks/swrOptions.d.ts

@@ -0,0 +1,5 @@
+export declare const STATIC_SWR_OPTIONS: {
+    readonly revalidateOnFocus: false;
+    readonly revalidateOnReconnect: false;
+    readonly revalidateIfStale: false;
+};

package/dist/LaunchProteinView/hooks/swrOptions.js

@@ -0,0 +1,8 @@
+// Shared SWR config for one-shot fetches that should never auto-revalidate
+// (structure files, computed protein sequences). keepPreviousData is opt-in
+// per-hook since it avoids result flicker when the key changes.
+export const STATIC_SWR_OPTIONS = {
+    revalidateOnFocus: false,
+    revalidateOnReconnect: false,
+    revalidateIfStale: false,
+};

package/dist/LaunchProteinView/hooks/useAlphaFoldDBSearch.js

@@ -2,24 +2,21 @@ import { useState } from 'react';
 import useAlphaFoldData from './useAlphaFoldData';
 import useAlphaFoldSequenceSearch from './useAlphaFoldSequenceSearch';
 import useDebouncedValue from './useDebouncedValue';
-import useIsoformProteinSequences from './useIsoformProteinSequences';
-import useTranscriptSelection from './useTranscriptSelection';
+import useTranscriptIsoformSelection from './useTranscriptIsoformSelection';
 import useUniProtSearch from './useUniProtSearch';
 import getSearchDescription from '../utils/getSearchDescription';
-import { extractFeatureIdentifiers, getId, getTranscriptFeatures, stripStopCodon, } from '../utils/util';
+import { extractFeatureIdentifiers, stripStopCodon } from '../utils/util';
 export default function useAlphaFoldDBSearch({ feature, view, }) {
     const [lookupMode, setLookupMode] = useState('auto');
     const [manualUniprotId, setManualUniprotId] = useState('');
     const geneIds = extractFeatureIdentifiers(feature);
-    const [selectedQueryId, setSelectedQueryId] = useState(geneIds.recognizedIds[0] ?? 'auto');
+    const [selectedQueryId, setSelectedQueryId] = useState('auto');
     const [sequenceSearchType, setSequenceSearchType] = useState('md5');
     const [selectedUniprotId, setSelectedUniprotId] = useState();
-    const transcriptOptions = getTranscriptFeatures(feature);
     const featureUniprotId = geneIds.uniprotId;
     const effectiveLookupMode = lookupMode === 'auto' && featureUniprotId ? 'feature' : lookupMode;
     const isSequenceMode = effectiveLookupMode === 'sequence';
     const isAutoMode = effectiveLookupMode === 'auto';
-    const { isoformSequences, isLoading: isIsoformLoading, error: isoformError, } = useIsoformProteinSequences({ feature, view });
     const { entries: uniprotEntries, isLoading: isLookupLoading, error: lookupError, } = useUniProtSearch({
         recognizedIds: geneIds.recognizedIds,
         geneId: geneIds.geneId,
@@ -41,16 +38,12 @@ export default function useAlphaFoldDBSearch({ feature, view, }) {
     const { isLoading: isAlphaFoldLoading, error: alphaFoldError, url: alphaFoldUrl, confidenceUrl: alphaFoldConfidenceUrl, structureSequence: alphaFoldStructureSequence, } = useAlphaFoldData({
         uniprotId: isSequenceMode ? undefined : uniprotId,
     });
-    const { userSelection: effectiveTranscriptId, setUserSelection } = useTranscriptSelection({
-        options: transcriptOptions,
-        isoformSequences,
+    const { transcripts: transcriptOptions, isoformSequences, isLoading: isIsoformLoading, error: isoformError, selectedTranscriptId: effectiveTranscriptId, setSelectedTranscriptId: setUserSelection, selectedTranscript, selectedIsoform: userSelectedProteinSequence, } = useTranscriptIsoformSelection({
+        feature,
+        view,
         structureSequence: alphaFoldStructureSequence,
         resetKey: uniprotId,
     });
-    const selectedTranscript = transcriptOptions.find(f => getId(f) === effectiveTranscriptId);
-    const userSelectedProteinSequence = effectiveTranscriptId
-        ? isoformSequences?.[effectiveTranscriptId]
-        : undefined;
     const { uniprotId: seqSearchUniprotId, cifUrl: seqSearchUrl, plddtDocUrl: seqSearchConfidenceUrl, structureSequence: seqSearchStructureSequence, isLoading: isSequenceSearchLoading, error: sequenceSearchError, } = useAlphaFoldSequenceSearch({
         sequence: userSelectedProteinSequence?.seq,
         searchType: sequenceSearchType,

package/dist/LaunchProteinView/hooks/useAlphaFoldData.js

@@ -1,13 +1,11 @@
-import useRemoteStructureFileSequence from './useRemoteStructureFileSequence';
+import useStructureFileSequence from './useStructureFileSequence';
 import { getAlphaFoldConfidenceUrl, getAlphaFoldStructureUrl, } from '../utils/launchViewUtils';
 export default function useAlphaFoldData({ uniprotId, }) {
     const url = uniprotId ? getAlphaFoldStructureUrl(uniprotId) : undefined;
     const confidenceUrl = uniprotId
         ? getAlphaFoldConfidenceUrl(uniprotId)
         : undefined;
-    const { sequences, isLoading, error } = useRemoteStructureFileSequence({
-        url,
-    });
+    const { sequences, isLoading, error } = useStructureFileSequence({ url });
     return {
         isLoading,
         error,

package/dist/LaunchProteinView/hooks/useAlphaFoldSequenceSearch.js

@@ -1,5 +1,6 @@
 import { useMemo } from 'react';
 import useSWR from 'swr';
+import { STATIC_SWR_OPTIONS } from './swrOptions';
 import { jsonfetch } from '../../fetchUtils';
 import { md5 } from '../utils/md5';
 import { stripStopCodon } from '../utils/util';
@@ -14,9 +15,7 @@ export default function useAlphaFoldSequenceSearch({ sequence, searchType, enabl
     const { data, error, isLoading } = useSWR(enabled && searchValue
         ? `https://alphafold.ebi.ac.uk/api/sequence/summary?id=${encodeURIComponent(searchValue)}&type=${searchType}`
         : null, jsonfetch, {
-        revalidateOnFocus: false,
-        revalidateOnReconnect: false,
-        revalidateIfStale: false,
+        ...STATIC_SWR_OPTIONS,
         keepPreviousData: true,
     });
     return {

package/dist/LaunchProteinView/hooks/useIsoformProteinSequences.js

@@ -1,4 +1,6 @@
+import { getSession } from '@jbrowse/core/util';
 import useSWR from 'swr';
+import { STATIC_SWR_OPTIONS } from './swrOptions';
 import { fetchProteinSeq } from '../utils/calculateProteinSequence';
 import { getTranscriptFeatures } from '../utils/util';
 export default function useIsoformProteinSequences({ feature, view, }) {
@@ -7,7 +9,11 @@ export default function useIsoformProteinSequences({ feature, view, }) {
         const errors = [];
         const results = await Promise.all(transcripts.map(async (f) => {
             try {
-                const seq = await fetchProteinSeq({ view, feature: f });
+                const seq = await fetchProteinSeq({
+                    session: getSession(view),
+                    assemblyName: view?.assemblyNames?.[0],
+                    feature: f,
+                });
                 return seq ? [f.id(), { feature: f, seq }] : undefined;
             }
             catch (e) {
@@ -27,9 +33,7 @@ export default function useIsoformProteinSequences({ feature, view, }) {
         }
         return Object.fromEntries(entries);
     }, {
-        revalidateOnFocus: false,
-        revalidateOnReconnect: false,
-        revalidateIfStale: false,
+        ...STATIC_SWR_OPTIONS,
         keepPreviousData: true,
     });
     return { isLoading, isoformSequences: data, error };

package/dist/LaunchProteinView/hooks/{useRemoteStructureFileSequence.d.ts → useStructureFileSequence.d.ts}

@@ -1,4 +1,5 @@
-export default function useRemoteStructureFileSequence({ url, }: {
+export default function useStructureFileSequence({ file, url, }: {
+    file?: File;
     url?: string;
 }): {
     error: any;

package/dist/LaunchProteinView/hooks/useStructureFileSequence.js

@@ -0,0 +1,47 @@
+import useSWR from 'swr';
+import { STATIC_SWR_OPTIONS } from './swrOptions';
+import { addStructureFromData } from '../../ProteinView/addStructureFromData';
+import { addStructureFromURL } from '../../ProteinView/addStructureFromURL';
+import { extractStructureSequences } from '../../ProteinView/extractStructureSequences';
+import { withTemporaryMolstarPlugin } from '../../ProteinView/withTemporaryMolstarPlugin';
+function detectStructureFormat(fileName) {
+    const dot = fileName.lastIndexOf('.');
+    const ext = dot >= 0 ? fileName.slice(dot + 1).toLowerCase() : '';
+    if (ext === 'cif' || ext === 'mmcif' || ext === 'bcif') {
+        return 'mmcif';
+    }
+    return 'pdb';
+}
+async function fetchSequences({ file, url }) {
+    return withTemporaryMolstarPlugin(async (plugin) => {
+        const { model } = file
+            ? await addStructureFromData({
+                data: await file.text(),
+                plugin,
+                format: detectStructureFormat(file.name),
+            })
+            : await addStructureFromURL({ url: url, plugin });
+        return extractStructureSequences(model);
+    });
+}
+// Extract protein sequences from a structure given either a local File or a
+// remote URL (exactly one is expected). Used directly for user-provided
+// structures and wrapped by useAlphaFoldData for AlphaFoldDB URLs.
+export default function useStructureFileSequence({ file, url, }) {
+    const key = file
+        ? ['structure-file', file.name, file.size, file.lastModified]
+        : url
+            ? ['structure-url', url]
+            : null;
+    const { data, error, isLoading } = useSWR(key, async () => {
+        const seq = await fetchSequences({ file, url });
+        if (!seq) {
+            throw new Error('no sequences detected in file');
+        }
+        return seq;
+    }, {
+        ...STATIC_SWR_OPTIONS,
+        keepPreviousData: true,
+    });
+    return { error, isLoading, sequences: data };
+}

package/dist/LaunchProteinView/hooks/useTranscriptIsoformSelection.d.ts

@@ -0,0 +1,24 @@
+import type { Feature } from '@jbrowse/core/util';
+export default function useTranscriptIsoformSelection({ feature, view, structureSequence, resetKey, }: {
+    feature: Feature;
+    view?: {
+        assemblyNames?: string[];
+    };
+    structureSequence?: string;
+    resetKey?: string;
+}): {
+    transcripts: Feature[];
+    isoformSequences: Record<string, {
+        feature: Feature;
+        seq: string;
+    }> | undefined;
+    isLoading: boolean;
+    error: any;
+    selectedTranscriptId: string | undefined;
+    setSelectedTranscriptId: import("react").Dispatch<import("react").SetStateAction<string | undefined>>;
+    selectedTranscript: Feature | undefined;
+    selectedIsoform: {
+        feature: Feature;
+        seq: string;
+    } | undefined;
+};

package/dist/LaunchProteinView/hooks/useTranscriptIsoformSelection.js

@@ -0,0 +1,33 @@
+import useIsoformProteinSequences from './useIsoformProteinSequences';
+import useTranscriptSelection from './useTranscriptSelection';
+import { getId, getTranscriptFeatures } from '../utils/util';
+// Bundles the transcript-isoform wiring shared by all three launch tabs:
+// list transcripts, fetch their protein sequences, auto/manually select one,
+// and resolve the selection back to its feature + sequence.
+export default function useTranscriptIsoformSelection({ feature, view, structureSequence, resetKey, }) {
+    const transcripts = getTranscriptFeatures(feature);
+    const { isoformSequences, isLoading, error } = useIsoformProteinSequences({
+        feature,
+        view,
+    });
+    const { userSelection, setUserSelection } = useTranscriptSelection({
+        options: transcripts,
+        isoformSequences,
+        structureSequence,
+        resetKey,
+    });
+    const selectedTranscript = transcripts.find(f => getId(f) === userSelection);
+    const selectedIsoform = userSelection
+        ? isoformSequences?.[userSelection]
+        : undefined;
+    return {
+        transcripts,
+        isoformSequences,
+        isLoading,
+        error,
+        selectedTranscriptId: userSelection,
+        setSelectedTranscriptId: setUserSelection,
+        selectedTranscript,
+        selectedIsoform,
+    };
+}

package/dist/LaunchProteinView/hooks/useUniProtSearch.js

@@ -1,4 +1,5 @@
 import useSWR from 'swr';
+import { STATIC_SWR_OPTIONS } from './swrOptions';
 import { searchUniProtEntries } from '../services/lookupMethods';
 import { isRecognizedDatabaseId } from '../utils/util';
 export default function useUniProtSearch({ recognizedIds = [], geneId, geneName, selectedQueryId = 'auto', enabled = true, }) {
@@ -29,9 +30,7 @@ export default function useUniProtSearch({ recognizedIds = [], geneId, geneName,
         geneId,
         geneName: geneNameToSearch,
     }), {
-        revalidateOnFocus: false,
-        revalidateOnReconnect: false,
-        revalidateIfStale: false,
+        ...STATIC_SWR_OPTIONS,
         keepPreviousData: true,
     });
     return {

package/dist/LaunchProteinView/utils/calculateProteinSequence.d.ts

@@ -1,4 +1,4 @@
-import type { Feature } from '@jbrowse/core/util';
+import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
 export interface Feat {
     start: number;
     end: number;
@@ -20,9 +20,8 @@ export declare function getProteinSequence({ feature, seq, }: {
     seq: string;
     feature: Feature;
 }): string;
-export declare function fetchProteinSeq({ feature, view, }: {
+export declare function fetchProteinSeq({ feature, session, assemblyName, }: {
     feature: Feature;
-    view: {
-        assemblyNames?: string[];
-    } | undefined;
+    session: AbstractSessionModel;
+    assemblyName: string | undefined;
 }): Promise<string | undefined>;