npm - jbrowse-plugin-protein3d - Versions diffs - 0.0.3 → 0.0.5 - Mend

jbrowse-plugin-protein3d 0.0.3 → 0.0.5

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package/dist/LaunchProteinView/components/ManualUniProtIDEntry.js ADDED Viewed

@@ -0,0 +1,225 @@
+import React, { useEffect, useState } from 'react';
+import { observer } from 'mobx-react';
+import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import { getContainingView, getSession, isSessionWithAddTracks, } from '@jbrowse/core/util';
+import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui';
+// locals
+import { getId, getGeneDisplayName, getTranscriptDisplayName, getTranscriptFeatures, } from './util';
+// components
+import TranscriptSelector from './TranscriptSelector';
+import AlphaFoldDBSearchStatus from './AlphaFoldDBSearchStatus';
+// hooks
+import useRemoteStructureFileSequence from './useRemoteStructureFileSequence';
+import useIsoformProteinSequences from './useIsoformProteinSequences';
+const useStyles = makeStyles()(theme => ({
+    dialogContent: {
+        marginTop: theme.spacing(6),
+        width: '80em',
+    },
+}));
+const ManualUniProtIDEntry = observer(function ({ feature, model, handleClose, }) {
+    const { classes } = useStyles();
+    const session = getSession(model);
+    // 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 [userSelection, setUserSelection] = useState();
+    const view = getContainingView(model);
+    const selectedTranscript = options.find(val => getId(val) === userSelection);
+    const { isoformSequences, isLoading: isIsoformProteinSequencesLoading, error: isoformProteinSequencesError, } = useIsoformProteinSequences({
+        feature,
+        view,
+    });
+    const userSelectedProteinSequence = isoformSequences?.[userSelection ?? ''];
+    const [uniprotId, setUniprotId] = useState('');
+    const url = uniprotId
+        ? `https://alphafold.ebi.ac.uk/files/AF-${uniprotId}-F1-model_v4.cif`
+        : undefined;
+    const { sequences: structureSequences, isLoading: isRemoteStructureSequenceLoading, error: remoteStructureSequenceError, } = useRemoteStructureFileSequence({ url });
+    const e = isoformProteinSequencesError || remoteStructureSequenceError;
+    const structureSequence = structureSequences?.[0];
+    useEffect(() => {
+        if (isoformSequences !== undefined) {
+            const ret = options.find(f => isoformSequences[f.id()]?.seq.replaceAll('*', '') ==
+                structureSequence) ?? options.find(f => !!isoformSequences[f.id()]);
+            setUserSelection(ret?.id());
+        }
+    }, [options, structureSequence, isoformSequences]);
+    return (React.createElement(React.Fragment, null,
+        React.createElement(DialogContent, { className: classes.dialogContent },
+            e ? React.createElement(ErrorMessage, { error: e }) : null,
+            React.createElement(Typography, null, "Manually enter a UniProt ID"),
+            isRemoteStructureSequenceLoading ? (React.createElement(LoadingEllipses, { variant: "h6", message: "Loading sequence from remote structure file" })) : null,
+            React.createElement(TextField, { label: "UniProt ID", value: uniprotId, onChange: event => {
+                    setUniprotId(event.target.value);
+                } }),
+            isIsoformProteinSequencesLoading ? (React.createElement(LoadingEllipses, { variant: "h6", message: "Loading protein sequences from transcript isoforms" })) : null,
+            isoformSequences && structureSequence && selectedTranscript ? (React.createElement(React.Fragment, null,
+                React.createElement(TranscriptSelector, { val: userSelection ?? '', setVal: setUserSelection, structureSequence: structureSequence, feature: feature, isoforms: options, isoformSequences: isoformSequences }),
+                React.createElement(AlphaFoldDBSearchStatus, { uniprotId: uniprotId, selectedTranscript: selectedTranscript, structureSequence: structureSequence, isoformSequences: isoformSequences }))) : null),
+        React.createElement(DialogActions, null,
+            React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
+                    handleClose();
+                } }, "Cancel"),
+            React.createElement(Button, { variant: "contained", color: "primary", disabled: !uniprotId || !userSelectedProteinSequence || !selectedTranscript, onClick: () => {
+                    session.addView('ProteinView', {
+                        type: 'ProteinView',
+                        isFloating: true,
+                        structures: [
+                            {
+                                url,
+                                userProvidedTranscriptSequence: userSelectedProteinSequence?.seq,
+                                feature: selectedTranscript?.toJSON(),
+                                connectedViewId: view.id,
+                            },
+                        ],
+                        displayName: [
+                            'Protein view',
+                            uniprotId,
+                            getGeneDisplayName(feature),
+                            getTranscriptDisplayName(selectedTranscript),
+                        ].join(' - '),
+                    });
+                    handleClose();
+                } }, "Launch 3-D protein structure view"),
+            React.createElement(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: `${type}-LinearBasicDisplay`,
+                                                type: 'LinearBasicDisplay',
+                                                jexlFilters: [`get(feature,'type')=='${type}'`],
+                                            },
+                                        ],
+                                    });
+                                });
+                                session.addTrackConf({
+                                    type: 'FeatureTrack',
+                                    trackId: 'Antigen',
+                                    name: 'Antigen',
+                                    adapter: {
+                                        type: 'Gff3Adapter',
+                                        gffLocation: {
+                                            uri: `https://www.ebi.ac.uk/proteins/api/antigen/${uniprotId}?format=gff`,
+                                        },
+                                    },
+                                    assemblyNames: [uniprotId],
+                                });
+                                session.addTrackConf({
+                                    type: 'FeatureTrack',
+                                    trackId: 'Variation',
+                                    name: 'Variation',
+                                    adapter: {
+                                        type: 'UniProtVariationAdapter',
+                                        location: {
+                                            uri: `https://www.ebi.ac.uk/proteins/api/variation/${uniprotId}.json`,
+                                        },
+                                    },
+                                    assemblyNames: [uniprotId],
+                                });
+                                session.addTrackConf({
+                                    type: 'QuantitativeTrack',
+                                    trackId: 'AlphaFold confidence',
+                                    name: 'AlphaFold confidence',
+                                    adapter: {
+                                        type: 'AlphaFoldConfidenceAdapter',
+                                        location: {
+                                            uri: `https://alphafold.ebi.ac.uk/files/AF-${uniprotId}-F1-confidence_v4.json`,
+                                        },
+                                    },
+                                    assemblyNames: [uniprotId],
+                                });
+                                session.addTrackConf({
+                                    type: 'MultiQuantitativeTrack',
+                                    trackId: 'AlphaMissense scores',
+                                    name: 'AlphaMissense scores',
+                                    assemblyNames: [uniprotId],
+                                    adapter: {
+                                        type: 'AlphaMissensePathogenicityAdapter',
+                                        location: {
+                                            uri: `https://alphafold.ebi.ac.uk/files/AF-${uniprotId}-F1-aa-substitutions.csv`,
+                                        },
+                                    },
+                                    displays: [
+                                        {
+                                            type: 'MultiLinearWiggleDisplay',
+                                            displayId: '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(' - '),
+                                });
+                                await view.navToLocString(uniprotId, uniprotId);
+                            }
+                            catch (e) {
+                                console.error(e);
+                                session.notifyError(`${e}`, e);
+                            }
+                        })();
+                    }
+                    handleClose();
+                } }, "Launch linear protein annotation view"))));
+});
+export default ManualUniProtIDEntry;
+//# sourceMappingURL=ManualUniProtIDEntry.js.map

package/dist/LaunchProteinView/components/ManualUniProtIDEntry.js.map ADDED Viewed

@@ -0,0 +1 @@

+ 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package/dist/LaunchProteinView/components/TranscriptSelector.js CHANGED Viewed

@@ -7,7 +7,9 @@ function TextField2({ children, ...rest }) {
         React.createElement(TextField, { ...rest }, children)));
 }
 export default function TranscriptSelector({ val, setVal, isoforms, isoformSequences, structureSequence, feature, }) {
-    return (React.createElement(TextField2, { value: val, onChange: event => setVal(event.target.value), label: "Choose transcript isoform", select: true },
+    return (React.createElement(TextField2, { value: val, onChange: event => {
+            setVal(event.target.value);
+        }, label: "Choose transcript isoform", select: true },
         isoforms
             .filter(f => !!isoformSequences[f.id()])
             .filter(f => isoformSequences[f.id()].seq.replaceAll('*', '') ===

package/dist/LaunchProteinView/components/TranscriptSelector.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"TranscriptSelector.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/TranscriptSelector.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,SAAS,EAAkB,MAAM,eAAe,CAAA;AAGnE,SAAS;AACT,OAAO,EAAE,kBAAkB,EAAE,wBAAwB,EAAE,MAAM,QAAQ,CAAA;AAErE,SAAS,UAAU,CAAC,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAkB;IACvD,OAAO,CACL;QACE,oBAAC,SAAS,OAAK,IAAI,IAAG,QAAQ,CAAa,CACvC,CACP,CAAA;AACH,CAAC;AAED,MAAM,CAAC,OAAO,UAAU,kBAAkB,CAAC,EACzC,GAAG,EACH,MAAM,EACN,QAAQ,EACR,gBAAgB,EAChB,iBAAiB,EACjB,OAAO,GAQR;IACC,OAAO,CACL,oBAAC,UAAU,IACT,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE;YAChB,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;QAC5B,CAAC,EACD,KAAK,EAAC,2BAA2B,EACjC,MAAM;QAEL,QAAQ;aACN,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;aACvC,MAAM,CACL,CAAC,CAAC,EAAE,CACF,gBAAgB,CAAC,CAAC,CAAC,EAAE,EAAE,CAAE,CAAC,GAAG,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC;YACjD,iBAAiB,CACpB;aACA,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CACR,oBAAC,QAAQ,IAAC,KAAK,EAAE,CAAC,CAAC,EAAE,EAAE,EAAE,GAAG,EAAE,CAAC,CAAC,EAAE,EAAE;YACjC,kBAAkB,CAAC,OAAO,CAAC;;YAAK,wBAAwB,CAAC,CAAC,CAAC;;YAC3D,gBAAgB,CAAC,CAAC,CAAC,EAAE,EAAE,CAAE,CAAC,GAAG,CAAC,MAAM;+CAE5B,CACZ,CAAC;QACH,QAAQ;aACN,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;aACvC,MAAM,CACL,CAAC,CAAC,EAAE,CACF,gBAAgB,CAAC,CAAC,CAAC,EAAE,EAAE,CAAE,CAAC,GAAG,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC;YACjD,iBAAiB,CACpB;aACA,IAAI,CACH,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CACP,gBAAgB,CAAC,CAAC,CAAC,EAAE,EAAE,CAAE,CAAC,GAAG,CAAC,MAAM;YACpC,gBAAgB,CAAC,CAAC,CAAC,EAAE,EAAE,CAAE,CAAC,GAAG,CAAC,MAAM,CACvC;aACA,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CACR,oBAAC,QAAQ,IAAC,KAAK,EAAE,CAAC,CAAC,EAAE,EAAE,EAAE,GAAG,EAAE,CAAC,CAAC,EAAE,EAAE;YACjC,kBAAkB,CAAC,OAAO,CAAC;;YAAK,wBAAwB,CAAC,CAAC,CAAC;;YAC3D,gBAAgB,CAAC,CAAC,CAAC,EAAE,EAAE,CAAE,CAAC,GAAG,CAAC,MAAM;kBAC5B,CACZ,CAAC;QACH,QAAQ;aACN,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;aACtC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CACR,oBAAC,QAAQ,IAAC,KAAK,EAAE,CAAC,CAAC,EAAE,EAAE,EAAE,GAAG,EAAE,CAAC,CAAC,EAAE,EAAE,EAAE,QAAQ;YAC3C,kBAAkB,CAAC,OAAO,CAAC;;YAAK,wBAAwB,CAAC,CAAC,CAAC;yBAEnD,CACZ,CAAC,CACO,CACd,CAAA;AACH,CAAC"}

package/dist/LaunchProteinView/components/UserProvidedStructure.js CHANGED Viewed

@@ -50,12 +50,11 @@ const UserProvidedStructure = observer(function ({ feature, model, handleClose,
         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;
+    const { sequences: structureSequences1, error: error3 } = useLocalStructureFileSequence({ file });
+    const { sequences: structureSequences2, error: error4 } = useRemoteStructureFileSequence({ url: structureURL });
+    const structureName = file?.name ?? structureURL.slice(structureURL.lastIndexOf('/') + 1);
+    const structureSequences = structureSequences1 ?? structureSequences2;
+    const structureSequence = structureSequences?.[0];
     useEffect(() => {
         if (isoformSequences !== undefined) {
             const ret = options.find(f => isoformSequences[f.id()]?.seq.replaceAll('*', '') ==
@@ -73,19 +72,23 @@ const UserProvidedStructure = observer(function ({ feature, model, handleClose,
                     "Open your structure file ",
                     React.createElement(HelpButton, null)),
                 React.createElement(FormControl, { component: "fieldset" },
-                    React.createElement(RadioGroup, { value: choice, onChange: event => setChoice(event.target.value) },
+                    React.createElement(RadioGroup, { value: choice, onChange: event => {
+                            setChoice(event.target.value);
+                        } },
                         React.createElement(FormControlLabel, { value: "url", control: React.createElement(Radio, null), label: "URL" }),
                         React.createElement(FormControlLabel, { value: "file", control: React.createElement(Radio, null), label: "File" }),
                         React.createElement(FormControlLabel, { value: "pdb", control: React.createElement(Radio, null), label: "PDB ID" }))),
                 choice === 'url' ? (React.createElement("div", null,
                     React.createElement(Typography, null, "Open a PDB/mmCIF/etc. file from remote URL"),
-                    React.createElement(TextField, { label: "URL", value: structureURL, onChange: event => setStructureURL(event.target.value) }))) : null,
+                    React.createElement(TextField, { label: "URL", value: structureURL, onChange: event => {
+                            setStructureURL(event.target.value);
+                        } }))) : null,
                 choice === 'file' ? (React.createElement("div", { style: { paddingTop: 20 } },
                     React.createElement(Typography, null, "Open a PDB/mmCIF/etc. file from your local drive"),
                     React.createElement(Button, { variant: "outlined", component: "label" },
                         "Choose File",
                         React.createElement("input", { type: "file", hidden: true, onChange: ({ target }) => {
-                                const file = target?.files?.[0];
+                                const file = target.files?.[0];
                                 if (file) {
                                     setFile(file);
                                 }
@@ -98,12 +101,16 @@ const UserProvidedStructure = observer(function ({ feature, model, handleClose,
             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
+                    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(DialogActions, null,
-            React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel"),
+            React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
+                    handleClose();
+                } }, "Cancel"),
             React.createElement(Button, { variant: "contained", color: "primary", disabled: !(structureURL || file) || !protein || !selectedTranscript, onClick: () => {
                     // eslint-disable-next-line @typescript-eslint/no-floating-promises
                     ;
@@ -125,7 +132,7 @@ const UserProvidedStructure = observer(function ({ feature, model, handleClose,
                             setError(e);
                         }
                     })();
-                } }, "Submit"))));
+                } }, "Launch 3-D protein structure view"))));
 });
 export default UserProvidedStructure;
 //# sourceMappingURL=UserProvidedStructure.js.map

package/dist/LaunchProteinView/components/UserProvidedStructure.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ 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package/dist/LaunchProteinView/components/calculateProteinSequence.js CHANGED Viewed

@@ -8,7 +8,7 @@ export function calculateProteinSequence({ cds, sequence, codonTable, }) {
     let protein = '';
     for (let i = 0; i < str.length; i += 3) {
         // use & symbol for undefined codon, or partial slice
-        protein += codonTable[str.slice(i, i + 3)] || '&';
+        protein += codonTable[str.slice(i, i + 3)] ?? '&';
     }
     return protein;
 }
@@ -52,8 +52,10 @@ export async function fetchProteinSeq({ feature, view, }) {
     const refName = feature.get('refName');
     const session = getSession(view);
     const { assemblyManager, rpcManager } = session;
-    const [assemblyName] = view?.assemblyNames ?? [];
-    const assembly = await assemblyManager.waitForAssembly(assemblyName);
+    const assemblyName = view?.assemblyNames?.[0];
+    const assembly = assemblyName
+        ? await assemblyManager.waitForAssembly(assemblyName)
+        : undefined;
     if (!assembly) {
         throw new Error('assembly not found');
     }

package/dist/LaunchProteinView/components/calculateProteinSequence.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LaunchProteinView/components/useLocalStructureFileSequence.d.ts CHANGED Viewed

@@ -3,5 +3,5 @@ export default function useLocalStructureFileSequence({ file, }: {
 }): {
     error: unknown;
     isLoading: boolean;
-    seq: string | undefined;
+    sequences: string[] | undefined;
 };

package/dist/LaunchProteinView/components/useLocalStructureFileSequence.js CHANGED Viewed

@@ -1,23 +1,38 @@
 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';
+import { addStructureFromData } from '../../ProteinView/addStructureFromData';
 async function structureFileSequenceFetcher(file, format) {
     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;
+    try {
+        const { model } = await addStructureFromData({
+            data: await file.text(),
+            plugin: p,
+            format,
+        });
+        return model.obj?.data.sequence.sequences.map(s => {
+            let seq = '';
+            const arr = s.sequence.label.toArray();
+            // eslint-disable-next-line unicorn/no-for-loop,@typescript-eslint/prefer-for-of
+            for (let i = 0; i < arr.length; i++) {
+                seq += arr[i];
+            }
+            return seq;
+        });
+    }
+    finally {
+        p.unmount();
+        ret.remove();
+    }
 }
 export default function useLocalStructureFileSequence({ file, }) {
     const [error, setError] = useState();
     const [isLoading, setLoading] = useState(false);
-    const [seq, setSeq] = useState();
+    const [sequences, setSequences] = useState();
     useEffect(() => {
         // eslint-disable-next-line @typescript-eslint/no-floating-promises
         ;
@@ -27,7 +42,12 @@ export default function useLocalStructureFileSequence({ file, }) {
                     setLoading(true);
                     const ext = file.name.slice(file.name.lastIndexOf('.') + 1) || 'pdb';
                     const seq = await structureFileSequenceFetcher(file, (ext === 'cif' ? 'mmcif' : ext));
-                    setSeq(seq);
+                    if (seq) {
+                        setSequences(seq);
+                    }
+                    else {
+                        throw new Error('no sequences detected in file');
+                    }
                 }
             }
             catch (e) {
@@ -39,6 +59,6 @@ export default function useLocalStructureFileSequence({ file, }) {
             }
         })();
     }, [file]);
-    return { error, isLoading, seq };
+    return { error, isLoading, sequences };
 }
 //# sourceMappingURL=useLocalStructureFileSequence.js.map

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package/dist/LaunchProteinView/components/useRemoteStructureFileSequence.d.ts CHANGED Viewed

@@ -3,5 +3,5 @@ export default function useRemoteStructureFileSequence({ url, }: {
 }): {
     error: unknown;
     isLoading: boolean;
-    seq: string | undefined;
+    sequences: string[] | undefined;
 };

package/dist/LaunchProteinView/components/useRemoteStructureFileSequence.js CHANGED Viewed

@@ -1,22 +1,34 @@
 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';
+import { addStructureFromURL } from '../../ProteinView/addStructureFromURL';
 async function structureFileSequenceFetcher(url) {
     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;
+    try {
+        const { model } = await addStructureFromURL({ url, plugin: p });
+        return model.obj?.data.sequence.sequences.map(s => {
+            let seq = '';
+            const arr = s.sequence.label.toArray();
+            // eslint-disable-next-line unicorn/no-for-loop,@typescript-eslint/prefer-for-of
+            for (let i = 0; i < arr.length; i++) {
+                seq += arr[i];
+            }
+            return seq;
+        });
+    }
+    finally {
+        p.unmount();
+        ret.remove();
+    }
 }
 export default function useRemoteStructureFileSequence({ url, }) {
     const [error, setError] = useState();
     const [isLoading, setLoading] = useState(false);
-    const [seq, setSeq] = useState();
+    const [sequences, setSequences] = useState();
     useEffect(() => {
         // eslint-disable-next-line @typescript-eslint/no-floating-promises
         ;
@@ -25,7 +37,12 @@ export default function useRemoteStructureFileSequence({ url, }) {
                 if (url) {
                     setLoading(true);
                     const seq = await structureFileSequenceFetcher(url);
-                    setSeq(seq);
+                    if (seq) {
+                        setSequences(seq);
+                    }
+                    else {
+                        throw new Error('no sequences detected in file');
+                    }
                 }
             }
             catch (e) {
@@ -37,6 +54,6 @@ export default function useRemoteStructureFileSequence({ url, }) {
             }
         })();
     }, [url]);
-    return { error, isLoading, seq };
+    return { error, isLoading, sequences };
 }
 //# sourceMappingURL=useRemoteStructureFileSequence.js.map

package/dist/LaunchProteinView/components/useRemoteStructureFileSequence.js.map CHANGED Viewed

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package/dist/LaunchProteinView/components/util.js CHANGED Viewed

@@ -7,7 +7,7 @@ export function getTranscriptFeatures(feature) {
         : subfeatures;
 }
 export function stripTrailingVersion(s) {
-    return s?.replace(/\.[^/.]+$/, '');
+    return s?.replace(/\.[^./]+$/, '');
 }
 export function z(n) {
     return n.toLocaleString('en-US');