jbrowse-plugin-protein3d 0.0.2 → 0.0.4

package/dist/LaunchProteinView/components/TranscriptSelector.js

@@ -1,24 +1,41 @@
 import React from 'react';
 import { MenuItem, TextField } from '@mui/material';
 // locals
-import { getGeneDisplayName, getTranscriptDisplayName } from '../util';
+import { getGeneDisplayName, getTranscriptDisplayName } from './util';
 function TextField2({ children, ...rest }) {
     return (React.createElement("div", null,
         React.createElement(TextField, { ...rest }, children)));
 }
-export default function TranscriptSelector({ val, setVal, options, feature, seqs, }) {
-    return (React.createElement(TextField2, { value: val, onChange: event => setVal(event.target.value), label: "Choose transcript isoform", select: true },
-        options
-            .filter(f => !!seqs[f.id()])
+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 },
+        isoforms
+            .filter(f => !!isoformSequences[f.id()])
+            .filter(f => isoformSequences[f.id()].seq.replaceAll('*', '') ===
+            structureSequence)
             .map(f => (React.createElement(MenuItem, { value: f.id(), key: f.id() },
             getGeneDisplayName(feature),
             " - ",
             getTranscriptDisplayName(f),
             " (",
-            seqs[f.id()].length,
+            isoformSequences[f.id()].seq.length,
+            "aa) (matches structure residues)"))),
+        isoforms
+            .filter(f => !!isoformSequences[f.id()])
+            .filter(f => isoformSequences[f.id()].seq.replaceAll('*', '') !==
+            structureSequence)
+            .sort((a, b) => isoformSequences[b.id()].seq.length -
+            isoformSequences[a.id()].seq.length)
+            .map(f => (React.createElement(MenuItem, { value: f.id(), key: f.id() },
+            getGeneDisplayName(feature),
+            " - ",
+            getTranscriptDisplayName(f),
+            " (",
+            isoformSequences[f.id()].seq.length,
             "aa)"))),
-        options
-            .filter(f => !seqs[f.id()])
+        isoforms
+            .filter(f => !isoformSequences[f.id()])
             .map(f => (React.createElement(MenuItem, { value: f.id(), key: f.id(), disabled: true },
             getGeneDisplayName(feature),
             " - ",

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

@@ -1 +1 @@
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+{"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

@@ -1,14 +1,19 @@
 import React, { useEffect, useState } from 'react';
 import { observer } from 'mobx-react';
-import { Button, DialogActions, Radio, RadioGroup, DialogContent, TextField, FormControlLabel, FormControl, Link, Typography, } from '@mui/material';
+import { Button, DialogActions, DialogContent, FormControlLabel, FormControl, Link, Radio, RadioGroup, TextField, Typography, } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
 import { getContainingView, getSession, } from '@jbrowse/core/util';
 import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui';
 // locals
-import { getGeneDisplayName, getId, getTranscriptDisplayName, getTranscriptFeatures, } from '../util';
+import { getGeneDisplayName, getId, getTranscriptDisplayName, getTranscriptFeatures, } 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: {
         marginTop: theme.spacing(6),
@@ -29,82 +34,97 @@ const UserProvidedStructure = observer(function ({ feature, model, handleClose,
     const { classes } = useStyles();
     const session = getSession(model);
     const [file, setFile] = useState();
+    const [pdbId, setPdbId] = useState('');
     const [choice, setChoice] = useState('file');
     const [error2, setError] = useState();
     const [structureURL, setStructureURL] = useState('');
-    const [selection, setSelection] = useState();
+    const [userSelection, setUserSelection] = useState();
+    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);
-    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 { 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 (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]);
-    const e = error || error2;
+    }, [options, structureSequence, isoformSequences]);
+    const e = error || error2 || error3 || error4;
     return (React.createElement(React.Fragment, null,
         React.createElement(DialogContent, { className: classes.dialogContent },
             e ? React.createElement(ErrorMessage, { error: e }) : null,
             React.createElement(HelpText, null),
-            seqs ? (React.createElement(React.Fragment, null,
-                React.createElement(TranscriptSelector, { val: selection ?? '', setVal: setSelection, options: options, feature: feature, seqs: seqs }),
-                selectedTranscript ? (React.createElement(TextField, { variant: "outlined", multiline: true, minRows: 5, maxRows: 10, fullWidth: true, value: `>${selectedTranscript.get('name') || selectedTranscript.get('id')}\n${protein}`, InputProps: {
-                        readOnly: true,
-                        classes: {
-                            input: classes.textAreaFont,
-                        },
-                    } })) : null)) : (React.createElement("div", { style: { margin: 20 } },
-                React.createElement(LoadingEllipses, { title: "Loading protein sequences", variant: "h6" }))),
             React.createElement("div", { style: { display: 'flex', margin: 30 } },
+                React.createElement(Typography, null,
+                    "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: "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);
                                 }
-                            } })))) : null)),
+                            } })))) : null,
+                choice === 'pdb' ? (React.createElement(TextField, { value: pdbId, onChange: event => {
+                        const s = event.target.value;
+                        setPdbId(s);
+                        setStructureURL(`https://files.rcsb.org/download/${s}.cif`);
+                    }, label: "PDB ID" })) : null),
+            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(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
                     ;
                     (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) {

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

@@ -1 +1 @@
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package/dist/LaunchProteinView/{calculateProteinSequence.js → components/calculateProteinSequence.js}

@@ -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

@@ -0,0 +1 @@
+{"version":3,"file":"calculateProteinSequence.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/calculateProteinSequence.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,6BAA6B,CAAA;AACrD,OAAO,EAEL,iBAAiB,EACjB,kBAAkB,EAClB,UAAU,EACV,MAAM,GACP,MAAM,oBAAoB,CAAA;AAQ3B,MAAM,UAAU,MAAM,CAAC,QAAgB,EAAE,QAAgB;IACvD,OAAO,QAAQ,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;AACzE,CAAC;AAED,MAAM,UAAU,wBAAwB,CAAC,EACvC,GAAG,EACH,QAAQ,EACR,UAAU,GAKX;IACC,MAAM,GAAG,GAAG,MAAM,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAA;IACjC,IAAI,OAAO,GAAG,EAAE,CAAA;IAChB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;QACvC,qDAAqD;QACrD,OAAO,IAAI,UAAU,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,GAAG,CAAA;IACnD,CAAC;IACD,OAAO,OAAO,CAAA;AAChB,CAAC;AAED,MAAM,UAAU,OAAO,CAAC,IAAY,EAAE,MAAc;IAClD,OAAO,IAAI;SACR,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;QACX,GAAG,GAAG;QACN,KAAK,EAAE,MAAM,GAAG,GAAG,CAAC,GAAG;QACvB,GAAG,EAAE,MAAM,GAAG,GAAG,CAAC,KAAK;KACxB,CAAC,CAAC;SACF,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,CAAA;AACtC,CAAC;AAED,sDAAsD;AACtD,SAAS,SAAS,CAAC,IAAU;IAC3B,OAAO,GAAG,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,GAAG,EAAE,CAAA;AACpC,CAAC;AAED,sDAAsD;AACtD,MAAM,UAAU,MAAM,CAAC,IAAY;IACjC,OAAO,IAAI,CAAC,MAAM,CAChB,CAAC,IAAI,EAAE,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC,CAAC,GAAG,IAAI,SAAS,CAAC,IAAI,CAAC,KAAK,SAAS,CAAC,GAAG,CAAC,GAAG,GAAG,CAAC,CAAE,CAAC,CACzE,CAAA;AACH,CAAC;AAED,MAAM,UAAU,kBAAkB,CAAC,EACjC,OAAO,EACP,GAAG,GAIJ;IACC,mBAAmB;IACnB,MAAM,CAAC,GAAG,OAAO,CAAC,MAAM,EAMvB,CAAA;IACD,MAAM,GAAG,GAAG,MAAM,CAChB,CAAC,CAAC,WAAW;SACV,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC;SACjC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;QACX,GAAG,GAAG;QACN,KAAK,EAAE,GAAG,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK;QAC1B,GAAG,EAAE,GAAG,CAAC,GAAG,GAAG,CAAC,CAAC,KAAK;KACvB,CAAC,CAAC;SACF,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,KAAK,CAAC,CACjC,CAAA;IAED,OAAO,wBAAwB,CAAC;QAC9B,GAAG,EAAE,CAAC,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG;QACrD,QAAQ,EAAE,CAAC,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG;QAC7C,UAAU,EAAE,kBAAkB,CAAC,iBAAiB,CAAC;KAClD,CAAC,CAAA;AACJ,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,eAAe,CAAC,EACpC,OAAO,EACP,IAAI,GAIL;IACC,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IAClC,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;IAC9B,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,CAAA;IACtC,MAAM,OAAO,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;IAChC,MAAM,EAAE,eAAe,EAAE,UAAU,EAAE,GAAG,OAAO,CAAA;IAC/C,MAAM,YAAY,GAAG,IAAI,EAAE,aAAa,EAAE,CAAC,CAAC,CAAC,CAAA;IAC7C,MAAM,QAAQ,GAAG,YAAY;QAC3B,CAAC,CAAC,MAAM,eAAe,CAAC,eAAe,CAAC,YAAY,CAAC;QACrD,CAAC,CAAC,SAAS,CAAA;IACb,IAAI,CAAC,QAAQ,EAAE,CAAC;QACd,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAA;IACvC,CAAC;IACD,MAAM,SAAS,GAAG,aAAa,CAAA;IAC/B,MAAM,KAAK,GAAG,MAAM,UAAU,CAAC,IAAI,CAAC,SAAS,EAAE,iBAAiB,EAAE;QAChE,aAAa,EAAE,OAAO,CAAC,QAAQ,EAAE,CAAC,UAAU,EAAE,SAAS,CAAC,CAAC;QACzD,SAAS;QACT,OAAO,EAAE;YACP;gBACE,KAAK;gBACL,GAAG;gBACH,OAAO,EAAE,QAAQ,CAAC,mBAAmB,CAAC,OAAO,CAAC;gBAC9C,YAAY;aACb;SACF;KACF,CAAC,CAAA;IAEF,MAAM,CAAC,IAAI,CAAC,GAAG,KAAkB,CAAA;IACjC,MAAM,GAAG,GAAG,IAAI,EAAE,GAAG,CAAC,KAAK,CAAuB,CAAA;IAClD,OAAO,GAAG,CAAC,CAAC,CAAC,kBAAkB,CAAC,EAAE,GAAG,EAAE,OAAO,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;AAC/D,CAAC"}

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

@@ -0,0 +1,14 @@
+import { Feature } from '@jbrowse/core/util';
+export default function useIsoformProteinSequences({ feature, view, }: {
+    feature: Feature;
+    view?: {
+        assemblyNames?: string[];
+    };
+}): {
+    isLoading: boolean;
+    isoformSequences: Record<string, {
+        feature: Feature;
+        seq: string;
+    }> | undefined;
+    error: unknown;
+};

package/dist/LaunchProteinView/{useProteinSequences.js → components/useIsoformProteinSequences.js}

@@ -2,29 +2,34 @@ import { useEffect, useState } from 'react';
 // locals
 import { getTranscriptFeatures } from './util';
 import { fetchProteinSeq } from './calculateProteinSequence';
-export default function useAllSequences({ feature, view, }) {
+export default function useIsoformProteinSequences({ feature, view, }) {
     const [error, setError] = useState();
-    const [seqs, setSeqs] = useState();
+    const [isoformSequences, setIsoformSequences] = useState();
+    const [isLoading, setLoading] = useState(false);
     useEffect(() => {
         // eslint-disable-next-line @typescript-eslint/no-floating-promises
         ;
         (async () => {
             try {
+                setLoading(true);
                 const ret = [];
                 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 };
 }
-//# sourceMappingURL=useProteinSequences.js.map
+//# sourceMappingURL=useIsoformProteinSequences.js.map

package/dist/LaunchProteinView/components/useIsoformProteinSequences.js.map

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

@@ -0,0 +1,7 @@
+export default function useLocalStructureFileSequence({ file, }: {
+    file?: File;
+}): {
+    error: unknown;
+    isLoading: boolean;
+    sequences: string[] | undefined;
+};

package/dist/LaunchProteinView/components/useLocalStructureFileSequence.js

@@ -0,0 +1,64 @@
+import { useEffect, useState } from 'react';
+import { createPluginUI } from 'molstar/lib/mol-plugin-ui';
+import { renderReact18 } from 'molstar/lib/mol-plugin-ui/react18';
+import { addStructureFromData } from '../../ProteinView/addStructureFromData';
+async function structureFileSequenceFetcher(file, format) {
+    const ret = document.createElement('div');
+    const p = await createPluginUI({
+        target: ret,
+        render: renderReact18,
+    });
+    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 [sequences, setSequences] = useState();
+    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));
+                    if (seq) {
+                        setSequences(seq);
+                    }
+                    else {
+                        throw new Error('no sequences detected in file');
+                    }
+                }
+            }
+            catch (e) {
+                console.error(e);
+                setError(e);
+            }
+            finally {
+                setLoading(false);
+            }
+        })();
+    }, [file]);
+    return { error, isLoading, sequences };
+}
+//# sourceMappingURL=useLocalStructureFileSequence.js.map

package/dist/LaunchProteinView/components/useLocalStructureFileSequence.js.map

@@ -0,0 +1 @@
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package/dist/LaunchProteinView/{useMyGeneInfo.d.ts → components/useMyGeneInfoUniprotIdLookup.d.ts}

@@ -1,7 +1,7 @@
 export default function useMyGeneInfo({ id }: {
     id: string;
 }): {
-    loading: boolean;
-    result: string | undefined;
+    isLoading: boolean;
+    uniprotId: string | undefined;
     error: unknown;
 };

package/dist/LaunchProteinView/{useMyGeneInfo.js → components/useMyGeneInfoUniprotIdLookup.js}

@@ -1,29 +1,34 @@
 import { useEffect, useState } from 'react';
-import { jsonfetch } from '../fetchUtils';
+import { jsonfetch } from '../../fetchUtils';
 import { stripTrailingVersion } from './util';
 export default function useMyGeneInfo({ id }) {
     const [result, setResult] = useState();
     const [error, setError] = useState();
-    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,
+    };
 }
-//# sourceMappingURL=useMyGeneInfo.js.map
+//# sourceMappingURL=useMyGeneInfoUniprotIdLookup.js.map

package/dist/LaunchProteinView/components/useMyGeneInfoUniprotIdLookup.js.map

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

@@ -0,0 +1,7 @@
+export default function useRemoteStructureFileSequence({ url, }: {
+    url?: string;
+}): {
+    error: unknown;
+    isLoading: boolean;
+    sequences: string[] | undefined;
+};

package/dist/LaunchProteinView/components/useRemoteStructureFileSequence.js

@@ -0,0 +1,59 @@
+import { useEffect, useState } from 'react';
+import { createPluginUI } from 'molstar/lib/mol-plugin-ui';
+import { renderReact18 } from 'molstar/lib/mol-plugin-ui/react18';
+import { addStructureFromURL } from '../../ProteinView/addStructureFromURL';
+async function structureFileSequenceFetcher(url) {
+    const ret = document.createElement('div');
+    const p = await createPluginUI({
+        target: ret,
+        render: renderReact18,
+    });
+    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 [sequences, setSequences] = useState();
+    useEffect(() => {
+        // eslint-disable-next-line @typescript-eslint/no-floating-promises
+        ;
+        (async () => {
+            try {
+                if (url) {
+                    setLoading(true);
+                    const seq = await structureFileSequenceFetcher(url);
+                    if (seq) {
+                        setSequences(seq);
+                    }
+                    else {
+                        throw new Error('no sequences detected in file');
+                    }
+                }
+            }
+            catch (e) {
+                console.error(e);
+                setError(e);
+            }
+            finally {
+                setLoading(false);
+            }
+        })();
+    }, [url]);
+    return { error, isLoading, sequences };
+}
+//# sourceMappingURL=useRemoteStructureFileSequence.js.map

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

@@ -0,0 +1 @@
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package/dist/LaunchProteinView/{util.d.ts → components/util.d.ts}

@@ -1,17 +1,7 @@
 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 declare function getTranscriptFeatures(feature: Feature): Feature[];
 export declare function stripTrailingVersion(s?: string): string | undefined;
 export declare function z(n: number): string;
-export declare function createMapFromData(data?: Row[]): Map<string, string>;
 export declare function getDisplayName(f: Feature): string;
 export declare function getId(val?: Feature): string;
 export declare function getTranscriptDisplayName(val?: Feature): string;