jbrowse-plugin-msaview 2.2.3 → 2.2.5

package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js

@@ -1,15 +1,14 @@
 import React, { useState } from 'react';
 import { ErrorMessage, FileSelector } from '@jbrowse/core/ui';
 import { getContainingView, getSession, } from '@jbrowse/core/util';
-import { openLocation } from '@jbrowse/core/util/io';
-import { Button, DialogActions, DialogContent, FormControl, FormControlLabel, Radio, RadioGroup, } from '@mui/material';
+import { Alert, Button, DialogActions, DialogContent, FormControl, FormControlLabel, Radio, RadioGroup, } from '@mui/material';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
 import { launchView } from './launchView';
 import TextField2 from '../../../components/TextField2';
-import { getGeneDisplayName, getId, getTranscriptFeatures } from '../../util';
+import { getGeneDisplayName } from '../../util';
 import TranscriptSelector from '../TranscriptSelector';
-import { useFeatureSequence } from '../useFeatureSequence';
+import { useTranscriptSelection } from '../useTranscriptSelection';
 const useStyles = makeStyles()({
     dialogContent: {
         width: '80em',
@@ -28,14 +27,8 @@ const ManualMSALoader = observer(function PreLoadedMSA2({ model, feature, handle
     const [treeText, setTreeText] = useState('');
     const [msaFileLocation, setMsaFileLocation] = useState();
     const [treeFileLocation, setTreeFileLocation] = useState();
-    const options = getTranscriptFeatures(feature);
-    const [userSelection, setUserSelection] = useState(getId(options[0]));
-    const ret = options.find(val => userSelection === getId(val));
-    const selectedTranscript = options.find(val => getId(val) === userSelection);
-    const { proteinSequence, error: error2 } = useFeatureSequence({
-        view,
-        feature: selectedTranscript,
-    });
+    const [querySeqName, setQuerySeqName] = useState('');
+    const { options, setSelectedId, selectedTranscript, proteinSequence, error: error2, } = useTranscriptSelection({ feature, view });
     const e = launchViewError ?? error2;
     return (React.createElement(React.Fragment, null,
         React.createElement(DialogContent, { className: classes.dialogContent },
@@ -55,45 +48,44 @@ const ManualMSALoader = observer(function PreLoadedMSA2({ model, feature, handle
                 React.createElement(TextField2, { variant: "outlined", name: "Tree", multiline: true, minRows: 5, maxRows: 10, fullWidth: true, placeholder: "Paste newick tree (optional)", value: treeText, onChange: event => {
                         setTreeText(event.target.value);
                     } })))),
-            React.createElement(TranscriptSelector, { feature: feature, options: options, selectedTranscriptId: userSelection, onTranscriptChange: setUserSelection, proteinSequence: proteinSequence })),
+            React.createElement(TranscriptSelector, { feature: feature, options: options, selectedTranscript: selectedTranscript, onTranscriptChange: setSelectedId, proteinSequence: proteinSequence }),
+            React.createElement(TextField2, { variant: "outlined", name: "MSA row name", fullWidth: true, required: true, style: { marginTop: 20 }, placeholder: "Row name in MSA that corresponds to the selected transcript", helperText: "Required: Specify the name of the row in your MSA that should be aligned with the selected transcript", value: querySeqName, onChange: event => {
+                    setQuerySeqName(event.target.value);
+                } }),
+            !querySeqName.trim() && (React.createElement(Alert, { severity: "warning", style: { marginTop: 10 } }, "Without specifying the MSA row name, clicking on the MSA will not navigate to the corresponding genome position, and hovering highlights will not work."))),
         React.createElement(DialogActions, null,
-            React.createElement(Button, { color: "primary", variant: "contained", disabled: !ret ||
+            React.createElement(Button, { color: "primary", variant: "contained", disabled: !selectedTranscript ||
                     (inputMethod === 'file' && !msaFileLocation) ||
                     (inputMethod === 'text' && !msaText.trim()), onClick: () => {
-                    // eslint-disable-next-line @typescript-eslint/no-floating-promises
-                    ;
-                    (async () => {
-                        try {
-                            if (!ret) {
-                                return;
-                            }
-                            setLaunchViewError(undefined);
-                            launchView({
-                                session,
-                                newViewTitle: getGeneDisplayName(ret),
-                                view,
-                                feature: ret,
-                                data: inputMethod === 'file'
-                                    ? {
-                                        msa: msaFileLocation
-                                            ? await openLocation(msaFileLocation).readFile('utf8')
-                                            : '',
-                                        tree: treeFileLocation
-                                            ? await openLocation(treeFileLocation).readFile('utf8')
-                                            : undefined,
-                                    }
-                                    : {
+                    try {
+                        if (!selectedTranscript) {
+                            return;
+                        }
+                        setLaunchViewError(undefined);
+                        launchView({
+                            session,
+                            newViewTitle: getGeneDisplayName(selectedTranscript),
+                            view,
+                            feature: selectedTranscript,
+                            querySeqName: querySeqName.trim() || undefined,
+                            ...(inputMethod === 'file'
+                                ? {
+                                    msaFilehandle: msaFileLocation,
+                                    treeFilehandle: treeFileLocation,
+                                }
+                                : {
+                                    data: {
                                         msa: msaText,
-                                        tree: treeText,
+                                        tree: treeText || undefined,
                                     },
-                            });
-                            handleClose();
-                        }
-                        catch (e) {
-                            console.error(e);
-                            setLaunchViewError(e);
-                        }
-                    })();
+                                }),
+                        });
+                        handleClose();
+                    }
+                    catch (e) {
+                        console.error(e);
+                        setLaunchViewError(e);
+                    }
                 } }, "Submit"),
             React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => {
                     handleClose();

package/dist/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ManualMSALoader.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,YAAY,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC7D,OAAO,EAIL,iBAAiB,EACjB,UAAU,GACX,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EACL,KAAK,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,WAAW,EACX,gBAAgB,EAChB,KAAK,EACL,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,EAAE,UAAU,EAAE,MAAM,cAAc,CAAA;AACzC,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAA;AAC/C,OAAO,kBAAkB,MAAM,uBAAuB,CAAA;AACtD,OAAO,EAAE,sBAAsB,EAAE,MAAM,2BAA2B,CAAA;AAIlE,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,aAAa,EAAE;QACb,KAAK,EAAE,MAAM;KACd;IACD,YAAY,EAAE;QACZ,UAAU,EAAE,aAAa;KAC1B;CACF,CAAC,CAAA;AAEF,MAAM,eAAe,GAAG,QAAQ,CAAC,SAAS,aAAa,CAAC,EACtD,KAAK,EACL,OAAO,EACP,WAAW,GAKZ;IACC,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,IAAI,GAAG,iBAAiB,CAAC,KAAK,CAA0B,CAAA;IAC9D,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,eAAe,EAAE,kBAAkB,CAAC,GAAG,QAAQ,EAAW,CAAA;IACjE,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,QAAQ,CAAkB,MAAM,CAAC,CAAA;IACvE,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IAC1C,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IAC5C,MAAM,CAAC,eAAe,EAAE,kBAAkB,CAAC,GAAG,QAAQ,EAAgB,CAAA;IACtE,MAAM,CAAC,gBAAgB,EAAE,mBAAmB,CAAC,GAAG,QAAQ,EAAgB,CAAA;IACxE,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IACpD,MAAM,EACJ,OAAO,EACP,aAAa,EACb,kBAAkB,EAClB,eAAe,EACf,KAAK,EAAE,MAAM,GACd,GAAG,sBAAsB,CAAC,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC,CAAA;IAE7C,MAAM,CAAC,GAAG,eAAe,IAAI,MAAM,CAAA;IACnC,OAAO,CACL;QACE,oBAAC,aAAa,IAAC,SAAS,EAAE,OAAO,CAAC,aAAa;YAC5C,CAAC,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,CAAC,GAAI,CAAC,CAAC,CAAC,IAAI;YACtC,oBAAC,WAAW,IAAC,SAAS,EAAC,UAAU;gBAC/B,oBAAC,UAAU,IACT,GAAG,QACH,KAAK,EAAE,WAAW,EAClB,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,cAAc,CAAC,KAAK,CAAC,MAAM,CAAC,KAAwB,CAAC,CAAA;oBACvD,CAAC;oBAED,oBAAC,gBAAgB,IACf,KAAK,EAAC,MAAM,EACZ,OAAO,EAAE,oBAAC,KAAK,OAAG,EAClB,KAAK,EAAC,YAAY,GAClB;oBACF,oBAAC,gBAAgB,IACf,KAAK,EAAC,MAAM,EACZ,OAAO,EAAE,oBAAC,KAAK,OAAG,EAClB,KAAK,EAAC,YAAY,GAClB,CACS,CACD;YAEd,6BAAK,KAAK,EAAE,EAAE,YAAY,EAAE,EAAE,EAAE,IAC7B,WAAW,KAAK,MAAM,CAAC,CAAC,CAAC,CACxB,6BAAK,KAAK,EAAE,EAAE,QAAQ,EAAE,GAAG,EAAE;gBAC3B,oBAAC,YAAY,IACX,IAAI,EAAC,6EAA6E,EAClF,MAAM,QACN,QAAQ,EAAE,eAAe,EACzB,WAAW,EAAE,kBAAkB,GAC/B;gBACF,oBAAC,YAAY,IACX,IAAI,EAAC,oDAAoD,EACzD,MAAM,QACN,QAAQ,EAAE,gBAAgB,EAC1B,WAAW,EAAE,mBAAmB,GAChC,CACE,CACP,CAAC,CAAC,CAAC,CACF;gBACE,oBAAC,UAAU,IACT,OAAO,EAAC,UAAU,EAClB,IAAI,EAAC,KAAK,EACV,SAAS,QACT,OAAO,EAAE,CAAC,EACV,KAAK,EAAE,EAAE,YAAY,EAAE,MAAM,EAAE,EAC/B,OAAO,EAAE,EAAE,EACX,SAAS,QACT,WAAW,EAAC,gBAAgB,EAC5B,KAAK,EAAE,OAAO,EACd,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,UAAU,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;oBAChC,CAAC,GACD;gBACF,oBAAC,UAAU,IACT,OAAO,EAAC,UAAU,EAClB,IAAI,EAAC,MAAM,EACX,SAAS,QACT,OAAO,EAAE,CAAC,EACV,OAAO,EAAE,EAAE,EACX,SAAS,QACT,WAAW,EAAC,8BAA8B,EAC1C,KAAK,EAAE,QAAQ,EACf,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,WAAW,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;oBACjC,CAAC,GACD,CACD,CACJ,CACG;YAEN,oBAAC,kBAAkB,IACjB,OAAO,EAAE,OAAO,EAChB,OAAO,EAAE,OAAO,EAChB,kBAAkB,EAAE,kBAAkB,EACtC,kBAAkB,EAAE,aAAa,EACjC,eAAe,EAAE,eAAe,GAChC;YAEF,oBAAC,UAAU,IACT,OAAO,EAAC,UAAU,EAClB,IAAI,EAAC,cAAc,EACnB,SAAS,QACT,QAAQ,QACR,KAAK,EAAE,EAAE,SAAS,EAAE,EAAE,EAAE,EACxB,WAAW,EAAC,6DAA6D,EACzE,UAAU,EAAC,uGAAuG,EAClH,KAAK,EAAE,YAAY,EACnB,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,eAAe,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBACrC,CAAC,GACD;YAED,CAAC,YAAY,CAAC,IAAI,EAAE,IAAI,CACvB,oBAAC,KAAK,IAAC,QAAQ,EAAC,SAAS,EAAC,KAAK,EAAE,EAAE,SAAS,EAAE,EAAE,EAAE,8JAI1C,CACT,CACa;QAEhB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,KAAK,EAAC,SAAS,EACf,OAAO,EAAC,WAAW,EACnB,QAAQ,EACN,CAAC,kBAAkB;oBACnB,CAAC,WAAW,KAAK,MAAM,IAAI,CAAC,eAAe,CAAC;oBAC5C,CAAC,WAAW,KAAK,MAAM,IAAI,CAAC,OAAO,CAAC,IAAI,EAAE,CAAC,EAE7C,OAAO,EAAE,GAAG,EAAE;oBACZ,IAAI,CAAC;wBACH,IAAI,CAAC,kBAAkB,EAAE,CAAC;4BACxB,OAAM;wBACR,CAAC;wBAED,kBAAkB,CAAC,SAAS,CAAC,CAAA;wBAC7B,UAAU,CAAC;4BACT,OAAO;4BACP,YAAY,EAAE,kBAAkB,CAAC,kBAAkB,CAAC;4BACpD,IAAI;4BACJ,OAAO,EAAE,kBAAkB;4BAC3B,YAAY,EAAE,YAAY,CAAC,IAAI,EAAE,IAAI,SAAS;4BAC9C,GAAG,CAAC,WAAW,KAAK,MAAM;gCACxB,CAAC,CAAC;oCACE,aAAa,EAAE,eAAe;oCAC9B,cAAc,EAAE,gBAAgB;iCACjC;gCACH,CAAC,CAAC;oCACE,IAAI,EAAE;wCACJ,GAAG,EAAE,OAAO;wCACZ,IAAI,EAAE,QAAQ,IAAI,SAAS;qCAC5B;iCACF,CAAC;yBACP,CAAC,CAAA;wBAEF,WAAW,EAAE,CAAA;oBACf,CAAC;oBAAC,OAAO,CAAC,EAAE,CAAC;wBACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;wBAChB,kBAAkB,CAAC,CAAC,CAAC,CAAA;oBACvB,CAAC;gBACH,CAAC,aAGM;YACT,oBAAC,MAAM,IACL,KAAK,EAAC,WAAW,EACjB,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;oBACZ,WAAW,EAAE,CAAA;gBACf,CAAC,aAGM,CACK,CACf,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,eAAe,CAAA"}

package/dist/LaunchMsaView/components/ManualMSALoader/launchView.d.ts

@@ -1,12 +1,13 @@
 import { AbstractSessionModel, Feature, FileLocation } from '@jbrowse/core/util';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-export declare function launchView({ session, newViewTitle, view, feature, msaFileLocation, treeFileLocation, data, }: {
+export declare function launchView({ session, newViewTitle, view, feature, msaFilehandle, treeFilehandle, querySeqName, data, }: {
     session: AbstractSessionModel;
     newViewTitle: string;
     view: LinearGenomeViewModel;
     feature: Feature;
-    msaFileLocation?: FileLocation;
-    treeFileLocation?: FileLocation;
+    msaFilehandle?: FileLocation;
+    treeFilehandle?: FileLocation;
+    querySeqName?: string;
     data?: {
         msa: string;
         tree?: string;

package/dist/LaunchMsaView/components/ManualMSALoader/launchView.js

@@ -1,11 +1,12 @@
-export function launchView({ session, newViewTitle, view, feature, msaFileLocation, treeFileLocation, data, }) {
+export function launchView({ session, newViewTitle, view, feature, msaFilehandle, treeFilehandle, querySeqName, data, }) {
     session.addView('MsaView', {
         type: 'MsaView',
         displayName: newViewTitle,
         connectedViewId: view.id,
         connectedFeature: feature.toJSON(),
-        msaFileLocation,
-        treeFileLocation,
+        msaFilehandle,
+        treeFilehandle,
+        querySeqName,
         data,
     });
 }

package/dist/LaunchMsaView/components/ManualMSALoader/launchView.js.map

@@ -1 +1 @@
-{"version":3,"file":"launchView.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/ManualMSALoader/launchView.ts"],"names":[],"mappings":"AAIA,MAAM,UAAU,UAAU,CAAC,EACzB,OAAO,EACP,YAAY,EACZ,IAAI,EACJ,OAAO,EACP,eAAe,EACf,gBAAgB,EAChB,IAAI,GAYL;IACC,OAAO,CAAC,OAAO,CAAC,SAAS,EAAE;QACzB,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,YAAY;QACzB,eAAe,EAAE,IAAI,CAAC,EAAE;QACxB,gBAAgB,EAAE,OAAO,CAAC,MAAM,EAAE;QAClC,eAAe;QACf,gBAAgB;QAChB,IAAI;KACL,CAAC,CAAA;AACJ,CAAC"}
+{"version":3,"file":"launchView.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/ManualMSALoader/launchView.ts"],"names":[],"mappings":"AAIA,MAAM,UAAU,UAAU,CAAC,EACzB,OAAO,EACP,YAAY,EACZ,IAAI,EACJ,OAAO,EACP,aAAa,EACb,cAAc,EACd,YAAY,EACZ,IAAI,GAaL;IACC,OAAO,CAAC,OAAO,CAAC,SAAS,EAAE;QACzB,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,YAAY;QACzB,eAAe,EAAE,IAAI,CAAC,EAAE;QACxB,gBAAgB,EAAE,OAAO,CAAC,MAAM,EAAE;QAClC,aAAa;QACb,cAAc;QACd,YAAY;QACZ,IAAI;KACL,CAAC,CAAA;AACJ,CAAC"}

package/dist/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.d.ts

@@ -0,0 +1,9 @@
+import React from 'react';
+import { Feature } from '@jbrowse/core/util';
+import type { AbstractTrackModel } from '@jbrowse/core/util';
+declare const CachedBlastResults: ({ model, handleClose, feature, }: {
+    model: AbstractTrackModel;
+    handleClose: () => void;
+    feature: Feature;
+}) => React.JSX.Element;
+export default CachedBlastResults;

package/dist/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.js

@@ -0,0 +1,76 @@
+import React, { useEffect, useState } from 'react';
+import { getContainingView } from '@jbrowse/core/util';
+import DeleteIcon from '@mui/icons-material/Delete';
+import { Button, IconButton, List, ListItem, ListItemButton, ListItemText, Typography, } from '@mui/material';
+import { observer } from 'mobx-react';
+import { blastLaunchViewFromCache } from './blastLaunchView';
+import { clearAllCachedResults, deleteCachedResult, getAllCachedResults, } from '../../../utils/blastCache';
+const CachedBlastResults = observer(function ({ model, handleClose, feature, }) {
+    const [results, setResults] = useState([]);
+    const [loading, setLoading] = useState(true);
+    const view = getContainingView(model);
+    const geneId = feature.get('id');
+    useEffect(() => {
+        // eslint-disable-next-line @typescript-eslint/no-floating-promises
+        ;
+        (async () => {
+            try {
+                const cached = await getAllCachedResults();
+                setResults(cached.filter(r => r.geneId === geneId));
+                setLoading(false);
+            }
+            catch (e) {
+                console.error(e);
+            }
+        })();
+    }, [geneId]);
+    const handleDelete = async (id) => {
+        await deleteCachedResult(id);
+        setResults(r => r.filter(result => result.id !== id));
+    };
+    const handleClearAll = async () => {
+        await clearAllCachedResults();
+        setResults([]);
+    };
+    const handleUseCached = (cached) => {
+        blastLaunchViewFromCache({
+            view,
+            cached,
+            newViewTitle: `BLAST - ${cached.geneId ?? cached.transcriptId ?? 'Unknown gene'}`,
+        });
+        handleClose();
+    };
+    if (loading) {
+        return React.createElement(Typography, null, "Loading cached results...");
+    }
+    if (results.length === 0) {
+        return (React.createElement(Typography, { color: "textSecondary" }, "No cached BLAST results found for this gene. Run a BLAST query to cache results."));
+    }
+    return (React.createElement("div", null,
+        React.createElement("div", { style: {
+                display: 'flex',
+                justifyContent: 'space-between',
+                alignItems: 'center',
+                marginBottom: 8,
+            } },
+            React.createElement(Typography, { variant: "subtitle1" },
+                "Cached BLAST Results (",
+                results.length,
+                ")"),
+            React.createElement(Button, { size: "small", color: "error", onClick: () => {
+                    // eslint-disable-next-line @typescript-eslint/no-floating-promises
+                    handleClearAll();
+                } }, "Clear All")),
+        React.createElement(List, { dense: true, style: { maxHeight: 300, overflow: 'auto' } }, results.map(result => (React.createElement(ListItem, { key: result.id, disablePadding: true, secondaryAction: React.createElement(IconButton, { edge: "end", size: "small", onClick: e => {
+                    e.stopPropagation();
+                    // eslint-disable-next-line @typescript-eslint/no-floating-promises
+                    handleDelete(result.id);
+                } },
+                React.createElement(DeleteIcon, { fontSize: "small" })) },
+            React.createElement(ListItemButton, { onClick: () => {
+                    handleUseCached(result);
+                } },
+                React.createElement(ListItemText, { primary: `${result.geneId ?? result.transcriptId ?? 'Unknown'} - ${result.blastDatabase}/${result.blastProgram} (${result.msaAlgorithm})`, secondary: `${new Date(result.timestamp).toLocaleString()} - Seq: ${result.proteinSequence.slice(0, 30)}...` }))))))));
+});
+export default CachedBlastResults;
+//# sourceMappingURL=CachedBlastResults.js.map

package/dist/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.js.map

@@ -0,0 +1 @@
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package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js

@@ -1,14 +1,17 @@
 import React, { useEffect, useState } from 'react';
 import { ErrorMessage } from '@jbrowse/core/ui';
 import { getContainingView, } from '@jbrowse/core/util';
-import { Button, DialogActions, DialogContent, MenuItem, Typography, } from '@mui/material';
+import ExpandMoreIcon from '@mui/icons-material/ExpandMore';
+import { Accordion, AccordionDetails, AccordionSummary, Button, DialogActions, DialogContent, MenuItem, Typography, } from '@mui/material';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
+import CachedBlastResults from './CachedBlastResults';
 import { blastLaunchView } from './blastLaunchView';
 import TextField2 from '../../../components/TextField2';
-import { getGeneDisplayName, getId, getTranscriptDisplayName, getTranscriptFeatures, } from '../../util';
+import { getAllCachedResults } from '../../../utils/blastCache';
+import { getGeneDisplayName, getTranscriptDisplayName } from '../../util';
 import TranscriptSelector from '../TranscriptSelector';
-import { useFeatureSequence } from '../useFeatureSequence';
+import { useTranscriptSelection } from '../useTranscriptSelection';
 const useStyles = makeStyles()({
     dialogContent: {
         width: '80em',
@@ -26,20 +29,31 @@ const NCBIBlastAutomaticPanel = observer(function ({ handleClose, feature, model
     const [launchViewError, setLaunchViewError] = useState();
     const [selectedBlastDatabase, setSelectedBlastDatabase] = useState('nr');
     const [selectedMsaAlgorithm, setSelectedMsaAlgorithm] = useState('clustalo');
-    const options = getTranscriptFeatures(feature);
-    const [selectedTranscriptId, setSelectedTranscriptId] = useState(getId(options[0]));
     const [selectedBlastProgram, setSelectedBlastProgram] = useState('quick-blastp');
-    const selectedTranscript = options.find(val => getId(val) === selectedTranscriptId);
-    const { error: proteinSequenceError, proteinSequence } = useFeatureSequence({
-        view,
-        feature: selectedTranscript,
-    });
+    const [hasCachedResults, setHasCachedResults] = useState(false);
+    const [error, setError] = useState();
+    const geneId = feature.get('id');
+    useEffect(() => {
+        // eslint-disable-next-line @typescript-eslint/no-floating-promises
+        ;
+        (async () => {
+            try {
+                const results = await getAllCachedResults();
+                setHasCachedResults(results.some(r => r.geneId === geneId));
+            }
+            catch (e) {
+                console.error(e);
+                setError(e);
+            }
+        })();
+    }, [geneId]);
+    const { options, setSelectedId, selectedTranscript, proteinSequence, error: proteinSequenceError, } = useTranscriptSelection({ feature, view });
     useEffect(() => {
         if (selectedBlastDatabase === 'nr_cluster_seq') {
             setSelectedBlastProgram('blastp');
         }
     }, [selectedBlastDatabase]);
-    const e = proteinSequenceError ?? launchViewError;
+    const e = proteinSequenceError ?? launchViewError ?? error;
     const style = { width: 150 };
     return (React.createElement(React.Fragment, null,
         React.createElement(DialogContent, { className: classes.dialogContent },
@@ -59,11 +73,19 @@ const NCBIBlastAutomaticPanel = observer(function ({ handleClose, feature, model
                         marginLeft: 4,
                         alignContent: 'center',
                     } }, "Can only use blastp on nr_cluster_seq")) : null),
-            React.createElement(TranscriptSelector, { feature: feature, options: options, selectedTranscriptId: selectedTranscriptId, onTranscriptChange: setSelectedTranscriptId, proteinSequence: proteinSequence }),
-            React.createElement(Typography, { style: { marginTop: 20 } }, "This panel will automatically submit a query to NCBI. Using blastp can take 10+ minutes to run, quick-blastp is generally a lot faster but is not available for the clustered database. After completion, all the hits will be run through a multiple sequence alignment. Note: we are not able to currently run NCBI COBALT automatically on the BLAST results, even though that is the method NCBI uses on their website. If you need a COBALT alignment, please use the manual approach of submitting BLAST yourself and downloading the resulting files")),
+            React.createElement(TranscriptSelector, { feature: feature, options: options, selectedTranscript: selectedTranscript, onTranscriptChange: setSelectedId, proteinSequence: proteinSequence }),
+            React.createElement(Typography, { style: { marginTop: 20 } }, "This panel will automatically submit a query to NCBI. Using blastp can take 10+ minutes to run, quick-blastp is generally a lot faster but is not available for the clustered database. After completion, all the hits will be run through a multiple sequence alignment. Note: we are not able to currently run NCBI COBALT automatically on the BLAST results, even though that is the method NCBI uses on their website. If you need a COBALT alignment, please use the manual approach of submitting BLAST yourself and downloading the resulting files"),
+            hasCachedResults ? (React.createElement(Accordion, { style: { marginTop: 20 } },
+                React.createElement(AccordionSummary, { expandIcon: React.createElement(ExpandMoreIcon, null) },
+                    React.createElement(Typography, null, "Previous BLAST Results")),
+                React.createElement(AccordionDetails, null,
+                    React.createElement(CachedBlastResults, { model: model, handleClose: handleClose, feature: feature })))) : null),
         React.createElement(DialogActions, null,
             React.createElement(Button, { color: "primary", variant: "contained", onClick: () => {
                     try {
+                        if (!selectedTranscript) {
+                            return;
+                        }
                         setLaunchViewError(undefined);
                         blastLaunchView({
                             feature: selectedTranscript,

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js.map

@@ -1 +1 @@
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+{"version":3,"file":"NCBIBlastAutomaticPanel.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAElD,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC/C,OAAO,EAGL,iBAAiB,GAClB,MAAM,oBAAoB,CAAA;AAC3B,OAAO,cAAc,MAAM,gCAAgC,CAAA;AAC3D,OAAO,EACL,SAAS,EACT,gBAAgB,EAChB,gBAAgB,EAChB,MAAM,EACN,aAAa,EACb,aAAa,EACb,QAAQ,EACR,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,kBAAkB,MAAM,sBAAsB,CAAA;AACrD,OAAO,EAAE,eAAe,EAAE,MAAM,mBAAmB,CAAA;AACnD,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,EAAE,mBAAmB,EAAE,MAAM,2BAA2B,CAAA;AAC/D,OAAO,EAAE,kBAAkB,EAAE,wBAAwB,EAAE,MAAM,YAAY,CAAA;AACzE,OAAO,kBAAkB,MAAM,uBAAuB,CAAA;AACtD,OAAO,EAAE,sBAAsB,EAAE,MAAM,2BAA2B,CAAA;AAIlE,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,aAAa,EAAE;QACb,KAAK,EAAE,MAAM;KACd;IACD,YAAY,EAAE;QACZ,UAAU,EAAE,aAAa;KAC1B;CACF,CAAC,CAAA;AAEF,MAAM,oBAAoB,GAAG,CAAC,IAAI,EAAE,gBAAgB,CAAU,CAAA;AAC9D,MAAM,aAAa,GAAG,CAAC,UAAU,EAAE,QAAQ,EAAE,QAAQ,EAAE,OAAO,CAAU,CAAA;AACxE,MAAM,aAAa,GAAG,CAAC,QAAQ,EAAE,cAAc,CAAU,CAAA;AAMzD,MAAM,uBAAuB,GAAG,QAAQ,CAAC,UAAU,EACjD,WAAW,EACX,OAAO,EACP,KAAK,EACL,QAAQ,EACR,OAAO,GAOR;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,IAAI,GAAG,iBAAiB,CAAC,KAAK,CAA0B,CAAA;IAC9D,MAAM,CAAC,eAAe,EAAE,kBAAkB,CAAC,GAAG,QAAQ,EAAW,CAAA;IACjE,MAAM,CAAC,qBAAqB,EAAE,wBAAwB,CAAC,GACrD,QAAQ,CAAwB,IAAI,CAAC,CAAA;IACvC,MAAM,CAAC,oBAAoB,EAAE,uBAAuB,CAAC,GACnD,QAAQ,CAAiB,UAAU,CAAC,CAAA;IACtC,MAAM,CAAC,oBAAoB,EAAE,uBAAuB,CAAC,GACnD,QAAQ,CAAiB,cAAc,CAAC,CAAA;IAC1C,MAAM,CAAC,gBAAgB,EAAE,mBAAmB,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAC/D,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAAW,CAAA;IAE7C,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,CAAA;IAChC,SAAS,CAAC,GAAG,EAAE;QACb,mEAAmE;QACnE,CAAC;QAAA,CAAC,KAAK,IAAI,EAAE;YACX,IAAI,CAAC;gBACH,MAAM,OAAO,GAAG,MAAM,mBAAmB,EAAE,CAAA;gBAC3C,mBAAmB,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,KAAK,MAAM,CAAC,CAAC,CAAA;YAC7D,CAAC;YAAC,OAAO,CAAC,EAAE,CAAC;gBACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;gBAChB,QAAQ,CAAC,CAAC,CAAC,CAAA;YACb,CAAC;QACH,CAAC,CAAC,EAAE,CAAA;IACN,CAAC,EAAE,CAAC,MAAM,CAAC,CAAC,CAAA;IAEZ,MAAM,EACJ,OAAO,EACP,aAAa,EACb,kBAAkB,EAClB,eAAe,EACf,KAAK,EAAE,oBAAoB,GAC5B,GAAG,sBAAsB,CAAC,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC,CAAA;IAE7C,SAAS,CAAC,GAAG,EAAE;QACb,IAAI,qBAAqB,KAAK,gBAAgB,EAAE,CAAC;YAC/C,uBAAuB,CAAC,QAAQ,CAAC,CAAA;QACnC,CAAC;IACH,CAAC,EAAE,CAAC,qBAAqB,CAAC,CAAC,CAAA;IAC3B,MAAM,CAAC,GAAG,oBAAoB,IAAI,eAAe,IAAI,KAAK,CAAA;IAC1D,MAAM,KAAK,GAAG,EAAE,KAAK,EAAE,GAAG,EAAE,CAAA;IAC5B,OAAO,CACL;QACE,oBAAC,aAAa,IAAC,SAAS,EAAE,OAAO,CAAC,aAAa;YAC5C,QAAQ;YACR,CAAC,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,CAAC,GAAI,CAAC,CAAC,CAAC,IAAI;YACtC,oBAAC,UAAU,IACT,OAAO,EAAC,UAAU,EAClB,KAAK,EAAC,gBAAgB,EACtB,KAAK,EAAE,KAAK,EACZ,MAAM,QACN,KAAK,EAAE,qBAAqB,EAC5B,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,wBAAwB,CACtB,KAAK,CAAC,MAAM,CAAC,KAA8C,CAC5D,CAAA;gBACH,CAAC,IAEA,oBAAoB,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CAC/B,oBAAC,QAAQ,IAAC,KAAK,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,IAC3B,GAAG,CACK,CACZ,CAAC,CACS;YAEb,oBAAC,UAAU,IACT,OAAO,EAAC,UAAU,EAClB,KAAK,EAAC,eAAe,EACrB,KAAK,EAAE,KAAK,EACZ,MAAM,QACN,KAAK,EAAE,oBAAoB,EAC3B,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,uBAAuB,CACrB,KAAK,CAAC,MAAM,CAAC,KAAuC,CACrD,CAAA;gBACH,CAAC,IAEA,aAAa,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CACxB,oBAAC,QAAQ,IAAC,KAAK,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,IAC3B,GAAG,CACK,CACZ,CAAC,CACS;YAEb,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;gBAC7B,oBAAC,UAAU,IACT,OAAO,EAAC,UAAU,EAClB,KAAK,EAAC,eAAe,EACrB,QAAQ,EAAE,qBAAqB,KAAK,gBAAgB,EACpD,KAAK,EAAE,KAAK,EACZ,MAAM,QACN,KAAK,EAAE,oBAAoB,EAC3B,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,uBAAuB,CACrB,KAAK,CAAC,MAAM,CAAC,KAAuC,CACrD,CAAA;oBACH,CAAC,IAEA,aAAa,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CACxB,oBAAC,QAAQ,IAAC,KAAK,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,IAC3B,GAAG,CACK,CACZ,CAAC,CACS;gBACZ,qBAAqB,KAAK,gBAAgB,CAAC,CAAC,CAAC,CAC5C,oBAAC,UAAU,IACT,OAAO,EAAC,WAAW,EACnB,KAAK,EAAE;wBACL,UAAU,EAAE,CAAC;wBACb,YAAY,EAAE,QAAQ;qBACvB,4CAGU,CACd,CAAC,CAAC,CAAC,IAAI,CACJ;YAEN,oBAAC,kBAAkB,IACjB,OAAO,EAAE,OAAO,EAChB,OAAO,EAAE,OAAO,EAChB,kBAAkB,EAAE,kBAAkB,EACtC,kBAAkB,EAAE,aAAa,EACjC,eAAe,EAAE,eAAe,GAChC;YAEF,oBAAC,UAAU,IAAC,KAAK,EAAE,EAAE,SAAS,EAAE,EAAE,EAAE,kiBASvB;YAEZ,gBAAgB,CAAC,CAAC,CAAC,CAClB,oBAAC,SAAS,IAAC,KAAK,EAAE,EAAE,SAAS,EAAE,EAAE,EAAE;gBACjC,oBAAC,gBAAgB,IAAC,UAAU,EAAE,oBAAC,cAAc,OAAG;oBAC9C,oBAAC,UAAU,iCAAoC,CAC9B;gBACnB,oBAAC,gBAAgB;oBACf,oBAAC,kBAAkB,IACjB,KAAK,EAAE,KAAK,EACZ,WAAW,EAAE,WAAW,EACxB,OAAO,EAAE,OAAO,GAChB,CACe,CACT,CACb,CAAC,CAAC,CAAC,IAAI,CACM;QAChB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,KAAK,EAAC,SAAS,EACf,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;oBACZ,IAAI,CAAC;wBACH,IAAI,CAAC,kBAAkB,EAAE,CAAC;4BACxB,OAAM;wBACR,CAAC;wBACD,kBAAkB,CAAC,SAAS,CAAC,CAAA;wBAC7B,eAAe,CAAC;4BACd,OAAO,EAAE,kBAAkB;4BAC3B,IAAI;4BACJ,YAAY,EAAE,WAAW,kBAAkB,CAAC,OAAO,CAAC,MAAM,wBAAwB,CAAC,kBAAkB,CAAC,EAAE;4BACxG,WAAW,EAAE;gCACX,OAAO;gCACP,YAAY,EAAE,oBAAoB;gCAClC,aAAa,EAAE,qBAAqB;gCACpC,YAAY,EAAE,oB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package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.js

@@ -1,13 +1,13 @@
-import React, { useState } from 'react';
+import React from 'react';
 import { ErrorMessage } from '@jbrowse/core/ui';
 import { getContainingView, shorten2 } from '@jbrowse/core/util';
 import { Button, DialogActions, DialogContent, Typography } from '@mui/material';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
 import ExternalLink from '../../../components/ExternalLink';
-import { getId, getTranscriptFeatures } from '../../util';
+import { cleanProteinSequence } from '../../util';
 import TranscriptSelector from '../TranscriptSelector';
-import { useFeatureSequence } from '../useFeatureSequence';
+import { useTranscriptSelection } from '../useTranscriptSelection';
 const useStyles = makeStyles()({
     dialogContent: {
         width: '80em',
@@ -24,21 +24,15 @@ const useStyles = makeStyles()({
 const NCBIBlastManualPanel = observer(function ({ handleClose, feature, model, children, baseUrl, }) {
     const { classes } = useStyles();
     const view = getContainingView(model);
-    const options = getTranscriptFeatures(feature);
-    const [userSelection, setUserSelection] = useState(getId(options[0]));
-    const selectedTranscript = options.find(val => getId(val) === userSelection);
-    const { proteinSequence, error } = useFeatureSequence({
-        view,
-        feature: selectedTranscript,
-    });
-    const s2 = proteinSequence.replaceAll('*', '').replaceAll('&', '');
+    const { options, setSelectedId, selectedTranscript, proteinSequence, error } = useTranscriptSelection({ feature, view });
+    const s2 = cleanProteinSequence(proteinSequence);
     const link = `${baseUrl}?PAGE_TYPE=BlastSearch&PAGE=Proteins&PROGRAM=blastp&QUERY=${s2}`;
     const link2 = `${baseUrl}?PAGE_TYPE=BlastSearch&PAGE=Proteins&PROGRAM=blastp&QUERY=${shorten2(s2, 10)}`;
     return (React.createElement(React.Fragment, null,
         React.createElement(DialogContent, { className: classes.dialogContent },
             children,
             error ? React.createElement(ErrorMessage, { error: error }) : null,
-            React.createElement(TranscriptSelector, { feature: feature, options: options, selectedTranscriptId: userSelection, onTranscriptChange: setUserSelection, proteinSequence: proteinSequence }),
+            React.createElement(TranscriptSelector, { feature: feature, options: options, selectedTranscript: selectedTranscript, onTranscriptChange: setSelectedId, proteinSequence: proteinSequence }),
             proteinSequence ? (React.createElement("div", { className: classes.ncbiLink },
                 "Link to NCBI BLAST: ",
                 React.createElement(ExternalLink, { href: link }, link2))) : null,

package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.js.map

@@ -1 +1 @@
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package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.d.ts

@@ -1,5 +1,6 @@
 import { Feature } from '@jbrowse/core/util';
 import type { JBrowsePluginMsaViewModel } from '../../../MsaViewPanel/model';
+import type { CachedBlastResult } from '../../../utils/blastCache';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 export declare function blastLaunchView({ newViewTitle, view, feature, blastParams, }: {
     newViewTitle: string;
@@ -7,3 +8,8 @@ export declare function blastLaunchView({ newViewTitle, view, feature, blastPara
     feature: Feature;
     blastParams: Record<string, unknown>;
 }): JBrowsePluginMsaViewModel;
+export declare function blastLaunchViewFromCache({ newViewTitle, view, cached, }: {
+    newViewTitle: string;
+    view: LinearGenomeViewModel;
+    cached: CachedBlastResult;
+}): JBrowsePluginMsaViewModel;

package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.js

@@ -11,4 +11,19 @@ export function blastLaunchView({ newViewTitle, view, feature, blastParams, }) {
         blastParams,
     });
 }
+export function blastLaunchViewFromCache({ newViewTitle, view, cached, }) {
+    return getSession(view).addView('MsaView', {
+        type: 'MsaView',
+        displayName: newViewTitle,
+        connectedViewId: view.id,
+        drawNodeBubbles: true,
+        colWidth: 10,
+        rowHeight: 12,
+        data: {
+            msa: cached.msa,
+            tree: cached.tree,
+            treeMetadata: cached.treeMetadata,
+        },
+    });
+}
 //# sourceMappingURL=blastLaunchView.js.map

package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.js.map

@@ -1 +1 @@
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+{"version":3,"file":"blastLaunchView.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.ts"],"names":[],"mappings":"AAAA,OAAO,EAAW,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAMxD,MAAM,UAAU,eAAe,CAAC,EAC9B,YAAY,EACZ,IAAI,EACJ,OAAO,EACP,WAAW,GAMZ;IACC,OAAO,UAAU,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,SAAS,EAAE;QACzC,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,YAAY;QACzB,eAAe,EAAE,IAAI,CAAC,EAAE;QACxB,gBAAgB,EAAE,OAAO,CAAC,MAAM,EAAE;QAClC,eAAe,EAAE,IAAI;QACrB,QAAQ,EAAE,EAAE;QACZ,SAAS,EAAE,EAAE;QACb,WAAW;KACZ,CAA8B,CAAA;AACjC,CAAC;AAED,MAAM,UAAU,wBAAwB,CAAC,EACvC,YAAY,EACZ,IAAI,EACJ,MAAM,GAKP;IACC,OAAO,UAAU,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,SAAS,EAAE;QACzC,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,YAAY;QACzB,eAAe,EAAE,IAAI,CAAC,EAAE;QACxB,eAAe,EAAE,IAAI;QACrB,QAAQ,EAAE,EAAE;QACZ,SAAS,EAAE,EAAE;QACb,IAAI,EAAE;YACJ,GAAG,EAAE,MAAM,CAAC,GAAG;YACf,IAAI,EAAE,MAAM,CAAC,IAAI;YACjB,YAAY,EAAE,MAAM,CAAC,YAAY;SAClC;KACF,CAA8B,CAAA;AACjC,CAAC"}

package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js

@@ -1,4 +1,4 @@
-import React, { useEffect, useMemo, useState } from 'react';
+import React, { useState } from 'react';
 import { readConfObject } from '@jbrowse/core/configuration';
 import { ErrorMessage, LoadingEllipses, SanitizedHTML } from '@jbrowse/core/ui';
 import { getContainingView, getEnv, getSession, } from '@jbrowse/core/util';
@@ -7,12 +7,11 @@ import { observer } from 'mobx-react';
 import useSWR from 'swr';
 import { makeStyles } from 'tss-react/mui';
 import TextField2 from '../../../components/TextField2';
-import { getGeneDisplayName, getId, getTranscriptFeatures } from '../../util';
+import { getGeneDisplayName } from '../../util';
 import TranscriptSelector from '../TranscriptSelector';
-import { useFeatureSequence } from '../useFeatureSequence';
+import { useTranscriptSelection } from '../useTranscriptSelection';
 import { swrFlags } from './consts';
 import { fetchMSA, fetchMSAList } from './fetchMSAData';
-import { findValidTranscriptId } from './findValidTranscriptId';
 import { preCalculatedLaunchView } from './preCalculatedLaunchView';
 const useStyles = makeStyles()({
     dialogContent: {
@@ -25,16 +24,7 @@ const PreLoadedMSA = observer(function PreLoadedMSA2({ model, feature, handleClo
     const { classes } = useStyles();
     const { pluginManager } = getEnv(model);
     const { assemblyNames } = view;
-    const transcripts = getTranscriptFeatures(feature);
-    const [selectedTranscriptId, setSelectedTranscriptId] = useState(getId(transcripts[0]));
     const [viewError, setViewError] = useState();
-    const selectedTranscript = selectedTranscriptId
-        ? transcripts.find(val => getId(val) === selectedTranscriptId)
-        : undefined;
-    const { proteinSequence, error: proteinSequenceError } = useFeatureSequence({
-        view,
-        feature: selectedTranscript,
-    });
     const { jbrowse } = session;
     const datasets = readConfObject(jbrowse, ['msa', 'datasets']);
     const [selectedDatasetId, setSelectedDatasetId] = useState(datasets?.[0]?.datasetId);
@@ -45,28 +35,16 @@ const PreLoadedMSA = observer(function PreLoadedMSA2({ model, feature, handleClo
             pluginManager,
         })
         : undefined, swrFlags);
-    const { data: msaData, isLoading: msaDataLoading, error: msaDataFetchError, } = useSWR(selectedTranscriptId && selectedDatasetId
-        ? `${selectedTranscriptId}-${selectedTranscriptId}-${msaList?.length}-msa`
-        : 'none-msa', () => selectedTranscriptId && selectedDataset && msaList
+    const { options: transcripts, selectedId, setSelectedId, selectedTranscript, proteinSequence, error: proteinSequenceError, validSet, } = useTranscriptSelection({ feature, view, validIds: msaList });
+    const { data: msaData, isLoading: msaDataLoading, error: msaDataFetchError, } = useSWR(selectedId && selectedDatasetId
+        ? `${selectedId}-${selectedId}-${msaList?.length}-msa`
+        : 'none-msa', () => selectedId && selectedDataset && msaList
         ? fetchMSA({
-            msaId: selectedTranscriptId,
+            msaId: selectedId,
             config: selectedDataset.adapter,
             pluginManager,
         })
         : undefined, swrFlags);
-    const validSet = useMemo(() => new Set(msaList), [msaList]);
-    // Update selectedTranscriptId when msaList changes
-    useEffect(() => {
-        if (msaList && msaList.length > 0) {
-            const validId = findValidTranscriptId({
-                transcriptsList: transcripts,
-                validMsaList: msaList,
-            });
-            if (validId && validId !== selectedTranscriptId) {
-                setSelectedTranscriptId(validId);
-            }
-        }
-    }, [msaList, transcripts, selectedTranscriptId]);
     const e = msaListFetchError ?? msaDataFetchError ?? proteinSequenceError ?? viewError;
     if (e) {
         console.error(e);
@@ -76,20 +54,20 @@ const PreLoadedMSA = observer(function PreLoadedMSA2({ model, feature, handleClo
             e ? React.createElement(ErrorMessage, { error: e }) : null,
             React.createElement(TextField2, { select: true, label: "Select MSA dataset", value: selectedDatasetId, onChange: event => {
                     setSelectedDatasetId(event.target.value);
-                } }, datasets && datasets.length > 0 ? (datasets.map(d => (React.createElement(MenuItem, { key: d.datasetId, value: d.datasetId }, d.name)))) : (React.createElement(MenuItem, null, "No MSA datasets found"))),
+                } }, datasets?.map(d => (React.createElement(MenuItem, { key: d.datasetId, value: d.datasetId }, d.name)))),
             selectedDataset ? (React.createElement("div", { style: { marginTop: 50 } },
-                !msaListLoading && msaDataLoading ? (React.createElement(LoadingEllipses, { variant: "h6", message: `Loading MSA for (${selectedTranscriptId})` })) : null,
+                !msaListLoading && msaDataLoading ? (React.createElement(LoadingEllipses, { variant: "h6", message: `Loading MSA for (${selectedId})` })) : null,
                 msaListLoading ? (React.createElement(LoadingEllipses, { variant: "h6", message: `Loading available MSAs for (${selectedDataset.name})` })) : null,
                 msaList ? (React.createElement("div", null,
                     React.createElement(SanitizedHTML, { html: selectedDataset.description }),
-                    React.createElement(TranscriptSelector, { feature: feature, options: transcripts, selectedTranscriptId: selectedTranscriptId, onTranscriptChange: setSelectedTranscriptId, proteinSequence: proteinSequence, validSet: validSet }))) : null)) : null),
+                    React.createElement(TranscriptSelector, { feature: feature, options: transcripts, selectedTranscript: selectedTranscript, onTranscriptChange: setSelectedId, proteinSequence: proteinSequence, validSet: validSet }))) : null)) : null),
         React.createElement(DialogActions, null,
             React.createElement(Button, { color: "primary", variant: "contained", disabled: !selectedTranscript || !msaData?.length, onClick: () => {
                     try {
                         if (!selectedTranscript || !msaData) {
                             return;
                         }
-                        const querySeqName = `${selectedTranscriptId}_${assemblyNames[0]}`;
+                        const querySeqName = `${selectedId}_${assemblyNames[0]}`;
                         preCalculatedLaunchView({
                             session,
                             newViewTitle: getGeneDisplayName(selectedTranscript),