jbrowse-plugin-protein3d 0.4.11 → 0.4.13

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

@@ -0,0 +1,5 @@
+import React from 'react';
+export default function LaunchSettingsDialog({ open, onClose, }: {
+    open: boolean;
+    onClose: () => void;
+}): React.JSX.Element;

package/dist/LaunchProteinView/components/LaunchSettingsDialog.js

@@ -0,0 +1,23 @@
+import React, { useState } from 'react';
+import { Button, Checkbox, Dialog, DialogActions, DialogContent, DialogTitle, FormControlLabel, FormGroup, Typography, } from '@mui/material';
+import { getLaunchSideBySide, setLaunchSideBySide } from '../utils/sideBySide';
+// Small, self-contained launch settings (NOT the global preferences dialog):
+// just the options that affect how this protein view opens.
+export default function LaunchSettingsDialog({ open, onClose, }) {
+    const [sideBySide, setSideBySide] = useState(() => getLaunchSideBySide());
+    return (React.createElement(Dialog, { open: open, onClose: () => {
+            onClose();
+        } },
+        React.createElement(DialogTitle, null, "Launch settings"),
+        React.createElement(DialogContent, null,
+            React.createElement(FormGroup, null,
+                React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: sideBySide }), label: "Open protein view side-by-side with the genome view", onChange: (_, checked) => {
+                        setSideBySide(checked);
+                        setLaunchSideBySide(checked);
+                    } })),
+            React.createElement(Typography, { variant: "body2", color: "text.secondary" }, "When enabled, launching a protein view places it to the right of the connected genome view in a split layout instead of stacking it below.")),
+        React.createElement(DialogActions, null,
+            React.createElement(Button, { variant: "contained", onClick: () => {
+                    onClose();
+                } }, "Close"))));
+}

package/dist/LaunchProteinView/components/ProteinViewActions.js

@@ -1,13 +1,16 @@
 import React, { useState } from 'react';
 import { ErrorMessage } from '@jbrowse/core/ui';
 import ArrowDropDownIcon from '@mui/icons-material/ArrowDropDown';
-import { Button, ButtonGroup, Typography } from '@mui/material';
+import SettingsIcon from '@mui/icons-material/Settings';
+import { Button, ButtonGroup, IconButton, Tooltip, Typography } from '@mui/material';
 import LaunchOptionsDialog from './LaunchOptionsDialog';
+import LaunchSettingsDialog from './LaunchSettingsDialog';
 import SequenceMismatchNotice from './SequenceMismatchNotice';
 import { getLaunchMissingReasons, safeLaunch } from '../utils/launchHelpers';
 import { hasMsaViewPlugin, launch1DProteinView, launch3DProteinView, launch3DProteinViewWithMsa, launchMsaView, } from '../utils/launchViewUtils';
 export default function ProteinViewActions({ handleClose, uniprotId, userSelectedProteinSequence, selectedTranscript, url, confidenceUrl, feature, view, session, alignmentAlgorithm, onAlignmentAlgorithmChange, sequencesMatch, isLoading, error, }) {
     const [dialogOpen, setDialogOpen] = useState(false);
+    const [settingsOpen, setSettingsOpen] = useState(false);
     const [launchError, setLaunchError] = useState();
     // Disable launch while loading — SWR's keepPreviousData would otherwise let
     // a user click Launch on stale results (wrong UniProt ID) during a refetch.
@@ -87,6 +90,11 @@ export default function ProteinViewActions({ handleClose, uniprotId, userSelecte
     return (React.createElement(React.Fragment, null,
         launchError ? React.createElement(ErrorMessage, { error: launchError }) : null,
         sequencesMatch === false ? (React.createElement(SequenceMismatchNotice, { alignmentAlgorithm: alignmentAlgorithm, onAlignmentAlgorithmChange: onAlignmentAlgorithmChange })) : null,
+        React.createElement(Tooltip, { title: "Launch settings" },
+            React.createElement(IconButton, { size: "small", "aria-label": "Launch settings", onClick: () => {
+                    setSettingsOpen(true);
+                } },
+                React.createElement(SettingsIcon, { fontSize: "small" }))),
         React.createElement(Button, { variant: "contained", color: "secondary", size: "small", onClick: () => {
                 handleClose();
             } }, "Cancel"),
@@ -97,5 +105,8 @@ export default function ProteinViewActions({ handleClose, uniprotId, userSelecte
                     setDialogOpen(true);
                 }, "aria-label": "More launch options" },
                 React.createElement(ArrowDropDownIcon, null))),
-        React.createElement(LaunchOptionsDialog, { open: dialogOpen, onClose: closeMenu, options: launchOptions })));
+        React.createElement(LaunchOptionsDialog, { open: dialogOpen, onClose: closeMenu, options: launchOptions }),
+        React.createElement(LaunchSettingsDialog, { open: settingsOpen, onClose: () => {
+                setSettingsOpen(false);
+            } })));
 }

package/dist/LaunchProteinView/hooks/useAlphaFoldDBSearch.js

@@ -35,7 +35,7 @@ export default function useAlphaFoldDBSearch({ feature, view, }) {
             : effectiveLookupMode === 'manual'
                 ? debouncedManualUniprotId
                 : undefined;
-    const { isLoading: isAlphaFoldLoading, error: alphaFoldError, url: alphaFoldUrl, confidenceUrl: alphaFoldConfidenceUrl, structureSequence: alphaFoldStructureSequence, } = useAlphaFoldData({
+    const { isLoading: isAlphaFoldLoading, isValidating: isAlphaFoldValidating, error: alphaFoldError, url: alphaFoldUrl, confidenceUrl: alphaFoldConfidenceUrl, structureSequence: alphaFoldStructureSequence, } = useAlphaFoldData({
         uniprotId: isSequenceMode ? undefined : uniprotId,
     });
     const { transcripts: transcriptOptions, isoformSequences, isLoading: isIsoformLoading, error: isoformError, selectedTranscriptId: effectiveTranscriptId, setSelectedTranscriptId: setUserSelection, selectedTranscript, selectedIsoform: userSelectedProteinSequence, } = useTranscriptIsoformSelection({
@@ -44,7 +44,7 @@ export default function useAlphaFoldDBSearch({ feature, view, }) {
         structureSequence: alphaFoldStructureSequence,
         resetKey: uniprotId,
     });
-    const { uniprotId: seqSearchUniprotId, cifUrl: seqSearchUrl, plddtDocUrl: seqSearchConfidenceUrl, structureSequence: seqSearchStructureSequence, isLoading: isSequenceSearchLoading, error: sequenceSearchError, } = useAlphaFoldSequenceSearch({
+    const { uniprotId: seqSearchUniprotId, cifUrl: seqSearchUrl, plddtDocUrl: seqSearchConfidenceUrl, structureSequence: seqSearchStructureSequence, isLoading: isSequenceSearchLoading, isValidating: isSequenceSearchValidating, error: sequenceSearchError, } = useAlphaFoldSequenceSearch({
         sequence: userSelectedProteinSequence?.seq,
         searchType: sequenceSearchType,
         enabled: isSequenceMode,
@@ -58,6 +58,13 @@ export default function useAlphaFoldDBSearch({ feature, view, }) {
         ? seqSearchStructureSequence
         : alphaFoldStructureSequence;
     const finalUniprotId = isSequenceMode ? seqSearchUniprotId : uniprotId;
+    // While a structure fetch is in flight, finalStructureSequence may still be
+    // the previous selection's sequence (keepPreviousData). Comparing that stale
+    // sequence to the freshly-selected transcript would give a wrong match, so
+    // the match is treated as unknown until the fetch settles.
+    const isStructureValidating = isSequenceMode
+        ? isSequenceSearchValidating
+        : isAlphaFoldValidating;
     const loadingStatuses = [
         isLookupLoading && 'Looking up UniProt ID',
         isIsoformLoading && 'Loading protein sequences from transcript isoforms',
@@ -104,7 +111,9 @@ export default function useAlphaFoldDBSearch({ feature, view, }) {
         showStructureSelectors: !!isoformSequences &&
             !!selectedTranscript &&
             (isSequenceMode || !!(finalStructureSequence && finalUniprotId)),
-        sequencesMatch: userSelectedProteinSequence?.seq && finalStructureSequence
+        sequencesMatch: !isStructureValidating &&
+            userSelectedProteinSequence?.seq &&
+            finalStructureSequence
             ? stripStopCodon(userSelectedProteinSequence.seq) ===
                 finalStructureSequence
             : undefined,

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

@@ -2,6 +2,7 @@ export default function useAlphaFoldData({ uniprotId, }: {
     uniprotId?: string;
 }): {
     isLoading: boolean;
+    isValidating: boolean;
     error: any;
     url: string | undefined;
     confidenceUrl: string | undefined;

package/dist/LaunchProteinView/hooks/useAlphaFoldData.js

@@ -5,9 +5,10 @@ export default function useAlphaFoldData({ uniprotId, }) {
     const confidenceUrl = uniprotId
         ? getAlphaFoldConfidenceUrl(uniprotId)
         : undefined;
-    const { sequences, isLoading, error } = useStructureFileSequence({ url });
+    const { sequences, isLoading, isValidating, error } = useStructureFileSequence({ url });
     return {
         isLoading,
+        isValidating,
         error,
         url,
         confidenceUrl,

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

@@ -19,6 +19,7 @@ export default function useAlphaFoldSequenceSearch({ sequence, searchType, enabl
     enabled?: boolean;
 }): {
     isLoading: boolean;
+    isValidating: boolean;
     result: SequenceSummaryResponse | undefined;
     uniprotId: string | undefined;
     cifUrl: string | undefined;

package/dist/LaunchProteinView/hooks/useAlphaFoldSequenceSearch.js

@@ -12,7 +12,7 @@ export default function useAlphaFoldSequenceSearch({ sequence, searchType, enabl
         const cleanSeq = stripStopCodon(sequence.toUpperCase());
         return searchType === 'md5' ? md5(cleanSeq) : cleanSeq;
     }, [sequence, searchType]);
-    const { data, error, isLoading } = useSWR(enabled && searchValue
+    const { data, error, isLoading, isValidating } = useSWR(enabled && searchValue
         ? `https://alphafold.ebi.ac.uk/api/sequence/summary?id=${encodeURIComponent(searchValue)}&type=${searchType}`
         : null, jsonfetch, {
         ...STATIC_SWR_OPTIONS,
@@ -20,6 +20,7 @@ export default function useAlphaFoldSequenceSearch({ sequence, searchType, enabl
     });
     return {
         isLoading,
+        isValidating,
         result: data,
         uniprotId: data?.uniprotAccession,
         cifUrl: data?.cifUrl,

package/dist/LaunchProteinView/hooks/useFoldseekSearch.js

@@ -1,4 +1,4 @@
-import { useState } from 'react';
+import { useEffect, useRef, useState } from 'react';
 import { DEFAULT_DATABASES, predict3Di, submitFoldseekSearch, waitForFoldseekResults, } from '../services/foldseekApi';
 export default function useFoldseekSearch() {
     const [results, setResults] = useState();
@@ -7,46 +7,81 @@ export default function useFoldseekSearch() {
     const [isPredicting, setIsPredicting] = useState(false);
     const [error, setError] = useState();
     const [statusMessage, setStatusMessage] = useState('');
+    // Aborts the in-flight request (3Di prediction or the up-to-3-minute Foldseek
+    // poll) when the dialog closes/unmounts, so it stops hitting the external API
+    // and stops updating dead state.
+    const abortRef = useRef(null);
+    useEffect(() => {
+        return () => {
+            abortRef.current?.abort();
+        };
+    }, []);
+    const startOperation = () => {
+        abortRef.current?.abort();
+        const controller = new AbortController();
+        abortRef.current = controller;
+        return controller.signal;
+    };
     const predictStructure = async (aaSequence) => {
+        const signal = startOperation();
         setIsPredicting(true);
         setError(undefined);
         setStatusMessage('Predicting 3Di structure...');
         try {
-            const result = await predict3Di(aaSequence);
+            const result = await predict3Di({ aaSequence, signal });
             setPredictData(result);
             return result;
         }
         catch (e) {
-            console.error(e);
-            setError(e);
+            if (!signal.aborted) {
+                console.error(e);
+                setError(e);
+            }
             return undefined;
         }
         finally {
-            setIsPredicting(false);
-            setStatusMessage('');
+            if (!signal.aborted) {
+                setIsPredicting(false);
+                setStatusMessage('');
+            }
         }
     };
     const search = async (aaSeq, di3Seq, databases = DEFAULT_DATABASES) => {
+        const signal = startOperation();
         setIsLoading(true);
         setError(undefined);
         setStatusMessage('Submitting search...');
         try {
-            const ticket = await submitFoldseekSearch(aaSeq, di3Seq, databases);
-            const result = await waitForFoldseekResults(ticket.id, setStatusMessage);
+            const ticket = await submitFoldseekSearch({
+                aaSequence: aaSeq,
+                di3Sequence: di3Seq,
+                databases,
+                signal,
+            });
+            const result = await waitForFoldseekResults({
+                ticketId: ticket.id,
+                onStatusChange: setStatusMessage,
+                signal,
+            });
             setResults(result);
             return result;
         }
         catch (e) {
-            console.error(e);
-            setError(e);
+            if (!signal.aborted) {
+                console.error(e);
+                setError(e);
+            }
             return undefined;
         }
         finally {
-            setIsLoading(false);
-            setStatusMessage('');
+            if (!signal.aborted) {
+                setIsLoading(false);
+                setStatusMessage('');
+            }
         }
     };
     const reset = () => {
+        abortRef.current?.abort();
         setResults(undefined);
         setPredictData(undefined);
         setError(undefined);

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

@@ -4,5 +4,6 @@ export default function useStructureFileSequence({ file, url, }: {
 }): {
     error: any;
     isLoading: boolean;
+    isValidating: boolean;
     sequences: string[] | undefined;
 };

package/dist/LaunchProteinView/hooks/useStructureFileSequence.js

@@ -33,7 +33,7 @@ export default function useStructureFileSequence({ file, url, }) {
         : url
             ? ['structure-url', url]
             : null;
-    const { data, error, isLoading } = useSWR(key, async () => {
+    const { data, error, isLoading, isValidating } = useSWR(key, async () => {
         const seq = await fetchSequences({ file, url });
         if (!seq) {
             throw new Error('no sequences detected in file');
@@ -43,5 +43,8 @@ export default function useStructureFileSequence({ file, url, }) {
         ...STATIC_SWR_OPTIONS,
         keepPreviousData: true,
     });
-    return { error, isLoading, sequences: data };
+    // isValidating distinguishes "fetching for the current key" from the stale
+    // data keepPreviousData keeps around during a key change. Consumers comparing
+    // this sequence against another need it to avoid matching against stale data.
+    return { error, isLoading, isValidating, sequences: data };
 }

package/dist/LaunchProteinView/services/foldseekApi.d.ts

@@ -64,12 +64,23 @@ export interface FoldseekResult {
     };
     results: FoldseekDatabaseResult[];
 }
-export declare function predict3Di(aaSequence: string): Promise<{
+export declare function predict3Di({ aaSequence, signal, }: {
+    aaSequence: string;
+    signal?: AbortSignal;
+}): Promise<{
     aaSequence: string;
     di3Sequence: string;
 }>;
-export declare function submitFoldseekSearch(aaSequence: string, di3Sequence: string, databases: FoldseekDatabaseId[]): Promise<FoldseekTicketResponse>;
-export declare function pollFoldseekStatus(ticketId: string): Promise<FoldseekTicketResponse>;
+export declare function submitFoldseekSearch({ aaSequence, di3Sequence, databases, signal, }: {
+    aaSequence: string;
+    di3Sequence: string;
+    databases: FoldseekDatabaseId[];
+    signal?: AbortSignal;
+}): Promise<FoldseekTicketResponse>;
+export declare function pollFoldseekStatus({ ticketId, signal, }: {
+    ticketId: string;
+    signal?: AbortSignal;
+}): Promise<FoldseekTicketResponse>;
 interface FoldseekApiResponse {
     mode: string;
     queries: {
@@ -82,6 +93,13 @@ interface FoldseekApiResponse {
         taxonomyreports: unknown[];
     }[];
 }
-export declare function getFoldseekResults(ticketId: string): Promise<FoldseekApiResponse>;
-export declare function waitForFoldseekResults(ticketId: string, onStatusChange?: (status: string) => void): Promise<FoldseekResult>;
+export declare function getFoldseekResults({ ticketId, signal, }: {
+    ticketId: string;
+    signal?: AbortSignal;
+}): Promise<FoldseekApiResponse>;
+export declare function waitForFoldseekResults({ ticketId, onStatusChange, signal, }: {
+    ticketId: string;
+    onStatusChange?: (status: string) => void;
+    signal?: AbortSignal;
+}): Promise<FoldseekResult>;
 export {};

package/dist/LaunchProteinView/services/foldseekApi.js

@@ -13,7 +13,7 @@ export const DEFAULT_DATABASES = [
     'pdb100',
     'afdb-swissprot',
 ];
-export async function predict3Di(aaSequence) {
+export async function predict3Di({ aaSequence, signal, }) {
     // Clean the sequence - remove FASTA header, whitespace, stop codons, and non-AA chars
     const cleanSequence = aaSequence
         .split('\n')
@@ -23,7 +23,7 @@ export async function predict3Di(aaSequence) {
         .replace(/\*/g, '') // Remove stop codons before querying 3Di
         .toUpperCase()
         .replace(/[^ACDEFGHIKLMNPQRSTVWY]/g, ''); // Keep only valid amino acids
-    const response = await fetch(`https://3di.foldseek.com/predict/${encodeURIComponent(cleanSequence)}`);
+    const response = await fetch(`https://3di.foldseek.com/predict/${encodeURIComponent(cleanSequence)}`, { signal });
     if (!response.ok) {
         throw new Error(`3Di prediction failed: ${response.status} ${await response.text()}`);
     }
@@ -35,7 +35,7 @@ export async function predict3Di(aaSequence) {
         .trim();
     return { aaSequence: cleanSequence, di3Sequence: cleanDi3 };
 }
-export async function submitFoldseekSearch(aaSequence, di3Sequence, databases) {
+export async function submitFoldseekSearch({ aaSequence, di3Sequence, databases, signal, }) {
     // Submit both AA and 3Di sequences (with trailing newline like working example)
     const fastaContent = `>query\n${aaSequence}\n>3DI\n${di3Sequence}\n`;
     const params = new URLSearchParams();
@@ -51,14 +51,18 @@ export async function submitFoldseekSearch(aaSequence, di3Sequence, databases) {
             'Content-Type': 'application/x-www-form-urlencoded',
         },
         body: params,
+        signal,
     });
-    const responseData = await response.json();
+    // Read the body as text first so a non-JSON error page (e.g. a gateway/500
+    // HTML response) surfaces the real status instead of an opaque JSON
+    // SyntaxError that hides it.
+    const text = await response.text();
     if (!response.ok) {
-        throw new Error(`Foldseek submission failed: ${response.status} ${JSON.stringify(responseData)}`);
+        throw new Error(`Foldseek submission failed: ${response.status} ${text}`);
     }
-    return responseData;
+    return JSON.parse(text);
 }
-export async function pollFoldseekStatus(ticketId) {
+export async function pollFoldseekStatus({ ticketId, signal, }) {
     // Use the /tickets endpoint (plural) with POST
     const params = new URLSearchParams();
     params.append('tickets[]', ticketId);
@@ -68,6 +72,7 @@ export async function pollFoldseekStatus(ticketId) {
             'Content-Type': 'application/x-www-form-urlencoded',
         },
         body: params,
+        signal,
     });
     if (!response.ok) {
         throw new Error(`Failed to poll ticket status: ${response.status}`);
@@ -80,21 +85,24 @@ export async function pollFoldseekStatus(ticketId) {
     }
     return result;
 }
-export async function getFoldseekResults(ticketId) {
-    return jsonfetch(`https://search.foldseek.com/api/result/${ticketId}/0`);
+export async function getFoldseekResults({ ticketId, signal, }) {
+    return jsonfetch(`https://search.foldseek.com/api/result/${ticketId}/0`, { signal });
 }
-export async function waitForFoldseekResults(ticketId, onStatusChange) {
+export async function waitForFoldseekResults({ ticketId, onStatusChange, signal, }) {
     const maxAttempts = 180;
     let attempts = 0;
     while (attempts < maxAttempts) {
-        const status = await pollFoldseekStatus(ticketId);
+        if (signal?.aborted) {
+            throw signal.reason;
+        }
+        const status = await pollFoldseekStatus({ ticketId, signal });
         if (status.status === 'ERROR') {
             console.error('[Foldseek] Search error:', status);
             throw new Error(`Foldseek search failed: ${status.error ?? 'Unknown error'}`);
         }
         if (status.status === 'COMPLETE') {
             onStatusChange?.('Fetching results...');
-            const apiResponse = await getFoldseekResults(ticketId);
+            const apiResponse = await getFoldseekResults({ ticketId, signal });
             // Transform API response to our format
             const results = {
                 query: apiResponse.queries[0] ?? { header: '', sequence: '' },
@@ -106,7 +114,7 @@ export async function waitForFoldseekResults(ticketId, onStatusChange) {
             return results;
         }
         onStatusChange?.(`Search ${status.status.toLowerCase()}... (${attempts + 1}s)`);
-        await timeout(1000);
+        await timeout(1000, signal);
         attempts++;
     }
     throw new Error('Foldseek search timed out');

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

@@ -21,13 +21,14 @@ interface LaunchViewParams {
     uniprotId?: string;
 }
 export declare function formatViewName(prefix: string, feature: Feature, selectedTranscript?: Feature, uniprotId?: string): string;
-export declare function launch3DProteinView({ session, view, feature, selectedTranscript, uniprotId, url, data, userProvidedTranscriptSequence, alignmentAlgorithm, displayName, connectedMsaViewId, }: LaunchViewParams & {
+export declare function launch3DProteinView({ session, view, feature, selectedTranscript, uniprotId, url, data, userProvidedTranscriptSequence, alignmentAlgorithm, displayName, connectedMsaViewId, sideBySide, }: LaunchViewParams & {
     url?: string;
     data?: string;
     userProvidedTranscriptSequence?: string;
     alignmentAlgorithm?: string;
     displayName?: string;
     connectedMsaViewId?: string;
+    sideBySide?: boolean;
 }): import("@jbrowse/core/util").AbstractViewModel;
 export declare function launch1DProteinView({ session, view, feature, selectedTranscript, uniprotId, confidenceUrl, }: LaunchViewParams & {
     confidenceUrl?: string;

package/dist/LaunchProteinView/utils/launchViewUtils.js

@@ -1,4 +1,5 @@
 import { isSessionWithAddTracks } from '@jbrowse/core/util';
+import { getLaunchSideBySide, launchViewSideBySide } from './sideBySide';
 import { getGeneDisplayName, getTranscriptDisplayName } from './util';
 import { launchProteinAnnotationView } from '../components/launchProteinAnnotationView';
 export const ALPHAFOLD_VERSION = 'v6';
@@ -58,7 +59,7 @@ export function formatViewName(prefix, feature, selectedTranscript, uniprotId) {
         .filter(s => !!s)
         .join(' - ');
 }
-export function launch3DProteinView({ session, view, feature, selectedTranscript, uniprotId, url, data, userProvidedTranscriptSequence, alignmentAlgorithm, displayName, connectedMsaViewId, }) {
+export function launch3DProteinView({ session, view, feature, selectedTranscript, uniprotId, url, data, userProvidedTranscriptSequence, alignmentAlgorithm, displayName, connectedMsaViewId, sideBySide, }) {
     const snap = {
         type: 'ProteinView',
         alignmentAlgorithm,
@@ -75,7 +76,11 @@ export function launch3DProteinView({ session, view, feature, selectedTranscript
         displayName: displayName ??
             formatViewName('Protein view', feature, selectedTranscript, uniprotId),
     };
-    return session.addView('ProteinView', snap);
+    const proteinView = session.addView('ProteinView', snap);
+    if (sideBySide ?? getLaunchSideBySide()) {
+        launchViewSideBySide(session, proteinView.id);
+    }
+    return proteinView;
 }
 export async function launch1DProteinView({ session, view, feature, selectedTranscript, uniprotId, confidenceUrl, }) {
     if (!uniprotId || !isSessionWithAddTracks(session)) {

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

@@ -0,0 +1,11 @@
+import type { AbstractSessionModel } from '@jbrowse/core/util';
+export declare function getLaunchSideBySide(): boolean;
+export declare function setLaunchSideBySide(value: boolean): void;
+/**
+ * Place a freshly-added view to the right of the others in a workspaces (tiled)
+ * layout. Mirrors the "Move to split view" view-menu action: queue a splitRight
+ * pending move for this view, then enable workspaces so TiledViewsContainer
+ * consumes the move on mount (other views land in the left panel, this one in a
+ * new right panel). No-op on sessions without workspaces support.
+ */
+export declare function launchViewSideBySide(session: AbstractSessionModel, viewId: string): void;

package/dist/LaunchProteinView/utils/sideBySide.js

@@ -0,0 +1,33 @@
+// Self-contained launch preference (NOT the global/core preferences system):
+// whether a protein view launched from a genome feature opens side-by-side with
+// its connected genome view (left genome | right protein) instead of stacked.
+const SIDE_BY_SIDE_KEY = 'proteinView-launchSideBySide';
+// Default to side-by-side: a connected genome+protein pair reads best as a
+// left/right split. Users can turn it off in the launch dialog's settings.
+const DEFAULT_SIDE_BY_SIDE = true;
+export function getLaunchSideBySide() {
+    const stored = localStorage.getItem(SIDE_BY_SIDE_KEY);
+    return stored === null ? DEFAULT_SIDE_BY_SIDE : stored === 'true';
+}
+export function setLaunchSideBySide(value) {
+    localStorage.setItem(SIDE_BY_SIDE_KEY, value ? 'true' : 'false');
+}
+function isSessionWithWorkspaces(session) {
+    return ('setUseWorkspaces' in session &&
+        typeof session.setUseWorkspaces === 'function' &&
+        'setPendingMove' in session &&
+        typeof session.setPendingMove === 'function');
+}
+/**
+ * Place a freshly-added view to the right of the others in a workspaces (tiled)
+ * layout. Mirrors the "Move to split view" view-menu action: queue a splitRight
+ * pending move for this view, then enable workspaces so TiledViewsContainer
+ * consumes the move on mount (other views land in the left panel, this one in a
+ * new right panel). No-op on sessions without workspaces support.
+ */
+export function launchViewSideBySide(session, viewId) {
+    if (isSessionWithWorkspaces(session)) {
+        session.setPendingMove({ type: 'splitRight', viewId });
+        session.setUseWorkspaces(true);
+    }
+}

package/dist/LaunchProteinViewExtensionPoint/index.js

@@ -1,4 +1,5 @@
 import { resolveShortLaunch } from './resolveShortLaunch';
+import { getLaunchSideBySide, launchViewSideBySide, } from '../LaunchProteinView/utils/sideBySide';
 export default function LaunchProteinViewExtensionPointF(pluginManager) {
     pluginManager.addToExtensionPoint('LaunchView-ProteinView', 
     // LaunchView extension points are typed as transformers `(extendee, props)
@@ -6,7 +7,7 @@ export default function LaunchProteinViewExtensionPointF(pluginManager) {
     // handlers and ignores the return value. Casting away the signature
     // mismatch rather than fabricating a fake return.
     // @ts-expect-error
-    async ({ session, url, uniprotId, transcriptId, userProvidedTranscriptSequence, feature, connectedViewId, connectedView, alignmentAlgorithm, displayName, height, showControls, showHighlight, zoomToBaseLevel, }) => {
+    async ({ session, url, uniprotId, transcriptId, userProvidedTranscriptSequence, feature, connectedViewId, connectedView, alignmentAlgorithm, displayName, height, showControls, showHighlight, zoomToBaseLevel, sideBySide, }) => {
         // Short-URL form: `uniprotId` + `transcriptId` + `connectedView` (no
         // explicit `url`/`feature`/sequence). Derive the structure URL, the
         // transcript feature, and the translated sequence from the connected
@@ -37,6 +38,9 @@ export default function LaunchProteinViewExtensionPointF(pluginManager) {
         // `connectedView` is supplied we create the LinearGenomeView here and wire
         // its id, letting a single spec entry produce a connected genome+protein
         // pair (e.g. hover a variant to highlight the residue).
+        // a connected view this launch created itself can be split beside the
+        // protein view; a pre-existing connectedViewId is left in place
+        const ownsConnectedView = !connectedViewId && !!connectedView;
         const resolvedConnectedViewId = connectedViewId ??
             (connectedView
                 ? session.addView('LinearGenomeView', {
@@ -44,7 +48,7 @@ export default function LaunchProteinViewExtensionPointF(pluginManager) {
                     init: connectedView,
                 }).id
                 : undefined);
-        session.addView('ProteinView', {
+        const proteinView = session.addView('ProteinView', {
             type: 'ProteinView',
             alignmentAlgorithm,
             displayName,
@@ -63,5 +67,8 @@ export default function LaunchProteinViewExtensionPointF(pluginManager) {
                 },
             ],
         });
+        if (ownsConnectedView && (sideBySide ?? getLaunchSideBySide())) {
+            launchViewSideBySide(session, proteinView.id);
+        }
     });
 }

package/dist/ProteinView/applyColorTheme.d.ts

@@ -31,7 +31,7 @@ export declare const COLOR_SCHEMES: readonly [{
     readonly label: "Molecule type";
 }];
 export type ProteinColorScheme = (typeof COLOR_SCHEMES)[number]['value'];
-export declare const COLOR_SCHEME_VALUES: ("uncertainty" | "hydrophobicity" | "chain-id" | "molecule-type" | "residue-name" | "secondary-structure" | "default" | "plddt-confidence")[];
+export declare const COLOR_SCHEME_VALUES: ("default" | "plddt-confidence" | "chain-id" | "secondary-structure" | "hydrophobicity" | "residue-name" | "uncertainty" | "molecule-type")[];
 export declare function applyColorTheme({ plugin, colorScheme, }: {
     plugin: PluginContext;
     colorScheme: ProteinColorScheme;

package/dist/ProteinView/loadStructureData.d.ts

@@ -0,0 +1,18 @@
+import type { PluginContext } from 'molstar/lib/mol-plugin/context';
+export interface StructureData {
+    sequences?: string[];
+    confidence?: number[];
+}
+/**
+ * Loads a structure (from inline data or a URL) into the given Molstar plugin
+ * and pulls out its per-chain sequences and per-residue confidence. Pure with
+ * respect to the model — it only touches the plugin and returns plain data, so
+ * callers own the decision of whether/where to store the result.
+ */
+export declare function loadStructureData({ structure, plugin, }: {
+    structure: {
+        data?: string;
+        url?: string;
+    };
+    plugin: PluginContext;
+}): Promise<StructureData>;

package/dist/ProteinView/loadStructureData.js

@@ -0,0 +1,22 @@
+import { addStructureFromData } from './addStructureFromData';
+import { addStructureFromURL } from './addStructureFromURL';
+import { extractPerResidueConfidence } from './extractPerResidueConfidence';
+import { extractStructureSequences } from './extractStructureSequences';
+/**
+ * Loads a structure (from inline data or a URL) into the given Molstar plugin
+ * and pulls out its per-chain sequences and per-residue confidence. Pure with
+ * respect to the model — it only touches the plugin and returns plain data, so
+ * callers own the decision of whether/where to store the result.
+ */
+export async function loadStructureData({ structure, plugin, }) {
+    const { model } = structure.data
+        ? await addStructureFromData({ data: structure.data, plugin })
+        : structure.url
+            ? await addStructureFromURL({ url: structure.url, plugin })
+            : { model: undefined };
+    const sequences = model ? extractStructureSequences(model) : undefined;
+    const confidence = model
+        ? extractPerResidueConfidence(model, sequences?.[0]?.length)
+        : undefined;
+    return { sequences, confidence };
+}

package/dist/ProteinView/model.d.ts

@@ -19,7 +19,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     displayName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     minimized: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-}, "colorScheme" | "structures" | "type" | "id" | "init" | "zoomToBaseLevel" | "alignmentAlgorithm" | "connectedMsaViewId" | "showHighlight" | "showAlignment" | "showProteinTracks" | "autoScrollAlignment" | "compactTracks" | "showControls" | "height"> & {
+}, "colorScheme" | "structures" | "id" | "type" | "init" | "zoomToBaseLevel" | "alignmentAlgorithm" | "connectedMsaViewId" | "showHighlight" | "showAlignment" | "showProteinTracks" | "autoScrollAlignment" | "compactTracks" | "showControls" | "height"> & {
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("@jbrowse/mobx-state-tree").ISimpleType<"ProteinView">;
     structures: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -641,7 +641,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     showHighlight: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     zoomToBaseLevel: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     autoScrollAlignment: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    colorScheme: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<"uncertainty" | "hydrophobicity" | "chain-id" | "molecule-type" | "residue-name" | "secondary-structure" | "default" | "plddt-confidence">, [undefined]>;
+    colorScheme: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<"default" | "plddt-confidence" | "chain-id" | "secondary-structure" | "hydrophobicity" | "residue-name" | "uncertainty" | "molecule-type">, [undefined]>;
     showAlignment: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     showProteinTracks: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     compactTracks: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;