jbrowse-plugin-protein3d 0.5.6 → 0.5.7

package/dist/LaunchProteinView/components/FoldseekActionMenu.js

@@ -1,10 +1,9 @@
 import React, { useState } from 'react';
 import { ErrorMessage } from '@jbrowse/core/ui';
-import { isSessionWithAddTracks } from '@jbrowse/core/util';
 import { Button, Menu, MenuItem } from '@mui/material';
 import { useSafeLaunch } from '../hooks/useSafeLaunch';
 import { caCoordsToPdb, hasValidCaCoords } from '../utils/caCoordsToPdb';
-import { getConfidenceUrlFromTarget, getUniprotIdFromAlphaFoldTarget, hasMsaViewPlugin, launch1DProteinView, launch3DProteinView, launchMsaView, } from '../utils/launchViewUtils';
+import { getConditionalProteinLaunches, getConfidenceUrlFromTarget, getUniprotIdFromAlphaFoldTarget, launch3DProteinView, } from '../utils/launchViewUtils';
 export default function FoldseekActionMenu({ hit, session, view, feature, selectedTranscript, userProvidedTranscriptSequence, onClose, }) {
     const [anchorEl, setAnchorEl] = useState(null);
     const open = Boolean(anchorEl);
@@ -29,28 +28,19 @@ export default function FoldseekActionMenu({ hit, session, view, feature, select
             userProvidedTranscriptSequence,
         });
     });
-    const handleLaunchMSA = runLaunch(() => {
-        launchMsaView(baseParams);
+    const { launch1D, launchMsa } = getConditionalProteinLaunches({
+        ...baseParams,
+        confidenceUrl: getConfidenceUrlFromTarget(hit.target),
     });
     const canLoad = !!hit.structureUrl || hasValidCaCoords(hit.tCa, hit.tSeq);
     if (!canLoad) {
         return React.createElement("span", null, "-");
     }
-    // 1D launch needs an add-tracks session and a uniprotId; narrowing both here
-    // gates the menu item and types its handler from a single condition.
-    const addTracksSession = isSessionWithAddTracks(session) ? session : undefined;
     return (React.createElement(React.Fragment, null,
         launchError ? React.createElement(ErrorMessage, { error: launchError }) : null,
         React.createElement(Button, { size: "small", variant: "outlined", onClick: handleClick }, "Load"),
         React.createElement(Menu, { anchorEl: anchorEl, open: open, onClose: handleMenuClose },
             React.createElement(MenuItem, { onClick: handleLaunch3D }, "Launch 3D protein view"),
-            addTracksSession && uniprotId ? (React.createElement(MenuItem, { onClick: runLaunch(() => launch1DProteinView({
-                    session: addTracksSession,
-                    view,
-                    feature,
-                    selectedTranscript,
-                    uniprotId,
-                    confidenceUrl: getConfidenceUrlFromTarget(hit.target),
-                })) }, "Launch 1D protein annotation view")) : null,
-            uniprotId && hasMsaViewPlugin() ? (React.createElement(MenuItem, { onClick: handleLaunchMSA }, "Launch MSA view (AlphaFoldDB a3m)")) : null)));
+            launch1D ? (React.createElement(MenuItem, { onClick: runLaunch(launch1D) }, "Launch 1D protein annotation view")) : null,
+            launchMsa ? (React.createElement(MenuItem, { onClick: runLaunch(launchMsa) }, "Launch MSA view (AlphaFoldDB a3m)")) : null)));
 }

package/dist/LaunchProteinView/components/FoldseekResultsTable.js

@@ -3,7 +3,7 @@ import { Paper, Table, TableBody, TableCell, TableContainer, TableHead, TableRow
 import { makeStyles } from 'tss-react/mui';
 import FoldseekActionMenu from './FoldseekActionMenu';
 import { getStructureUrlFromTarget } from '../utils/launchViewUtils';
-const useStyles = makeStyles()({
+const useStyles = makeStyles()(theme => ({
     root: {
         display: 'flex',
         flexDirection: 'column',
@@ -14,13 +14,16 @@ const useStyles = makeStyles()({
     },
     headerCell: {
         fontWeight: 'bold',
-        backgroundColor: '#f5f5f5',
+        backgroundColor: theme.palette.mode === 'dark'
+            ? theme.palette.grey[900]
+            : theme.palette.grey[100],
     },
     noResults: {
         padding: 16,
         textAlign: 'center',
     },
-});
+}));
+const MAX_HITS = 100;
 function flattenResults(results) {
     const hits = results.results.flatMap(dbResult => (dbResult.alignments ?? []).flat().map(alignment => ({
         ...alignment,
@@ -28,11 +31,12 @@ function flattenResults(results) {
         structureUrl: getStructureUrlFromTarget(alignment.target, dbResult.db),
     })));
     hits.sort((a, b) => (a.eval ?? Infinity) - (b.eval ?? Infinity));
-    return hits.slice(0, 100);
+    return hits;
 }
 export default function FoldseekResultsTable({ results, session, view, feature, selectedTranscript, userProvidedTranscriptSequence, onClose, }) {
     const { classes } = useStyles();
-    const flatHits = flattenResults(results);
+    const allHits = flattenResults(results);
+    const flatHits = allHits.slice(0, MAX_HITS);
     if (flatHits.length === 0) {
         return (React.createElement(Paper, { className: classes.noResults },
             React.createElement(Typography, null, "No similar structures found")));
@@ -40,8 +44,11 @@ export default function FoldseekResultsTable({ results, session, view, feature,
     return (React.createElement("div", { className: classes.root },
         React.createElement(Typography, { variant: "subtitle2" },
             "Found ",
-            flatHits.length,
-            " similar structures"),
+            allHits.length,
+            " similar structures",
+            allHits.length > flatHits.length
+                ? ` (showing top ${flatHits.length})`
+                : ''),
         React.createElement(TableContainer, { component: Paper, className: classes.tableContainer },
             React.createElement(Table, { size: "small", stickyHeader: true },
                 React.createElement(TableHead, null,

package/dist/LaunchProteinView/components/ProteinViewActions.js

@@ -1,6 +1,5 @@
 import React, { useState } from 'react';
 import { ErrorMessage } from '@jbrowse/core/ui';
-import { isSessionWithAddTracks } from '@jbrowse/core/util';
 import ArrowDropDownIcon from '@mui/icons-material/ArrowDropDown';
 import SettingsIcon from '@mui/icons-material/Settings';
 import { Button, ButtonGroup, IconButton, Tooltip, Typography } from '@mui/material';
@@ -9,36 +8,31 @@ import LaunchSettingsDialog from './LaunchSettingsDialog';
 import SequenceMismatchNotice from './SequenceMismatchNotice';
 import { useSafeLaunch } from '../hooks/useSafeLaunch';
 import { getLaunchMissingReasons } from '../utils/launchHelpers';
-import { hasMsaViewPlugin, launch1DProteinView, launch3DProteinView, launch3DProteinViewWithMsa, launchMsaView, } from '../utils/launchViewUtils';
+import { getConditionalProteinLaunches, launch3DProteinView, launch3DProteinViewWithMsa, } 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);
-    // Disable launch while loading — SWR's keepPreviousData would otherwise let
-    // a user click Launch on stale results (wrong UniProt ID) during a refetch.
-    const canLaunch = !isLoading &&
-        !!uniprotId &&
-        !!userSelectedProteinSequence &&
-        !!selectedTranscript;
     const missingReasons = getLaunchMissingReasons({
         uniprotId,
         userSelectedProteinSequence,
         selectedTranscript,
-        isLoading,
-        error,
     });
+    // Disable launch while loading — SWR's keepPreviousData would otherwise let
+    // a user click Launch on stale results (wrong UniProt ID) during a refetch.
+    const canLaunch = !isLoading && missingReasons.length === 0;
+    // Suppress the derived reasons while loading or while a real upstream error
+    // is displayed above via <ErrorMessage> — a duplicate hint would mislead.
+    const showMissingReasons = !isLoading && !error && missingReasons.length > 0;
     const closeMenu = () => {
         setDialogOpen(false);
     };
     const { runLaunch, launchError } = useSafeLaunch(handleClose, closeMenu);
-    const baseParams = {
+    const launch3DParams = {
         session,
         view,
         feature,
         selectedTranscript,
         uniprotId,
-    };
-    const launch3DParams = {
-        ...baseParams,
         url,
         userProvidedTranscriptSequence: userSelectedProteinSequence?.seq,
         alignmentAlgorithm,
@@ -46,18 +40,14 @@ export default function ProteinViewActions({ handleClose, uniprotId, userSelecte
     const handleLaunch3DView = runLaunch(() => {
         launch3DProteinView(launch3DParams);
     });
-    const handleLaunchMsa = runLaunch(() => {
-        launchMsaView(baseParams);
-    });
-    const handleLaunch3DWithMsa = runLaunch(() => {
-        launch3DProteinViewWithMsa(launch3DParams);
+    const { launch1D, launchMsa } = getConditionalProteinLaunches({
+        session,
+        view,
+        feature,
+        selectedTranscript,
+        uniprotId,
+        confidenceUrl,
     });
-    // The 1D annotation view needs an add-tracks session and a known uniprotId.
-    // Narrowing here is the single source of truth: the option only exists when
-    // both hold, and its handler is type-checked against those narrowed values —
-    // so a 1D launch that can't work is unrepresentable rather than a silent
-    // no-op.
-    const addTracksSession = isSessionWithAddTracks(session) ? session : undefined;
     const launchOptions = [
         {
             key: '3d',
@@ -65,36 +55,29 @@ export default function ProteinViewActions({ handleClose, uniprotId, userSelecte
             description: 'View protein structure with genome-to-structure coordinate mapping',
             onClick: handleLaunch3DView,
         },
-        ...(addTracksSession && uniprotId
+        ...(launch1D
             ? [
                 {
                     key: '1d',
                     title: 'Launch 1D protein annotation view',
                     description: 'View protein features and annotations as a linear track',
-                    onClick: runLaunch(() => launch1DProteinView({
-                        session: addTracksSession,
-                        view,
-                        feature,
-                        selectedTranscript,
-                        uniprotId,
-                        confidenceUrl,
-                    })),
+                    onClick: runLaunch(launch1D),
                 },
             ]
             : []),
-        ...(hasMsaViewPlugin()
+        ...(launchMsa
             ? [
                 {
                     key: 'msa',
                     title: 'Launch MSA view',
                     description: 'View AlphaFold a3m multiple sequence alignment',
-                    onClick: handleLaunchMsa,
+                    onClick: runLaunch(launchMsa),
                 },
                 {
                     key: '3d-msa',
                     title: 'Launch 3D structure + MSA view',
                     description: 'Launch both views with AlphaFold a3m MSA',
-                    onClick: handleLaunch3DWithMsa,
+                    onClick: runLaunch(() => launch3DProteinViewWithMsa(launch3DParams)),
                 },
             ]
             : []),
@@ -110,7 +93,7 @@ export default function ProteinViewActions({ handleClose, uniprotId, userSelecte
         React.createElement(Button, { variant: "contained", color: "secondary", size: "small", onClick: () => {
                 handleClose();
             } }, "Cancel"),
-        !canLaunch && missingReasons.length > 0 ? (React.createElement(Typography, { variant: "body2", color: "error", sx: { mr: 2 } }, missingReasons.join('. '))) : null,
+        showMissingReasons ? (React.createElement(Typography, { variant: "body2", color: "error", sx: { mr: 2 } }, missingReasons.join('. '))) : null,
         React.createElement(ButtonGroup, { variant: "contained", color: "primary", size: "small" },
             React.createElement(Button, { disabled: !canLaunch, onClick: handleLaunch3DView }, "Launch"),
             React.createElement(Button, { disabled: !canLaunch, onClick: () => {

package/dist/LaunchProteinView/components/UniProtResultsTable.js

@@ -2,36 +2,38 @@ import React from 'react';
 import { Chip, Paper, Radio, Table, TableBody, TableCell, TableContainer, TableHead, TableRow, Typography, } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
 import ExternalLink from '../../components/ExternalLink';
-const useStyles = makeStyles()({
+const useStyles = makeStyles()(theme => ({
     tableContainer: {
         maxHeight: 200,
     },
     headerCell: {
         fontWeight: 'bold',
-        backgroundColor: '#f5f5f5',
+        backgroundColor: theme.palette.mode === 'dark'
+            ? theme.palette.grey[900]
+            : theme.palette.grey[100],
     },
     selectedRow: {
-        backgroundColor: '#e3f2fd',
+        backgroundColor: theme.palette.action.selected,
     },
     clickableRow: {
         cursor: 'pointer',
         '&:hover': {
-            backgroundColor: '#f5f5f5',
+            backgroundColor: theme.palette.action.hover,
         },
     },
     reviewedChip: {
-        backgroundColor: '#4caf50',
-        color: 'white',
+        backgroundColor: theme.palette.success.main,
+        color: theme.palette.success.contrastText,
         fontSize: '0.7rem',
         height: 20,
     },
     unreviewedChip: {
-        backgroundColor: '#ff9800',
-        color: 'white',
+        backgroundColor: theme.palette.warning.main,
+        color: theme.palette.warning.contrastText,
         fontSize: '0.7rem',
         height: 20,
     },
-});
+}));
 export default function UniProtResultsTable({ entries, selectedAccession, onSelect, }) {
     const { classes, cx } = useStyles();
     return entries.length === 0 ? null : (React.createElement("div", null,

package/dist/LaunchProteinView/components/UserProvidedStructure.js

@@ -8,6 +8,7 @@ import SequenceMismatchNotice from './SequenceMismatchNotice';
 import StructureSourcePicker from './StructureSourcePicker';
 import TranscriptSelector from './TranscriptSelector';
 import ExternalLink from '../../components/ExternalLink';
+import { useSafeLaunch } from '../hooks/useSafeLaunch';
 import useStructureFileSequence from '../hooks/useStructureFileSequence';
 import useTranscriptIsoformSelection from '../hooks/useTranscriptIsoformSelection';
 import { launch3DProteinView } from '../utils/launchViewUtils';
@@ -33,43 +34,34 @@ const UserProvidedStructure = observer(function UserProvidedStructure({ feature,
     const [file, setFile] = useState();
     const [pdbId, setPdbId] = useState('');
     const [choice, setChoice] = useState('file');
-    const [submitError, setSubmitError] = useState();
     const [structureURL, setStructureURL] = useState('');
+    const { runLaunch, launchError } = useSafeLaunch(handleClose);
     const activeFile = choice === 'file' ? file : undefined;
     const activeURL = choice === 'file' ? '' : structureURL;
     const { sequences: structureSequences, error: fileError } = useStructureFileSequence({ file: activeFile, url: activeURL });
     const structureName = activeFile?.name ?? activeURL.slice(activeURL.lastIndexOf('/') + 1);
     const structureSequence = structureSequences?.[0];
     const { transcripts: options, isoformSequences, selectedTranscriptId: userSelection, setSelectedTranscriptId: setUserSelection, selectedTranscript, selectedIsoform: protein, error: isoformError, } = useTranscriptIsoformSelection({ feature, view, structureSequence });
-    const error = isoformError ?? submitError ?? fileError;
+    const error = isoformError ?? launchError ?? fileError;
     const canLaunch = !!(activeURL || activeFile) && !!protein && !!selectedTranscript;
     const sequencesDiffer = !!protein?.seq &&
         !!structureSequence &&
         stripStopCodon(protein.seq) !== structureSequence;
-    const handleLaunch = async () => {
-        if (!protein || !selectedTranscript) {
-            return;
-        }
-        try {
+    const handleLaunch = runLaunch(async () => {
+        if (protein && selectedTranscript) {
             const structureData = activeFile ? await activeFile.text() : undefined;
-            const url = activeURL ? activeURL : undefined;
             launch3DProteinView({
                 session,
                 view,
                 feature,
                 selectedTranscript,
-                url,
+                url: activeURL ? activeURL : undefined,
                 data: structureData,
                 userProvidedTranscriptSequence: protein.seq,
                 alignmentAlgorithm,
             });
-            handleClose();
-        }
-        catch (e) {
-            console.error(e);
-            setSubmitError(e);
         }
-    };
+    });
     return (React.createElement(React.Fragment, null,
         React.createElement(DialogContent, { className: classes.dialogContent },
             error ? React.createElement(ErrorMessage, { error: error }) : null,
@@ -84,7 +76,7 @@ const UserProvidedStructure = observer(function UserProvidedStructure({ feature,
                     handleClose();
                 } }, "Cancel"),
             React.createElement(Button, { variant: "contained", color: "primary", disabled: !canLaunch, onClick: () => {
-                    void handleLaunch();
+                    handleLaunch();
                 } }, "Launch 3-D protein structure view"))));
 });
 export default UserProvidedStructure;

package/dist/LaunchProteinView/components/launchProteinAnnotationView.js

@@ -11,7 +11,7 @@ export async function launchProteinAnnotationView({ session, feature, selectedTr
     });
     const view = session.addView('LinearGenomeView', {
         type: 'LinearGenomeView',
-        displayName: formatViewName('Protein view', feature, selectedTranscript, uniprotId),
+        displayName: formatViewName('Protein annotations', feature, selectedTranscript, uniprotId),
     });
     // Register for linked highlighting between 1D and 3D views
     if (connectedViewId && selectedTranscript) {

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

@@ -4,6 +4,6 @@
  * runs the launch via safeLaunch, and surfaces failures inline.
  */
 export declare function useSafeLaunch(onSuccess: () => void, onBeforeLaunch?: () => void): {
-    runLaunch: (fn: () => void | Promise<void>) => () => void;
+    runLaunch: (fn: () => unknown) => () => void;
     launchError: unknown;
 };

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

@@ -3,24 +3,19 @@
  * Used to wrap `session.addView(...)` calls so MST validation errors don't
  * fall silently into the React error boundary.
  */
-export declare function safeLaunch(fn: () => void | Promise<void>, onSuccess?: () => void, onError?: (e: unknown) => void): Promise<void>;
+export declare function safeLaunch(fn: () => unknown, onSuccess?: () => void, onError?: (e: unknown) => void): Promise<void>;
 interface LaunchRequirements {
     uniprotId?: string;
     userSelectedProteinSequence?: {
         seq: string;
     };
     selectedTranscript?: unknown;
-    isLoading?: boolean;
-    /**
-     * If a real error already surfaced (e.g. from UniProt lookup), suppress the
-     * derived "No UniProt ID found" reason — the underlying error is already
-     * shown via <ErrorMessage> and the duplicate hint is misleading.
-     */
-    error?: unknown;
 }
 /**
- * Compute user-facing reasons the Launch button is disabled. Suppressed
- * while loading or while a real upstream error is being displayed.
+ * The requirements a launch needs, as user-facing reasons for any that are
+ * unmet. An empty array means the launch can proceed. Callers decide whether to
+ * surface these (e.g. suppressed while loading or while a real upstream error
+ * is already shown via <ErrorMessage>, where a duplicate hint would mislead).
  */
-export declare function getLaunchMissingReasons({ uniprotId, userSelectedProteinSequence, selectedTranscript, isLoading, error, }: LaunchRequirements): string[];
+export declare function getLaunchMissingReasons({ uniprotId, userSelectedProteinSequence, selectedTranscript, }: LaunchRequirements): string[];
 export {};

package/dist/LaunchProteinView/utils/launchHelpers.js

@@ -14,16 +14,15 @@ export async function safeLaunch(fn, onSuccess, onError) {
     }
 }
 /**
- * Compute user-facing reasons the Launch button is disabled. Suppressed
- * while loading or while a real upstream error is being displayed.
+ * The requirements a launch needs, as user-facing reasons for any that are
+ * unmet. An empty array means the launch can proceed. Callers decide whether to
+ * surface these (e.g. suppressed while loading or while a real upstream error
+ * is already shown via <ErrorMessage>, where a duplicate hint would mislead).
  */
-export function getLaunchMissingReasons({ uniprotId, userSelectedProteinSequence, selectedTranscript, isLoading, error, }) {
-    if (isLoading || error) {
-        return [];
-    }
+export function getLaunchMissingReasons({ uniprotId, userSelectedProteinSequence, selectedTranscript, }) {
     return [
         !uniprotId && 'No UniProt ID found',
-        !userSelectedProteinSequence &&
+        !userSelectedProteinSequence?.seq &&
             'Could not compute protein sequence (feature may be missing CDS subfeatures)',
         !selectedTranscript && 'No transcript selected',
     ].filter((s) => typeof s === 'string');

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

@@ -1,10 +1,10 @@
+import type { AbstractSessionModel, Feature, SessionWithAddTracks } from '@jbrowse/core/util';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 declare global {
     interface Window {
         JBrowsePluginMsaView?: unknown;
     }
 }
-import type { AbstractSessionModel, Feature, SessionWithAddTracks } from '@jbrowse/core/util';
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 export declare const ALPHAFOLD_VERSION = "v6";
 export declare function getAlphaFoldStructureUrl(uniprotId: string, version?: string): string;
 export declare function getAlphaFoldConfidenceUrl(uniprotId: string, version?: string): string;
@@ -41,5 +41,11 @@ export declare function launchMsaView({ session, view, feature, selectedTranscri
     displayName?: string;
 }): import("@jbrowse/core/util").AbstractViewModel | undefined;
 export declare function hasMsaViewPlugin(): boolean;
+export declare function getConditionalProteinLaunches({ session, view, feature, selectedTranscript, uniprotId, confidenceUrl, }: LaunchViewParams & {
+    confidenceUrl?: string;
+}): {
+    launch1D: (() => Promise<void>) | undefined;
+    launchMsa: (() => import("@jbrowse/core/util").AbstractViewModel | undefined) | undefined;
+};
 export declare function launch3DProteinViewWithMsa(params: LaunchViewParams & Launch3DExtraParams): import("@jbrowse/core/util").AbstractViewModel | undefined;
 export {};

package/dist/LaunchProteinView/utils/launchViewUtils.js

@@ -1,3 +1,4 @@
+import { isSessionWithAddTracks } from '@jbrowse/core/util';
 import { maybeLaunchSideBySide } from './sideBySide';
 import { getGeneDisplayName, getTranscriptDisplayName } from './util';
 import { launchProteinAnnotationView } from '../components/launchProteinAnnotationView';
@@ -120,6 +121,36 @@ export function launchMsaView({ session, view, feature, selectedTranscript, unip
 export function hasMsaViewPlugin() {
     return window.JBrowsePluginMsaView !== undefined;
 }
+// The 1D-annotation and MSA launches share identical availability rules across
+// the AlphaFold and Foldseek launch menus: the 1D view needs an add-tracks
+// session and a uniprotId, the MSA view needs the msaview plugin and a
+// uniprotId. Returning each as a ready-to-run thunk (or undefined when
+// unavailable) is the single source of truth — an unavailable action is
+// unrepresentable rather than a menu item that silently no-ops.
+export function getConditionalProteinLaunches({ session, view, feature, selectedTranscript, uniprotId, confidenceUrl, }) {
+    const addTracksSession = isSessionWithAddTracks(session) ? session : undefined;
+    return {
+        launch1D: addTracksSession && uniprotId
+            ? () => launch1DProteinView({
+                session: addTracksSession,
+                view,
+                feature,
+                selectedTranscript,
+                uniprotId,
+                confidenceUrl,
+            })
+            : undefined,
+        launchMsa: uniprotId && hasMsaViewPlugin()
+            ? () => launchMsaView({
+                session,
+                view,
+                feature,
+                selectedTranscript,
+                uniprotId,
+            })
+            : undefined,
+    };
+}
 export function launch3DProteinViewWithMsa(params) {
     const { uniprotId } = params;
     if (!uniprotId) {