jbrowse-plugin-protein3d 0.4.12 → 0.4.14

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/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/components/FeatureBar.js

@@ -84,7 +84,7 @@ const FeatureBar = observer(function FeatureBar({ feature, model, }) {
     const { left, width } = getFeatureGeometry(feature, structurePositionToAlignmentMap);
     const color = getFeatureColor(feature.type);
     return (React.createElement(Tooltip, { title: React.createElement(FeatureTooltipContent, { feature: feature }), followCursor: true },
-        React.createElement("div", { onClick: () => {
+        React.createElement("div", { "data-testid": `protein-feature-${feature.type}`, "data-feature-id": feature.uniqueId, "data-feature-start": feature.start, "data-feature-end": feature.end, onClick: () => {
                 handleClick();
             }, onMouseEnter: () => {
                 handleMouseEnter();

package/dist/config.json

@@ -2,7 +2,7 @@
   "plugins": [
     {
       "name": "Protein3d",
-      "url": "https://jbrowse.org/plugins/jbrowse-plugin-protein3d/0.4.12/dist/jbrowse-plugin-protein3d.umd.production.min.js"
+      "url": "https://jbrowse.org/plugins/jbrowse-plugin-protein3d/latest/dist/jbrowse-plugin-protein3d.umd.production.min.js"
     }
   ],
   "assemblies": [