jbrowse-plugin-protein3d 0.8.3 → 0.9.0

package/dist/LaunchProteinView/components/FoldseekActionMenu.js

@@ -29,7 +29,7 @@ export default function FoldseekActionMenu({ hit, session, view, feature, select
             userProvidedTranscriptSequence,
         });
     });
-    const { launch1D, launchMsa } = getConditionalProteinLaunches({
+    const { launch1D } = getConditionalProteinLaunches({
         ...baseParams,
         confidenceUrl: getConfidenceUrlFromTarget(hit.target),
     });
@@ -42,6 +42,5 @@ export default function FoldseekActionMenu({ hit, session, view, feature, select
         React.createElement(Button, { size: "small", variant: "outlined", onClick: handleClick }, "Load"),
         React.createElement(Menu, { anchorEl: anchorEl, open: open, onClose: handleMenuClose },
             React.createElement(MenuItem, { "data-testid": "protein-launch-option-3d", onClick: handleLaunch3D }, PROTEIN_LAUNCH_LABELS['3d']),
-            launch1D ? (React.createElement(MenuItem, { "data-testid": "protein-launch-option-1d", onClick: runLaunch(launch1D) }, PROTEIN_LAUNCH_LABELS['1d'])) : null,
-            launchMsa ? (React.createElement(MenuItem, { "data-testid": "protein-launch-option-msa", onClick: runLaunch(launchMsa) }, PROTEIN_LAUNCH_LABELS.msa)) : null)));
+            launch1D ? (React.createElement(MenuItem, { "data-testid": "protein-launch-option-1d", onClick: runLaunch(launch1D) }, PROTEIN_LAUNCH_LABELS['1d'])) : null)));
 }

package/dist/LaunchProteinView/components/ProteinViewActions.js

@@ -8,7 +8,7 @@ import LaunchSettingsDialog from './LaunchSettingsDialog';
 import SequenceMismatchNotice from './SequenceMismatchNotice';
 import { useSafeLaunch } from '../hooks/useSafeLaunch';
 import { getLaunchMissingReasons } from '../utils/launchHelpers';
-import { PROTEIN_LAUNCH_LABELS, getConditionalProteinLaunches, launch3DProteinView, launch3DProteinViewWithMsa, } from '../utils/launchViewUtils';
+import { PROTEIN_LAUNCH_LABELS, getConditionalProteinLaunches, launch3DProteinView, } 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);
@@ -40,7 +40,7 @@ export default function ProteinViewActions({ handleClose, uniprotId, userSelecte
     const handleLaunch3DView = runLaunch(() => {
         launch3DProteinView(launch3DParams);
     });
-    const { launch1D, launchMsa } = getConditionalProteinLaunches({
+    const { launch1D } = getConditionalProteinLaunches({
         session,
         view,
         feature,
@@ -65,22 +65,6 @@ export default function ProteinViewActions({ handleClose, uniprotId, userSelecte
                 },
             ]
             : []),
-        ...(launchMsa
-            ? [
-                {
-                    key: 'msa',
-                    title: PROTEIN_LAUNCH_LABELS.msa,
-                    description: 'View AlphaFold a3m multiple sequence alignment',
-                    onClick: runLaunch(launchMsa),
-                },
-                {
-                    key: '3d-msa',
-                    title: PROTEIN_LAUNCH_LABELS['3d-msa'],
-                    description: 'Launch both views with AlphaFold a3m MSA',
-                    onClick: runLaunch(() => launch3DProteinViewWithMsa(launch3DParams)),
-                },
-            ]
-            : []),
     ];
     return (React.createElement(React.Fragment, null,
         launchError ? React.createElement(ErrorMessage, { error: launchError }) : null,

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

@@ -1,11 +1,6 @@
 import type { AlignmentAlgorithm } from '../../ProteinView/types';
 import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-declare global {
-    interface Window {
-        JBrowsePluginMsaView?: unknown;
-    }
-}
 interface LaunchViewParams {
     session: AbstractSessionModel;
     view: LinearGenomeViewModel;
@@ -28,14 +23,10 @@ export declare function launch3DProteinView({ session, view, feature, selectedTr
 export declare const PROTEIN_LAUNCH_LABELS: {
     readonly '3d': "Launch 3D protein structure view";
     readonly '1d': "Launch 1D protein annotation view";
-    readonly msa: "Launch MSA view (AlphaFold a3m)";
-    readonly '3d-msa': "Launch 3D structure + MSA view";
 };
 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

@@ -1,6 +1,5 @@
 import { isSessionWithAddTracks } from '@jbrowse/core/util';
 import { maybeLaunchSideBySide } from './sideBySide';
-import { getAlphaFoldMsaUrl } from './structureUrls';
 import { getGeneDisplayName, getTranscriptDisplayName } from './util';
 import { proteinViewSnapshot } from '../../ProteinView/proteinViewSpec';
 import { launchProteinAnnotationView } from '../components/launchProteinAnnotationView';
@@ -50,56 +49,19 @@ async function launch1DProteinView({ session, view, feature, selectedTranscript,
         connectedViewId: view.id,
     });
 }
-// CROSS-REPO DEPENDENCY: the 'MsaView' view type is registered by
-// jbrowse-plugin-msaview, which wraps the `react-msaview` library. The top-level
-// props here (colorSchemeName, connectedViewId, connectedFeature) are native
-// react-msaview model properties applied directly from the snapshot; only `init`
-// (msaUrl) is a declarative launch contract that the plugin resolves once and
-// clears. These are NOT type-checked here because we only depend on it at runtime
-// (gated by hasMsaViewPlugin()). If react-msaview renames these, the launch
-// silently degrades. Keep in step with that repo.
-function launchMsaView({ session, view, feature, selectedTranscript, uniprotId, displayName, }) {
-    if (!uniprotId) {
-        return undefined;
-    }
-    return session.addView('MsaView', {
-        type: 'MsaView',
-        displayName: displayName ??
-            formatViewName('MSA view', feature, selectedTranscript, uniprotId),
-        connectedViewId: view.id,
-        connectedFeature: selectedTranscript?.toJSON(),
-        colorSchemeName: 'percent_identity',
-        init: {
-            msaUrl: getAlphaFoldMsaUrl(uniprotId),
-        },
-    });
-}
-function hasMsaViewPlugin() {
-    return window.JBrowsePluginMsaView !== undefined;
-}
 // What the launches below are CALLED, shared for the same reason their
-// availability is: the AlphaFold and Foldseek menus offer the same three
-// actions, and had drifted to different names for two of them ("Launch 3D
-// protein structure view" vs "Launch 3D protein view", and an MSA item that
-// named its source on one menu and not the other). Two names for one action
-// reads as two actions.
-//
-// The MSA item says "(AlphaFold a3m)" rather than a bare "Launch MSA view"
-// because msaview contributes a gene right-click item by that exact name, and
-// the two build different things: msaview's is one row per species from NCBI's
-// orthologs, this one is the deep unlabelled alignment AlphaFold folded from.
+// availability is: the AlphaFold and Foldseek menus offer the same actions, and
+// had drifted to different names ("Launch 3D protein structure view" vs "Launch
+// 3D protein view"). Two names for one action reads as two actions.
 export const PROTEIN_LAUNCH_LABELS = {
     '3d': 'Launch 3D protein structure view',
     '1d': 'Launch 1D protein annotation view',
-    msa: 'Launch MSA view (AlphaFold a3m)',
-    '3d-msa': 'Launch 3D structure + MSA view',
 };
-// 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.
+// The 1D-annotation launch has the same availability rule on both the AlphaFold
+// and Foldseek launch menus: a session it can add tracks to, and a uniprotId.
+// Returning it 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 {
@@ -113,25 +75,5 @@ export function getConditionalProteinLaunches({ session, view, feature, selected
                 confidenceUrl,
             })
             : undefined,
-        launchMsa: uniprotId && hasMsaViewPlugin()
-            ? () => launchMsaView({
-                session,
-                view,
-                feature,
-                selectedTranscript,
-                uniprotId,
-            })
-            : undefined,
     };
 }
-export function launch3DProteinViewWithMsa(params) {
-    const { uniprotId } = params;
-    if (!uniprotId) {
-        return undefined;
-    }
-    const msaView = launchMsaView(params);
-    return launch3DProteinView({
-        ...params,
-        connectedMsaViewId: msaView?.id,
-    });
-}

package/dist/LaunchProteinView/utils/sideBySide.js

@@ -23,19 +23,36 @@ function isSessionWithWorkspaces(session) {
     // Missing BOTH is an embedded session: it has no workspaces, there is nothing
     // to ask for, and silence is the right answer.
     //
-    // Missing ONE is a host that has workspaces but has changed how a view is
-    // placed in them — and silence there is how this broke before. jbrowse-web
-    // folded `setPendingMove` into its layout `init`, this guard went false, and
-    // the plugin simply stopped asking for the split: no error, no missing
-    // feature, just two views quietly stacking instead of sitting side by side.
-    // Nobody noticed for weeks. Feature detection cannot ask the host to announce
-    // a change, but it can tell "not supported here" from "supported, and gone".
+    // Missing ONE is a host that has workspaces but places views some other way —
+    // and silence there is how this broke before. jbrowse-web folded
+    // `setPendingMove` into its layout `init`, this guard went false, and the
+    // plugin simply stopped asking for the split: no error, no missing feature,
+    // just two views quietly stacking. Nobody noticed for weeks. Feature
+    // detection cannot ask the host to announce a change, but it can tell "not
+    // supported here" from "supported, and gone".
+    //
+    // Two very different hosts produce this one shape, and nothing on the session
+    // tells them apart, so the message carries both rather than the guess:
+    //
+    // - Releases through v4.3.0, where placement is `setPendingMoveToSplitRight`,
+    //   a module function in @jbrowse/app-core's DockviewContext, not a session
+    //   action. Nothing is wrong and nothing needs fixing; this plugin targets v5+
+    //   and does not reach for v4's door. Measured 2026-08-17: v4.3.0 and latest
+    //   stack, main splits.
+    // - A newer host that moved the action out from under us, which is the
+    //   regression this warning exists to catch.
+    //
+    // Do not quiet the first case by sniffing the version. The alarm is only worth
+    // having if it fires on a shape it cannot explain, and these two shapes are
+    // identical.
     if (canEnable !== canPlace && !warnedPartial) {
         warnedPartial = true;
         console.warn(`jbrowse-plugin-protein3d: this session supports workspaces but not ` +
             `${canPlace ? 'setUseWorkspaces' : 'setPendingMove'}, so the ` +
-            `side-by-side launch was skipped and the views will stack. The host's ` +
-            `session API changed; the plugin needs updating to match.`);
+            `side-by-side launch was skipped and the views will stack. Expected on ` +
+            `releases through v4.3.0, which place views through @jbrowse/app-core ` +
+            `instead; on a newer host it means the session API moved and the plugin ` +
+            `needs updating to match.`);
     }
     return canEnable && canPlace;
 }

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

@@ -3,7 +3,6 @@ export declare function uniprotFastaUrl(uniprotId: string): string;
 export declare function uniprotEntryUrl(uniprotId: string): string;
 export declare function getAlphaFoldStructureUrl(uniprotId: string, version?: string): string;
 export declare function getAlphaFoldConfidenceUrl(uniprotId: string, version?: string): string;
-export declare function getAlphaFoldMsaUrl(uniprotId: string, version?: string): string;
 export declare function getPdbStructureUrl(pdbId: string): string;
 /**
  * Resolve the `{ uniprotId }` / `{ pdbId }` shorthand to a concrete structure

package/dist/LaunchProteinView/utils/structureUrls.js

@@ -21,9 +21,6 @@ export function getAlphaFoldStructureUrl(uniprotId, version = ALPHAFOLD_VERSION)
 export function getAlphaFoldConfidenceUrl(uniprotId, version = ALPHAFOLD_VERSION) {
     return `https://alphafold.ebi.ac.uk/files/AF-${uniprotId}-F1-confidence_${version}.json`;
 }
-export function getAlphaFoldMsaUrl(uniprotId, version = ALPHAFOLD_VERSION) {
-    return `https://alphafold.ebi.ac.uk/files/msa/AF-${uniprotId}-F1-msa_${version}.a3m`;
-}
 export function getPdbStructureUrl(pdbId) {
     return `https://files.rcsb.org/download/${pdbId}.cif`;
 }