jbrowse-plugin-msaview 2.6.3 → 2.6.5

package/dist/AddHighlightModel/MsaToGenomeHighlight.js

@@ -3,7 +3,6 @@ import { getSession } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
 import { hasHoverPosition, useStyles } from './util';
 import { isMsaView } from '../MsaViewPanel/model';
-import { getCanonicalRefName } from '../MsaViewPanel/util';
 const MsaToGenomeHighlight = observer(function MsaToGenomeHighlight2({ model, }) {
     const { views, hovered } = getSession(model);
     const msaView = views
@@ -17,16 +16,16 @@ const MsaToGenomeHighlight = observer(function MsaToGenomeHighlight2({ model, })
 // Inner component: handles the scroll-dependent rendering
 const MsaToGenomeHighlightRenderer = observer(function ({ model, highlights, }) {
     const { classes } = useStyles();
-    const { assemblyManager } = getSession(model);
     const { offsetPx } = model;
     return (React.createElement(React.Fragment, null, highlights.map((r, idx) => {
-        const refName = getCanonicalRefName({
-            assemblyManager,
-            assemblyNames: model.assemblyNames,
-            refName: r.refName,
-        });
-        const s = model.bpToPx({ refName, coord: r.start });
-        const e = model.bpToPx({ refName, coord: r.end });
+        // Use the highlight's own refName, which is already in the connected
+        // view's coordinate space (it comes from the connectedFeature the
+        // launcher set on this LGV). Do NOT canonicalize: bpToPx matches
+        // displayed regions by exact refName with no alias resolution, so
+        // rewriting e.g. "chr17" to the assembly-canonical "17" misses a view
+        // whose regions are "chr17". (GenomeMouseoverHighlight does the same.)
+        const s = model.bpToPx({ refName: r.refName, coord: r.start });
+        const e = model.bpToPx({ refName: r.refName, coord: r.end });
         if (s && e) {
             const width = Math.max(Math.abs(e.offsetPx - s.offsetPx), 4);
             const left = Math.min(s.offsetPx, e.offsetPx) - offsetPx;

package/dist/MsaViewPanel/afterCreateAutoruns.d.ts

@@ -18,8 +18,6 @@ export declare function processInit(self: JBrowsePluginMsaViewModel): void;
  * column the user is hovering directly in the MSA.
  */
 export declare function syncGenomeHoverToMsaColumn(self: JBrowsePluginMsaViewModel): () => void;
-export declare function highlightConnectedStructures(self: JBrowsePluginMsaViewModel): void;
-export declare function autoConnectStructures(self: JBrowsePluginMsaViewModel): void;
 /**
  * Mirror a connected 3D protein view's hovered residue onto the MSA's
  * highlighted columns. Returns the autorun body and keeps a flag tracking

package/dist/MsaViewPanel/afterCreateAutoruns.js

@@ -4,7 +4,7 @@ import { fetchIndexedMsa } from './fetchIndexedMsa';
 import { genomeToMSA } from './genomeToMSA';
 import { loadProteinDomains } from './loadProteinDomains';
 import { cleanupOldData, generateDataStoreId, retrieveMsaData, storeMsaData, } from './msaDataStore';
-import { gappedToUngappedPosition, getProteinViews, structureMatchesMsa, } from './structureConnection';
+import { getProteinViews } from './structureConnection';
 import { getUniprotIdFromAlphaFoldUrl } from './util';
 export function loadStoredData(self) {
     const { dataStoreId, rows } = self;
@@ -183,68 +183,6 @@ export function syncGenomeHoverToMsaColumn(self) {
         }
     };
 }
-export function highlightConnectedStructures(self) {
-    const { mouseCol, connectedProteinViews } = self;
-    if (connectedProteinViews.length === 0) {
-        return;
-    }
-    for (const conn of connectedProteinViews) {
-        const structure = conn.proteinView.structures[conn.structureIdx];
-        if (!structure) {
-            continue;
-        }
-        if (mouseCol === undefined) {
-            structure.clearHighlightFromExternal?.();
-            continue;
-        }
-        const seq = self.getSequenceByRowName(conn.msaRowName);
-        if (!seq) {
-            continue;
-        }
-        const msaUngapped = gappedToUngappedPosition(seq, mouseCol);
-        if (msaUngapped === undefined) {
-            structure.clearHighlightFromExternal?.();
-            continue;
-        }
-        const structurePos = conn.msaToStructure[msaUngapped];
-        if (structurePos === undefined) {
-            structure.clearHighlightFromExternal?.();
-        }
-        else {
-            structure.highlightFromExternal?.(structurePos);
-        }
-    }
-}
-export function autoConnectStructures(self) {
-    const { connectedViewId, uniprotId, rows, connectedStructures } = self;
-    if (rows.length === 0) {
-        return;
-    }
-    for (const view of getProteinViews(getSession(self).views)) {
-        for (let structureIdx = 0; structureIdx < view.structures.length; structureIdx++) {
-            const structure = view.structures[structureIdx];
-            if (!structure) {
-                continue;
-            }
-            if (!structureMatchesMsa({ structure, connectedViewId, uniprotId })) {
-                continue;
-            }
-            const alreadyConnected = connectedStructures.some(c => c.proteinViewId === view.id && c.structureIdx === structureIdx);
-            if (alreadyConnected) {
-                continue;
-            }
-            if (!structure.structureSequences?.[0]) {
-                continue;
-            }
-            try {
-                self.connectToStructure(view.id, structureIdx);
-            }
-            catch (e) {
-                console.error('Failed to auto-connect to ProteinView:', e);
-            }
-        }
-    }
-}
 /**
  * Mirror a connected 3D protein view's hovered residue onto the MSA's
  * highlighted columns. Returns the autorun body and keeps a flag tracking

package/dist/MsaViewPanel/model.d.ts

@@ -1,5 +1,4 @@
 export type { MSAFormat } from 'msa-parsers';
-import type { ProteinView, StructureConnection } from './structureConnection';
 import type { MafRegion, MsaViewInitState } from './types';
 import type { BlastDatabase, BlastProgram, MsaAlgorithm } from '../LaunchMsaView/components/NCBIBlastQuery/consts';
 import type { Feature } from '@jbrowse/core/util';
@@ -159,7 +158,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     featureFilters: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
     relativeTo: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     highlightColumns: import("@jbrowse/mobx-state-tree").IType<number[] | undefined, number[] | undefined, number[] | undefined>;
-}, "init" | "querySeqName" | "zoomToBaseLevel" | "connectedViewId" | "connectedFeature" | "blastParams" | "uniprotId" | "connectedStructures" | "dataStoreId" | "mafRegion"> & {
+}, "init" | "querySeqName" | "zoomToBaseLevel" | "connectedViewId" | "connectedFeature" | "blastParams" | "uniprotId" | "dataStoreId" | "mafRegion"> & {
     connectedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     connectedFeature: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
     blastParams: import("@jbrowse/mobx-state-tree").IType<BlastParams | undefined, BlastParams | undefined, BlastParams | undefined>;
@@ -167,7 +166,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     uniprotId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     zoomToBaseLevel: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     init: import("@jbrowse/mobx-state-tree").IType<MsaViewInitState | undefined, MsaViewInitState | undefined, MsaViewInitState | undefined>;
-    connectedStructures: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<StructureConnection, StructureConnection, StructureConnection>>;
     dataStoreId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     mafRegion: import("@jbrowse/mobx-state-tree").IType<MafRegion | undefined, MafRegion | undefined, MafRegion | undefined>;
 }, {
@@ -386,43 +384,92 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
         name: string;
         accession: string;
         description: string;
+        featureType: string | undefined;
         start: number;
         end: number;
+        strand: number | undefined;
     }>;
     readonly tidyInterProAnnotations: {
         id: string;
         name: string;
         accession: string;
         description: string;
+        featureType: string | undefined;
         start: number;
         end: number;
+        strand: number | undefined;
     }[];
     readonly tidyFilteredInterProAnnotations: {
         id: string;
         name: string;
         accession: string;
         description: string;
+        featureType: string | undefined;
         start: number;
         end: number;
+        strand: number | undefined;
     }[];
     readonly tidyFilteredGatheredInterProAnnotations: Record<string, {
         id: string;
         name: string;
         accession: string;
         description: string;
+        featureType: string | undefined;
         start: number;
         end: number;
+        strand: number | undefined;
     }[]>;
 } & {
     readonly showVerticalScrollbar: boolean;
 } & {
     readonly verticalScrollbarWidth: 0 | 20;
+    readonly segmentDomainTypes: {
+        id: string;
+        name: string;
+        accession: string;
+        description: string;
+        featureType: string | undefined;
+        start: number;
+        end: number;
+        strand: number | undefined;
+    }[];
+    readonly categoricalDomainTypes: {
+        id: string;
+        name: string;
+        accession: string;
+        description: string;
+        featureType: string | undefined;
+        start: number;
+        end: number;
+        strand: number | undefined;
+    }[];
     readonly fillPalette: {
-        [k: string]: string;
+        [x: string]: string;
     };
     readonly strokePalette: {
         [k: string]: string;
     };
+    readonly segmentLabels: Map<string, string>;
+    readonly visibleDomainTypes: {
+        id: string;
+        name: string;
+        accession: string;
+        description: string;
+        featureType: string | undefined;
+        start: number;
+        end: number;
+        strand: number | undefined;
+    }[];
+    readonly mouseOverDomains: {
+        id: string;
+        name: string;
+        accession: string;
+        description: string;
+        featureType: string | undefined;
+        start: number;
+        end: number;
+        strand: number | undefined;
+    }[];
     getRowData(name: string): {
         data: {
             name?: string;
@@ -478,12 +525,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
      * #getter
      */
     readonly connectedView: MaybeLGV;
-    /**
-     * #getter
-     */
-    readonly connectedProteinViews: (StructureConnection & {
-        proteinView: ProteinView;
-    })[];
 } & {
     /**
      * #getter
@@ -546,18 +587,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
      * #action
      */
     handleMsaClick(coord: number): void;
-    /**
-     * #action
-     */
-    connectToStructure(proteinViewId: string, structureIdx: number, msaRowName?: string): void;
-    /**
-     * #action
-     */
-    disconnectFromStructure(proteinViewId: string, structureIdx: number): void;
-    /**
-     * #action
-     */
-    disconnectAllStructures(): void;
 } & {
     /**
      * #action
@@ -567,17 +596,12 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     /**
      * #method
      */
-    extraViewMenuItems(): ({
+    extraViewMenuItems(): {
         label: string;
         checked: boolean;
         type: string;
         onClick: () => void;
-    } | {
-        label: string;
-        onClick: () => void;
-        checked?: undefined;
-        type?: undefined;
-    })[];
+    }[];
 } & {
     afterCreate(): void;
 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{

package/dist/MsaViewPanel/model.js

@@ -1,16 +1,11 @@
-import { lazy } from 'react';
 import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes';
 import { getSession } from '@jbrowse/core/util';
 import { addDisposer, types } from '@jbrowse/mobx-state-tree';
 import { genomeToTranscriptSeqMapping } from 'g2p_mapper';
 import { autorun } from 'mobx';
 import { MSAModelF } from 'react-msaview';
-import { autoConnectStructures, autoLoadProteinDomains, highlightConnectedStructures, launchBlastIfNeeded, loadStoredData, observeProteinHighlights, processInit, runCleanup, storeDataToIndexedDB, syncGenomeHoverToMsaColumn, } from './afterCreateAutoruns';
+import { autoLoadProteinDomains, launchBlastIfNeeded, loadStoredData, observeProteinHighlights, processInit, runCleanup, storeDataToIndexedDB, syncGenomeHoverToMsaColumn, } from './afterCreateAutoruns';
 import { msaCoordToGenomeCoord } from './msaCoordToGenomeCoord';
-import { buildAlignmentMaps, runPairwiseAlignment } from './pairwiseAlignment';
-import { getProteinViews } from './structureConnection';
-import { getCanonicalRefName } from './util';
-const ConnectStructureDialog = lazy(() => import('./components/ConnectStructureDialog'));
 /**
  * #stateModel MsaViewPlugin
  * extends
@@ -47,10 +42,6 @@ export default function stateModelFactory() {
          * #property
          */
         init: types.frozen(),
-        /**
-         * #property
-         */
-        connectedStructures: types.array(types.frozen()),
         /**
          * #property
          */
@@ -118,20 +109,6 @@ export default function stateModelFactory() {
             const { views } = getSession(self);
             return views.find(f => f.id === self.connectedViewId);
         },
-        /**
-         * #getter
-         */
-        get connectedProteinViews() {
-            const proteinViews = getProteinViews(getSession(self).views);
-            const result = [];
-            for (const conn of self.connectedStructures) {
-                const proteinView = proteinViews.find(v => v.id === conn.proteinViewId);
-                if (proteinView) {
-                    result.push({ ...conn, proteinView });
-                }
-            }
-            return result;
-        },
     }))
         .views(self => ({
         /**
@@ -233,71 +210,20 @@ export default function stateModelFactory() {
          */
         handleMsaClick(coord) {
             const { connectedView, zoomToBaseLevel } = self;
-            const { assemblyManager } = getSession(self);
             const r2 = msaCoordToGenomeCoord({ model: self, coord });
             if (!r2 || !connectedView) {
                 return;
             }
+            // Use the genome coord's own refName for both nav paths — it matches the
+            // connected view's displayed regions. Canonicalizing (e.g. "chr17"->"17")
+            // can miss a view whose regions are an alias (same as the bpToPx path).
             if (zoomToBaseLevel) {
                 connectedView.navTo(r2);
             }
             else {
-                const r = getCanonicalRefName({
-                    assemblyManager,
-                    assemblyNames: connectedView.assemblyNames,
-                    refName: r2.refName,
-                });
-                connectedView.centerAt(r2.start, r);
-            }
-        },
-        /**
-         * #action
-         */
-        connectToStructure(proteinViewId, structureIdx, msaRowName) {
-            const rowName = msaRowName ?? self.querySeqName;
-            const msaSequence = self.getSequenceByRowName(rowName);
-            if (!msaSequence) {
-                throw new Error(`MSA row "${rowName}" not found`);
-            }
-            const ungappedMsaSequence = msaSequence.replaceAll('-', '');
-            const proteinView = getProteinViews(getSession(self).views).find(v => v.id === proteinViewId);
-            if (!proteinView) {
-                throw new Error(`ProteinView "${proteinViewId}" not found`);
-            }
-            const structure = proteinView.structures[structureIdx];
-            if (!structure) {
-                throw new Error(`Structure at index ${structureIdx} not found`);
-            }
-            const structureSequence = structure.structureSequences?.[0];
-            if (!structureSequence) {
-                throw new Error('Structure sequence not available');
-            }
-            const alignment = runPairwiseAlignment(ungappedMsaSequence, structureSequence);
-            const { seq1ToSeq2 } = buildAlignmentMaps(alignment);
-            const connection = {
-                proteinViewId,
-                structureIdx,
-                msaRowName: rowName,
-                msaToStructure: Object.fromEntries(seq1ToSeq2),
-            };
-            self.connectedStructures.push(connection);
-        },
-        /**
-         * #action
-         */
-        disconnectFromStructure(proteinViewId, structureIdx) {
-            const idx = self.connectedStructures.findIndex(c => c.proteinViewId === proteinViewId &&
-                c.structureIdx === structureIdx);
-            if (idx !== -1) {
-                self.connectedStructures.splice(idx, 1);
+                connectedView.centerAt(r2.start, r2.refName);
             }
         },
-        /**
-         * #action
-         */
-        disconnectAllStructures() {
-            self.connectedStructures.clear();
-        },
     }))
         .actions(self => {
         const superSetMouseClickPos = self.setMouseClickPos.bind(self);
@@ -327,28 +253,6 @@ export default function stateModelFactory() {
                         self.setZoomToBaseLevel(!self.zoomToBaseLevel);
                     },
                 },
-                {
-                    label: 'Connect to protein structure...',
-                    onClick: () => {
-                        getSession(self).queueDialog(handleClose => [
-                            ConnectStructureDialog,
-                            {
-                                model: self,
-                                handleClose,
-                            },
-                        ]);
-                    },
-                },
-                ...(self.connectedStructures.length > 0
-                    ? [
-                        {
-                            label: 'Disconnect from protein structures',
-                            onClick: () => {
-                                self.disconnectAllStructures();
-                            },
-                        },
-                    ]
-                    : []),
             ];
         },
     }))
@@ -360,8 +264,6 @@ export default function stateModelFactory() {
                 storeDataToIndexedDB,
                 launchBlastIfNeeded,
                 processInit,
-                highlightConnectedStructures,
-                autoConnectStructures,
                 autoLoadProteinDomains,
             ]) {
                 addDisposer(self, autorun(() => {

package/dist/MsaViewPanel/structureConnection.d.ts

@@ -7,11 +7,6 @@ export interface ProteinViewStructure {
         start: number;
         end: number;
     }[];
-    hoverPosition?: {
-        structureSeqPos?: number;
-    };
-    clearHighlightFromExternal?: () => void;
-    highlightFromExternal?: (pos: number) => void;
 }
 export interface ProteinView {
     type: 'ProteinView';
@@ -26,39 +21,6 @@ export declare function isProteinView(view: unknown): view is ProteinView;
 export declare function getProteinViews(views: {
     type: string;
 }[]): ProteinView[];
-/**
- * Whether a 3D structure belongs to a given alignment — the single source of
- * truth for pairing an MsaView with a ProteinView's structure. A structure
- * matches when it either:
- *  - shares the alignment's genome view (both pinned to the same
- *    LinearGenomeView via `connectedViewId` — the genome-centric gene-explorer
- *    flow, the same key genome↔MSA and genome↔structure already bridge through),
- *    or
- *  - shares the alignment's UniProt accession (the BLAST/AlphaFold flow, which
- *    has no genome view to bridge through).
- *
- * The residue map itself is built by sequence (connectToStructure pairwise-
- * aligns the query row against the structure), so neither key is mechanically
- * required — they only scope WHICH structure pairs with the alignment.
- */
-export declare function structureMatchesMsa({ structure, connectedViewId, uniprotId, }: {
-    structure: Pick<ProteinViewStructure, 'connectedViewId' | 'uniprotId'>;
-    connectedViewId?: string;
-    uniprotId?: string;
-}): boolean;
-/**
- * Represents a connection between the MSA view and a protein structure
- */
-export interface StructureConnection {
-    /** ID of the ProteinView containing the structure */
-    proteinViewId: string;
-    /** Index of the structure within the ProteinView's structures array */
-    structureIdx: number;
-    /** Name of the MSA row that corresponds to this structure */
-    msaRowName: string;
-    /** Map from MSA ungapped position to structure sequence position */
-    msaToStructure: Record<number, number>;
-}
 /**
  * Helper to convert gapped MSA column to ungapped position for a specific row
  */

package/dist/MsaViewPanel/structureConnection.js

@@ -8,26 +8,6 @@ export function isProteinView(view) {
 export function getProteinViews(views) {
     return views.filter(isProteinView);
 }
-/**
- * Whether a 3D structure belongs to a given alignment — the single source of
- * truth for pairing an MsaView with a ProteinView's structure. A structure
- * matches when it either:
- *  - shares the alignment's genome view (both pinned to the same
- *    LinearGenomeView via `connectedViewId` — the genome-centric gene-explorer
- *    flow, the same key genome↔MSA and genome↔structure already bridge through),
- *    or
- *  - shares the alignment's UniProt accession (the BLAST/AlphaFold flow, which
- *    has no genome view to bridge through).
- *
- * The residue map itself is built by sequence (connectToStructure pairwise-
- * aligns the query row against the structure), so neither key is mechanically
- * required — they only scope WHICH structure pairs with the alignment.
- */
-export function structureMatchesMsa({ structure, connectedViewId, uniprotId, }) {
-    const sharesGenomeView = !!connectedViewId && structure.connectedViewId === connectedViewId;
-    const sharesUniprot = !!uniprotId && structure.uniprotId === uniprotId;
-    return sharesGenomeView || sharesUniprot;
-}
 /**
  * Helper to convert gapped MSA column to ungapped position for a specific row
  */

package/dist/MsaViewPanel/structureConnection.test.js

@@ -1,39 +1,5 @@
 import { describe, expect, test } from 'vitest';
-import { gappedToUngappedPosition, structureMatchesMsa, } from './structureConnection';
-describe('structureMatchesMsa', () => {
-    test('matches on a shared genome view alone (no UniProt id)', () => {
-        expect(structureMatchesMsa({
-            structure: { connectedViewId: 'lgv-TP53' },
-            connectedViewId: 'lgv-TP53',
-        })).toBe(true);
-    });
-    test('matches on a shared UniProt id alone (no genome view)', () => {
-        expect(structureMatchesMsa({
-            structure: { uniprotId: 'P04637' },
-            uniprotId: 'P04637',
-        })).toBe(true);
-    });
-    test('shared genome view wins even when UniProt ids differ', () => {
-        expect(structureMatchesMsa({
-            structure: { connectedViewId: 'lgv-TP53', uniprotId: 'OTHER' },
-            connectedViewId: 'lgv-TP53',
-            uniprotId: 'P04637',
-        })).toBe(true);
-    });
-    test('no match when neither key matches', () => {
-        expect(structureMatchesMsa({
-            structure: { connectedViewId: 'lgv-OTHER', uniprotId: 'OTHER' },
-            connectedViewId: 'lgv-TP53',
-            uniprotId: 'P04637',
-        })).toBe(false);
-    });
-    test('two undefined connectedViewIds do not count as a shared genome view', () => {
-        // both sides lacking a genome view must NOT auto-pair on `undefined ===
-        // undefined`; only an explicit shared id (or UniProt id) connects
-        expect(structureMatchesMsa({ structure: {} })).toBe(false);
-        expect(structureMatchesMsa({ structure: { uniprotId: 'P04637' } })).toBe(false);
-    });
-});
+import { gappedToUngappedPosition } from './structureConnection';
 describe('gappedToUngappedPosition', () => {
     test('returns correct ungapped position for non-gap character', () => {
         const seq = 'M-KA-A';