jbrowse-plugin-msaview 2.2.3 → 2.2.4

package/dist/MsaViewPanel/model.js

@@ -1,12 +1,56 @@
+import { lazy } from 'react';
 import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes';
 import { getSession } from '@jbrowse/core/util';
+import { addDisposer, cast, types } from '@jbrowse/mobx-state-tree';
 import { genomeToTranscriptSeqMapping } from 'g2p_mapper';
 import { autorun } from 'mobx';
-import { addDisposer, cast, types } from 'mobx-state-tree';
 import { MSAModelF } from 'react-msaview';
 import { doLaunchBlast } from './doLaunchBlast';
 import { genomeToMSA } from './genomeToMSA';
 import { msaCoordToGenomeCoord } from './msaCoordToGenomeCoord';
+import { cleanupOldData, generateDataStoreId, retrieveMsaData, storeMsaData, } from './msaDataStore';
+import { buildAlignmentMaps, runPairwiseAlignment } from './pairwiseAlignment';
+import { gappedToUngappedPosition, mapToRecord, ungappedToGappedPosition, } from './structureConnection';
+import { getUniprotIdFromAlphaFoldUrl } from './util';
+const ConnectStructureDialog = lazy(() => import('./components/ConnectStructureDialog'));
+/**
+ * Highlights residues in connected protein structures based on current MSA hover position
+ */
+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;
+        }
+        // Clear highlight if mouse left MSA
+        if (mouseCol === undefined) {
+            structure.clearHighlightFromExternal?.();
+            continue;
+        }
+        const seq = self.getSequenceByRowName(conn.msaRowName);
+        if (!seq) {
+            continue;
+        }
+        // Convert gapped MSA column to ungapped position
+        const msaUngapped = gappedToUngappedPosition(seq, mouseCol);
+        if (msaUngapped === undefined) {
+            structure.clearHighlightFromExternal?.();
+            continue;
+        }
+        // Map to structure position and highlight
+        const structurePos = conn.msaToStructure[msaUngapped];
+        if (structurePos === undefined) {
+            structure.clearHighlightFromExternal?.();
+        }
+        else {
+            structure.highlightFromExternal?.(structurePos);
+        }
+    }
+}
 /**
  * #stateModel MsaViewPlugin
  * extends
@@ -39,10 +83,43 @@ export default function stateModelFactory() {
          * #property
          */
         querySeqName: 'QUERY',
+        /**
+         * #property
+         * UniProt ID extracted from AlphaFold MSA URL
+         */
+        uniprotId: types.maybe(types.string),
         /**
          * #property
          */
         zoomToBaseLevel: false,
+        /**
+         * #property
+         * used for loading the MSA view via session snapshots, e.g.
+         * {
+         *   "type": "MsaView",
+         *   "init": {
+         *     "msaUrl": "https://example.com/alignment.fa",
+         *     "treeUrl": "https://example.com/tree.nh",
+         *     "querySeqName": "ENST00000123_hg38"
+         *   }
+         * }
+         */
+        init: types.frozen(),
+        /**
+         * #property
+         * connections to protein 3D structure views for synchronized highlighting
+         */
+        connectedStructures: types.array(types.frozen()),
+        /**
+         * #property
+         * Reference ID for MSA data stored in IndexedDB (for large datasets)
+         */
+        dataStoreId: types.maybe(types.string),
+        /**
+         * #property
+         * MAF region for coordinate mapping (used when launched from MAF viewer)
+         */
+        mafRegion: types.frozen(),
     }))
         .volatile(() => ({
         /**
@@ -57,25 +134,26 @@ export default function stateModelFactory() {
          * #volatile
          */
         error: undefined,
+        /**
+         * #volatile
+         * True when loading MSA data from IndexedDB
+         */
+        loadingStoredData: false,
     }))
         .views(self => ({
         /**
          * #method
+         * Get a row by name, returns [name, sequence] or undefined
          */
-        ungappedCoordMap(rowName, position) {
-            const row = self.rows.find(f => f[0] === rowName);
-            const seq = row?.[1];
-            if (seq && position < seq.length) {
-                let i = 0;
-                let j = 0;
-                for (; j < position; j++, i++) {
-                    while (seq[i] === '-') {
-                        i++;
-                    }
-                }
-                return i;
-            }
-            return undefined;
+        getRowByName(rowName) {
+            return self.rows.find(r => r[0] === rowName);
+        },
+        /**
+         * #method
+         * Get the sequence for a row by name
+         */
+        getSequenceByRowName(rowName) {
+            return self.rows.find(r => r[0] === rowName)?.[1];
         },
     }))
         .views(self => ({
@@ -87,34 +165,81 @@ export default function stateModelFactory() {
                 ? genomeToTranscriptSeqMapping(self.connectedFeature)
                 : undefined;
         },
-    }))
-        .views(self => ({
         /**
          * #getter
          */
-        get mouseCol2() {
-            return genomeToMSA({ model: self });
+        get processing() {
+            return !!self.progress;
         },
         /**
          * #getter
          */
-        get clickCol2() {
+        get connectedView() {
+            const { views } = getSession(self);
+            return views.find(f => f.id === self.connectedViewId);
+        },
+        /**
+         * #getter
+         * Get connected protein views with their full model references
+         */
+        get connectedProteinViews() {
+            const { views } = getSession(self);
+            return self.connectedStructures
+                .map(conn => {
+                const proteinView = views.find((v) => v.id === conn.proteinViewId);
+                return proteinView ? { ...conn, proteinView } : undefined;
+            })
+                .filter((c) => !!c);
+        },
+    }))
+        .views(self => ({
+        /**
+         * #getter
+         * Get the MSA column that corresponds to the currently hovered structure position
+         * Returns the first match from any connected structure
+         */
+        get structureHoverCol() {
+            for (const conn of self.connectedProteinViews) {
+                const structure = conn.proteinView?.structures?.[conn.structureIdx];
+                const structurePos = structure?.hoverPosition?.structureSeqPos;
+                if (structurePos !== undefined) {
+                    const msaUngapped = conn.structureToMsa[structurePos];
+                    if (msaUngapped !== undefined) {
+                        const seq = self.getSequenceByRowName(conn.msaRowName);
+                        if (seq) {
+                            // Convert ungapped position to global column, then to visible column
+                            const globalCol = ungappedToGappedPosition(seq, msaUngapped);
+                            if (globalCol !== undefined) {
+                                return self.globalColToVisibleCol(globalCol);
+                            }
+                        }
+                    }
+                }
+            }
             return undefined;
         },
     }))
         .views(self => ({
         /**
          * #getter
+         * Returns a secondary highlight column from either:
+         * 1. Structure hover (from connected protein 3D view)
+         * 2. Genome hover (from connected linear genome view)
          */
-        get processing() {
-            return !!self.progress;
+        get mouseCol2() {
+            // Check structure hover first
+            const structureCol = self.structureHoverCol;
+            if (structureCol !== undefined) {
+                return structureCol;
+            }
+            // Fall back to genome hover
+            return genomeToMSA({ model: self });
         },
         /**
          * #getter
          */
-        get connectedView() {
-            const { views } = getSession(self);
-            return views.find(f => f.id === self.connectedViewId);
+        get clickCol2() {
+            return undefined;
         },
     }))
         .actions(self => ({
@@ -166,6 +291,42 @@ export default function stateModelFactory() {
         setBlastParams(args) {
             self.blastParams = args;
         },
+        /**
+         * #action
+         */
+        setInit(arg) {
+            self.init = arg;
+        },
+        /**
+         * #action
+         */
+        setQuerySeqName(arg) {
+            self.querySeqName = arg;
+        },
+        /**
+         * #action
+         */
+        setUniprotId(arg) {
+            self.uniprotId = arg;
+        },
+        /**
+         * #action
+         */
+        setDataStoreId(arg) {
+            self.dataStoreId = arg;
+        },
+        /**
+         * #action
+         */
+        setMafRegion(arg) {
+            self.mafRegion = arg;
+        },
+        /**
+         * #action
+         */
+        setLoadingStoredData(arg) {
+            self.loadingStoredData = arg;
+        },
         /**
          * #action
          */
@@ -186,10 +347,63 @@ export default function stateModelFactory() {
                 connectedView.centerAt(r2.start, r);
             }
         },
+        /**
+         * #action
+         * Connect to a protein structure for synchronized highlighting
+         */
+        connectToStructure(proteinViewId, structureIdx, msaRowName) {
+            const rowName = msaRowName ?? self.querySeqName;
+            const msaSequence = self.getSequenceByRowName(rowName);
+            if (!msaSequence) {
+                throw new Error(`MSA row "${rowName}" not found`);
+            }
+            const ungappedMsaSequence = msaSequence.replaceAll('-', '');
+            const { views } = getSession(self);
+            const proteinView = views.find((v) => v.id === proteinViewId);
+            if (!proteinView) {
+                throw new Error(`ProteinView "${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, seq2ToSeq1 } = buildAlignmentMaps(alignment);
+            const connection = {
+                proteinViewId,
+                structureIdx,
+                msaRowName: rowName,
+                msaToStructure: mapToRecord(seq1ToSeq2),
+                structureToMsa: mapToRecord(seq2ToSeq1),
+            };
+            self.connectedStructures.push(connection);
+        },
+        /**
+         * #action
+         * Disconnect from a protein structure
+         */
+        disconnectFromStructure(proteinViewId, structureIdx) {
+            const idx = self.connectedStructures.findIndex(c => c.proteinViewId === proteinViewId &&
+                c.structureIdx === structureIdx);
+            if (idx !== -1) {
+                self.connectedStructures.splice(idx, 1);
+            }
+        },
+        /**
+         * #action
+         * Disconnect from all protein structures
+         */
+        disconnectAllStructures() {
+            self.connectedStructures.clear();
+        },
     }))
         .actions(self => {
         // store reference to the original action from react-msaview
-        const superSetMouseClickPos = self.setMouseClickPos;
+        const superSetMouseClickPos = self.setMouseClickPos.bind(self);
         return {
             /**
              * #action
@@ -218,24 +432,95 @@ 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();
+                            },
+                        },
+                    ]
+                    : []),
             ];
         },
-        /**
-         * #getter
-         */
-        get processing() {
-            return !!self.progress;
-        },
-        /**
-         * #getter
-         */
-        get connectedView() {
-            const { views } = getSession(self);
-            return views.find(f => f.id === self.connectedViewId);
-        },
     }))
         .actions(self => ({
         afterCreate() {
+            // Clean up old IndexedDB entries on startup
+            cleanupOldData().catch((e) => {
+                console.error('Failed to cleanup old MSA data:', e);
+            });
+            // Load MSA data from IndexedDB if dataStoreId exists and no data loaded
+            addDisposer(self, autorun(async () => {
+                const { dataStoreId, rows } = self;
+                if (dataStoreId && rows.length === 0) {
+                    try {
+                        self.setLoadingStoredData(true);
+                        const storedData = await retrieveMsaData(dataStoreId);
+                        if (storedData) {
+                            if (storedData.msa) {
+                                self.setMSA(storedData.msa);
+                            }
+                            if (storedData.tree) {
+                                self.setTree(storedData.tree);
+                            }
+                        }
+                    }
+                    catch (e) {
+                        console.error('Failed to load MSA data from IndexedDB:', e);
+                    }
+                    finally {
+                        self.setLoadingStoredData(false);
+                    }
+                }
+            }));
+            // Store MSA data to IndexedDB when loaded from inline data (no filehandle)
+            // This ensures data persists across page refreshes even when
+            // react-msaview's postProcessSnapshot would strip it
+            addDisposer(self, autorun(async () => {
+                const { rows, dataStoreId } = self;
+                // Only store if we have data and don't already have a dataStoreId
+                if (rows.length > 0 && !dataStoreId) {
+                    // Only store if there's no filehandle (filehandles can reload from source)
+                    const hasFilehandle = !!(self.msaFilehandle ?? self.treeFilehandle);
+                    if (hasFilehandle) {
+                        return;
+                    }
+                    const msaData = self.data.msa;
+                    const treeData = self.data.tree;
+                    // Only store if we have actual data
+                    if (msaData || treeData) {
+                        try {
+                            const newId = generateDataStoreId();
+                            const success = await storeMsaData(newId, {
+                                msa: msaData,
+                                tree: treeData,
+                                treeMetadata: self.data.treeMetadata,
+                            });
+                            // Only set dataStoreId if storage was successful
+                            if (success) {
+                                self.setDataStoreId(newId);
+                            }
+                        }
+                        catch (e) {
+                            console.error('Failed to store MSA data to IndexedDB:', e);
+                        }
+                    }
+                }
+            }));
             addDisposer(self, autorun(async () => {
                 if (self.blastParams) {
                     try {
@@ -256,6 +541,56 @@ export default function stateModelFactory() {
                     }
                 }
             }));
+            // process init parameter for loading MSA from session snapshots
+            addDisposer(self, autorun(async () => {
+                const { init } = self;
+                if (init) {
+                    try {
+                        self.setError(undefined);
+                        const { msaData, msaUrl, treeData, treeUrl, querySeqName } = init;
+                        // Extract uniprotId from AlphaFold MSA URL and set querySeqName
+                        if (msaUrl) {
+                            const id = getUniprotIdFromAlphaFoldUrl(msaUrl);
+                            if (id) {
+                                self.setUniprotId(id);
+                                // AlphaFold MSA files use 'query' as the row name
+                                self.setQuerySeqName('query');
+                            }
+                        }
+                        // User-provided querySeqName takes precedence
+                        if (querySeqName) {
+                            self.setQuerySeqName(querySeqName);
+                        }
+                        if (msaData) {
+                            self.setMSA(msaData);
+                        }
+                        else if (msaUrl) {
+                            const response = await fetch(msaUrl);
+                            if (!response.ok) {
+                                throw new Error(`Failed to fetch MSA: ${response.status}`);
+                            }
+                            const data = await response.text();
+                            self.setMSA(data);
+                        }
+                        if (treeData) {
+                            self.setTree(treeData);
+                        }
+                        else if (treeUrl) {
+                            const response = await fetch(treeUrl);
+                            if (!response.ok) {
+                                throw new Error(`Failed to fetch tree: ${response.status}`);
+                            }
+                            const data = await response.text();
+                            self.setTree(data);
+                        }
+                        self.setInit(undefined);
+                    }
+                    catch (e) {
+                        self.setError(e);
+                        console.error(e);
+                    }
+                }
+            }));
             // this adds highlights to the genome view when mouse-ing over the MSA
             addDisposer(self, autorun(() => {
                 const { mouseCol, mouseClickCol } = self;
@@ -267,6 +602,99 @@ export default function stateModelFactory() {
                     : msaCoordToGenomeCoord({ model: self, coord: mouseClickCol });
                 self.setConnectedHighlights([r1, r2].filter(f => !!f));
             }));
+            // this highlights residues in connected protein structures when mousing over the MSA
+            addDisposer(self, autorun(() => {
+                highlightConnectedStructures(self);
+            }));
+            // auto-connect to compatible ProteinViews
+            addDisposer(self, autorun(() => {
+                const { views } = getSession(self);
+                const { connectedViewId, uniprotId, rows, connectedStructures } = self;
+                // Need MSA loaded and a uniprotId to auto-connect
+                if (!uniprotId || rows.length === 0) {
+                    return;
+                }
+                // Find ProteinViews that share the same connectedViewId
+                for (const view of views) {
+                    const v = view;
+                    if (v.type !== 'ProteinView' || !v.structures) {
+                        continue;
+                    }
+                    for (let structureIdx = 0; structureIdx < v.structures.length; structureIdx++) {
+                        const structure = v.structures[structureIdx];
+                        // Check if structure shares the same genome view connection
+                        if (structure.connectedViewId !== connectedViewId) {
+                            continue;
+                        }
+                        // Check if structure has matching uniprotId
+                        if (structure.uniprotId !== uniprotId) {
+                            continue;
+                        }
+                        // Check if already connected
+                        const alreadyConnected = connectedStructures.some(c => c.proteinViewId === v.id && c.structureIdx === structureIdx);
+                        if (alreadyConnected) {
+                            continue;
+                        }
+                        // Check if structure sequence is available
+                        if (!structure.structureSequences?.[0]) {
+                            continue;
+                        }
+                        // Auto-connect
+                        try {
+                            self.connectToStructure(v.id, structureIdx);
+                        }
+                        catch (e) {
+                            console.error('Failed to auto-connect to ProteinView:', e);
+                        }
+                    }
+                }
+            }));
+            // Observe protein3d genome highlights and update MSA highlighted columns
+            // This enables communication via the linear genome view coordinates
+            addDisposer(self, autorun(() => {
+                const { views } = getSession(self);
+                const { connectedViewId, transcriptToMsaMap, querySeqName } = self;
+                if (!connectedViewId || !transcriptToMsaMap) {
+                    return;
+                }
+                const columns = [];
+                // Find ProteinViews that share the same connected genome view
+                for (const view of views) {
+                    const v = view;
+                    if (v.type !== 'ProteinView' || !v.structures) {
+                        continue;
+                    }
+                    for (const structure of v.structures) {
+                        // Check if structure is connected to same genome view
+                        if (structure.connectedViewId !== connectedViewId) {
+                            continue;
+                        }
+                        // Check if structure has hover genome highlights
+                        const highlights = structure.hoverGenomeHighlights;
+                        if (!highlights || highlights.length === 0) {
+                            continue;
+                        }
+                        // Map genome coordinates to MSA columns
+                        const { g2p } = transcriptToMsaMap;
+                        for (const highlight of highlights) {
+                            for (let coord = highlight.start; coord < highlight.end; coord++) {
+                                const proteinPos = g2p[coord];
+                                if (proteinPos !== undefined) {
+                                    const col = self.seqPosToGlobalCol(querySeqName, proteinPos);
+                                    if (!columns.includes(col)) {
+                                        columns.push(col);
+                                    }
+                                }
+                            }
+                        }
+                    }
+                }
+                // Convert global column indices to visible column indices
+                const visibleColumns = columns
+                    .map(col => self.globalColToVisibleCol(col))
+                    .filter((col) => col !== undefined);
+                self.setHighlightedColumns(visibleColumns.length > 0 ? visibleColumns : undefined);
+            }));
         },
     }));
 }

package/dist/MsaViewPanel/model.js.map

@@ -1 +1 @@
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package/dist/MsaViewPanel/msaCoordToGenomeCoord.d.ts

@@ -1,12 +1,17 @@
+import type { MafRegion } from './types';
 export declare function msaCoordToGenomeCoord({ model, coord: mouseCol, }: {
     model: {
         querySeqName: string;
-        transcriptToMsaMap: any;
+        transcriptToMsaMap: {
+            refName: string;
+            p2g: Record<number, number>;
+        } | undefined;
+        mafRegion?: MafRegion;
         rows: string[][];
     };
     coord: number;
 }): {
-    refName: any;
+    refName: string;
     start: number;
     end: number;
 } | undefined;