jbrowse-plugin-msaview 2.2.11 → 2.3.2

package/dist/MsaViewPanel/model.js

@@ -5,52 +5,12 @@ import { addDisposer, cast, types } from '@jbrowse/mobx-state-tree';
 import { genomeToTranscriptSeqMapping } from 'g2p_mapper';
 import { autorun } from 'mobx';
 import { MSAModelF } from 'react-msaview';
-import { doLaunchBlast } from './doLaunchBlast';
+import { autoConnectStructures, highlightConnectedStructures, launchBlastIfNeeded, loadStoredData, observeProteinHighlights, processInit, runCleanup, storeDataToIndexedDB, updateGenomeHighlights, } from './afterCreateAutoruns';
 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';
+import { mapToRecord, ungappedToGappedPosition } from './structureConnection';
 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
@@ -85,7 +45,6 @@ export default function stateModelFactory() {
         querySeqName: 'QUERY',
         /**
          * #property
-         * UniProt ID extracted from AlphaFold MSA URL
          */
         uniprotId: types.maybe(types.string),
         /**
@@ -94,30 +53,18 @@ export default function stateModelFactory() {
         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(),
     }))
@@ -136,21 +83,18 @@ export default function stateModelFactory() {
         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
          */
         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];
@@ -180,7 +124,6 @@ export default function stateModelFactory() {
         },
         /**
          * #getter
-         * Get connected protein views with their full model references
          */
         get connectedProteinViews() {
             const { views } = getSession(self);
@@ -195,8 +138,6 @@ export default function stateModelFactory() {
         .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) {
@@ -207,7 +148,6 @@ export default function stateModelFactory() {
                     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);
@@ -222,17 +162,12 @@ export default function stateModelFactory() {
         .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 mouseCol2() {
-            // Check structure hover first
             const structureCol = self.structureHoverCol;
             if (structureCol !== undefined) {
                 return structureCol;
             }
-            // Fall back to genome hover
             return genomeToMSA({ model: self });
         },
         /**
@@ -349,7 +284,6 @@ export default function stateModelFactory() {
         },
         /**
          * #action
-         * Connect to a protein structure for synchronized highlighting
          */
         connectToStructure(proteinViewId, structureIdx, msaRowName) {
             const rowName = msaRowName ?? self.querySeqName;
@@ -384,7 +318,6 @@ export default function stateModelFactory() {
         },
         /**
          * #action
-         * Disconnect from a protein structure
          */
         disconnectFromStructure(proteinViewId, structureIdx) {
             const idx = self.connectedStructures.findIndex(c => c.proteinViewId === proteinViewId &&
@@ -395,19 +328,16 @@ export default function stateModelFactory() {
         },
         /**
          * #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.bind(self);
         return {
             /**
              * #action
-             * overrides base setMouseClickPos to trigger navigation
              */
             setMouseClickPos(col, row) {
                 superSetMouseClickPos(col, row);
@@ -420,7 +350,6 @@ export default function stateModelFactory() {
         .views(self => ({
         /**
          * #method
-         * overrides base
          */
         extraViewMenuItems() {
             return [
@@ -459,242 +388,21 @@ export default function stateModelFactory() {
     }))
         .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 {
-                        self.setProgress('Submitting query');
-                        self.setError(undefined);
-                        const data = await doLaunchBlast({
-                            self,
-                        });
-                        self.setData(data);
-                        self.setBlastParams(undefined);
-                    }
-                    catch (e) {
-                        self.setError(e);
-                        console.error(e);
-                    }
-                    finally {
-                        self.setProgress('');
-                    }
-                }
-            }));
-            // 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;
-                const r1 = mouseCol === undefined
-                    ? undefined
-                    : msaCoordToGenomeCoord({ model: self, coord: mouseCol });
-                const r2 = mouseClickCol === undefined
-                    ? undefined
-                    : 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);
-            }));
+            runCleanup();
+            for (const fn of [
+                loadStoredData,
+                storeDataToIndexedDB,
+                launchBlastIfNeeded,
+                processInit,
+                updateGenomeHighlights,
+                highlightConnectedStructures,
+                autoConnectStructures,
+                observeProteinHighlights,
+            ]) {
+                addDisposer(self, autorun(() => {
+                    fn(self);
+                }));
+            }
         },
     }));
 }

package/dist/MsaViewPanel/model.js.map

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

@@ -5,10 +5,9 @@ export declare function storeMsaData(id: string, data: {
     treeMetadata?: string;
 }): Promise<boolean>;
 export declare function retrieveMsaData(id: string): Promise<{
-    msa?: string;
-    tree?: string;
-    treeMetadata?: string;
+    msa: string | undefined;
+    tree: string | undefined;
+    treeMetadata: string | undefined;
 } | undefined>;
 export declare function deleteMsaData(id: string): Promise<void>;
 export declare function cleanupOldData(maxAgeMs?: number): Promise<number>;
-export declare function isIndexedDBAvailable(): boolean;