jbrowse-plugin-msaview 2.6.3 → 2.6.4

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "2.6.3";
+export declare const version = "2.6.4";

package/dist/version.js

@@ -1 +1 @@
-export const version = '2.6.3';
+export const version = '2.6.4';

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "2.6.3",
+  "version": "2.6.4",
   "license": "MIT",
   "name": "jbrowse-plugin-msaview",
   "repository": {

package/src/AddHighlightModel/MsaToGenomeHighlight.tsx

@@ -5,7 +5,6 @@ import { observer } from 'mobx-react'
 
 import { hasHoverPosition, useStyles } from './util'
 import { isMsaView } from '../MsaViewPanel/model'
-import { getCanonicalRefName } from '../MsaViewPanel/util'
 
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
@@ -38,19 +37,19 @@ const MsaToGenomeHighlightRenderer = observer(function ({
   highlights: { refName: string; start: number; end: number }[]
 }) {
   const { classes } = useStyles()
-  const { assemblyManager } = getSession(model)
   const { offsetPx } = model
 
   return (
     <>
       {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/src/MsaViewPanel/afterCreateAutoruns.ts

@@ -10,11 +10,7 @@ import {
   retrieveMsaData,
   storeMsaData,
 } from './msaDataStore'
-import {
-  gappedToUngappedPosition,
-  getProteinViews,
-  structureMatchesMsa,
-} from './structureConnection'
+import { getProteinViews } from './structureConnection'
 import { getUniprotIdFromAlphaFoldUrl } from './util'
 
 import type { JBrowsePluginMsaViewModel } from './model'
@@ -199,85 +195,6 @@ export function syncGenomeHoverToMsaColumn(self: JBrowsePluginMsaViewModel) {
   }
 }
 
-export function highlightConnectedStructures(self: JBrowsePluginMsaViewModel) {
-  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: JBrowsePluginMsaViewModel) {
-  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/src/MsaViewPanel/model.ts

@@ -1,5 +1,3 @@
-import { lazy } from 'react'
-
 import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes'
 import { getSession } from '@jbrowse/core/util'
 import { addDisposer, types } from '@jbrowse/mobx-state-tree'
@@ -12,9 +10,7 @@ import { MSAModelF } from 'react-msaview'
 export type { MSAFormat } from 'msa-parsers'
 
 import {
-  autoConnectStructures,
   autoLoadProteinDomains,
-  highlightConnectedStructures,
   launchBlastIfNeeded,
   loadStoredData,
   observeProteinHighlights,
@@ -24,11 +20,7 @@ import {
   syncGenomeHoverToMsaColumn,
 } from './afterCreateAutoruns'
 import { msaCoordToGenomeCoord } from './msaCoordToGenomeCoord'
-import { buildAlignmentMaps, runPairwiseAlignment } from './pairwiseAlignment'
-import { getProteinViews } from './structureConnection'
-import { getCanonicalRefName } from './util'
 
-import type { ProteinView, StructureConnection } from './structureConnection'
 import type { MafRegion, MsaViewInitState } from './types'
 import type {
   BlastDatabase,
@@ -39,10 +31,6 @@ import type { Feature } from '@jbrowse/core/util'
 import type { Instance } from '@jbrowse/mobx-state-tree'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
-const ConnectStructureDialog = lazy(
-  () => import('./components/ConnectStructureDialog'),
-)
-
 type LGV = LinearGenomeViewModel
 
 type MaybeLGV = LGV | undefined
@@ -106,11 +94,6 @@ export default function stateModelFactory() {
          */
         init: types.frozen<MsaViewInitState | undefined>(),
 
-        /**
-         * #property
-         */
-        connectedStructures: types.array(types.frozen<StructureConnection>()),
-
         /**
          * #property
          */
@@ -194,24 +177,6 @@ export default function stateModelFactory() {
         const { views } = getSession(self)
         return views.find(f => f.id === self.connectedViewId) as MaybeLGV
       },
-
-      /**
-       * #getter
-       */
-      get connectedProteinViews() {
-        const proteinViews = getProteinViews(getSession(self).views)
-        const result: (StructureConnection & { proteinView: ProteinView })[] =
-          []
-        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 => ({
@@ -315,94 +280,22 @@ export default function stateModelFactory() {
        */
       handleMsaClick(coord: number) {
         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)
+          connectedView.centerAt(r2.start, r2.refName)
         }
       },
 
-      /**
-       * #action
-       */
-      connectToStructure(
-        proteinViewId: string,
-        structureIdx: number,
-        msaRowName?: string,
-      ) {
-        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: StructureConnection = {
-          proteinViewId,
-          structureIdx,
-          msaRowName: rowName,
-          msaToStructure: Object.fromEntries(seq1ToSeq2),
-        }
-
-        self.connectedStructures.push(connection)
-      },
-
-      /**
-       * #action
-       */
-      disconnectFromStructure(proteinViewId: string, structureIdx: number) {
-        const idx = self.connectedStructures.findIndex(
-          c =>
-            c.proteinViewId === proteinViewId &&
-            c.structureIdx === structureIdx,
-        )
-        if (idx !== -1) {
-          self.connectedStructures.splice(idx, 1)
-        }
-      },
-
-      /**
-       * #action
-       */
-      disconnectAllStructures() {
-        self.connectedStructures.clear()
-      },
     }))
     .actions(self => {
       const superSetMouseClickPos = self.setMouseClickPos.bind(self)
@@ -434,28 +327,6 @@ 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()
-                  },
-                },
-              ]
-            : []),
         ]
       },
     }))
@@ -468,8 +339,6 @@ export default function stateModelFactory() {
           storeDataToIndexedDB,
           launchBlastIfNeeded,
           processInit,
-          highlightConnectedStructures,
-          autoConnectStructures,
           autoLoadProteinDomains,
         ]) {
           addDisposer(

package/src/MsaViewPanel/structureConnection.test.ts

@@ -1,58 +1,6 @@
 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', () => {

package/src/MsaViewPanel/structureConnection.ts

@@ -4,9 +4,6 @@ export interface ProteinViewStructure {
   uniprotId?: string
   structureSequences?: string[]
   hoverGenomeHighlights?: { start: number; end: number }[]
-  hoverPosition?: { structureSeqPos?: number }
-  clearHighlightFromExternal?: () => void
-  highlightFromExternal?: (pos: number) => void
 }
 
 export interface ProteinView {
@@ -28,50 +25,6 @@ export function getProteinViews(views: { type: string }[]): ProteinView[] {
   return (views as unknown[]).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,
-}: {
-  structure: Pick<ProteinViewStructure, 'connectedViewId' | 'uniprotId'>
-  connectedViewId?: string
-  uniprotId?: string
-}) {
-  const sharesGenomeView =
-    !!connectedViewId && structure.connectedViewId === connectedViewId
-  const sharesUniprot = !!uniprotId && structure.uniprotId === uniprotId
-  return sharesGenomeView || sharesUniprot
-}
-
-/**
- * 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/src/version.ts

@@ -1 +1 @@
-export const version = '2.6.3'
+export const version = '2.6.4'

package/dist/MsaViewPanel/autoConnectStructures.test.d.ts

@@ -1 +0,0 @@
-export {};

package/dist/MsaViewPanel/autoConnectStructures.test.js

@@ -1,60 +0,0 @@
-import { getSession } from '@jbrowse/core/util';
-import { beforeEach, describe, expect, test, vi } from 'vitest';
-import { autoConnectStructures } from './afterCreateAutoruns';
-// Integration coverage for the autorun itself — the structure-matching matrix
-// lives in structureConnection.test.ts (structureMatchesMsa). Here we check the
-// autorun wires a match through to connectToStructure and respects its guards.
-// Mock only getSession; keep the rest of the util module real so the
-// afterCreateAutoruns import graph still loads.
-vi.mock('@jbrowse/core/util', async (importOriginal) => ({
-    ...(await importOriginal()),
-    getSession: vi.fn(),
-}));
-const mockGetSession = vi.mocked(getSession);
-function makeModel(opts) {
-    const connected = [];
-    const model = {
-        connectedViewId: opts.connectedViewId,
-        uniprotId: opts.uniprotId,
-        rows: [['hg38', 'MKATEST']],
-        connectedStructures: connected,
-        connectToStructure: (proteinViewId, structureIdx) => {
-            connected.push({ proteinViewId, structureIdx });
-        },
-    };
-    return { model, connected };
-}
-function withStructure(structure) {
-    const view = {
-        type: 'ProteinView',
-        id: 'pv1',
-        structures: [{ ...structure, structureSequences: ['MKATEST'] }],
-    };
-    mockGetSession.mockReturnValue({
-        views: [view],
-    });
-}
-describe('autoConnectStructures', () => {
-    beforeEach(() => {
-        vi.clearAllMocks();
-    });
-    test('connects a matching structure (genome-view link, no UniProt id)', () => {
-        const { model, connected } = makeModel({ connectedViewId: 'lgv-TP53' });
-        withStructure({ connectedViewId: 'lgv-TP53' });
-        autoConnectStructures(model);
-        expect(connected).toEqual([{ proteinViewId: 'pv1', structureIdx: 0 }]);
-    });
-    test('does not connect a non-matching structure', () => {
-        const { model, connected } = makeModel({ connectedViewId: 'lgv-TP53' });
-        withStructure({ connectedViewId: 'lgv-OTHER' });
-        autoConnectStructures(model);
-        expect(connected).toEqual([]);
-    });
-    test('does not connect before the alignment has loaded (no rows)', () => {
-        const { model, connected } = makeModel({ connectedViewId: 'lgv-TP53' });
-        model.rows = [];
-        withStructure({ connectedViewId: 'lgv-TP53' });
-        autoConnectStructures(model);
-        expect(connected).toEqual([]);
-    });
-});

package/dist/MsaViewPanel/components/ConnectStructureDialog.d.ts

@@ -1,7 +0,0 @@
-import React from 'react';
-import type { JBrowsePluginMsaViewModel } from '../model';
-declare const ConnectStructureDialog: ({ model, handleClose, }: {
-    model: JBrowsePluginMsaViewModel;
-    handleClose: () => void;
-}) => React.JSX.Element;
-export default ConnectStructureDialog;

package/dist/MsaViewPanel/components/ConnectStructureDialog.js

@@ -1,60 +0,0 @@
-import React, { useState } from 'react';
-import { Dialog, ErrorMessage } from '@jbrowse/core/ui';
-import { getSession } from '@jbrowse/core/util';
-import { Button, DialogActions, DialogContent, FormControl, InputLabel, MenuItem, Select, Typography, } from '@mui/material';
-import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
-import { getProteinViews } from '../structureConnection';
-const useStyles = makeStyles()(theme => ({
-    formControl: {
-        marginBottom: theme.spacing(2),
-    },
-}));
-const ConnectStructureDialog = observer(function ConnectStructureDialog({ model, handleClose, }) {
-    const { classes } = useStyles();
-    const session = getSession(model);
-    const [selectedViewId, setSelectedViewId] = useState('');
-    const [selectedStructureIdx, setSelectedStructureIdx] = useState(0);
-    const [selectedMsaRow, setSelectedMsaRow] = useState(model.querySeqName);
-    const [error, setError] = useState();
-    const proteinViews = getProteinViews(session.views);
-    const selectedView = proteinViews.find(v => v.id === selectedViewId);
-    const structures = selectedView?.structures ?? [];
-    const msaRowNames = model.rows.map(r => r[0]);
-    const handleConnect = () => {
-        if (!selectedViewId) {
-            setError('Please select a protein view');
-            return;
-        }
-        try {
-            model.connectToStructure(selectedViewId, selectedStructureIdx, selectedMsaRow);
-            handleClose();
-        }
-        catch (e) {
-            setError(e instanceof Error ? e.message : String(e));
-        }
-    };
-    return (React.createElement(Dialog, { maxWidth: "sm", title: "Connect to Protein Structure", open: true, onClose: handleClose },
-        React.createElement(DialogContent, null, proteinViews.length === 0 ? (React.createElement(Typography, { color: "textSecondary" }, "No protein views are currently open. Please open a protein structure view first.")) : (React.createElement(React.Fragment, null,
-            React.createElement(FormControl, { fullWidth: true, className: classes.formControl },
-                React.createElement(InputLabel, null, "Protein View"),
-                React.createElement(Select, { value: selectedViewId, label: "Protein View", onChange: e => {
-                        setSelectedViewId(e.target.value);
-                        setSelectedStructureIdx(0);
-                    } }, proteinViews.map(view => (React.createElement(MenuItem, { key: view.id, value: view.id }, view.displayName ?? `ProteinView ${view.id}`))))),
-            structures.length > 1 ? (React.createElement(FormControl, { fullWidth: true, className: classes.formControl },
-                React.createElement(InputLabel, null, "Structure"),
-                React.createElement(Select, { value: selectedStructureIdx, label: "Structure", onChange: e => {
-                        setSelectedStructureIdx(e.target.value);
-                    } }, structures.map((structure, idx) => (React.createElement(MenuItem, { key: idx, value: idx }, structure.url ?? `Structure ${idx + 1}`)))))) : null,
-            React.createElement(FormControl, { fullWidth: true, className: classes.formControl },
-                React.createElement(InputLabel, null, "MSA Row"),
-                React.createElement(Select, { value: selectedMsaRow, label: "MSA Row", onChange: e => {
-                        setSelectedMsaRow(e.target.value);
-                    } }, msaRowNames.map(name => (React.createElement(MenuItem, { key: name, value: name }, name))))),
-            error ? React.createElement(ErrorMessage, { error: error }) : null))),
-        React.createElement(DialogActions, null,
-            React.createElement(Button, { onClick: handleClose }, "Cancel"),
-            React.createElement(Button, { onClick: handleConnect, variant: "contained", disabled: proteinViews.length === 0 || !selectedViewId }, "Connect"))));
-});
-export default ConnectStructureDialog;

package/dist/MsaViewPanel/pairwiseAlignment.d.ts

@@ -1,20 +0,0 @@
-interface AlignmentResult {
-    alignedSeq1: string;
-    alignedSeq2: string;
-    score: number;
-}
-export interface AlignmentRow {
-    id: string;
-    seq: string;
-}
-export interface PairwiseAlignment {
-    consensus: string;
-    alns: readonly [AlignmentRow, AlignmentRow];
-}
-export declare function needlemanWunsch(seq1: string, seq2: string, gapOpen?: number, gapExtend?: number): AlignmentResult;
-export declare function runPairwiseAlignment(seq1: string, seq2: string): PairwiseAlignment;
-export declare function buildAlignmentMaps(pairwiseAlignment: PairwiseAlignment): {
-    seq1ToSeq2: Map<number, number>;
-    seq2ToSeq1: Map<number, number>;
-};
-export {};