jbrowse-plugin-msaview 2.6.2 → 2.6.4

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "2.6.2";
+export declare const version = "2.6.4";

package/dist/version.js

@@ -1 +1 @@
-export const version = '2.6.2';
+export const version = '2.6.4';

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "2.6.2",
+  "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/LaunchMsaViewExtensionPoint/index.ts

@@ -46,18 +46,25 @@ export default function LaunchMsaViewExtensionPointF(
         )
       }
 
-      // all data sources flow through `init` so processInit is the single place
-      // that resolves them (AlphaFold detection, native filehandle loading, etc.)
+      // inline data and the tree URL are native react-msaview snapshot props, set
+      // directly. Only sources needing launch-time resolution go through `init`:
+      // msaUrl (AlphaFold sniff) and the name-indexed bgzip block (no native loader).
       session.addView('MsaView', {
         type: 'MsaView',
         ...rest,
+        data,
+        ...(treeFileLocation
+          ? {
+              treeFilehandle: {
+                ...treeFileLocation,
+                locationType: 'UriLocation',
+              },
+            }
+          : {}),
         init: {
-          msaData: data?.msa,
-          treeData: data?.tree,
           msaUrl: msaFileLocation?.uri,
           msaIndexedLocation,
           msaName,
-          treeUrl: treeFileLocation?.uri,
           querySeqName,
         },
       })

package/src/MsaViewPanel/afterCreateAutoruns.ts

@@ -10,10 +10,7 @@ import {
   retrieveMsaData,
   storeMsaData,
 } from './msaDataStore'
-import {
-  gappedToUngappedPosition,
-  getProteinViews,
-} from './structureConnection'
+import { getProteinViews } from './structureConnection'
 import { getUniprotIdFromAlphaFoldUrl } from './util'
 
 import type { JBrowsePluginMsaViewModel } from './model'
@@ -128,22 +125,15 @@ export function autoLoadProteinDomains(self: JBrowsePluginMsaViewModel) {
   }
 }
 
-// Resolve the declarative `init` launch contract once. Inline strings go straight
-// to the data model; URLs are handed to react-msaview's native filehandle loaders
-// (openLocation + progress + abort + CORS-proxy) rather than a hand-rolled fetch;
-// the bgzip name-indexed block is the one source with no native loader.
+// Resolve the declarative `init` launch contract once, then clear it. msaUrl is
+// handed to react-msaview's native filehandle loader (openLocation + progress +
+// abort + CORS-proxy) and sniffed for an AlphaFold uniprotId; the bgzip
+// name-indexed block is the one source with no native loader, so it's fetched
+// here. Inline data and tree URLs arrive as native snapshot props, not via init.
 export function processInit(self: JBrowsePluginMsaViewModel) {
   const { init } = self
   if (init) {
-    const {
-      msaData,
-      msaUrl,
-      msaIndexedLocation,
-      msaName,
-      treeData,
-      treeUrl,
-      querySeqName,
-    } = init
+    const { msaUrl, msaIndexedLocation, msaName, querySeqName } = init
     void (async () => {
       try {
         self.setError(undefined)
@@ -159,9 +149,7 @@ export function processInit(self: JBrowsePluginMsaViewModel) {
           self.setQuerySeqName(querySeqName)
         }
 
-        if (msaData) {
-          self.setMSA(msaData)
-        } else if (msaUrl) {
+        if (msaUrl) {
           self.setMSAFilehandle({ uri: msaUrl, locationType: 'UriLocation' })
         } else if (msaIndexedLocation && msaName) {
           const fasta = await fetchIndexedMsa({
@@ -177,12 +165,6 @@ export function processInit(self: JBrowsePluginMsaViewModel) {
           }
         }
 
-        if (treeData) {
-          self.setTree(treeData)
-        } else if (treeUrl) {
-          self.setTreeFilehandle({ uri: treeUrl, locationType: 'UriLocation' })
-        }
-
         self.setInit(undefined)
       } catch (e) {
         self.setError(e)
@@ -213,89 +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 (!uniprotId || 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 (structure.connectedViewId !== connectedViewId) {
-        continue
-      }
-
-      if (structure.uniprotId !== 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.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 {
@@ -28,20 +25,6 @@ export function getProteinViews(views: { type: string }[]): ProteinView[] {
   return (views as unknown[]).filter(isProteinView)
 }
 
-/**
- * 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/MsaViewPanel/types.ts

@@ -1,19 +1,24 @@
-// Declarative launch contract, resolved once by processInit. This is also a
-// cross-repo contract: jbrowse-plugin-protein3d builds an MsaView snapshot
-// directly with `init: { msaUrl }`, so these keys must stay stable.
+// Declarative launch contract, resolved once by processInit, then cleared. Only
+// sources that need launch-time resolution belong here. Inline data and tree URLs
+// do NOT: they are native react-msaview snapshot props (`data`, `treeFilehandle`)
+// applied directly from the addView snapshot, no resolution required.
+//
+// Cross-repo contract: jbrowse-plugin-protein3d builds an MsaView snapshot directly
+// with `init: { msaUrl }`, so these keys must stay stable.
 export interface MsaViewInitState {
-  msaData?: string
+  // resolved here (not as a native msaFilehandle) so the AlphaFold-URL → uniprotId
+  // sniff runs once at launch; querySeqName is coupled to it (AlphaFold files name
+  // the query row 'query'), which is why it rides along in init rather than being a
+  // plain top-level prop.
   msaUrl?: string
+  querySeqName?: string
   // a single bgzip `.fa.gz` of per-transcript FASTA blocks; its `.gzi` and name
   // index `.idx` (name<TAB>offset<TAB>length) are found by suffix. `msaName`
   // selects one transcript's block by name (a random read), so one genome-scale
-  // alignment serves any gene without per-gene files or coordinates. See
-  // react-msaview's gene-explorer.
+  // alignment serves any gene without per-gene files or coordinates. This is the
+  // one alignment source with no native loader. See react-msaview's gene-explorer.
   msaIndexedLocation?: { uri: string }
   msaName?: string
-  treeData?: string
-  treeUrl?: string
-  querySeqName?: string
 }
 
 export interface MafRegion {

package/src/version.ts

@@ -1 +1 @@
-export const version = '2.6.2'
+export const version = '2.6.4'

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 {};