jbrowse-plugin-msaview 2.3.5 → 2.3.8

package/src/MsaViewPanel/components/MsaViewPanel.tsx

@@ -3,17 +3,25 @@ import React from 'react'
 import { LoadingEllipses } from '@jbrowse/core/ui'
 import { observer } from 'mobx-react'
 import { MSAView } from 'react-msaview'
+import { makeStyles } from 'tss-react/mui'
 
 import { ErrorBoundary } from './ErrorBoundary'
 import LoadingBLAST from './LoadingBLAST'
 
 import type { JBrowsePluginMsaViewModel } from '../model'
 
+const useStyles = makeStyles()({
+  loadingContainer: {
+    padding: 20,
+  },
+})
+
 const MsaViewPanel = observer(function MsaViewPanel2({
   model,
 }: {
   model: JBrowsePluginMsaViewModel
 }) {
+  const { classes } = useStyles()
   const { blastParams, loadingStoredData } = model
   return (
     <ErrorBoundary>
@@ -21,7 +29,7 @@ const MsaViewPanel = observer(function MsaViewPanel2({
         {blastParams ? (
           <LoadingBLAST model={model} baseUrl={blastParams.baseUrl} />
         ) : loadingStoredData ? (
-          <div style={{ padding: 20 }}>
+          <div className={classes.loadingContainer}>
             <LoadingEllipses message="Loading MSA data" variant="h6" />
           </div>
         ) : (

package/src/MsaViewPanel/model.ts

@@ -21,9 +21,13 @@ import {
 import { genomeToMSA } from './genomeToMSA'
 import { msaCoordToGenomeCoord } from './msaCoordToGenomeCoord'
 import { buildAlignmentMaps, runPairwiseAlignment } from './pairwiseAlignment'
-import { mapToRecord, ungappedToGappedPosition } from './structureConnection'
+import {
+  isProteinView,
+  mapToRecord,
+  ungappedToGappedPosition,
+} from './structureConnection'
 
-import type { StructureConnection } from './structureConnection'
+import type { ProteinView, StructureConnection } from './structureConnection'
 import type { MafRegion, MsaViewInitState } from './types'
 import type { Feature } from '@jbrowse/core/util'
 import type { Instance } from '@jbrowse/mobx-state-tree'
@@ -195,18 +199,19 @@ export default function stateModelFactory() {
        */
       get connectedProteinViews() {
         const { views } = getSession(self)
-        return self.connectedStructures
-          .map(conn => {
-            const proteinView = views.find(
-              (v: unknown) =>
-                (v as Record<string, unknown>).id === conn.proteinViewId,
-            )
-            return proteinView ? { ...conn, proteinView } : undefined
-          })
-          .filter(
-            (c): c is StructureConnection & { proteinView: any } =>
-              c !== undefined,
+        const unknownViews = views as unknown[]
+        const result: (StructureConnection & { proteinView: ProteinView })[] =
+          []
+        for (const conn of self.connectedStructures) {
+          const proteinView = unknownViews.find(
+            (v): v is ProteinView =>
+              isProteinView(v) && v.id === conn.proteinViewId,
           )
+          if (proteinView) {
+            result.push({ ...conn, proteinView })
+          }
+        }
+        return result
       },
     }))
 
@@ -216,7 +221,7 @@ export default function stateModelFactory() {
        */
       get structureHoverCol(): number | undefined {
         for (const conn of self.connectedProteinViews) {
-          const structure = conn.proteinView?.structures?.[conn.structureIdx]
+          const structure = conn.proteinView.structures[conn.structureIdx]
           const structurePos = structure?.hoverPosition?.structureSeqPos
           if (structurePos !== undefined) {
             const msaUngapped = conn.structureToMsa[structurePos]
@@ -380,14 +385,14 @@ export default function stateModelFactory() {
 
         const { views } = getSession(self)
 
-        const proteinView = views.find(
-          (v: any) => v.id === proteinViewId,
-        ) as any
+        const proteinView = (views as unknown[]).find(
+          (v): v is ProteinView => isProteinView(v) && v.id === proteinViewId,
+        )
         if (!proteinView) {
           throw new Error(`ProteinView "${proteinViewId}" not found`)
         }
 
-        const structure = proteinView.structures?.[structureIdx]
+        const structure = proteinView.structures[structureIdx]
         if (!structure) {
           throw new Error(`Structure at index ${structureIdx} not found`)
         }

package/src/MsaViewPanel/pairwiseAlignment.ts

@@ -1,9 +1,7 @@
 import BLOSUM62 from './blosum62'
 
 function getScore(a: string, b: string) {
-  const upper_a = a.toUpperCase()
-  const upper_b = b.toUpperCase()
-  return BLOSUM62[upper_a]?.[upper_b] ?? -4
+  return BLOSUM62[a.toUpperCase()]?.[b.toUpperCase()] ?? -4
 }
 
 const GAP_OPEN = -10
@@ -75,10 +73,12 @@ export function needlemanWunsch(
   let i = m
   let j = n
 
-  const finalScores = [M[m]![n]!, Ix[m]![n]!, Iy[m]![n]!]
-  const score = Math.max(...finalScores)
+  const mScore = M[m]![n]!
+  const ixScore = Ix[m]![n]!
+  const iyScore = Iy[m]![n]!
+  const score = Math.max(mScore, ixScore, iyScore)
   let currentMatrix: 'M' | 'Ix' | 'Iy' =
-    score === M[m]![n]! ? 'M' : score === Ix[m]![n]! ? 'Ix' : 'Iy'
+    score === mScore ? 'M' : score === ixScore ? 'Ix' : 'Iy'
 
   while (i > 0 || j > 0) {
     if (currentMatrix === 'M' && i > 0 && j > 0) {

package/src/MsaViewPanel/structureConnection.ts

@@ -1,3 +1,26 @@
+export interface ProteinViewStructure {
+  url?: string
+  connectedViewId?: string
+  uniprotId?: string
+  structureSequences?: string[]
+  hoverGenomeHighlights?: { start: number; end: number }[]
+  hoverPosition?: { structureSeqPos?: number }
+  clearHighlightFromExternal?: () => void
+  highlightFromExternal?: (pos: number) => void
+}
+
+export interface ProteinView {
+  type: 'ProteinView'
+  id: string
+  displayName?: string
+  structures: ProteinViewStructure[]
+}
+
+export function isProteinView(view: unknown): view is ProteinView {
+  const v = view as Record<string, unknown>
+  return v.type === 'ProteinView' && Array.isArray(v.structures)
+}
+
 /**
  * Represents a connection between the MSA view and a protein structure
  */

package/src/version.ts

@@ -1 +1 @@
-export const version = '2.3.5'
+export const version = '2.3.8'