jbrowse-plugin-msaview 2.3.3 → 2.3.8

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) {
@@ -88,10 +88,11 @@ export function needlemanWunsch(
       const matchScore = getScore(seq1[i - 1]!, seq2[j - 1]!)
       const prevM = M[i - 1]![j - 1]!
       const prevIx = Ix[i - 1]![j - 1]!
+      const currentScore = M[i]![j]!
 
-      if (M[i]![j]! === prevM + matchScore) {
+      if (currentScore === prevM + matchScore) {
         currentMatrix = 'M'
-      } else if (M[i]![j]! === prevIx + matchScore) {
+      } else if (currentScore === prevIx + matchScore) {
         currentMatrix = 'Ix'
       } else {
         currentMatrix = 'Iy'
@@ -102,13 +103,17 @@ export function needlemanWunsch(
       alignedSeq1 = seq1[i - 1] + alignedSeq1
       alignedSeq2 = '-' + alignedSeq2
 
-      currentMatrix = Ix[i]![j]! === M[i - 1]![j]! + gapOpen ? 'M' : 'Ix'
+      const ixScore = Ix[i]![j]!
+      const mScore = M[i - 1]![j]! + gapOpen
+      currentMatrix = ixScore === mScore ? 'M' : 'Ix'
       i--
     } else if (j > 0) {
       alignedSeq1 = '-' + alignedSeq1
       alignedSeq2 = seq2[j - 1] + alignedSeq2
 
-      currentMatrix = Iy[i]![j]! === M[i]![j - 1]! + gapOpen ? 'M' : 'Iy'
+      const iyScore = Iy[i]![j]!
+      const mScore = M[i]![j - 1]! + gapOpen
+      currentMatrix = iyScore === mScore ? 'M' : 'Iy'
       j--
     } else {
       break

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/utils/blastCache.ts

@@ -40,11 +40,10 @@ function createCacheKey(
   blastProgram: string,
   transcriptId?: string,
 ) {
-  const seqKey = proteinSequence.slice(0, 100)
   if (transcriptId) {
-    return `${blastDatabase}:${blastProgram}:${transcriptId}:${seqKey}`
+    return `${blastDatabase}:${blastProgram}:${transcriptId}:${proteinSequence}`
   }
-  return `${blastDatabase}:${blastProgram}:${seqKey}`
+  return `${blastDatabase}:${blastProgram}:${proteinSequence}`
 }
 
 export async function getCachedBlastResult({

package/src/version.ts

@@ -1 +1 @@
-export const version = '2.3.3'
+export const version = '2.3.8'