jbrowse-plugin-msaview 2.6.2 → 2.6.4

package/src/MsaViewPanel/pairwiseAlignment.ts

@@ -1,182 +0,0 @@
-import BLOSUM62 from './blosum62'
-
-function getScore(a: string, b: string) {
-  return BLOSUM62[a.toUpperCase()]?.[b.toUpperCase()] ?? -4
-}
-
-const GAP_OPEN = -10
-const GAP_EXTEND = -0.5
-
-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 function needlemanWunsch(
-  seq1: string,
-  seq2: string,
-  gapOpen = GAP_OPEN,
-  gapExtend = GAP_EXTEND,
-): AlignmentResult {
-  const m = seq1.length
-  const n = seq2.length
-
-  const M: number[][] = []
-  const Ix: number[][] = []
-  const Iy: number[][] = []
-
-  for (let i = 0; i <= m; i++) {
-    M[i] = []
-    Ix[i] = []
-    Iy[i] = []
-    for (let j = 0; j <= n; j++) {
-      M[i]![j] = -Infinity
-      Ix[i]![j] = -Infinity
-      Iy[i]![j] = -Infinity
-    }
-  }
-
-  M[0]![0] = 0
-  for (let i = 1; i <= m; i++) {
-    Ix[i]![0] = gapOpen + (i - 1) * gapExtend
-  }
-  for (let j = 1; j <= n; j++) {
-    Iy[0]![j] = gapOpen + (j - 1) * gapExtend
-  }
-
-  for (let i = 1; i <= m; i++) {
-    for (let j = 1; j <= n; j++) {
-      const matchScore = getScore(seq1[i - 1]!, seq2[j - 1]!)
-
-      M[i]![j] =
-        Math.max(M[i - 1]![j - 1]!, Ix[i - 1]![j - 1]!, Iy[i - 1]![j - 1]!) +
-        matchScore
-
-      Ix[i]![j] = Math.max(M[i - 1]![j]! + gapOpen, Ix[i - 1]![j]! + gapExtend)
-      Iy[i]![j] = Math.max(M[i]![j - 1]! + gapOpen, Iy[i]![j - 1]! + gapExtend)
-    }
-  }
-
-  let alignedSeq1 = ''
-  let alignedSeq2 = ''
-  let i = m
-  let j = n
-
-  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 === mScore ? 'M' : score === ixScore ? 'Ix' : 'Iy'
-
-  while (i > 0 || j > 0) {
-    if (currentMatrix === 'M' && i > 0 && j > 0) {
-      alignedSeq1 = seq1[i - 1] + alignedSeq1
-      alignedSeq2 = seq2[j - 1] + alignedSeq2
-
-      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 (currentScore === prevM + matchScore) {
-        currentMatrix = 'M'
-      } else if (currentScore === prevIx + matchScore) {
-        currentMatrix = 'Ix'
-      } else {
-        currentMatrix = 'Iy'
-      }
-      i--
-      j--
-    } else if (currentMatrix === 'Ix' && i > 0) {
-      alignedSeq1 = seq1[i - 1] + alignedSeq1
-      alignedSeq2 = '-' + alignedSeq2
-
-      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
-
-      const iyScore = Iy[i]![j]!
-      const mScore = M[i]![j - 1]! + gapOpen
-      currentMatrix = iyScore === mScore ? 'M' : 'Iy'
-      j--
-    } else {
-      break
-    }
-  }
-
-  return { alignedSeq1, alignedSeq2, score }
-}
-
-function buildConsensus(alignedSeq1: string, alignedSeq2: string) {
-  let consensus = ''
-  for (let i = 0; i < alignedSeq1.length; i++) {
-    const a = alignedSeq1[i]!
-    const b = alignedSeq2[i]!
-    const match = a !== '-' && b !== '-' && a.toUpperCase() === b.toUpperCase()
-    consensus += match ? '|' : ' '
-  }
-  return consensus
-}
-
-export function runPairwiseAlignment(
-  seq1: string,
-  seq2: string,
-): PairwiseAlignment {
-  const { alignedSeq1, alignedSeq2 } = needlemanWunsch(seq1, seq2)
-
-  return {
-    consensus: buildConsensus(alignedSeq1, alignedSeq2),
-    alns: [
-      { id: 'msa', seq: alignedSeq1 },
-      { id: 'structure', seq: alignedSeq2 },
-    ],
-  }
-}
-
-export function buildAlignmentMaps(pairwiseAlignment: PairwiseAlignment) {
-  const seq1 = pairwiseAlignment.alns[0].seq
-  const seq2 = pairwiseAlignment.alns[1].seq
-
-  if (seq1.length !== seq2.length) {
-    throw new Error('Aligned sequences must have same length')
-  }
-
-  let pos1 = 0
-  let pos2 = 0
-  const seq1ToSeq2 = new Map<number, number>()
-  const seq2ToSeq1 = new Map<number, number>()
-
-  for (let i = 0; i < seq1.length; i++) {
-    const c1 = seq1[i]
-    const c2 = seq2[i]
-
-    if (c1 !== '-' && c2 !== '-') {
-      seq1ToSeq2.set(pos1, pos2)
-      seq2ToSeq1.set(pos2, pos1)
-      pos1++
-      pos2++
-    } else if (c1 === '-') {
-      pos2++
-    } else {
-      pos1++
-    }
-  }
-
-  return { seq1ToSeq2, seq2ToSeq1 }
-}