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Accellerate a bit LCS computation

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This commit is contained in:
Eric Coissac
2022-10-27 17:30:55 +02:00
parent f3ddac0f50
commit 6429f24c57
1 changed files with 91 additions and 26 deletions
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117
pkg/obialign/lcs.go
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@ -22,12 +22,12 @@ func min(a, b int) int {
type LCSMatrix struct {
matrix []int16 // Score matrix
lenght []int16 // Alignment length matrix
ll int // Length of the longest sequence
l int // Length of the shortest sequence
delta int // ll - l
extra int
w int
//lenght []int16 // Alignment length matrix
ll int // Length of the longest sequence
l int // Length of the shortest sequence
delta int // ll - l
extra int
w int
}
func NewLCSMatrix(matrix *LCSMatrix, L, l int, maxError int) *LCSMatrix {
@ -42,15 +42,15 @@ func NewLCSMatrix(matrix *LCSMatrix, L, l int, maxError int) *LCSMatrix {
delta := L - l
extra := ((maxError - delta) / 2) + 1
needed := L * (1 + delta + 2*extra)
needed := (L * (1 + delta + 2*extra)) * 2
if needed > matrix.Cap() {
matrix.matrix = make([]int16, needed)
matrix.lenght = make([]int16, needed)
//matrix.lenght = make([]int16, needed)
}
matrix.matrix = matrix.matrix[:needed]
matrix.lenght = matrix.lenght[:needed]
matrix.matrix = matrix.matrix[0:needed]
// matrix.lenght = matrix.lenght[:needed]
matrix.ll = L
matrix.l = l
@ -69,30 +69,98 @@ func (matrix *LCSMatrix) Length() int {
return len(matrix.matrix)
}
func (matrix *LCSMatrix) Get(i, j int) (int16, int16) {
func (matrix *LCSMatrix) Get(i, j int) (int, int) {
ij := max(0, i-matrix.extra)
sj := min(i+matrix.delta+matrix.extra, matrix.ll)
switch {
case i == 0:
return int16(0), int16(j)
return 0,j
case j == 0:
return int16(0), int16(i)
return 0,i
case j < ij || j > sj:
return -1, 30000
default:
return matrix.matrix[matrix.extra+matrix.w*(i-1)+(matrix.w-1)*(j-i)],
matrix.lenght[matrix.extra+matrix.w*(i-1)+(matrix.w-1)*(j-i)]
offset := (matrix.extra + matrix.w*(i-1) + (matrix.w-1)*(j-i)) * 2
return int(matrix.matrix[offset]), int(matrix.matrix[offset+1])
}
}
func (matrix *LCSMatrix) Set(i, j int, score, length int16) {
func (matrix *LCSMatrix) GetNeibourgh(i, j int) (
sd int, ld int,
sup int, lup int,
sleft int, lleft int) {
offset := matrix.extra + matrix.w*(j-2) + i - j
it := i - 1
jt := j - 1
ij0 := max(0, i-matrix.extra)
sj0 := min(i+matrix.delta+matrix.extra, matrix.ll)
ij1 := max(0, it-matrix.extra)
sj1 := min(it+matrix.delta+matrix.extra, matrix.ll)
switch {
case i == 1:
sd = 0
ld = jt
case j == 1:
sd = 0
ld = it
case jt < ij1 || jt > sj1:
sd = -1
ld = 30000
default:
sd = int(matrix.matrix[offset*2])
ld = int(matrix.matrix[offset*2+1])
}
offset++
switch {
case i == 0:
sleft = 0
lleft = jt
case j == 1:
sleft = 0
lleft = i
case jt < ij0 || jt > sj0:
sleft = -1
lleft = 30000
default:
sleft = int(matrix.matrix[offset*2])
lleft = int(matrix.matrix[offset*2+1])
}
offset += matrix.w - 2
switch {
case i == 1:
sup = 0
lup = j
case j == 0:
sup = 0
lup = it
case j < ij1 || j > sj1:
sup = -1
lup = 30000
default:
sup = int(matrix.matrix[offset*2])
lup = int(matrix.matrix[offset*2+1])
}
return
}
func (matrix *LCSMatrix) Set(i, j int, score, length int) {
ij := max(0, i-matrix.extra)
sj := min(i+matrix.delta+matrix.extra, matrix.ll)
if i > 0 && j > 0 && j >= ij && j <= sj {
matrix.matrix[matrix.extra+matrix.w*(i-1)+(matrix.w-1)*(j-i)] = score
matrix.lenght[matrix.extra+matrix.w*(i-1)+(matrix.w-1)*(j-i)] = length
offset := (matrix.extra + matrix.w*(i-1) + (matrix.w-1)*(j-i)) * 2
matrix.matrix[offset] = int16(score)
matrix.matrix[offset+1] = int16(length)
}
}
@ -100,7 +168,7 @@ func (matrix *LCSMatrix) Set(i, j int, score, length int16) {
// corresponding alignment
func LCSScore(seqA, seqB *obiseq.BioSequence, maxError int,
matrix *LCSMatrix) (int, int) {
if seqA.Length() == 0 {
log.Fatal("Sequence A has a length of 0")
}
@ -115,8 +183,6 @@ func LCSScore(seqA, seqB *obiseq.BioSequence, maxError int,
// swapped = true
}
if (seqA.Length() - seqB.Length()) > maxError {
return -1, -1
}
@ -132,7 +198,7 @@ func LCSScore(seqA, seqB *obiseq.BioSequence, maxError int,
ij := max(1, i-matrix.extra)
sj := min(i+matrix.delta+matrix.extra, matrix.ll)
for j := ij; j <= sj; j++ {
sd, ld := matrix.Get(i-1, j-1)
sd, ld, sup, lup, sleft, lleft := matrix.GetNeibourgh(i, j)
if i > lb {
log.Println("Error on seq B ", 1, matrix.l)
log.Println(i)
@ -150,8 +216,8 @@ func LCSScore(seqA, seqB *obiseq.BioSequence, maxError int,
if sb[i-1] == sa[j-1] {
sd++
}
sup, lup := matrix.Get(i-1, j)
sleft, lleft := matrix.Get(i, j-1)
// sup, lup := matrix.Get(i-1, j)
// sleft, lleft := matrix.Get(i, j-1)
switch {
case sd >= sup && sd >= sleft:
matrix.Set(i, j, sd, ld+1)
@ -165,11 +231,10 @@ func LCSScore(seqA, seqB *obiseq.BioSequence, maxError int,
s, l := matrix.Get(lb, la)
if (l - s) > int16(maxError) {
if (l - s) > maxError {
// log.Println(l,s,l-s,maxError)
return -1, -1
}
return int(s), int(l)
}