// Matrix computation function for semiglobal
func ComputeMatrix(a string, b string, scoreMatrix map[string]int, gp int) [][]int {
F := make([][]int, len(b)+1)
for i := 0; i < len(b)+1; i++ {
F[i] = make([]int, len(a)+1)
}
// initialize first row and column to 0
for j := 0; j < len(a)+1; j++ {
F[0][j] = 0
}
for i := 0; i < len(b)+1; i++ {
F[i][0] = 0
}
for i := 1; i < len(b)+1; i++ {
for j := 1; j < len(a)+1; j++ {
match := F[i-1][j-1] + utils.Score(a[j-1], b[i-1], scoreMatrix)
del := F[i-1][j] + gp
insert := F[i][j-1] + gp
// skip the gap penalty if it's the last row or column
if i == len(b) || j == len(a) {
del -= gp
insert -= gp
}
F[i][j] = utils.GetMax(match, del, insert)
}
}
return F
}
// Traceback for semiglobal
func GetTraceback(m [][]int, seqA string, seqB string, scoreMatrix map[string]int, gapPenalty int) (int, string, string) {
alignmentA := ""
alignmentB := ""
i := len(seqB)
j := len(seqA)
var gp int
for i > 0 || j > 0 {
// Set the gap penalty
if i == 0 || j == 0 || i == len(seqB) || j == len(seqA) {
gp = 0 // 0 for first or last row/column
} else {
gp = gapPenalty // otherwise use regular gap penalty
}
x := utils.GetMax(0, i-1)
y := utils.GetMax(0, j-1)
if i > 0 && j > 0 && m[i][j] == (m[i-1][j-1]+utils.Score(seqA[y], seqB[x], scoreMatrix)) {
alignmentA = string(seqA[y]) + alignmentA
alignmentB = string(seqB[x]) + alignmentB
i--
j--
} else if j > 0 && m[i][j] == (m[i][j-1]+gp) {
alignmentA = string(seqA[y]) + alignmentA
alignmentB = "-" + alignmentB
j--
} else if i > 0 && m[i][j] == (m[i-1][j]+gp) {
alignmentA = "-" + alignmentA
alignmentB = string(seqB[x]) + alignmentB
i--
}
}
return m[len(seqB)][len(seqA)], alignmentA, alignmentB
}
// Matrix computation for Smith-Waterman alignment
func ComputeMatrix(a string, b string, scoreMatrix map[string]int, gp int) [][]int {
F := make([][]int, len(b)+1)
for i := 0; i < len(b)+1; i++ {
F[i] = make([]int, len(a)+1)
}
for j := 0; j < len(a)+1; j++ {
F[0][j] = 0
}
for i := 0; i < len(b)+1; i++ {
F[i][0] = 0
}
for i := 1; i < len(b)+1; i++ {
for j := 1; j < len(a)+1; j++ {
match := F[i-1][j-1] + utils.Score(a[j-1], b[i-1], scoreMatrix)
del := F[i-1][j] + gp
insert := F[i][j-1] + gp
F[i][j] = utils.GetMax(match, del, insert, 0) // max with 0
}
}
return F
}
// Traceback for Smith-Waterman
func GetTraceback(m [][]int, seqA string, seqB string, scoreMatrix map[string]int, gp int) (int, string, string) {
alignmentA := ""
alignmentB := ""
i, j := getStartingPoint(m)
I, J := i, j
for i > 0 || j > 0 {
x := utils.GetMax(0, i-1)
y := utils.GetMax(0, j-1)
// stop if there's a 0 and no pointer that produced it...which only happens in the first row/column
if m[i][j] == 0 && (i == 0 || j == 0) {
break
}
if i > 0 && j > 0 && m[i][j] == (m[i-1][j-1]+utils.Score(seqA[y], seqB[x], scoreMatrix)) {
alignmentA = string(seqA[y]) + alignmentA
alignmentB = string(seqB[x]) + alignmentB
i--
j--
} else if j > 0 && m[i][j] == (m[i][j-1]+gp) {
alignmentA = string(seqA[y]) + alignmentA
alignmentB = "-" + alignmentB
j--
} else if i > 0 && m[i][j] == (m[i-1][j]+gp) {
alignmentA = "-" + alignmentA
alignmentB = string(seqB[x]) + alignmentB
i--
}
}
return m[I][J], alignmentA, alignmentB
}
// Get the traceback
func GetTraceback(m [][]int, seqA string, seqB string, scoreMatrix map[string]int, gp int) (int, string, string) {
alignmentA := ""
alignmentB := ""
i := len(seqB)
j := len(seqA)
for i > 0 || j > 0 {
// Compute and store the string indexes
x := utils.GetMax(0, i-1)
y := utils.GetMax(0, j-1)
// diagonal
if i > 0 && j > 0 && m[i][j] == (m[i-1][j-1]+utils.Score(seqA[y], seqB[x], scoreMatrix)) {
alignmentA = string(seqA[y]) + alignmentA
alignmentB = string(seqB[x]) + alignmentB
i--
j--
// left
} else if j > 0 && m[i][j] == (m[i][j-1]+gp) {
alignmentA = string(seqA[y]) + alignmentA
alignmentB = "-" + alignmentB
j--
// up
} else if i > 0 && m[i][j] == (m[i-1][j]+gp) {
alignmentA = "-" + alignmentA
alignmentB = string(seqB[x]) + alignmentB
i--
}
}
// return score and two alignments
return m[len(seqB)][len(seqA)], alignmentA, alignmentB
}