// 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 }
// 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 }
// 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 }
// 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 }