debug of obimultiplex

Former-commit-id: 1cf276840feb9d6135d96bd1bf63627d3085ae6e

pkg/obialign/locatepattern.go

@@ -0,0 +1,104 @@
+package obialign
+
+func buffIndex(i, j, width int) int {
+	return (i+1)*width + (j + 1)
+}
+func LocatePattern(pattern, sequence []byte) (int, int, int) {
+	width := len(pattern) + 1
+	buffsize := (len(pattern) + 1) * (len(sequence) + 1)
+	buffer := make([]int, buffsize)
+	path := make([]int, buffsize)
+
+	for j := 0; j < len(pattern); j++ {
+		idx := buffIndex(-1, j, width)
+		buffer[idx] = -j - 1
+		path[idx] = -1
+	}
+
+	for i := -1; i < len(sequence); i++ {
+		idx := buffIndex(i, -1, width)
+		buffer[idx] = 0
+		path[idx] = +1
+	}
+
+	path[0] = 0
+	jmax := len(pattern) - 1
+	for i := 0; i < len(sequence); i++ {
+		for j := 0; j < jmax; j++ {
+			match := -1
+			if _samenuc(pattern[j], sequence[i]) {
+				match = 0
+			}
+
+			idx := buffIndex(i, j, width)
+
+			diag := buffer[buffIndex(i-1, j-1, width)] + match
+			left := buffer[buffIndex(i, j-1, width)] - 1
+			up := buffer[buffIndex(i-1, j, width)] - 1
+
+			score := max(diag, up, left)
+
+			buffer[idx] = score
+
+			switch {
+			case score == left:
+				path[idx] = -1
+			case score == diag:
+				path[idx] = 0
+			case score == up:
+				path[idx] = +1
+			}
+		}
+	}
+
+	for i := 0; i < len(sequence); i++ {
+		idx := buffIndex(i, jmax, width)
+
+		match := -1
+		if _samenuc(pattern[jmax], sequence[i]) {
+			match = 0
+		}
+
+		diag := buffer[buffIndex(i-1, jmax-1, width)] + match
+		left := buffer[buffIndex(i, jmax-1, width)] - 1
+		up := buffer[buffIndex(i-1, jmax, width)]
+
+		score := max(diag, up, left)
+		buffer[idx] = score
+		switch {
+		case score == left:
+			path[idx] = -1
+		case score == diag:
+			path[idx] = 0
+		case score == up:
+			path[idx] = +1
+		}
+	}
+
+	i := len(sequence) - 1
+	j := jmax
+	end := -1
+	lali := 0
+	for i > -1 && j > 0 {
+		lali++
+		switch path[buffIndex(i, j, width)] {
+		case 0:
+			j--
+			if end == -1 {
+				end = i
+				lali = 1
+			}
+			i--
+		case 1:
+			i--
+		case -1:
+			j--
+			if end == -1 {
+				end = i
+				lali = 1
+			}
+		}
+
+	}
+	return i, end + 1, -buffer[buffIndex(len(sequence)-1, len(pattern)-1, width)]
+}