First commit

pkg/obialign/backtracking.go

@@ -0,0 +1,95 @@
+package obialign
+
+func __backtracking__(path_matrix []int, lseqA, lseqB int, path *[]int) []int {
+
+	needed := (lseqA + lseqB) * 2
+
+	if needed > cap(*path) {
+		*path = make([]int, 0, needed)
+	}
+
+	*path = (*path)[:cap(*path)]
+	p := cap(*path)
+
+	i := lseqA - 1
+	j := lseqB - 1
+
+	ldiag := 0
+	lup := 0
+	lleft := 0
+
+	for i > -1 || j > -1 {
+		step := __get_matrix__(&path_matrix, lseqA, i, j)
+		// log.Printf("I: %d J:%d -> %d\n", i, j, step)
+
+		switch {
+		case step == 0:
+			if lleft != 0 {
+				p--
+				(*path)[p] = ldiag
+				p--
+				(*path)[p] = lleft
+				lleft = 0
+				ldiag = 0
+			}
+			if lup != 0 {
+				p--
+				(*path)[p] = ldiag
+				p--
+				(*path)[p] = lup
+				lup = 0
+				ldiag = 0
+			}
+			ldiag++
+			i--
+			j--
+		case step > 0:
+			if lup != 0 {
+				p--
+				(*path)[p] = ldiag
+				p--
+				(*path)[p] = lup
+				lup = 0
+				ldiag = 0
+			}
+			lleft += step
+			j -= step
+		case step < 0:
+			if lleft != 0 {
+				p--
+				(*path)[p] = ldiag
+				p--
+				(*path)[p] = lleft
+				lleft = 0
+				ldiag = 0
+			}
+			lup += step
+			i += step
+		}
+	}
+
+	if lleft != 0 {
+		p--
+		(*path)[p] = ldiag
+		p--
+		(*path)[p] = lleft
+		ldiag = 0
+	}
+	if lup != 0 {
+		p--
+		(*path)[p] = ldiag
+		p--
+		(*path)[p] = lup
+		ldiag = 0
+	}
+	if ldiag != 0 {
+		p--
+		(*path)[p] = ldiag
+		p--
+		(*path)[p] = 0
+	}
+
+	*path = (*path)[p:cap((*path))]
+
+	return *path
+}