rewrite in go and compile to wasm

pkg/types.go

@@ -0,0 +1,214 @@
+package wfa
+
+import (
+	"fmt"
+	"math"
+)
+
+type Penalty struct {
+	M int
+	X int
+	O int
+	E int
+}
+
+type traceback byte
+
+const (
+	OpenIns traceback = iota
+	ExtdIns
+	OpenDel
+	ExtdDel
+	Sub
+	Ins
+	Del
+	End
+)
+
+type WavefrontComponent struct {
+	lo *PositiveSlice[int]                      // lo for each wavefront
+	hi *PositiveSlice[int]                      // hi for each wavefront
+	W  *PositiveSlice[*IntegerSlice[int]]       // wavefront diag distance for each wavefront
+	A  *PositiveSlice[*IntegerSlice[traceback]] // compact CIGAR for backtrace for each wavefront
+}
+
+func NewWavefrontComponent() WavefrontComponent {
+	// new wavefront component = {
+	// lo = [0]
+	// hi = [0]
+	// W = []
+	// A = []
+	// }
+	return WavefrontComponent{
+		lo: &PositiveSlice[int]{
+			data:  []int{0},
+			valid: []bool{true},
+		},
+		hi: &PositiveSlice[int]{
+			data:  []int{0},
+			valid: []bool{true},
+		},
+		W: &PositiveSlice[*IntegerSlice[int]]{},
+		A: &PositiveSlice[*IntegerSlice[traceback]]{},
+	}
+}
+
+// get value for wavefront=score, diag=k => returns ok, value
+func (w *WavefrontComponent) GetVal(score int, k int) (bool, int) {
+	// if W[score][k] is valid
+	if w.W.Valid(score) && w.W.Get(score).Valid(k) {
+		// return W[score][k]
+		return true, w.W.Get(score).Get(k)
+	} else {
+		return false, 0
+	}
+}
+
+// set value for wavefront=score, diag=k
+func (w *WavefrontComponent) SetVal(score int, k int, val int) {
+	// if W[score] is valid
+	if w.W.Valid(score) {
+		// W[score][k] = val
+		w.W.Get(score).Set(k, val)
+	} else {
+		// W[score] = []
+		w.W.Set(score, &IntegerSlice[int]{})
+		// W[score][k] = val
+		w.W.Get(score).Set(k, val)
+	}
+}
+
+// get alignment traceback for wavefront=score, diag=k => returns ok, value
+func (w *WavefrontComponent) GetTraceback(score int, k int) (bool, traceback) {
+	// if W[score][k] is valid
+	if w.A.Valid(score) && w.A.Get(score).Valid(k) {
+		// return W[score][k]
+		return true, w.A.Get(score).Get(k)
+	} else {
+		return false, 0
+	}
+}
+
+// set alignment traceback for wavefront=score, diag=k
+func (w *WavefrontComponent) SetTraceback(score int, k int, val traceback) {
+	// if A[score] is valid
+	if w.A.Valid(score) {
+		// A[score][k] = val
+		w.A.Get(score).Set(k, val)
+	} else {
+		// W[score] = []
+		w.A.Set(score, &IntegerSlice[traceback]{})
+		// W[score][k] = val
+		w.A.Get(score).Set(k, val)
+	}
+}
+
+// get hi for wavefront=score
+func (w *WavefrontComponent) GetHi(score int) (bool, int) {
+	// if hi[score] is valid
+	if w.hi.Valid(score) {
+		// return hi[score]
+		return true, w.hi.Get(score)
+	} else {
+		return false, 0
+	}
+}
+
+// set hi for wavefront=score
+func (w *WavefrontComponent) SetHi(score int, hi int) {
+	// hi[score] = hi
+	w.hi.Set(score, hi)
+}
+
+// get lo for wavefront=score
+func (w *WavefrontComponent) GetLo(score int) (bool, int) {
+	// if lo[score] is valid
+	if w.lo.Valid(score) {
+		// return lo[score]
+		return true, w.lo.Get(score)
+	} else {
+		return false, 0
+	}
+}
+
+// set hi for wavefront=score
+func (w *WavefrontComponent) SetLo(score int, lo int) {
+	// lo[score] = lo
+	w.lo.Set(score, lo)
+}
+
+type Result struct {
+	Score int
+	CIGAR string
+}
+
+func (w *WavefrontComponent) String(score int) string {
+	traceback_str := []string{"OI", "EI", "OD", "ED", "SB", "IN", "DL", "EN"}
+	s := "<"
+	min_lo := math.MaxInt
+	max_hi := math.MinInt
+
+	for i := 0; i <= score; i++ {
+		if w.lo.Valid(i) && w.lo.Get(i) < min_lo {
+			min_lo = w.lo.Get(i)
+		}
+		if w.hi.Valid(i) && w.hi.Get(i) > max_hi {
+			max_hi = w.hi.Get(i)
+		}
+	}
+
+	for k := min_lo; k <= max_hi; k++ {
+		s = s + fmt.Sprintf("%02d", k)
+		if k < max_hi {
+			s = s + "|"
+		}
+	}
+
+	s = s + ">\t<"
+
+	for k := min_lo; k <= max_hi; k++ {
+		s = s + fmt.Sprintf("%02d", k)
+		if k < max_hi {
+			s = s + "|"
+		}
+	}
+
+	s = s + ">\n"
+
+	for i := 0; i <= score; i++ {
+		s = s + "["
+		lo := w.lo.Get(i)
+		hi := w.hi.Get(i)
+		// print out wavefront matrix
+		for k := min_lo; k <= max_hi; k++ {
+			if w.W.Valid(i) && w.W.Get(i).Valid(k) {
+				s = s + fmt.Sprintf("%02d", w.W.Get(i).Get(k))
+			} else if k < lo || k > hi {
+				s = s + "--"
+			} else {
+				s = s + "  "
+			}
+
+			if k < max_hi {
+				s = s + "|"
+			}
+		}
+		s = s + "]\t["
+		// print out traceback matrix
+		for k := min_lo; k <= max_hi; k++ {
+			if w.A.Valid(i) && w.A.Get(i).Valid(k) {
+				s = s + traceback_str[w.A.Get(i).Get(k)]
+			} else if k < lo || k > hi {
+				s = s + "--"
+			} else {
+				s = s + "  "
+			}
+
+			if k < max_hi {
+				s = s + "|"
+			}
+		}
+		s = s + "]\n"
+	}
+	return s
+}