various optimizations to compute time,

add more profiling options to make test

Makefile

@@ -7,11 +7,19 @@ build: clean
 clean:
 	@echo "======================== Cleaning Project ======================"
 	go clean
-	rm -f dist/wfa.wasm
+	rm -f dist/wfa.wasm cover.prof cpu.prof mem.prof test.test
 
 test:
 	@echo "======================== Running Tests ========================="
-	go test -v -cover -coverpkg=./pkg/ -coverprofile coverage ./test/
+	go test -v -cover -coverpkg=./pkg/ -coverprofile cover.prof -cpuprofile cpu.prof -memprofile mem.prof ./test/
 	@echo "======================= Coverage Report ========================"
-	go tool cover -func=coverage
+	go tool cover -func=cover.prof
-	@rm -f coverage
+	@rm -f cover.prof
+	@echo "==================== CPU Performance Report ===================="
+	go tool pprof -top cpu.prof
+	@rm -f cpu.prof
+	@echo "=================== Memory Performance Report =================="
+	go tool pprof -top mem.prof
+	@rm -f mem.prof
+
+	@rm -f test.test

pkg/custom_slice.go

@@ -16,16 +16,12 @@ func (a *IntegerSlice[T]) TranslateIndex(idx int) int {
 
 func (a *IntegerSlice[T]) Valid(idx int) bool {
 	actualIdx := a.TranslateIndex(idx)
-	if actualIdx < len(a.valid) { // idx is in the slice
+	return 0 <= actualIdx && actualIdx < len(a.valid) && a.valid[actualIdx]
-		return a.valid[actualIdx]
-	} else { // idx is out of the slice
-		return false
-	}
 }
 
 func (a *IntegerSlice[T]) Get(idx int) T {
 	actualIdx := a.TranslateIndex(idx)
-	if actualIdx < len(a.valid) { // idx is in the slice
+	if 0 <= actualIdx && actualIdx < len(a.valid) && a.valid[actualIdx] { // idx is in the slice
 		return a.data[actualIdx]
 	} else { // idx is out of the slice
 		return a.defaultValue
@@ -36,12 +32,12 @@ func (a *IntegerSlice[T]) Set(idx int, value T) {
 	actualIdx := a.TranslateIndex(idx)
 	if actualIdx >= len(a.valid) { // idx is outside the slice
 		// expand data array to actualIdx
-		newData := make([]T, actualIdx+1)
+		newData := make([]T, 2*actualIdx+1)
 		copy(newData, a.data)
 		a.data = newData
 
 		// expand valid array to actualIdx
-		newValid := make([]bool, actualIdx+1)
+		newValid := make([]bool, 2*actualIdx+1)
 		copy(newValid, a.valid)
 		a.valid = newValid
 	}
@@ -50,6 +46,20 @@ func (a *IntegerSlice[T]) Set(idx int, value T) {
 	a.valid[actualIdx] = true
 }
 
+func (a *IntegerSlice[T]) Preallocate(lo int, hi int) {
+	actualLo := a.TranslateIndex(lo)
+	actualHi := a.TranslateIndex(hi)
+	size := max(actualHi, actualLo)
+
+	// expand data array to actualIdx
+	newData := make([]T, size+1)
+	a.data = newData
+
+	// expand valid array to actualIdx
+	newValid := make([]bool, size+1)
+	a.valid = newValid
+}
+
 type PositiveSlice[T any] struct {
 	data         []T
 	valid        []bool
@@ -62,16 +72,12 @@ func (a *PositiveSlice[T]) TranslateIndex(idx int) int {
 
 func (a *PositiveSlice[T]) Valid(idx int) bool {
 	actualIdx := a.TranslateIndex(idx)
-	if actualIdx >= 0 && actualIdx < len(a.valid) { // idx is in the slice
+	return 0 <= actualIdx && actualIdx < len(a.valid) && a.valid[actualIdx]
-		return a.valid[actualIdx]
-	} else { // idx is out of the slice
-		return false
-	}
 }
 
 func (a *PositiveSlice[T]) Get(idx int) T {
 	actualIdx := a.TranslateIndex(idx)
-	if actualIdx >= 0 && actualIdx < len(a.valid) { // idx is in the slice
+	if 0 <= actualIdx && actualIdx < len(a.valid) && a.valid[actualIdx] { // idx is in the slice
 		return a.data[actualIdx]
 	} else { // idx is out of the slice
 		return a.defaultValue
@@ -82,12 +88,12 @@ func (a *PositiveSlice[T]) Set(idx int, value T) {
 	actualIdx := a.TranslateIndex(idx)
 	if actualIdx < 0 || actualIdx >= len(a.valid) { // idx is outside the slice
 		// expand data array to actualIdx
-		newData := make([]T, actualIdx+1)
+		newData := make([]T, 2*actualIdx+1)
 		copy(newData, a.data)
 		a.data = newData
 
 		// expand valid array to actualIdx
-		newValid := make([]bool, actualIdx+1)
+		newValid := make([]bool, 2*actualIdx+1)
 		copy(newValid, a.valid)
 		a.valid = newValid
 	}
@@ -95,3 +101,15 @@ func (a *PositiveSlice[T]) Set(idx int, value T) {
 	a.data[actualIdx] = value
 	a.valid[actualIdx] = true
 }
+
+func (a *PositiveSlice[T]) Preallocate(hi int) {
+	size := hi
+
+	// expand data array to actualIdx
+	newData := make([]T, size+1)
+	a.data = newData
+
+	// expand valid array to actualIdx
+	newValid := make([]bool, size+1)
+	a.valid = newValid
+}

pkg/types.go

@@ -5,6 +5,11 @@ import (
 	"math"
 )
 
+type Result struct {
+	Score int
+	CIGAR string
+}
+
 type Penalty struct {
 	M int
 	X int
@@ -32,14 +37,14 @@ type WavefrontComponent struct {
 	A  *PositiveSlice[*IntegerSlice[traceback]] // compact CIGAR for backtrace for each wavefront
 }
 
-func NewWavefrontComponent() WavefrontComponent {
+func NewWavefrontComponent(preallocateSize int) WavefrontComponent {
 	// new wavefront component = {
 	// lo = [0]
 	// hi = [0]
 	// W = []
 	// A = []
 	// }
-	return WavefrontComponent{
+	w := WavefrontComponent{
 		lo: &PositiveSlice[int]{
 			data:  []int{0},
 			valid: []bool{true},
@@ -48,98 +53,73 @@ func NewWavefrontComponent() WavefrontComponent {
 			data:  []int{0},
 			valid: []bool{true},
 		},
-		W: &PositiveSlice[*IntegerSlice[int]]{},
+		W: &PositiveSlice[*IntegerSlice[int]]{
-		A: &PositiveSlice[*IntegerSlice[traceback]]{},
+			defaultValue: &IntegerSlice[int]{
+				data:  []int{},
+				valid: []bool{},
+			},
+		},
+		A: &PositiveSlice[*IntegerSlice[traceback]]{
+			defaultValue: &IntegerSlice[traceback]{
+				data:  []traceback{},
+				valid: []bool{},
+			},
+		},
 	}
+
+	w.lo.Preallocate(preallocateSize)
+	w.hi.Preallocate(preallocateSize)
+	w.W.Preallocate(preallocateSize)
+	w.A.Preallocate(preallocateSize)
+
+	return w
 }
 
 // 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
+	return w.W.Valid(score) && w.W.Get(score).Valid(k), w.W.Get(score).Get(k)
-	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
+	return w.A.Valid(score) && w.A.Get(score).Valid(k), w.A.Get(score).Get(k)
-	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) {
+func (w *WavefrontComponent) GetLoHi(score int) (bool, int, int) {
-	// if hi[score] is valid
+	// if lo[score] and hi[score] are valid
-	if w.hi.Valid(score) {
+	if w.lo.Valid(score) && w.hi.Valid(score) {
-		// return hi[score]
+		// return lo[score] hi[score]
-		return true, w.hi.Get(score)
+		return true, w.lo.Get(score), w.hi.Get(score)
 	} else {
-		return false, 0
+		return false, 0, 0
 	}
 }
 
 // set hi for wavefront=score
-func (w *WavefrontComponent) SetHi(score int, hi int) {
+func (w *WavefrontComponent) SetLoHi(score int, lo 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)
-}
+	// hi[score] = hi
+	w.hi.Set(score, hi)
 
-type Result struct {
+	// preemptively setup w.A
-	Score int
+	w.A.Set(score, &IntegerSlice[traceback]{})
-	CIGAR string
+	w.A.Get(score).Preallocate(lo, hi)
+
+	// preemptively setup w.W
+	w.W.Set(score, &IntegerSlice[int]{})
+	w.W.Get(score).Preallocate(lo, hi)
 }
 
 func (w *WavefrontComponent) String(score int) string {

pkg/utils.go

@@ -5,14 +5,12 @@ import (
 	"unicode/utf8"
 )
 
-func SafeMin(valids []bool, values []int) (bool, int) {
+func SafeMin(values []int, idx int) int {
-	ok, idx := SafeArgMin(valids, values)
+	return values[idx]
-	return ok, values[idx]
 }
 
-func SafeMax(valids []bool, values []int) (bool, int) {
+func SafeMax(values []int, idx int) int {
-	ok, idx := SafeArgMax(valids, values)
+	return values[idx]
-	return ok, values[idx]
 }
 
 func SafeArgMax(valids []bool, values []int) (bool, int) {
@@ -66,50 +64,34 @@ func Splice(s string, c rune, idx int) string {
 	return s[:idx] + string(c) + s[idx:]
 }
 
-func NextLo(M WavefrontComponent, I WavefrontComponent, D WavefrontComponent, score int, penalties Penalty) int {
+func NextLoHi(M WavefrontComponent, I WavefrontComponent, D WavefrontComponent, score int, penalties Penalty) (int, int) {
 	x := penalties.X
 	o := penalties.O
 	e := penalties.E
 
-	a_ok, a := M.GetLo(score - x)
+	a_ok, a_lo, a_hi := M.GetLoHi(score - x)
-	b_ok, b := M.GetLo(score - o - e)
+	b_ok, b_lo, b_hi := M.GetLoHi(score - o - e)
-	c_ok, c := I.GetLo(score - e)
+	c_ok, c_lo, c_hi := I.GetLoHi(score - e)
-	d_ok, d := D.GetLo(score - e)
+	d_ok, d_lo, d_hi := D.GetLoHi(score - e)
 
-	ok, lo := SafeMin(
+	ok_lo, idx := SafeArgMin(
 		[]bool{a_ok, b_ok, c_ok, d_ok},
-		[]int{a, b, c, d},
+		[]int{a_lo, b_lo, c_lo, d_lo},
 	)
-	lo--
+	lo := SafeMin([]int{a_lo, b_lo, c_lo, d_lo}, idx) - 1
-	if ok {
-		M.SetLo(score, lo)
-		I.SetLo(score, lo)
-		D.SetLo(score, lo)
-	}
-	return lo
-}
 
-func NextHi(M WavefrontComponent, I WavefrontComponent, D WavefrontComponent, score int, penalties Penalty) int {
+	ok_hi, idx := SafeArgMax(
-	x := penalties.X
-	o := penalties.O
-	e := penalties.E
-
-	a_ok, a := M.GetHi(score - x)
-	b_ok, b := M.GetHi(score - o - e)
-	c_ok, c := I.GetHi(score - e)
-	d_ok, d := D.GetHi(score - e)
-
-	ok, hi := SafeMax(
 		[]bool{a_ok, b_ok, c_ok, d_ok},
-		[]int{a, b, c, d},
+		[]int{a_hi, b_hi, c_hi, d_hi},
 	)
-	hi++
+	hi := SafeMax([]int{a_hi, b_hi, c_hi, d_hi}, idx) + 1
-	if ok {
+
-		M.SetHi(score, hi)
+	if ok_lo && ok_hi {
-		I.SetHi(score, hi)
+		M.SetLoHi(score, lo, hi)
-		D.SetHi(score, hi)
+		I.SetLoHi(score, lo, hi)
+		D.SetLoHi(score, lo, hi)
 	}
-	return hi
+	return lo, hi
 }
 
 func NextI(M WavefrontComponent, I WavefrontComponent, score int, k int, penalties Penalty) {
@@ -119,13 +101,10 @@ func NextI(M WavefrontComponent, I WavefrontComponent, score int, k int, penalti
 	a_ok, a := M.GetVal(score-o-e, k-1)
 	b_ok, b := I.GetVal(score-e, k-1)
 
-	ok, nextIVal := SafeMax([]bool{a_ok, b_ok}, []int{a, b})
-	if ok {
-		I.SetVal(score, k, nextIVal+1) // important that the +1 is here
-	}
-
 	ok, nextITraceback := SafeArgMax([]bool{a_ok, b_ok}, []int{a, b})
+	nextIVal := SafeMax([]int{a, b}, nextITraceback) + 1 // important that the +1 is here
 	if ok {
+		I.SetVal(score, k, nextIVal)
 		I.SetTraceback(score, k, []traceback{OpenIns, ExtdIns}[nextITraceback])
 	}
 }
@@ -137,13 +116,13 @@ func NextD(M WavefrontComponent, D WavefrontComponent, score int, k int, penalti
 	a_ok, a := M.GetVal(score-o-e, k+1)
 	b_ok, b := D.GetVal(score-e, k+1)
 
-	ok, nextDVal := SafeMax([]bool{a_ok, b_ok}, []int{a, b})
+	ok, nextDTraceback := SafeArgMax(
-	if ok {
+		[]bool{a_ok, b_ok},
-		D.SetVal(score, k, nextDVal) // nothing special
+		[]int{a, b},
-	}
+	)
-
+	nextDVal := SafeMax([]int{a, b}, nextDTraceback) // nothing special
-	ok, nextDTraceback := SafeArgMax([]bool{a_ok, b_ok}, []int{a, b})
 	if ok {
+		D.SetVal(score, k, nextDVal)
 		D.SetTraceback(score, k, []traceback{OpenDel, ExtdDel}[nextDTraceback])
 	}
 }
@@ -156,13 +135,11 @@ func NextM(M WavefrontComponent, I WavefrontComponent, D WavefrontComponent, sco
 	b_ok, b := I.GetVal(score, k)
 	c_ok, c := D.GetVal(score, k)
 
-	ok, nextMVal := SafeMax([]bool{a_ok, b_ok, c_ok}, []int{a, b, c})
+	ok, nextMTraceback := SafeArgMax([]bool{a_ok, b_ok, c_ok}, []int{a, b, c})
+	nextMVal := SafeMax([]int{a, b, c}, nextMTraceback)
+
 	if ok {
 		M.SetVal(score, k, nextMVal)
-	}
-
-	ok, nextMTraceback := SafeArgMax([]bool{a_ok, b_ok, c_ok}, []int{a, b, c})
-	if ok {
 		M.SetTraceback(score, k, []traceback{Sub, Ins, Del}[nextMTraceback])
 	}
 }

pkg/wfa.go

@@ -6,13 +6,13 @@ func WFAlign(s1 string, s2 string, penalties Penalty, doCIGAR bool) Result {
 	A_k := m - n
 	A_offset := m
 	score := 0
-	M := NewWavefrontComponent()
+	estimatedScore := (max(n, m) * max(penalties.M, penalties.X, penalties.O, penalties.E)) / 4
+	M := NewWavefrontComponent(estimatedScore)
+	M.SetLoHi(0, 0, 0)
 	M.SetVal(0, 0, 0)
-	M.SetHi(0, 0)
-	M.SetLo(0, 0)
 	M.SetTraceback(0, 0, End)
-	I := NewWavefrontComponent()
+	I := NewWavefrontComponent(estimatedScore)
-	D := NewWavefrontComponent()
+	D := NewWavefrontComponent(estimatedScore)
 
 	for {
 		WFExtend(M, s1, n, s2, m, score)
@@ -36,8 +36,7 @@ func WFAlign(s1 string, s2 string, penalties Penalty, doCIGAR bool) Result {
 }
 
 func WFExtend(M WavefrontComponent, s1 string, n int, s2 string, m int, score int) {
-	_, lo := M.GetLo(score)
+	_, lo, hi := M.GetLoHi(score)
-	_, hi := M.GetHi(score)
 	for k := lo; k <= hi; k++ {
 		// v = M[score][k] - k
 		// h = M[score][k]
@@ -58,11 +57,8 @@ func WFExtend(M WavefrontComponent, s1 string, n int, s2 string, m int, score in
 }
 
 func WFNext(M WavefrontComponent, I WavefrontComponent, D WavefrontComponent, score int, penalties Penalty) {
-	// get this score's lo
+	// get this score's lo, hi
-	lo := NextLo(M, I, D, score, penalties)
+	lo, hi := NextLoHi(M, I, D, score, penalties)
-
-	// get this score's hi
-	hi := NextHi(M, I, D, score, penalties)
 
 	for k := lo; k <= hi; k++ {
 		NextI(M, I, score, k, penalties)