update go mod,

move Wavefront String method to debug file,
minor optimizations

go.mod

@@ -2,10 +2,14 @@ module wfa
 
 go 1.23.2
 
+require (
+	github.com/schollz/progressbar/v3 v3.17.0
+	golang.org/x/exp v0.0.0-20241009180824-f66d83c29e7c
+)
+
 require (
 	github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db // indirect
 	github.com/rivo/uniseg v0.4.7 // indirect
-	github.com/schollz/progressbar/v3 v3.16.1 // indirect
 	golang.org/x/sys v0.26.0 // indirect
 	golang.org/x/term v0.25.0 // indirect
 )

pkg/custom_slice.go

@@ -1,63 +1,59 @@
 package wfa
 
-type IntegerSlice[T any] struct {
+import (
-	data         []T
+	"golang.org/x/exp/constraints"
-	valid        []bool
+)
-	defaultValue T
+
+type Wavefront[T constraints.Integer] struct { // since wavefronts store diag distance, they should never be negative, and traceback data can be stored as uint8
+	data  []T
+	valid []bool
+	lo    int
 }
 
-func (a *IntegerSlice[T]) TranslateIndex(idx int) int {
+func NewWavefront[T constraints.Integer](lo int, hi int) *Wavefront[T] {
-	if idx >= 0 { // 0 -> 0, 1 -> 2, 2 -> 4, 3 -> 6, ...
+	a := &Wavefront[T]{}
-		return 2 * idx
-	} else { // -1 -> 1, -2 -> 3, -3 -> 5, ...
-		return (-2 * idx) - 1
-	}
-}
 
-func (a *IntegerSlice[T]) Valid(idx int) bool {
+	a.lo = lo
-	actualIdx := a.TranslateIndex(idx)
+	size := a.TranslateIndex(hi)
-	return 0 <= actualIdx && actualIdx < len(a.valid) && a.valid[actualIdx]
-}
 
-func (a *IntegerSlice[T]) Get(idx int) T {
-	actualIdx := a.TranslateIndex(idx)
-	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
-	}
-}
-
-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, 2*actualIdx+1)
-		copy(newData, a.data)
-		a.data = newData
-
-		// expand valid array to actualIdx
-		newValid := make([]bool, 2*actualIdx+1)
-		copy(newValid, a.valid)
-		a.valid = newValid
-	}
-
-	a.data[actualIdx] = value
-	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
+
+	return a
+}
+
+func (a *Wavefront[T]) TranslateIndex(idx int) int {
+	return idx - a.lo
+}
+
+func (a *Wavefront[T]) Valid(idx int) bool {
+	actualIdx := a.TranslateIndex(idx)
+	return 0 <= actualIdx && actualIdx < len(a.data) && a.valid[actualIdx]
+}
+
+func (a *Wavefront[T]) Get(idx int) T {
+	actualIdx := a.TranslateIndex(idx)
+	if 0 <= actualIdx && actualIdx < len(a.data) { // idx is in the slice
+		return a.data[actualIdx]
+	} else { // idx is out of the slice
+		return 0
+	}
+}
+
+func (a *Wavefront[T]) Set(idx int, value T) {
+	actualIdx := a.TranslateIndex(idx)
+
+	/* in theory idx is always in bounds because the wavefront is preallocated
+	if actualIdx < 0 || actualIdx >= len(a.data) {
+		return
+	}
+	*/
+
+	a.data[actualIdx] = value
+	a.valid[actualIdx] = true
 }
 
 type PositiveSlice[T any] struct {

pkg/debug.go

@@ -0,0 +1,79 @@
+//go:build debug
+
+package wfa
+
+import (
+	"fmt"
+	"math"
+)
+
+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
+}

pkg/types.go

@@ -1,10 +1,5 @@
 package wfa
 
-import (
-	"fmt"
-	"math"
-)
-
 type Result struct {
 	Score int
 	CIGAR string
@@ -31,10 +26,10 @@ const (
 )
 
 type WavefrontComponent struct {
-	lo *PositiveSlice[int]                      // lo for each wavefront
+	lo *PositiveSlice[int]                   // lo for each wavefront
-	hi *PositiveSlice[int]                      // hi for each wavefront
+	hi *PositiveSlice[int]                   // hi for each wavefront
-	W  *PositiveSlice[*IntegerSlice[int]]       // wavefront diag distance for each wavefront
+	W  *PositiveSlice[*Wavefront[int]]       // wavefront diag distance for each wavefront
-	A  *PositiveSlice[*IntegerSlice[traceback]] // compact CIGAR for backtrace for each wavefront
+	A  *PositiveSlice[*Wavefront[traceback]] // compact CIGAR for backtrace for each wavefront
 }
 
 func NewWavefrontComponent(preallocateSize int) WavefrontComponent {
@@ -53,16 +48,16 @@ func NewWavefrontComponent(preallocateSize int) WavefrontComponent {
 			data:  []int{0},
 			valid: []bool{true},
 		},
-		W: &PositiveSlice[*IntegerSlice[int]]{
+		W: &PositiveSlice[*Wavefront[int]]{
-			defaultValue: &IntegerSlice[int]{
+			defaultValue: &Wavefront[int]{
-				data:  []int{},
+				data:  []int{0},
-				valid: []bool{},
+				valid: []bool{false},
 			},
 		},
-		A: &PositiveSlice[*IntegerSlice[traceback]]{
+		A: &PositiveSlice[*Wavefront[traceback]]{
-			defaultValue: &IntegerSlice[traceback]{
+			defaultValue: &Wavefront[traceback]{
-				data:  []traceback{},
+				data:  []traceback{0},
-				valid: []bool{},
+				valid: []bool{false},
 			},
 		},
 	}
@@ -114,81 +109,10 @@ func (w *WavefrontComponent) SetLoHi(score int, lo int, hi int) {
 	w.hi.Set(score, hi)
 
 	// preemptively setup w.A
-	w.A.Set(score, &IntegerSlice[traceback]{})
+	a := NewWavefront[traceback](lo, hi)
-	w.A.Get(score).Preallocate(lo, hi)
+	w.A.Set(score, a)
 
 	// preemptively setup w.W
-	w.W.Set(score, &IntegerSlice[int]{})
+	b := NewWavefront[int](lo, hi)
-	w.W.Get(score).Preallocate(lo, hi)
+	w.W.Set(score, b)
-}
-
-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
 }

test/wfa_test.go

@@ -64,7 +64,7 @@ func TestWFA(t *testing.T) {
 			s2 := sequences.Text()
 			s2 = s2[1:]
 
-			x := wfa.WFAlign(s1, s2, testPenalties, false)
+			x := wfa.WFAlign(s1, s2, testPenalties, true)
 			gotScore := x.Score
 
 			if gotScore != -1*expectedScore {