package wfa import ( "math" "strings" "golang.org/x/exp/constraints" ) func UIntToString(num uint) string { // num assumed to be positive var builder strings.Builder for num > 0 { digit := num % 10 builder.WriteRune(rune('0' + digit)) num /= 10 } // Reverse the string as we built it in reverse order str := []rune(builder.String()) for i, j := 0, len(str)-1; i < j; i, j = i+1, j-1 { str[i], str[j] = str[j], str[i] } return string(str) } func RunLengthDecode(encoded string) string { decoded := strings.Builder{} length := len(encoded) i := 0 for i < length { // If the current character is a digit, we need to extract the run length runLength := 0 for i < length && encoded[i] >= '0' && encoded[i] <= '9' { runLength = runLength*10 + int(encoded[i]-'0') i++ } // The next character will be the character to repeat if i < length { char := encoded[i] for j := 0; j < runLength; j++ { decoded.WriteByte(char) } i++ // Move past the character } } return decoded.String() } func SafeMin[T constraints.Integer](values []T, idx int) T { return values[idx] } func SafeMax[T constraints.Integer](values []T, idx int) T { return values[idx] } func SafeArgMax[T constraints.Integer](valids []bool, values []T) (bool, int) { hasValid := false maxIndex := 0 maxValue := math.MinInt for i := 0; i < len(valids); i++ { if valids[i] && int(values[i]) > maxValue { hasValid = true maxIndex = i maxValue = int(values[i]) } } if hasValid { return true, maxIndex } else { return false, 0 } } func SafeArgMin[T constraints.Integer](valids []bool, values []T) (bool, int) { hasValid := false minIndex := 0 minValue := math.MaxInt for i := 0; i < len(valids); i++ { if valids[i] && int(values[i]) < minValue { hasValid = true minIndex = i minValue = int(values[i]) } } if hasValid { return true, minIndex } else { return false, 0 } } 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_lo, a_hi := M.GetLoHi(score - x) b_ok, b_lo, b_hi := M.GetLoHi(score - o - e) c_ok, c_lo, c_hi := I.GetLoHi(score - e) d_ok, d_lo, d_hi := D.GetLoHi(score - e) ok_lo, idx := SafeArgMin( []bool{a_ok, b_ok, c_ok, d_ok}, []int{a_lo, b_lo, c_lo, d_lo}, ) lo := SafeMin([]int{a_lo, b_lo, c_lo, d_lo}, idx) - 1 ok_hi, idx := SafeArgMax( []bool{a_ok, b_ok, c_ok, d_ok}, []int{a_hi, b_hi, c_hi, d_hi}, ) hi := SafeMax([]int{a_hi, b_hi, c_hi, d_hi}, idx) + 1 if ok_lo && ok_hi { M.SetLoHi(score, lo, hi) I.SetLoHi(score, lo, hi) D.SetLoHi(score, lo, hi) } return lo, hi } func NextI(M *WavefrontComponent, I *WavefrontComponent, score int, k int, penalties Penalty) { o := penalties.O e := penalties.E a_ok, a, _ := M.GetVal(score-o-e, k-1) b_ok, b, _ := I.GetVal(score-e, k-1) ok, nextITraceback := SafeArgMax([]bool{a_ok, b_ok}, []uint32{a, b}) nextIVal := SafeMax([]uint32{a, b}, nextITraceback) + 1 // important that the +1 is here if ok { I.SetVal(score, k, nextIVal, []Traceback{OpenIns, ExtdIns}[nextITraceback]) } } func NextD(M *WavefrontComponent, D *WavefrontComponent, score int, k int, penalties Penalty) { o := penalties.O e := penalties.E a_ok, a, _ := M.GetVal(score-o-e, k+1) b_ok, b, _ := D.GetVal(score-e, k+1) ok, nextDTraceback := SafeArgMax([]bool{a_ok, b_ok}, []uint32{a, b}) nextDVal := SafeMax([]uint32{a, b}, nextDTraceback) if ok { D.SetVal(score, k, nextDVal, []Traceback{OpenDel, ExtdDel}[nextDTraceback]) } } func NextM(M *WavefrontComponent, I *WavefrontComponent, D *WavefrontComponent, score int, k int, penalties Penalty) { x := penalties.X a_ok, a, _ := M.GetVal(score-x, k) a++ // important to have +1 here b_ok, b, _ := I.GetVal(score, k) c_ok, c, _ := D.GetVal(score, k) ok, nextMTraceback := SafeArgMax([]bool{a_ok, b_ok, c_ok}, []uint32{a, b, c}) nextMVal := SafeMax([]uint32{a, b, c}, nextMTraceback) if ok { M.SetVal(score, k, nextMVal, []Traceback{Sub, Ins, Del}[nextMTraceback]) } }