package wfa import ( "math" "unicode/utf8" ) func SafeMin(values []int, idx int) int { return values[idx] } func SafeMax(values []int, idx int) int { return values[idx] } func SafeArgMax(valids []bool, values []int) (bool, int) { hasValid := false maxIndex := 0 maxValue := math.MinInt for i := 0; i < len(valids); i++ { if valids[i] && values[i] > maxValue { hasValid = true maxIndex = i maxValue = values[i] } } if hasValid { return true, maxIndex } else { return false, 0 } } func SafeArgMin(valids []bool, values []int) (bool, int) { hasValid := false minIndex := 0 minValue := math.MaxInt for i := 0; i < len(valids); i++ { if valids[i] && values[i] < minValue { hasValid = true minIndex = i minValue = values[i] } } if hasValid { return true, minIndex } else { return false, 0 } } func Reverse(s string) string { size := len(s) buf := make([]byte, size) for start := 0; start < size; { r, n := utf8.DecodeRuneInString(s[start:]) start += n utf8.EncodeRune(buf[size-start:], r) } return string(buf) } func Splice(s string, c rune, idx int) string { return s[:idx] + string(c) + s[idx:] } 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}, []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]) } } 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}, []int{a, b}, ) nextDVal := SafeMax([]int{a, b}, nextDTraceback) // nothing special if ok { D.SetVal(score, k, nextDVal) D.SetTraceback(score, k, []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}, []int{a, b, c}) nextMVal := SafeMax([]int{a, b, c}, nextMTraceback) if ok { M.SetVal(score, k, nextMVal) M.SetTraceback(score, k, []traceback{Sub, Ins, Del}[nextMTraceback]) } }