package wfa import ( "math" "unicode/utf8" ) func SafeMin(valids []bool, values []int) (bool, int) { ok, idx := SafeArgMin(valids, values) return ok, values[idx] } func SafeMax(valids []bool, values []int) (bool, int) { ok, idx := SafeArgMax(valids, values) return ok, 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 NextLo(M WavefrontComponent, I WavefrontComponent, D WavefrontComponent, score int, penalties Penalty) int { x := penalties.X o := penalties.O e := penalties.E a_ok, a := M.GetLo(score - x) b_ok, b := M.GetLo(score - o - e) c_ok, c := I.GetLo(score - e) d_ok, d := D.GetLo(score - e) ok, lo := SafeMin( []bool{a_ok, b_ok, c_ok, d_ok}, []int{a, b, c, d}, ) lo-- 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 { 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}, ) hi++ if ok { M.SetHi(score, hi) I.SetHi(score, hi) D.SetHi(score, hi) } return 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, 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}) if ok { 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, nextDVal := SafeMax([]bool{a_ok, b_ok}, []int{a, b}) if ok { D.SetVal(score, k, nextDVal) // nothing special } ok, nextDTraceback := SafeArgMax([]bool{a_ok, b_ok}, []int{a, b}) if ok { 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, nextMVal := SafeMax([]bool{a_ok, b_ok, c_ok}, []int{a, b, c}) 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]) } }