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various optimizations to compute time,

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add more profiling options to make test
This commit is contained in:
Arthur Lu
2024-10-29 17:03:19 +00:00
parent aed3ac6f8f
commit a3beca4ed2
5 changed files with 132 additions and 153 deletions
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87
pkg/utils.go
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@@ -5,14 +5,12 @@ import (
"unicode/utf8"
)
func SafeMin(valids []bool, values []int) (bool, int) {
ok, idx := SafeArgMin(valids, values)
return ok, values[idx]
func SafeMin(values []int, idx int) int {
return values[idx]
}
func SafeMax(valids []bool, values []int) (bool, int) {
ok, idx := SafeArgMax(valids, values)
return ok, values[idx]
func SafeMax(values []int, idx int) int {
return 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)
b_ok, b := M.GetLo(score - o - e)
c_ok, c := I.GetLo(score - e)
d_ok, d := D.GetLo(score - 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 := 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--
if ok {
M.SetLo(score, lo)
I.SetLo(score, lo)
D.SetLo(score, lo)
}
return lo
}
lo := SafeMin([]int{a_lo, b_lo, c_lo, d_lo}, idx) - 1
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(
ok_hi, idx := SafeArgMax(
[]bool{a_ok, b_ok, c_ok, d_ok},
[]int{a, b, c, d},
[]int{a_hi, b_hi, c_hi, d_hi},
)
hi++
if ok {
M.SetHi(score, hi)
I.SetHi(score, hi)
D.SetHi(score, 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 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})
if ok {
D.SetVal(score, k, nextDVal) // nothing special
}
ok, nextDTraceback := SafeArgMax([]bool{a_ok, b_ok}, []int{a, b})
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])
}
}
@@ -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])
}
}