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major optimization by packing wavefront values

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This commit is contained in:
Arthur Lu
2024-11-05 18:28:28 +00:00
parent 8679c51fb0
commit 3da3ddf10c
6 changed files with 154 additions and 146 deletions
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53
pkg/utils.go
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@@ -3,25 +3,27 @@ package wfa
import (
"math"
"unicode/utf8"
"golang.org/x/exp/constraints"
)
func SafeMin(values []int, idx int) int {
func SafeMin[T constraints.Integer](values []T, idx int) T {
return values[idx]
}
func SafeMax(values []int, idx int) int {
func SafeMax[T constraints.Integer](values []T, idx int) T {
return values[idx]
}
func SafeArgMax(valids []bool, values []int) (bool, int) {
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] && values[i] > maxValue {
if valids[i] && int(values[i]) > maxValue {
hasValid = true
maxIndex = i
maxValue = values[i]
maxValue = int(values[i])
}
}
if hasValid {
@@ -31,15 +33,15 @@ func SafeArgMax(valids []bool, values []int) (bool, int) {
}
}
func SafeArgMin(valids []bool, values []int) (bool, int) {
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] && values[i] < minValue {
if valids[i] && int(values[i]) < minValue {
hasValid = true
minIndex = i
minValue = values[i]
minValue = int(values[i])
}
}
if hasValid {
@@ -98,14 +100,13 @@ func NextI(M WavefrontComponent, I WavefrontComponent, score int, k int, penalti
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)
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
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)
I.SetTraceback(score, k, []traceback{OpenIns, ExtdIns}[nextITraceback])
I.SetVal(score, k, nextIVal, []Traceback{OpenIns, ExtdIns}[nextITraceback])
}
}
@@ -113,33 +114,31 @@ func NextD(M WavefrontComponent, D WavefrontComponent, score int, k int, penalti
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)
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},
[]uint32{a, b},
)
nextDVal := SafeMax([]int{a, b}, nextDTraceback) // nothing special
nextDVal := SafeMax([]uint32{a, b}, nextDTraceback) // nothing special
if ok {
D.SetVal(score, k, nextDVal)
D.SetTraceback(score, k, []traceback{OpenDel, ExtdDel}[nextDTraceback])
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_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)
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)
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)
M.SetTraceback(score, k, []traceback{Sub, Ins, Del}[nextMTraceback])
M.SetVal(score, k, nextMVal, []Traceback{Sub, Ins, Del}[nextMTraceback])
}
}