mirror/erigon-pulse
1
0
Fork 0
mirror of https://gitlab.com/pulsechaincom/erigon-pulse.git synced 2024-12-28 14:47:16 +00:00
Code Issues Actions Packages Projects Releases Wiki Activity

gsa: remove terminator (make it closer to SAIS) #400

Browse Source
This commit is contained in:
Alex Sharov 2022-03-27 13:41:16 +07:00 committed by GitHub
parent 54629aaf7c
commit 8846b406eb
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
2 changed files with 36 additions and 49 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

23
sais/gsa/gsa_test.go
View File

@ -8,11 +8,15 @@ import (
)
func TestExampleGSA(t *testing.T) {
R := [][]byte{[]byte("hihihi")}
R := [][]byte{
[]byte("hihihi"),
[]byte("hihihi"),
[]byte("hihihi"),
}
str, n := ConcatAll(R)
sa := make([]uint, SaSize(n))
lcp := make([]int, LcpSize(n))
da := make([]int32, DaSize(n))
sa := make([]uint, n)
lcp := make([]int, n)
da := make([]int32, n)
_ = GSA(str, sa, lcp, da)
PrintArrays(str, sa, lcp, da, n)
}
@ -20,9 +24,10 @@ func TestExampleGSA(t *testing.T) {
func TestGSA(t *testing.T) {
R := [][]byte{{4, 5, 6, 4, 5, 6, 4, 5, 6}}
str, n := ConcatAll(R)
sa := make([]uint, SaSize(n))
sa := make([]uint, n)
lcp := make([]int, n)
_ = GSA(str, sa, lcp, nil)
da := make([]int32, n)
_ = GSA(str, sa, lcp, da)
assert.Equal(t, []uint{10, 9, 6, 3, 0, 7, 4, 1, 8, 5, 2}, sa[:n])
}
@ -57,9 +62,9 @@ func BenchmarkName2(b *testing.B) {
R = append(R, []byte("hihihi"))
}
str, n := ConcatAll(R)
sa := make([]uint, SaSize(n))
lcp := make([]int, LcpSize(n))
da := make([]int32, DaSize(n))
sa := make([]uint, n)
lcp := make([]int, n)
da := make([]int32, n)
b.ResetTimer()
for i := 0; i < b.N; i++ {
_ = GSA(str, sa, lcp, da)

62
sais/gsa/gsaca.go
View File

@ -2,6 +2,7 @@ package gsa
/*
#include "gsacak.h"
#cgo CFLAGS: -DTERMINATOR=0 -DM64=1 -Dm64=1
*/
import "C"
import (
@ -12,66 +13,47 @@ import (
// Implementation from https://github.com/felipelouza/gsufsort
// see also: https://almob.biomedcentral.com/track/pdf/10.1186/s13015-020-00177-y.pdf
// see also: https://almob.biomedcentral.com/track/pdf/10.1186/s13015-017-0117-9.pdf
func SaSize(l int) int {
var a uint
return l * int(unsafe.Sizeof(a))
}
func LcpSize(l int) int {
var a uint
return l * int(unsafe.Sizeof(a))
}
func DaSize(l int) int {
var a C.int_da
return l * int(unsafe.Sizeof(a))
}
func PrintArrays(str []byte, sa []uint, lcp []int, da []int32, n int) {
// remove terminator
sa = sa[1:]
lcp = lcp[1:]
terminatorDa := da[0]
da = da[1:]
n = n - 1
fmt.Printf("i\t")
if da != nil {
fmt.Printf("da\t")
}
fmt.Printf("sa\t")
if lcp != nil {
fmt.Printf("lcp\t")
}
fmt.Printf("gsa\t")
if da != nil {
fmt.Printf("gsa\t")
}
fmt.Printf("suffixes\t")
fmt.Printf("\n")
for i := 0; i < n; i++ {
fmt.Printf("%d\t", i)
fmt.Printf("%d\t", sa[i])
if lcp != nil {
fmt.Printf("%d\t", lcp[i])
}
if da != nil {
pos := sa[da[i]]
if da != nil { // gsa
pos := uint(terminatorDa)
if da[i] > 0 {
pos = sa[da[i]-1]
}
value := sa[i]
if da[i] != 0 {
value = sa[i] - pos - 1
}
fmt.Printf("(%d %d)\t", da[i], value)
} else {
fmt.Printf("%d\t", sa[i])
}
/*
if(gsa){
da_value = (light)?rankbv_rank1(rbv,SA[i]):DA[i];
printf("(%" PRIdA ", ", da_value);
//bwt
// char c = (SA[i])? T[SA[i]-1]-1:terminal;
// if(c==0) c = '$';
// printf("%c\t",c);
int_t pos;
if(last_end) pos=SA[da_value];
else pos=SA[da_value-1];
int_t value = (da_value==0)?SA[i]:SA[i]-pos-1;
printf("%" PRIdN ") \t", value);
}
*/
/*
if(bwt){
char c = (SA[i])? T[SA[i]-1]-1:terminal;
if(c==0) c = '$';
printf("%c\t",c);
}
*/
for j := sa[i]; int(j) < n; j++ {
if str[j] == 1 {
fmt.Printf("$")