CSA *csa_load(ifstream & fp) {
CSA *SA;
SA = (CSA *) malloc(sizeof(CSA));
csa_init(SA);
initranktables();
mkdecodetable();
SA->m = loadValue<int>(fp);
SA->two = loadValue<int>(fp);
SA->two2 = loadValue<int>(fp);
SA->l = loadValue<int>(fp);
SA->n = loadValue<int>(fp);
for(int i=0; i<(SIGMA+2); i++)
SA->K[i] = loadValue<int>(fp);
for(int i=0; i<(SIGMA+1); i++)
SA->C[i] = loadValue<int>(fp);
for(int i=0; i<(SIGMA+1); i++)
SA->C2[i] = loadValue<int>(fp);
#ifdef USE_MMAP
SA->p_size = loadValue<int>(fp);
SA->B = loadValue<unsigned short>(fp, SA->p_size);
SA->i_size = loadValue<int>(fp);
SA->r_size = loadValue<int>(fp);
SA->R = loadValue<int>(fp, SA->r_size);
SA->sa_size = loadValue<int>(fp);
SA->SA = loadValue<int>(fp, SA->sa_size);
SA->isa_size = loadValue<int>(fp);
SA->ISA = loadValue<int>(fp, SA->isa_size);
SA->mapp = NULL;
SA->mapi = NULL;
#endif
return SA;
}
int load_index(char *filename, void **index){
char fname1[128],fname2[128];
CSA *SA;
SA = (CSA *) malloc(sizeof(CSA));
initranktables();
mkdecodetable();
sprintf(fname1,"%s.psi",filename);
sprintf(fname2,"%s.idx",filename);
csa_read(SA,fname1,fname2);
(*index) = SA;
return 0;
}
i64 psi12_makeindex(CSA *csa, char *fname)
{
i64 psize,psize1,psize2;
i64 b, b2;
i64 i,j,x,xx;
i64 y,d,w;
int k;
FILE *f1,*f2;
char *fpsi, *fpsd;
//psi1_iterator *pi;
i64 runlen;
i64 maxrun;
i64 n,L;
psi1 *ps;
int id,id2;
FILE *out;
diskbuf *psi;
char *fbw, *flst;
SPARSEARRAY sx, sb;
int mm;
ps = (psi1 *)csa->psi_struc;
id = ps->id;
id2 = id & 0x3f;
k = strlen(fname);
fbw = mymalloc(k+5);
flst = mymalloc(k+5);
fpsi = mymalloc(k+5);
fpsd = mymalloc(k+5);
sprintf(fbw,"%s.bw",fname);
sprintf(flst,"%s.lst",fname);
switch (id2) {
case ID_DIFF_GAMMA_RR:
sprintf(fpsi,"%s.pxi",fname);
sprintf(fpsd,"%s.pxd",fname);
break;
}
out = create_tmp(0);
bw_to_psi(out,csa,fbw,flst,&k);
psi = open_diskbuf(out,k);
ps->last = getint_diskbuf(psi,0);
printf("last = %ld\n",ps->last);
n = csa->n;
L = ps->L;
if (L >= n) {
printf("L=%ld >= n=%ld\n",L,n);
exit(0);
}
maxrun = L;
mkdecodetable();
f1 = fopen(fpsi,"wb");
psize1 = 0;
f2 = fopen(fpsd,"wb");
psize2 = 0;
ps->k = k = (blog(n+1)+1+8-1)/8;
// pi = psi1_iterator_new(ps,0);
writeint(1,ID_PSI,f2);
writeint(1,k,f2); /* #bytes of integer */
writeint(k,n,f2);
writeint(k,L,f2);
psize2 += 1+1+2*k;
writeint(1,id,f2);
psize2 += 1;
if (id & ID_COMPPTR) {
mm = 0;
for (i=0; i<SIGMA; i++) {
if (csa->C[i] > 0) mm++;
}
SPARSEARRAY_construct_init(&sx, (mm+1)*(n+1), n/L+1);
SPARSEARRAY_construct_init(&sb, n, n/L+1);
}
b = b2 = 0;
mm = 0; xx = 0;
for (j=0; j<=n/L; j++) {
// display_progressbar("writing psi ",j,n/L);
if (j % 100000 == 0) {
printf("%ld %1.3f bpc\r",j,(double)psize2*8/(j+1)/L); fflush(stdout);
}
y = getint_diskbuf(psi,j*L);
if (id & ID_COMPPTR) {
if (y <= xx) {
mm++;
}
SPARSEARRAY_construct_set(&sx, j, mm*(n+1) + y);
SPARSEARRAY_construct_set(&sb, j, b);
xx = y;
} else {
// printf("%ld x=%ld sp=%ld\n",j,y,b);
writeint(k,y,f2);
writeint(k,b,f2);
psize2 += 2*k;
}
x = y;
runlen = 0;
b2 = 0;
for (i=j*L+1; i<(j+1)*L && i <= n; i++) { /* psi[j*L] are not encoded */
y = getint_diskbuf(psi,i);
d = y - x;
if (d <= 0) {
d += n+1;
}
if (i == j*L+1) {
if (d == 1) {setbit(Btmp,b2+1,1); runlen = 1;}
else {setbit(Btmp,b2+1,0); runlen = 0;}
b2++;
}
if (d > 1) {
if (runlen>0) {
// printf("d=%ld encode runlen=%ld\n",d,runlen);
w = ENCODENUM(Btmp,b2,runlen);
b2 += w;
runlen = 0;
}
// printf("encode d-1=%ld\n",d-1);
w = ENCODENUM(Btmp,b2,d-1);
b2 += w;
runlen = 1;
} else {
runlen++;
}
x = y;
}
if (runlen>0) {
// printf("encode runlen=%ld\n",runlen);
w = ENCODENUM(Btmp,b2,runlen);
b2 += w;
runlen = 0;
}
fwrite(Btmp,(b2+15) / 16,sizeof(short),f1);
psize1 += (b2+15)/16*sizeof(short);
b += (b2+15) / 16;
b2 = 0;
}
if (b2 > 0) {
fwrite(Btmp,(b2+15) / 16,sizeof(short),f1);
psize1 += (b2+15)/16*sizeof(short);
}
fwrite(Btmp,1,sizeof(short),f1); // getbitDで１ワード余計に読むため
psize1 += 1*sizeof(short);
if (id & ID_COMPPTR) {
SPARSEARRAY_construct_end(&sx, SDARRAY_SELECT1);
SPARSEARRAY_construct_end(&sb, SDARRAY_SELECT1);
SPARSEARRAY_write(&sx, f2);
SPARSEARRAY_write(&sb, f2);
}
psize = psize1 + psize2;
printf("size %ld (%1.3f bpc)\n",psize,(double)psize*8 / n);
fclose(f1);
fclose(f2);
// psi1_iterator_remove(pi);
close_diskbuf(psi);
fclose(out);
remove_tmp(0);
psi1_read(csa, fpsd);
free(fpsi);
free(fpsd);
free(fbw);
free(flst);
return psize;
}
i64 psi1_read(CSA *csa, char *fname)
{
FILE *f1;
i64 psize1,psize2;
i64 n;
int k,l,id,id2;
char *fpsi, *fpsd, *fname2;
psi1 *ps;
uchar *p,*q;
csa->psi_struc = ps = mymalloc(sizeof(psi1));
k = strlen(fname);
fname2 = mymalloc(k-4+1);
strncpy(fname2,fname,k-4);
fname2[k-4] = 0;
k -= 5;
initranktables();
mkdecodetable();
fpsi = mymalloc(k+5+1);
// fpsd = mymalloc(k+5);
// sprintf(fpsd,"%s.psd",fname2);
fpsd = fname;
// printf("psi_read: read %s\n",fpsd);
ps->mappsd = mymmap(fpsd);
if (ps->mappsd->addr==NULL) {
perror("psi1_read: mmap2\n");
exit(1);
}
p = q = (uchar *)ps->mappsd->addr;
psize1 = ps->mappsd->len;
id = getuint(p,0,1); p += 1;
if (id != ID_PSI) {
printf("read_psi: id = %d is not supported.\n",id);
exit(1);
}
ps->k = k = getuint(p,0,1); p += 1;
ps->n = n = getuint(p,0,k); p += k;
ps->L = l = getuint(p,0,k); p += k;
id = getuint(p,0,1); p += 1;
// printf("read_psi: psi_id = %d L = %d\n",id,l);
csa->id = ps->id = id;
id2 = id & 0x3f;
switch (id2) {
case ID_DIFF_GAMMA:
printf("#psi format = GAMMA L=%d C=%d\n",l,(id>>7));
sprintf(fpsi,"%s.psi",fname2);
break;
case ID_DIFF_GAMMA_RL:
printf("#psi format = GAMMA_RL L=%d C=%d\n",l,(id>>7));
sprintf(fpsi,"%s.pri",fname2);
break;
case ID_DIFF_GAMMA_SPARSE:
printf("#psi format = GAMMA_SPARSE L=%d C=%d\n",l,(id>>7));
sprintf(fpsi,"%s.psi",fname2);
break;
case ID_DIFF_GAMMA_RL_SPARSE:
printf("#psi format = GAMMA_RL_SPARSE L=%d C=%d\n",l,(id>>7));
sprintf(fpsi,"%s.pri",fname2);
break;
case ID_DIFF_GAMMA_RR:
printf("#psi format = GAMMA_RR L=%d C=%d\n",l,(id>>7));
sprintf(fpsi,"%s.pxi",fname2);
break;
default:
printf("read_csa: ID %d is not supported.\n",id);
break;
}
if (id & ID_COMPPTR) {
printf("COMPPTR\n");
ps->sx = mymalloc(sizeof(SPARSEARRAY));
ps->sb = mymalloc(sizeof(SPARSEARRAY));
SPARSEARRAY_read(ps->sx, &p);
SPARSEARRAY_read(ps->sb, &p);
} else {
ps->R = p;
}
// printf("psize = %ld\n",psize);
//// read psi
// printf("psi_read: map %s\n",fpsi);
ps->mappsi = mymmap(fpsi);
if (ps->mappsi->addr==NULL) {
perror("psi1_read: mmap1\n");
exit(1);
}
ps->B = (unsigned short *)ps->mappsi->addr;
psize2 = ps->mappsi->len;
// printf("psize2 = %ld\n",psize2);
// printf("psi1_read: psize1 = %ld psize2 = %ld\n",psize1,psize2);
ps->psize = psize1 + psize2;
free(fpsi);
// free(fpsd);
free(fname2);
// user-specific functions
csa->psi = psi1_psi;
if (id2 == ID_DIFF_GAMMA_RR) {
csa->psi = psi12_psi;
csa->psi_pred = csa_psi_pred_naive;
csa->psi_succ = csa_psi_succ_naive;
} else {
if ((id & ID_COMPPTR) || 0) {
csa->psi_pred = csa_psi_pred_naive;
csa->psi_succ = csa_psi_succ_naive;
} else {
csa->psi_succ = psi1_succ_tmp;
csa->psi_pred = psi1_pred_tmp;
// csa->psi_succ = csa_psi_succ_naive;
// csa->psi_pred = csa_psi_pred_naive;
}
}
// default functions
csa->LF = csa_LF_by_psi;
csa->lookup = csa_lookup;
csa->inverse = csa_inverse;
csa->text = csa_text;
csa->substring = csa_substring;
csa->T = csa_T;
csa->head = csa_head_rank;
csa->search = csa_search;
csa->searchsub = csa_searchsub;
return psize1 + psize2;
}
