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 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;
}
