unsigned long *csa_batchlookup2(CSA *SA,int l, int r) {
unsigned long *I; /* z */
int *V; /* vz */
int *J; /* Itz */
int v; /* [ */
int m; /* psivZ(testp) */
int q;
int i,j;
int two;
int *sa;
int f,s;
two = SA->two;
sa = SA->SA;
I = (unsigned long *)malloc((r-l+1)*sizeof(*I));
V = (int *)malloc((r-l+1+1)*sizeof(*V));
J = (int *)malloc((r-l+1+1)*sizeof(*J));
for (j=l; j<=r; j++) J[j-l] = -1;
for (j=l; j<=r; j++) I[j-l] = 0;
for (m=0,j=l; j<=r; j++) {
f = 0;
i = j; v = 0;
while (i % two !=0) {
i = csa_psi(SA,i);
v++;
m++;
if (l <= i && i <= r) {
V[j-l] = v;
J[i-l] = j;
f = 1;
break;
}
}
if (f==0) {
i = i / two;
I[j-l] = sa[i]-v;
}
}
for (j=l; j<=r; j++) {
if (I[j-l] != 0) {
q = j;
while (J[q-l] != -1) {
s = I[q-l];
i = J[q-l];
v = V[i-l];
I[i-l] = s - v;
J[q-l] = -1;
q = i;
}
}
}
for (j=l; j<=r; j++)
I[j-l]--;
free(V); free(J);
return I;
}
/*///////////////////////
//Accessing the indexed//
///////////////////////*/
int display(void *index, UCHAR *pattern, ULONG length, ULONG numc, ULONG *numocc, UCHAR **snippet_text, ULONG **snippet_lengths) {
int l,r;
int pos;
ULONG *occ, i, j, from, to, len, x;
UCHAR *text_aux;
CSA *SA=(CSA *) index;
csa_bsearch(pattern,length,SA,&l,&r);
*numocc = r-l+1;
occ = csa_batchlookup2(SA,l,r);
*snippet_lengths = (ULONG *) malloc((*numocc)*sizeof(ULONG));
if (!(*snippet_lengths)) return 1;
*snippet_text = (UCHAR *) malloc((*numocc)*(length+2*numc)*sizeof(UCHAR));
if (!(*snippet_text)) return 1;
text_aux=*snippet_text;
for (i=0;i<(*numocc);i++) {
x=occ[i];
if (x>numc) from = x-numc;
else from=0;
to= ((int)(x+length+numc-1)<(int)(SA->n-1)?(x+length+numc-1):(SA->n-1));
len =to-from+1;
pos = csa_inverse(SA,from+1);
for (j=0; (int)j<(int)len;j++) {
text_aux[j] = csa_T(SA,pos);
pos= csa_psi(SA,pos);
}
text_aux+=length+2*numc;
(*snippet_lengths)[i] = len;
}
free(occ);
return 0;
}
void csa_decode1line(unsigned char *p,CSA *SA,int suf,int maxlen) {
int i,k,m,pos;
unsigned char *tmp;
m = maxlen*2;
tmp = (unsigned char *)malloc(m+1);
if (tmp==NULL) {perror("csa_decode1line"); exit(1);}
k = suf - maxlen; if (k <= 0) k = 1;
pos = csa_inverse(SA,k);
i = 0;
while (i < m) {
tmp[i] = csa_T(SA,pos);
pos = csa_psi(SA,pos);
i++;
}
for (i = suf-k; i < m; i++) {
if (tmp[i] == 0x0a) {i--; break;}
}
m = i;
for (i = suf-k; i >= 0; i--) {
if (tmp[i] == 0x0a) {i++; break;}
}
if (m-i > maxlen) i = m-maxlen;
while (i < m) *p++ = tmp[i++];
*p = 0;
free(tmp);
}
void csa_decode2(unsigned char *p,CSA *SA,int pos,int len) {
int i;
i = 0;
while (i < len) {
*p++ = csa_T(SA,pos);
pos = csa_psi(SA,pos);
i++;
}
}
int csa_lookup(CSA *SA, int i) {
int v,two;
v = 0; two = SA->two;
while (i % two !=0) {
i = csa_psi(SA,i);
v++;
}
i = i / two;
return SA->SA[i]-v;
}
void csa_decode(unsigned char *p,CSA *SA,int suf,int len) {
int pos;
int i;
pos = csa_inverse(SA,suf);
i = 0;
while (i < len) {
*p++ = csa_T(SA,pos);
pos = csa_psi(SA,pos);
i++;
}
}
int csa_inverse(CSA *SA, int suf) {
int p,pos;
int two2;
two2 = SA->two2;
p = ((suf-1)/two2)*two2+1;
pos = SA->ISA[(suf-1)/two2];
while (p < suf) {
pos = csa_psi(SA,pos);
p++;
}
return pos;
}
int extract(void *index, ULONG from, ULONG to, UCHAR **snippet, ULONG *snippet_length){
CSA *SA=(CSA *) index;
ULONG n = SA->n;
int pos;
if (to >= n) to=n-1;
if (from > to) {
*snippet = NULL;
*snippet_length=0;
} else {
ULONG j;
ULONG len =to-from+1;
*snippet = (UCHAR *) malloc((len)*sizeof(UCHAR));
if (!(*snippet)) return 1;
pos = csa_inverse(SA,from+1);
for (j=0; j<len;j++) {
(*snippet)[j]=csa_T(SA,pos);
pos= csa_psi(SA,pos);
}
(*snippet_length)=len;
}
return 0;
}
int extract(void *index, ulong from, ulong to, uchar **snippet, ulong *snippet_length) {
CSA *SA=(CSA *) index;
ulong n = SA->n;
int pos;
if (to >= n) to=n-1;
if (from > to) {
*snippet = NULL;
*snippet_length=0;
}
else {
ulong j;
ulong len =to-from+1;
*snippet = (uchar *) malloc((len)*sizeof(uchar));
if (!(*snippet)) return 1;
pos = csa_inverse(SA,from+1);
for (j=0; j<len;j++) {
(*snippet)[j]=csa_T(SA,pos);
pos= csa_psi(SA,pos);
}
(*snippet_length)=len;
}
return 0;
}
size_t TextIndexCSA::getPsi(size_t i) const{
return csa_psi(csa,i+1)-1;
}
/* backward search */
int csa_bsearch(unsigned char *key,int keylen,CSA *SA,int *li,int *ri) {
int c,h,l,r,m,ll,rr,pl,pr;
int x,b,w,d,n,*R;
unsigned short *B;
int len;
c = key[keylen-1];
r = SA->C[c]; if (c>0) l = SA->C[c-1]+1; else l = 1;
len = 0;
if (l > r) goto end;
len++;
for (h = keylen-2; h >= 0; h--) {
pl = l; pr = r;
c = key[h];
r = SA->C[c]; if (c>0) l = SA->C[c-1]+1; else l = 1;
if (l > r) goto end;
#if 0
while (1) { // find maximum r such that Psi[r] <= pr
j = csa_psi(SA,r);
if (j <= pr) break;
r--;
//if (l > r) goto end;
}
#else
#if 0
ll = l; rr = r;
while (ll <= rr) {
m = (ll + rr) / 2;
if (csa_psi(SA,m) <= pr) ll = m+1; else rr = m-1;
}
r = ll-1;
#else
R = SA->R; B = SA->B; w = SA->l; n = SA->n;
ll = l / w + 1;
rr = r / w;
while (ll <= rr) {
m = (ll + rr) / 2;
if (R[m*2] <= pr) ll = m+1; else rr = m-1;
}
m = (ll-1)*w;
x = R[(m / w)*2];
b = R[(m / w)*2+1];
#if 1
while (m < l) {
b += DECODENUM(B,b,&d);
x += d;
//if (x > n) printf("??? \n");
if (x > n) {x = -1; m--;}
m++;
}
#endif
while (x <= pr && m <= r) {
b += DECODENUM(B,b,&d);
x += d;
//if (x > n) printf("??? \n");
m++;
}
r = m-1;
#endif
#endif
#if 0
while (1) { // find minimum l such that Psi[l] >= pl
j = csa_psi(SA,l);
if (j >= pl) break;
l++;
//if (l > r) goto end;
}
#else
#if 0
ll = l; rr = r;
while (ll <= rr) {
m = (ll + rr) / 2;
if (csa_psi(SA,m) >= pl) rr = m-1; else ll = m+1;
}
l = rr+1;
#else
//ll = l / w + 1;
ll = l / w;
rr = r / w;
while (ll <= rr) {
m = (ll + rr) / 2;
if (R[m*2] >= pl) rr = m-1; else ll = m+1;
}
m = rr*w;
x = R[(m / w)*2];
b = R[(m / w)*2+1];
while (m < l) {
b += DECODENUM(B,b,&d);
x += d;
if (x > n) {x = -1; m--;}
m++;
}
while (x < pl && m <= r) {
b += DECODENUM(B,b,&d);
x += d;
m++;
}
l = m;
#endif
#endif
if (l > r) goto end;
len++;
}
end:
*li = l; *ri = r;
return len;
}
int *csa_batchlookup3(CSA *SA,int l, int r,int len) {
int *I; /* z */
int *P; /* r i z */
int v; /* [ */
int m; /* SA */
int q;
int i,j;
int two;
int *sa;
int k,b,d,x,n,w;
unsigned short *B;
n = SA->n;
B = SA->B;
two = SA->two;
sa = SA->SA;
w = SA->l;
I =(int *) malloc((r-l+1+1)*sizeof(*I));
P =(int *) malloc((r-l+1+1)*sizeof(*I));
#if 1
x = SA->R[(l / w)*2];
b = SA->R[(l / w)*2+1];
j = l % w;
for (k=0; k<j; k++) {
b += DECODENUM(B,b,&d);
x += d;
if (x > n) {x = -1; k--;}
}
for (m = 0, q = 0, i = l; i <= r; i++) {
if (i % two == 0) {
I[1+m] = sa[i / two];
m++;
}
else {
P[q++] = x;
}
b += DECODENUM(B,b,&d);
x += d;
if (x > n) {
x = -1;
b += DECODENUM(B,b,&d);
x += d;
}
}
v = 1;
#else
for (q = 0, i = l; i <= r; i++) {
P[q++] = i;
}
v = 0;
m = 0;
#endif
while (q > 0 && v <= len) {
for (k = 0, j = 0; j < q; j++) {
i = P[j];
if (i % two == 0) {
I[1+m] = sa[i / two] - v;
m++;
}
else {
P[k++] = csa_psi(SA,i);
}
}
q = k;
v++;
}
for (j = 0; j < q; j++) {
I[1+m] = csa_lookup(SA,P[j])-v;
m++;
}
qsort(I+1, r-l+1, sizeof(int), intcompare);
I[0] = r-l+1;
free(P);
return I;
}
