int main(int argc,char * argv[])
{
const char * s1="xml.50MB";
const char * sa="xml.csa";
const char * s2="xml.txt";
if(argc==2)
{
CSA csa(atoi(argv[1]));
csa.Compress(s1,sa);
cout<<"compress is ok"<<endl;
csa.Decompress(sa,s2);
cout<<"decompress is ok"<<endl;
}
else
{
CSA csa;
csa.Compress(s1,sa);
cout<<"compress is ok"<<endl;
// time_t t1=clock();
csa.Decompress(sa,s2);
// time_t t2=clock();
// cout<<(t2-t1)/1000000.0<<endl;
cout<<"decompress is ok"<<endl;
}
return 0;
}
cst_node cst_nextchild(cst_node node, cst_node child)
{
int c;
i64 l, r;
i64 i, depth;
CSA *csa;
cst_node newnode;
csa = node.csa;
l = child.r+1;
depth = node.depth;
if (l > node.r) {
newnode.depth = -1;
newnode.l = 1;
newnode.r = 0;
return newnode;
}
for (i=0; i<depth; i++) {
l = csa->psi(csa, l);
}
c = csa->head(csa, l);
if (c == -1) {
newnode.csa = csa;
newnode.depth = depth+1;
newnode.l = newnode.r = node.l;
return newnode;
} else {
return cst_child(node, csa->AtoC[c]);
}
}
static VALUE // bug?
rb_csa_search_l(VALUE self, VALUE oc, VALUE range)
{
CSA *sa = csa_ptr(self);
i64 ll,rr;
int c;
i64 ret;
c = FIX2INT(oc);
#if USE_RANGE
ll = FIX2LONG(range_first(range));
rr = FIX2LONG(range_last(range)); if (range_exclude_end_p(range) == Qtrue) rr--;
#else
if (RALEN(range) != 2) {
return Qnil;
}
ll = FIX2LONG(RAPTR(range)[0]);
rr = FIX2LONG(RAPTR(range)[1]);
#endif
ret = sa->searchsub(c, sa, &ll, &rr);
if (ret == -1) return Qnil;
#if USE_RANGE
return rb_range_new(LONG2FIX(ll), LONG2FIX(rr), Qnil);
#else
return rb_ary_new3(2, LONG2FIX(ll), LONG2FIX(rr));
#endif
}
cst_node cst_canonize(cst_node node)
{
int c1,c2;
cst_node newnode;
i64 l, r;
i64 i, depth;
CSA *csa;
newnode = node;
csa = node.csa;
l = node.l; r = node.r;
depth = node.depth;
for (i=0; i<depth; i++) {
l = csa->psi(csa, l);
r = csa->psi(csa, r);
}
while (1) {
c1 = csa->head(csa, l);
c2 = csa->head(csa, r);
if (c1 != c2) break;
l = csa->psi(csa, l);
r = csa->psi(csa, r);
depth++;
}
newnode.depth = depth;
return newnode;
}
static VALUE
//rb_csa_text(VALUE self, VALUE oi, VALUE oj)
rb_csa_text(VALUE self, VALUE range)
{
CSA *sa = csa_ptr(self);
i64 i,j,n;
uchar *buf;
#if USE_RANGE
i = FIX2LONG(range_first(range));
j = FIX2LONG(range_last(range)); if (range_exclude_end_p(range) == Qtrue) j--;
#else
// i = FIX2LONG(oi);
// j = FIX2LONG(oj);
if (RALEN(range) != 2) {
return Qnil;
}
i = FIX2LONG(RAPTR(range)[0]);
j = FIX2LONG(RAPTR(range)[1]);
#endif
n = sa->n;
if (i < 0 || i > n || j < 0 || j > n) { // error
return Qnil;
}
buf = (uchar *)alloca(j-i+1+1);
sa->text(buf, sa, i, j);
buf[j-i+1] = 0;
return rb_str_new(buf, j-i+1);
}
int locate(void *index, uchar *pattern, ulong length, ulong **occ,
ulong *numocc)
{
CSA *csa;
i64 l,r;
ulong *buf,*buf2;
ulong i,oc;
i64 mlen;
csa = (CSA *)index;
mlen = csa->search(pattern, length, csa, &l, &r);
if (mlen < length) {
*numocc = 0;
return 0;
}
oc = (ulong)(r - l + 1);
buf = malloc((*numocc) * sizeof(ulong));
if (buf == NULL) {
printf("locate: not enough mem.\n");
exit(1);
}
for (i=0; i<oc; i++) {
buf[i] = csa->lookup(csa,l + i);
}
*numocc = oc;
*occ = buf;
return 0;
}
cst_node cst_firstchild(cst_node node)
{
int c;
i64 l;
i64 i, depth;
CSA *csa;
cst_node newnode;
csa = node.csa;
l = node.l;
depth = node.depth;
for (i=0; i<depth; i++) {
l = csa->psi(csa, l);
}
c = csa->head(csa, l);
if (c == -1) {
newnode.csa = csa;
newnode.depth = depth+1;
newnode.depth2 = depth+1;
newnode.l = newnode.r = node.l;
return newnode;
} else {
return cst_child(node, csa->AtoC[c]);
}
}
cst_node cst_suflink(cst_node node)
{
CSA *csa;
i64 l, r;
cst_node newnode;
csa = newnode.csa = node.csa;
l = node.l; r = node.r;
newnode.l = csa->psi(csa, l);
newnode.r = csa->psi(csa, r);
newnode.depth = node.depth;
return cst_parent(newnode);
}
int count(void *index, uchar *pattern, ulong length, ulong *numocc)
{
CSA *csa;
i64 l,r;
i64 mlen;
csa = (CSA *)index;
mlen = csa->search(pattern, length, csa, &l, &r);
if (mlen < length) {
*numocc = 0;
return 0;
}
*numocc = (ulong)(r - l + 1);
return 0;
}
static VALUE
rb_csa_inverse(VALUE self, VALUE oi)
{
CSA *sa = csa_ptr(self);
i64 i,j,n;
i = FIX2LONG(oi);
n = sa->n;
if (i < 0 || i > n) { // error
return Qnil;
}
j = sa->inverse(sa, i);
return LONG2FIX(j);
}
static VALUE
rb_csa_child_l(VALUE self, VALUE range)
{
CSA *sa = csa_ptr(self);
i64 l,r,ll,rr;
int c,i;
VALUE charset;
i64 ret;
#if USE_RANGE
ll = FIX2LONG(range_first(range));
rr = FIX2LONG(range_last(range)); if (range_exclude_end_p(range) == Qtrue) rr--;
#else
if (RALEN(range) != 2) {
return Qnil;
}
ll = FIX2LONG(RAPTR(range)[0]);
rr = FIX2LONG(RAPTR(range)[1]);
#endif
l = r = -1;
if (!rb_block_given_p()) charset = rb_ary_new();
for (i=0; i<sa->m; i++) {
c = sa->AtoC[i];
l = ll; r = rr;
ret = sa->searchsub(c, sa, &l, &r);
if (ret == 0) {
if (rb_block_given_p()) {
rb_yield(rb_ary_new3(2,INT2FIX(c),
#if USE_RANGE
rb_range_new(LONG2FIX(l), LONG2FIX(r), Qnil)));
#else
rb_ary_new3(2,LONG2FIX(l),LONG2FIX(r))));
#endif
} else {
rb_ary_push(charset,
rb_ary_new3(2,INT2FIX(c),
#if USE_RANGE
rb_range_new(LONG2FIX(l), LONG2FIX(r), Qnil)));
#else
rb_ary_new3(2,LONG2FIX(l),LONG2FIX(r))));
#endif
}
}
}
static VALUE
rb_csa_T(VALUE self, VALUE oi)
{
CSA *sa = csa_ptr(self);
i64 i, n;
int c;
i = FIX2LONG(oi);
n = sa->n;
if (i < 0 || i > n) { // error
return Qnil;
}
c = sa->T(sa, i);
return INT2FIX(c);
}
static VALUE
rb_csa_lf(VALUE self, VALUE oi)
{
CSA *sa = csa_ptr(self);
i64 i, n;
i64 p;
i = FIX2LONG(oi);
n = sa->n;
if (i < 0 || i > n) { // error
return Qnil;
}
p = sa->LF(sa, i);
return LONG2FIX(p);
}
static VALUE
rb_csa_search(VALUE self, VALUE okey)
{
CSA *sa = csa_ptr(self);
i64 n, l, keylen;
i64 i[2];
uchar *key;
key = StringValueCStr(okey);
keylen = RSLEN(okey);
if (sa->search(key, keylen, sa, &i[0], &i[1]) < keylen) return Qnil;
#if USE_RANGE
return rb_range_new(LONG2FIX(i[0]), LONG2FIX(i[1]), Qnil);
#else
return rb_ary_new3(2, LONG2FIX(i[0]), LONG2FIX(i[1]));
#endif
}
static VALUE
rb_csa_substring(VALUE self, VALUE orank, VALUE olen)
{
CSA *sa = csa_ptr(self);
i64 rank,len,n;
uchar *buf;
rank = FIX2LONG(orank);
len = FIX2LONG(olen);
n = sa->n;
if (rank < 0 || rank > n || len < 0) { // error
return Qnil;
}
buf = (uchar *)alloca(len+1);
len = sa->substring(buf, sa, rank, len);
buf[len] = 0;
return rb_str_new(buf, len);
}
int extract(void *index, ulong from, ulong to, uchar **snippet,
ulong *snippet_length)
{
CSA *csa;
uchar *text;
i64 i,len;
csa = (CSA *)index;
from++; to++;
if (to > csa->n) to = csa->n;
len = to - from + 1;
text = malloc(len);
csa->text(text,csa,from,to);
*snippet = text;
*snippet_length = (ulong)len;
return 0;
}
int cst_isunary(cst_node node)
{
int c1,c2;
i64 l, r;
i64 i, depth;
CSA *csa;
csa = node.csa;
l = node.l; r = node.r;
depth = node.depth;
for (i=0; i<depth; i++) {
l = csa->psi(csa, l);
r = csa->psi(csa, r);
}
c1 = csa->head(csa, l);
c2 = csa->head(csa, r);
return (c1 == c2);
}
cst_node cst_parent(cst_node node)
{
CSA *csa;
uchar *label;
cst_node parent;
i64 l, r;
i64 len;
csa = node.csa;
parent.csa = csa;
parent.depth = node.depth-1;
label = cst_pathlabel(node);
l = node.l; r = node.r;
if (csa->search(label, parent.depth, csa, &l, &r) != parent.depth) {
printf("cst_parent: ???\n");
}
parent.l = l; parent.r = r;
free(label);
return parent;
}
cst_node cst_weiner_link(cst_node node, int c)
{
CSA *csa;
cst_node newnode;
i64 ll, rr;
i64 len;
csa = newnode.csa = node.csa;
ll = node.l; rr = node.r;
if (csa->searchsub(c, node.csa, &ll, &rr) != 0) {
newnode.depth = -1;
newnode.l = 1;
newnode.r = 0;
} else {
newnode.depth = node.depth+1;
newnode.l = ll;
newnode.r = rr;
}
return newnode;
}
int main(int argc, char *argv[])
{
i64 i,n;
CSA csa;
mytimestruct before,after;
double t;
if (argc<2) {
fprintf(stderr, "syntax: suftest file\n");
return 1;
}
csa_read(&csa,argc,argv);
n = csa.n;
mygettime(&before);
{
int m;
FILE *out;
out = fopen("output.dec","w");
i = 0;
while (i < n) {
if ((i/PAGE) % PAGE == 0) {
fprintf(stderr,"%ld \r",i/PAGE); fflush(stderr);
}
m = PAGE;
if (i+m >= n) m = n-i;
csa.text(buf,&csa,i,i+m-1);
fwrite(buf,1,m,out);
i += m;
}
fwrite(buf,1,0,out);
fclose(out);
}
mygettime(&after);
t = mylaptime(&before,&after);
fprintf(stderr,"time %f sec\n",t);
return 0;
}
void csa_new_from_bwt(int argc, char *argv[])
{
i64 i,j,v,m;
FILE *f2;
i64 psize,isize;
i64 n;
int k;
char *fname,*fidx;
char *p;
int psi_id, idx_id;
CSA csa;
int sigma;
csa.sigma = 256; /* default alphabet size */
csa.k2 = 1;
// for (i=0; i<SIGMA+2; i++) csa.C[i] = 0;
// for (i=0; i<SIGMA; i++) csa.C[i] = 0;
fname = NULL; fidx = NULL;
psi_id = idx_id = -1;
for (i=1; i<argc; i++) {
p = argv[i];
if (p[0] == '-') {
p++;
switch (toupper(p[0])) {
case 'I':
// -I[n]:[D]:[D2]
p++;
idx_id = 0;
csa_options(&csa, p);
break;
case 'P':
// -P[n]:[L]
p++;
psi_id = 0;
psi_options(&csa, p);
break;
case 'C':
// -C[s]
p++;
sigma_options(&csa, p);
break;
default:
printf("??? no such option %s\n",argv[i]);
exit(1);
}
} else {
fname = argv[i];
k = strlen(fname);
fidx = mymalloc(k+5);
sprintf(fidx,"%s.idx",fname);
}
}
if (fname == NULL) {
printf("no input file.\n");
exit(0);
}
printf("sigma = %d k2 = %d\n", csa.sigma, csa.k2);
sigma = csa.sigma;
csa.C = mymalloc(sizeof(*csa.C)*sigma); //
csa.CtoA = mymalloc(sizeof(*csa.CtoA)*sigma); //
csa.AtoC = mymalloc(sizeof(*csa.AtoC)*sigma); //
csa.K = mymalloc(sizeof(*csa.K)*(sigma+2)); //
for (i=0; i<sigma; i++) csa.C[i] = 0;
psi_id = csa.id;
if (psi_id >= 0) {
printf("create psi: id=%d\n",psi_id);
}
if (idx_id >= 0) {
printf("create idx: id=%d D=%d D2=%d\n",idx_id,csa.D,csa.D2);
}
psize = 0;
if (psi_id >= 0) {
switch (psi_id & 0x3f) {
case ID_DIFF_GAMMA:
case ID_DIFF_GAMMA_RL:
case ID_DIFF_GAMMA_SPARSE:
case ID_DIFF_GAMMA_RL_SPARSE:
psize = psi1_makeindex(&csa, fname);
printf("n %ld\n",csa.n);
printf("Psi %ld bytes (%1.3f bpc)\n",
psize,(double)psize*8/csa.n);
break;
case ID_DIFF_GAMMA_RR:
psize = psi12_makeindex(&csa, fname);
printf("n %ld\n",csa.n);
printf("Psi %ld bytes (%1.3f bpc)\n",
psize,(double)psize*8/csa.n);
break;
case ID_BWT_DNA:
psize = lf_dna_makeindex(&csa, fname);
printf("n %ld\n",csa.n);
printf("BW %ld bytes (%1.3f bpc)\n",
psize,(double)psize*8/csa.n);
break;
case ID_BWT_DNA2:
psize = lf_dna2_makeindex(&csa, fname);
printf("n %ld\n",csa.n);
printf("BW %ld bytes (%1.3f bpc)\n",
psize,(double)psize*8/csa.n);
break;
case ID_BWT_BIT:
psize = lf_bit_makeindex(&csa, fname);
printf("n %ld\n",csa.n);
printf("BW %ld bytes (%1.3f bpc)\n",
psize,(double)psize*8/csa.n);
break;
case ID_BWT_WT:
case ID_BWT_WT_HUF:
case ID_BWT_WT_DENSE:
case ID_BWT_WT_SPARSE4:
case ID_BWT_WT_RR:
psize = lf_wt_makeindex(&csa, fname);
printf("n %ld\n",csa.n);
printf("BW %ld bytes (%1.3f bpc)\n",
psize,(double)psize*8/csa.n);
break;
#if 0
case ID_BWT_HUF:
psize = lf_bwt_makeindex(&csa, fname);
printf("n %ld\n",csa.n);
printf("BW %ld bytes (%1.3f bpc)\n",
psize,(double)psize*8/csa.n);
break;
#endif
case ID_SPARSE4:
psize = psi2_makeindex(&csa, fname);
printf("n %ld\n",csa.n);
printf("Psi %ld bytes (%1.3f bpc)\n",
psize,(double)psize*8/csa.n);
break;
default:
printf("psi_id = %d\n",psi_id);
exit(1);
}
}
csa.k = (blog(csa.n+1)+1+8-1)/8;
for (i=0; i<sigma; i++) csa.CtoA[i] = -1;
csa.K[-1+1] = 1;
for (m=0,v=1,i=0; i<sigma; i++) {
if (csa.C[i]>0) {
csa.AtoC[m] = i;
csa.CtoA[i] = m;
csa.K[m+1] = v;
// printf("i=%ld v = %ld C[i] = %ld\n",i,v,csa.C[i]);
v += csa.C[i];
m++;
}
}
csa.K[m+1] = v;
csa.m = m;
if (csa.D >= csa.n) {
printf("D=%d >= n=%ld\n",csa.D,csa.n);
exit(0);
}
if (csa.D2 >= csa.n) {
printf("D2=%d >= n=%ld\n",csa.D2,csa.n);
exit(0);
}
if (idx_id >= 0) {
n = csa.n;
k = csa.k;
//// compute SA and ISA
if (csa.D > 0) csa.SA = mymalloc(((n-1)/csa.D+1+1)*k);
if (csa.D2 > 0) csa.ISA = mymalloc(((n-1)/csa.D2+1+1)*k);
if (csa.D == 0 && csa.D2 == 0) goto brk;
switch (psi_id & 0x3f) {
case ID_DIFF_GAMMA:
case ID_DIFF_GAMMA_RL:
case ID_DIFF_GAMMA_SPARSE:
case ID_DIFF_GAMMA_RL_SPARSE:
case ID_SPARSE4:
case ID_DIFF_GAMMA_RR:
j = 0;
for (i=0; i<=n; i++) {
display_progressbar("making sa ",i,n);
j = csa.psi(&csa,j);
// sa[j] = i;
if (csa.D > 0 && j % csa.D == 0) {
putuint(csa.SA,j / csa.D,i,k);
}
if (csa.D2 > 0 && i % csa.D2 == 0) {
putuint(csa.ISA,i / csa.D2,j,k);
}
}
// putuint(csa.SA,0,n,k);
break;
case ID_BWT_DNA:
case ID_BWT_DNA2:
case ID_BWT_BIT:
case ID_BWT_WT:
case ID_BWT_WT_HUF:
case ID_BWT_WT_DENSE:
case ID_BWT_WT_SPARSE4:
case ID_BWT_WT_RR:
case ID_BWT_HUF:
j = 0;
for (i=n-1; i>=0; i--) {
display_progressbar("making sa ",i,n);
v = csa.LF(&csa,j);
// printf("LF[%ld] = %ld\n",j,v);
j = v;
if (csa.D > 0 && j % csa.D == 0) putuint(csa.SA, j/csa.D , i, k);
if (csa.D2 > 0 && i % csa.D2 == 0) putuint(csa.ISA, i/csa.D2, j, k);
}
// putuint(csa.SA,0,n,k);
if (csa.D > 0) putuint(csa.SA,0,n,k); // 2011-12-20
break;
default:
break;
}
brk:
//// write idx
f2 = fopen(fidx,"wb"); /* directory */
if (f2 == NULL) {
perror("csa2_new1: ");
exit(1);
}
isize = 0;
writeint(4,VERSION,f2); /* version */
isize += 4;
writeint(1,ID_HEADER,f2); // header ID
isize += 1;
isize = write_header(&csa, f2, isize);
if (csa.D > 0) {
writeint(1,ID_SA,f2);
isize += 1;
isize = write_sa(&csa, f2, isize);
}
if (csa.D2 > 0) {
writeint(1,ID_ISA,f2);
isize += 1;
isize = write_isa(&csa, f2, isize);
}
fclose(f2);
if (csa.D > 0) free(csa.SA);
if (csa.D2 > 0) free(csa.ISA);
printf("Total %ld bytes (%1.3f bpc)\n",(psize+isize),
(double)(psize+isize)*8/csa.n);
}
free(fidx);
}
void csa_new_from_bwt(CSA csa, char *fname, char *fidx, int psi_id, int idx_id, bool coded)
{
int k;
i64 i,j,v,m;
FILE *f2;
i64 psize,isize;
i64 n;
psi_id = csa.id;
if (psi_id >= 0) {
printf("create psi: id=%d\n",psi_id);
}
if (idx_id >= 0) {
printf("create idx: id=%d D=%d D2=%d\n",idx_id,csa.D,csa.D2);
}
psize = 0;
if (psi_id >= 0) {
switch (psi_id & 0x3f) {
case ID_DIFF_GAMMA:
case ID_DIFF_GAMMA_RL:
case ID_DIFF_GAMMA_SPARSE:
case ID_DIFF_GAMMA_RL_SPARSE:
psize = psi1_makeindex(&csa, fname);
printf("n %ld\n",csa.n);
printf("Psi %ld bytes (%1.3f bpc)\n",
psize,(double)psize*8/csa.n);
break;
case ID_DIFF_GAMMA_RR:
psize = psi12_makeindex(&csa, fname);
printf("n %ld\n",csa.n);
printf("Psi %ld bytes (%1.3f bpc)\n",
psize,(double)psize*8/csa.n);
break;
case ID_BWT_DNA:
psize = lf_dna_makeindex(&csa, fname, coded);
printf("n %ld\n",csa.n);
printf("BW %ld bytes (%1.3f bpc)\n",
psize,(double)psize*8/csa.n);
break;
case ID_BWT_BIT:
psize = lf_bit_makeindex(&csa, fname);
printf("n %ld\n",csa.n);
printf("BW %ld bytes (%1.3f bpc)\n",
psize,(double)psize*8/csa.n);
break;
case ID_BWT_WT:
case ID_BWT_WT_HUF:
case ID_BWT_WT_DENSE:
case ID_BWT_WT_SPARSE4:
case ID_BWT_WT_RR:
psize = lf_wt_makeindex(&csa, fname);
printf("n %ld\n",csa.n);
printf("BW %ld bytes (%1.3f bpc)\n",
psize,(double)psize*8/csa.n);
break;
#if 0
case ID_BWT_HUF:
psize = lf_bwt_makeindex(&csa, fname);
printf("n %ld\n",csa.n);
printf("BW %ld bytes (%1.3f bpc)\n",
psize,(double)psize*8/csa.n);
break;
#endif
case ID_SPARSE4:
psize = psi2_makeindex(&csa, fname);
printf("n %ld\n",csa.n);
printf("Psi %ld bytes (%1.3f bpc)\n",
psize,(double)psize*8/csa.n);
break;
default:
printf("psi_id = %d\n",psi_id);
exit(1);
}
}
csa.k = (blog(csa.n+1)+1+8-1)/8;
for (i=0; i<SIGMA; i++) csa.CtoA[i] = -1;
// csa.K[-1+1] = 0;
csa.K[-1+1] = 1;
for (m=0,v=1,i=0; i<SIGMA; i++) {
if (csa.C[i]>0) {
csa.AtoC[m] = i;
csa.CtoA[i] = m;
csa.K[m+1] = v;
// printf("i=%ld v = %ld C[i] = %ld\n",i,v,csa.C[i]);
v += csa.C[i];
m++;
}
}
csa.K[m+1] = v;
csa.m = m;
if (csa.D >= csa.n) {
printf("D=%d >= n=%ld\n",csa.D,csa.n);
exit(0);
}
if (csa.D2 >= csa.n) {
printf("D2=%d >= n=%ld\n",csa.D2,csa.n);
exit(0);
}
if (idx_id >= 0) {
n = csa.n;
k = csa.k;
//// compute SA and ISA
if (csa.D > 0) csa.SA = (uchar *) mymalloc(((n-1)/csa.D+1+1)*k);
if (csa.D2 > 0) csa.ISA = (uchar *) mymalloc(((n-1)/csa.D2+1+1)*k);
if (csa.D == 0 && csa.D2 == 0) goto brk;
switch (psi_id & 0x3f) {
case ID_DIFF_GAMMA:
case ID_DIFF_GAMMA_RL:
case ID_DIFF_GAMMA_SPARSE:
case ID_DIFF_GAMMA_RL_SPARSE:
case ID_SPARSE4:
case ID_DIFF_GAMMA_RR:
j = 0;
for (i=0; i<=n; i++) {
display_progressbar("making sa ",i,n);
j = csa.psi(&csa,j);
// sa[j] = i;
if (csa.D > 0 && j % csa.D == 0) {
putuint(csa.SA,j / csa.D,i,k);
}
if (csa.D2 > 0 && i % csa.D2 == 0) {
putuint(csa.ISA,i / csa.D2,j,k);
}
}
// putuint(csa.SA,0,n,k);
break;
case ID_BWT_DNA:
case ID_BWT_BIT:
case ID_BWT_WT:
case ID_BWT_WT_HUF:
case ID_BWT_WT_DENSE:
case ID_BWT_WT_SPARSE4:
case ID_BWT_WT_RR:
case ID_BWT_HUF:
j = 0;
for (i=n-1; i>=0; i--) {
display_progressbar("making sa ",i,n);
v = csa.LF(&csa,j);
// printf("LF[%ld] = %ld\n",j,v);
j = v;
if (csa.D > 0 && j % csa.D == 0) putuint(csa.SA, j/csa.D , i, k);
if (csa.D2 > 0 && i % csa.D2 == 0) putuint(csa.ISA, i/csa.D2, j, k);
}
putuint(csa.SA,0,n,k);
break;
default:
break;
}
brk:
//// write idx
f2 = fopen(fidx,"wb"); /* directory */
if (f2 == NULL) {
perror("csa2_new1: ");
exit(1);
}
isize = 0;
writeint(4,VERSION,f2); /* version */
isize += 4;
writeint(1,ID_HEADER,f2); // header ID
isize += 1;
isize = write_header(&csa, f2, isize);
if (csa.D > 0) {
writeint(1,ID_SA,f2);
isize += 1;
isize = write_sa(&csa, f2, isize);
}
if (csa.D2 > 0) {
writeint(1,ID_ISA,f2);
isize += 1;
isize = write_isa(&csa, f2, isize);
}
fclose(f2);
if (csa.D > 0) free(csa.SA);
if (csa.D2 > 0) free(csa.ISA);
printf("Total %ld bytes (%1.3f bpc)\n",(psize+isize),
(double)(psize+isize)*8/csa.n);
}
free(fidx);
}
int main(int argc, char *argv[])
{
i64 n;
CSA SA;
if (argc<3) {
fprintf(stderr, "syntax: %s {indexfiles}\n", argv[0]);
return 1;
}
csa_read(&SA,argc-1, argv+1);
n = SA.n;
#if 0
{
int i;
rank_t x;
unicode_t code;
uchar buf[6], *p;
x = SA.inverse(&SA, 0);
for (i = 0; i < 1000; i++) {
if (csa_utf8_T_psi(&SA, &x, &code) == -1) {
printf("???\n");
}
p = &buf[0];
unicode_to_string(&p, code);
buf[unicode_len(code)] = 0;
printf("%d code = %d (%s) rank = %ld\n", i, code, &buf[0], x);
}
for (i = 0; i < 1000; i++) {
if (csa_utf8_BW_LF(&SA, &x, &code) == -1) {
printf("???\n");
}
p = &buf[0];
unicode_to_string(&p, code);
buf[unicode_len(code)] = 0;
printf("%d code = %d (%s) rank = %ld\n", i, code, &buf[0], x);
}
}
#endif
#if 1
{
int i;
rank_t x;
unicode_t code;
uchar buf[6], *p;
CSAFILE *csafile;
csafile = csa_fdopen(&SA, NULL);
for (i = 0; i < 1000; i++) {
code = csa_fgetwc(csafile);
x = csafile->rank;
p = &buf[0];
unicode_to_string(&p, code);
buf[unicode_len(code)] = 0;
printf("%d code = %d (%s) rank = %ld\n", i, code, &buf[0], x);
}
for (i = 0; i < 1000; i++) {
code = csa_fgetwbw(csafile);
x = csafile->rank;
p = &buf[0];
unicode_to_string(&p, code);
buf[unicode_len(code)] = 0;
printf("%d code = %d (%s) rank = %ld\n", i, code, &buf[0], x);
}
}
#endif
return 0;
}
