-
+/* static_sequence_gmr_chunk.cpp
+ * Copyright (C) 2008, Francisco Claude, all rights reserved.
+ *
+ * gmr_chunk
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ *
+ */
+
#include "static_sequence_gmr_chunk.h"
+using std::max;
static_sequence_gmr_chunk::static_sequence_gmr_chunk(uint * sequence, uint chunk_length, static_bitsequence_builder *bmb, static_permutation_builder *pmb) {
sigma = 0;
for(uint i=0;i<chunk_length;i++) {
sigma = max(sigma,sequence[i]);
- }
- uint * X_bitmap = new uint[(1+chunk_length+sigma)/W+1];
+ }sigma++;
+ uint * X_bitmap = new uint[uint_len(1+chunk_length+sigma,1)];
assert(X_bitmap!=NULL);
- for(uint i=0;i<(1+sigma+chunk_length)/W+1;i++) X_bitmap[i]=0;
+ for(uint i=0;i<uint_len(1+chunk_length+sigma,1);i++) X_bitmap[i]=0;
uint pi_blen = bits(chunk_length-1);
- uint * pi = new uint[pi_blen*chunk_length/W+1];
+ uint * pi = new uint[uint_len(pi_blen,chunk_length)];
assert(pi!=NULL);
- for(uint i=0;i<pi_blen*chunk_length/W+1;i++) pi[i] = 0;
+ for(uint i=0;i<uint_len(pi_blen,chunk_length);i++) pi[i] = 0;
uint X_pos = 0;
- uint * counter = new uint[sigma+1];
- for(uint c=0;c<=sigma;c++) counter[c]=0;
+ uint * counter = new uint[sigma+2];
+ for(uint c=0;c<=sigma+1;c++) counter[c]=0;
for(uint i=0;i<chunk_length;i++) counter[sequence[i]+1]++;
for(uint c=0;c<sigma;c++) {
}
X_pos++;
for(uint i=0;i<chunk_length;i++) {
- bitput(pi, pi_blen*counter[sequence[i]], pi_blen, (uint)i);
+ set_field(pi, pi_blen,counter[sequence[i]], i);
counter[sequence[i]]++;
}
- this->X = new BitRankW32Int(X_bitmap, X_pos, true,20);
+ //cout << "pi_blen=" << pi_blen << endl;
+ this->X = bmb->build(X_bitmap,X_pos); //new BitRankW32Int(X_bitmap, X_pos, true,20);
assert(X!=NULL);
- this->permutation = createPerm(pi, chunk_length, t);
+ delete [] X_bitmap;
+ //cout << "a" << endl; cout.flush();
+ this->permutation = pmb->build(pi,chunk_length); //createPerm(pi, chunk_length, t);
+ //cout << "a" << endl; cout.flush();
assert(permutation!=NULL);
this->sigma = sigma;
- this->chunk_length = chunk_length;
+ this->len = chunk_length;
delete [] counter;
}
+static_sequence_gmr_chunk::static_sequence_gmr_chunk() {
+}
static_sequence_gmr_chunk::~static_sequence_gmr_chunk() {
delete X;
}
-uint static_sequence_gmr_chunk::caccess(uint j) {
- uint invPerm = inversePerm(permutation, j);
+uint static_sequence_gmr_chunk::access(uint j) {
+ uint invPerm = permutation->rev_pi(j); //inversePerm(permutation, j);
+ //cout << "invPerm=" << invPerm << endl;
uint rank_pos = X->select1(invPerm+1);
- uint ret = rank_pos - X->rank(rank_pos);// - 1;
+ //cout << "rank_pos=" << rank_pos << endl;
+ uint ret = rank_pos - X->rank1(rank_pos);// - 1;
+ //cout << "ret = " << ret << endl;
return ret;
}
-uint static_sequence_gmr_chunk::cselect(uint i, uint j) {
+uint static_sequence_gmr_chunk::select(uint i, uint j) {
uint pos = X->select0(i+1) + j - i -1;
- return getelemPerm(permutation, pos);
+ /*cout << "pos=" << pos << endl;
+ cout << "pos'=" << X->rank1(X->select0(i+1)+j) << endl;
+ cout << "perm_pos=" << permutation->pi(pos) << endl;*/
+ return permutation->pi(pos); //getelemPerm(permutation, pos);
}
-uint static_sequence_gmr_chunk::crank(uint i, uint j) {
+uint static_sequence_gmr_chunk::rank(uint i, uint j) {
uint ini = X->select0(i+1)-i;
uint ini_o = ini;
uint fin = X->select0(i+2);
if(fin<i+2) return 0;
fin = fin-(i+2);
if(fin<ini) return 0;
- if(getelemPerm(permutation,ini) > j) return 0;
- if(getelemPerm(permutation,ini) == j) return 1;
+ if(permutation->pi(ini) > j) return 0;
+ if(permutation->pi(ini) == j) return 1;
if(ini==fin) return 1;
while(ini < fin-1) {
uint med = (ini+fin)/2;
- uint elem = getelemPerm(permutation, med);
+ uint elem = permutation->pi(med); //getelemPerm(permutation, med);
if(elem >= j) fin = med;
else ini = med;
}
- while(fin>ini_o && getelemPerm(permutation, fin)>j) fin--;
+ while(fin>ini_o && permutation->pi(fin)>j) fin--;
return fin-ini_o+1;
}
uint static_sequence_gmr_chunk::size() {
- return sizeof(BitRankW32Int*)+sizeof(perm*)+(X->SpaceRequirementInBits()/8+sizeofPerm(permutation));
+ return sizeof(static_sequence_gmr_chunk)+permutation->size()+X->size();
+}
+
+uint static_sequence_gmr_chunk::save(FILE *fp) {
+ uint wr = GMR_CHUNK_HDR;
+ wr = fwrite(&wr,sizeof(uint),1,fp);
+ wr += fwrite(&len,sizeof(uint),1,fp);
+ wr += fwrite(&sigma,sizeof(uint),1,fp);
+ if(wr!=3) return 1;
+ if(X->save(fp)) return 1;
+ if(permutation->save(fp)) return 1;
+ return 0;
+}
+
+static_sequence_gmr_chunk * static_sequence_gmr_chunk::load(FILE *fp) {
+ uint rd;
+ if(fread(&rd,sizeof(uint),1,fp)!=1) return NULL;
+ if(rd!=GMR_CHUNK_HDR) return NULL;
+ static_sequence_gmr_chunk * ret = new static_sequence_gmr_chunk();
+ rd = fread(&ret->len,sizeof(uint),1,fp);
+ rd += fread(&ret->sigma,sizeof(uint),1,fp);
+ ret->X = static_bitsequence::load(fp);
+ ret->permutation = static_permutation::load(fp);
+ if(rd!=2 || ret->X==NULL || ret->permutation==NULL) {
+ /*cout << "rd=" << rd << endl;
+ cout << "X =" << ret->X << endl;
+ cout << "P =" << ret->permutation << endl;*/
+ delete ret;
+ return NULL;
+ }
+ return ret;
}
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