+++ /dev/null
-/* static_sequence_gmr.cpp
- * Copyright (C) 2008, Francisco Claude, all rights reserved.
- *
- * GMR
- *
- * 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.h>
-using std::max;
-static_sequence_gmr::static_sequence_gmr(uint * sequence, uint n, uint chunk_length, static_bitsequence_builder * bmb, static_sequence_builder * ssb) {
- len = n;
- if(len%chunk_length) len+=chunk_length-len%chunk_length;
- uint * new_seq = new uint[len];
- sigma = 0;
- for(uint i=0;i<n;i++){
- new_seq[i] = sequence[i]+1;
- sigma = max(sigma,new_seq[i]);
- }
- sigma++;
- for(uint i=n;i<len;i++)
- new_seq[i] = sigma;
- if(len!=n) sigma++;
- this->chunk_length = chunk_length;
- build(new_seq,bmb,ssb);
- delete [] new_seq;
-}
-
-static_sequence_gmr::static_sequence_gmr() {
-}
-
-static_sequence_gmr::~static_sequence_gmr() {
- delete B;
- for (uint i=0;i<len/chunk_length;i++)
- delete chunk[i];
- delete [] chunk;
-}
-
-
-void static_sequence_gmr::build(uint * sequence, static_bitsequence_builder * bmb, static_sequence_builder * ssb) {
- uint num_chunks = len/chunk_length;
- chunk = new static_sequence*[num_chunks];
- assert(chunk!=NULL);
- for (uint i=0;i<num_chunks;i++) {
- chunk[i] = ssb->build(sequence+i*chunk_length, chunk_length);
- //cout << "1." << i << endl; cout.flush();
- assert(chunk[i]!=NULL);
- }
- uint * ones = get_ones(sequence);
- uint *B_bitmap = new uint[(2+len+(unsigned long long)num_chunks*sigma)/W+1];
- assert(B_bitmap!=NULL);
- for (uint i=0;i<(2+len+(unsigned long long)num_chunks*sigma)/W+1;i++)
- B_bitmap[i] = 0;
- uint pos=0;
- for (unsigned long long i=0;i<(unsigned long long)num_chunks*sigma;i++) {
- for (uint j=0;j<ones[i];j++) {
- bitset(B_bitmap, pos);
- pos++;
- }
- pos++;
- }
- pos++;
- //cout << "5 pos=" << pos << endl; cout.flush();
- B = bmb->build(B_bitmap, pos);
- //cout << "6" << endl; cout.flush();
- delete [] B_bitmap;
- delete [] ones;
-}
-
-
-uint * static_sequence_gmr::get_ones(uint * sequence) {
- uint * ones = new uint[(unsigned long long)(len/chunk_length)*sigma];
- assert(ones!=NULL);
- for (uint i=0;i<(unsigned long long)(len/chunk_length)*sigma;i++) ones[i] = 0;
- for (uint i=0;i<len;i++) {
- uint whichChunk = (uint)(((unsigned long long)sequence[i]*len+i)/chunk_length);
- ones[whichChunk]++;
- }
- return ones;
-}
-
-
-uint static_sequence_gmr::rank(uint c, uint j) {
- c++;
- uint i = j/chunk_length;
- uint bp = (c)*(len/chunk_length);
- uint rank_pos = B->select0(bp);
- uint prev = rank_pos-bp+1;
- uint sum = B->rank1(B->select0(bp+i)) - prev;
- uint cr = chunk[i]->rank(c,j-i*chunk_length);
- /*if(c==0) {
- cout << "c=" << c << " j=" << j << endl;
- cout << "i=" << i << endl;
- cout << "bp=" << bp << endl;
- cout << "rank_pos=" << rank_pos << endl;
- cout << "prev=" << prev << endl;
- cout << "sum=" << sum << endl;
- cout << "cr=" << cr << endl;
- }*/
- return sum + cr;
-}
-
-
-uint static_sequence_gmr::select(uint c, uint j) {
- c++;
- uint rank_pos = B->select0(c*(len/chunk_length));
- uint prev = B->rank1(rank_pos);
- uint sel = prev+j;
- uint block = (B->select1(sel));
- uint i = block-sel+1;
- uint desp = B->rank1(B->select0((i)))-prev;
- if (desp+1==0) desp=0;
- uint rchunk = i%(len/chunk_length);
- /*if(j==90) {
- cout << "------------------------------" << endl;
- cout << "c=" << c << " j=" << j << endl;
- cout << "chunk_length=" << chunk_length << endl;
- cout << "rank_pos=" << rank_pos << endl;
- cout << "prev=" << prev << endl;
- cout << "sel=" << sel << endl;
- cout << "block=" << block << endl;
- cout << "i=" << i << endl;
- cout << "desp=" << desp << endl;
- cout << "rchunk=" << rchunk << endl;
- cout << "j-desp=" << j-desp << endl;
- }*/
- return (rchunk*chunk_length)+chunk[rchunk]->select(c, j-desp);
-}
-
-
-uint static_sequence_gmr::access(uint j) {
- return chunk[j/chunk_length]->access(j%chunk_length)-1;
-}
-
-
-uint static_sequence_gmr::size() {
- uint s = 0;
- for (uint i=0;i<len/chunk_length;i++)
- s += sizeof(void*)+chunk[i]->size();
- return s+B->size()+sizeof(static_sequence_gmr);
-}
-
-uint static_sequence_gmr::save(FILE *fp) {
- uint wr = GMR_HDR;
- wr = fwrite(&wr,sizeof(uint),1,fp);
- wr += fwrite(&len,sizeof(uint),1,fp);
- wr += fwrite(&sigma,sizeof(uint),1,fp);
- wr += fwrite(&chunk_length,sizeof(uint),1,fp);
- if(wr!=4) return 1;
- if(B->save(fp)) return 1;
- for(uint i=0;i<len/chunk_length;i++)
- if(chunk[i]->save(fp)) return 1;
- return 0;
-}
-
-static_sequence_gmr * static_sequence_gmr::load(FILE *fp) {
- uint rd;
- if(fread(&rd,sizeof(uint),1,fp)!=1) return NULL;
- if(rd!=GMR_HDR) return NULL;
- static_sequence_gmr * ret = new static_sequence_gmr();
- rd = fread(&ret->len,sizeof(uint),1,fp);
- rd += fread(&ret->sigma,sizeof(uint),1,fp);
- rd += fread(&ret->chunk_length,sizeof(uint),1,fp);
- if(rd!=3) {
- delete ret;
- return NULL;
- }
- ret->B = static_bitsequence::load(fp);
- if(ret->B==NULL) {
- delete ret;
- return NULL;
- }
- ret->chunk = new static_sequence*[ret->len/ret->chunk_length];
- for(uint i=0;i<ret->len/ret->chunk_length;i++) {
- ret->chunk[i] = static_sequence::load(fp);
- if(ret->chunk[i]==NULL) {
- delete ret;
- return NULL;
- }
- }
- return ret;
-}
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