+++ /dev/null
-/* static_bitsequence_rrr02_light.cpp
- * Copyright (C) 2008, Francisco Claude, all rights reserved.
- *
- * static_bitsequence_rrr02_light definition
- *
- * 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_bitsequence_rrr02_light.h>
-using std::min;
-using std::max;
-#define VARS_NEEDED uint C_len = len/BLOCK_SIZE_LIGHT + (len%BLOCK_SIZE_LIGHT!=0);\
-uint C_field_bits = bits(BLOCK_SIZE_LIGHT);\
-uint O_len = uint_len(1,O_bits_len);\
-uint C_sampling_len = C_len/sample_rate+2;\
-uint C_sampling_field_bits = bits(ones);\
-uint O_pos_len = C_len/sample_rate+1;\
-uint O_pos_field_bits = bits(O_bits_len);
-
-
-table_offset * static_bitsequence_rrr02_light::E = NULL;
-
-static_bitsequence_rrr02_light::static_bitsequence_rrr02_light() {
- ones=0;
- len=0;
- if(E==NULL) E = new table_offset(BLOCK_SIZE_LIGHT);
- E->use();
- C = NULL;
- O = NULL;
- C_sampling = NULL;
- O_pos = NULL;
- sample_rate = DEFAULT_SAMPLING_LIGHT;
- O_bits_len = 0;
-}
-
-static_bitsequence_rrr02_light::static_bitsequence_rrr02_light(uint * bitseq, uint len, uint sample_rate) {
- ones = 0;
- this->len = len;
- if(E==NULL) E = new table_offset(BLOCK_SIZE_LIGHT);
- E->use();
- // Table C
- uint C_len = len/BLOCK_SIZE_LIGHT + (len%BLOCK_SIZE_LIGHT!=0);
- uint C_field_bits = bits(BLOCK_SIZE_LIGHT);
- C = new uint[uint_len(C_len,C_field_bits)];
- for(uint i=0;i<uint_len(C_len,C_field_bits);i++)
- C[i] = 0;
- O_bits_len = 0;
- for(uint i=0;i<C_len;i++) {
- uint value = popcount(get_var_field(bitseq,i*BLOCK_SIZE_LIGHT,min((uint)len-1,(i+1)*BLOCK_SIZE_LIGHT-1)));
- assert(value<=BLOCK_SIZE_LIGHT);
- set_field(C,C_field_bits,i,value);
- ones += value;
- O_bits_len += E->get_log2binomial(BLOCK_SIZE_LIGHT,value);
- }
- // Table O
- uint O_len = uint_len(1,O_bits_len);
- O = new uint[O_len];
- for(uint i=0;i<O_len;i++)
- O[i] = 0;
- uint O_pos = 0;
- for(uint i=0;i<C_len;i++) {
- uint value = (ushort)get_var_field(bitseq,i*BLOCK_SIZE_LIGHT,min((uint)len-1,(i+1)*BLOCK_SIZE_LIGHT-1));
- set_var_field(O,O_pos,O_pos+E->get_log2binomial(BLOCK_SIZE_LIGHT,popcount(value))-1,E->compute_offset((ushort)value));
- O_pos += E->get_log2binomial(BLOCK_SIZE_LIGHT,popcount(value));
- }
- C_sampling = NULL;
- this->O_pos = NULL;
-
- create_sampling(sample_rate);
-}
-
-void static_bitsequence_rrr02_light::create_sampling(uint sample_rate) {
- this->sample_rate = sample_rate;
-/* for(uint i=0;i<C_len;i++) {
- O_bits_len += E->get_log2binomial(BLOCK_SIZE_LIGHT,get_field(C,C_field_bits,i));
- }*/
- // Sampling for C
- uint C_len = len/BLOCK_SIZE_LIGHT + (len%BLOCK_SIZE_LIGHT!=0);
- uint C_field_bits = bits(BLOCK_SIZE_LIGHT);
- uint C_sampling_len = C_len/sample_rate+2;
- uint C_sampling_field_bits = bits(ones);
- if(C_sampling!=NULL) delete [] C_sampling;
- C_sampling = new uint[max((uint)1,uint_len(C_sampling_len,C_sampling_field_bits))];
- for(uint i=0;i<max((uint)1,uint_len(C_sampling_len,C_sampling_field_bits));i++)
- C_sampling[i] = 0;
- uint sum = 0;
- for(uint i=0;i<C_len;i++) {
- if(i%sample_rate==0)
- set_field(C_sampling,C_sampling_field_bits,i/sample_rate,sum);
- sum += get_field(C,C_field_bits,i);
- }
- for(uint i=(C_len-1)/sample_rate+1;i<C_sampling_len;i++)
- set_field(C_sampling,C_sampling_field_bits,i,sum);
- // Sampling for O (table S) (Code separated from previous construction for readability)
- uint O_pos_len = C_len/sample_rate+1;
- uint O_pos_field_bits = bits(O_bits_len);
- if(O_pos!=NULL) delete [] O_pos;
- O_pos = new uint[uint_len(O_pos_len,O_pos_field_bits)];
- for(uint i=0;i<uint_len(O_pos_len,O_pos_field_bits);i++)
- O_pos[i] = 0;
- uint pos = 0;
- for(uint i=0;i<C_len;i++) {
- if(i%sample_rate==0)
- set_field(O_pos,O_pos_field_bits,i/sample_rate,pos);
- pos += E->get_log2binomial(BLOCK_SIZE_LIGHT,get_field(C,C_field_bits,i));
- }
-}
-
-bool static_bitsequence_rrr02_light::access(uint i) {
- uint C_field_bits = bits(BLOCK_SIZE_LIGHT);
- uint O_pos_field_bits = bits(O_bits_len);
- uint nearest_sampled_value = i/BLOCK_SIZE_LIGHT/sample_rate;
- uint pos_O = get_field(O_pos,O_pos_field_bits,nearest_sampled_value);
- uint pos = i/BLOCK_SIZE_LIGHT;
- for(uint k=nearest_sampled_value*sample_rate;k<pos;k++) {
- uint aux = get_field(C,C_field_bits,k);
- pos_O += E->get_log2binomial(BLOCK_SIZE_LIGHT,aux);
- }
- uint c = get_field(C,C_field_bits,pos);
- return ((1<<(i%BLOCK_SIZE_LIGHT))&E->short_bitmap(c,get_var_field(O,pos_O,pos_O+E->get_log2binomial(BLOCK_SIZE_LIGHT,c)-1)))!=0;
-}
-
-uint static_bitsequence_rrr02_light::rank0(uint i) {
- if(i+1==0) return 0;
- return 1+i-rank1(i);
-}
-
-uint static_bitsequence_rrr02_light::rank1(uint i) {
- uint C_field_bits = bits(BLOCK_SIZE_LIGHT);
- uint C_sampling_field_bits = bits(ones);
- uint O_pos_field_bits = bits(O_bits_len);
- if(i+1==0) return 0;
- uint nearest_sampled_value = i/BLOCK_SIZE_LIGHT/sample_rate;
- uint sum = get_field(C_sampling,C_sampling_field_bits,nearest_sampled_value);
- uint pos_O = get_field(O_pos,O_pos_field_bits,nearest_sampled_value);
- uint pos = i/BLOCK_SIZE_LIGHT;
- uint k=nearest_sampled_value*sample_rate;
- if(k%2==1 && k<pos) {
- uint aux = get_field(C,C_field_bits,k);
- sum += aux;
- pos_O += E->get_log2binomial(BLOCK_SIZE_LIGHT,aux);
- k++;
- }
- uchar * a = (uchar *)C;
- uint mask = 0x0F;
- a += k/2;
- while(k<(uint)max(0,(int)pos-1)) {
- assert(((*a)&mask)==get_field(C,C_field_bits,k));
- assert((*a)/16==get_field(C,C_field_bits,k+1));
- sum += ((*a)&mask)+(*a)/16;
- pos_O += E->get_log2binomial(BLOCK_SIZE_LIGHT,((*a)&mask))+E->get_log2binomial(BLOCK_SIZE_LIGHT,((*a)/16));
- a++;
- k+=2;
- }
- if(k<pos) {
- uint aux = get_field(C,C_field_bits,k);
- sum += aux;
- pos_O += E->get_log2binomial(BLOCK_SIZE_LIGHT,aux);
- k++;
- }
- uint c = get_field(C,C_field_bits,pos);
- sum += popcount(((2<<(i%BLOCK_SIZE_LIGHT))-1) & E->short_bitmap(c,get_var_field(O,pos_O,pos_O+E->get_log2binomial(BLOCK_SIZE_LIGHT,c)-1)));
- return sum;
-}
-
-uint static_bitsequence_rrr02_light::select0(uint i) {
- uint C_len = len/BLOCK_SIZE_LIGHT + (len%BLOCK_SIZE_LIGHT!=0);
- uint C_field_bits = bits(BLOCK_SIZE_LIGHT);
- uint C_sampling_len = C_len/sample_rate+2;
- uint C_sampling_field_bits = bits(ones);
- uint O_pos_field_bits = bits(O_bits_len);
- if(i==0) return -1;
- if(i>len-ones) return len;
- // Search over partial sums
- uint start=0;
- uint end=C_sampling_len-1;
- uint med, acc=0, pos;
- while(start<end-1) {
- med = (start+end)/2;
- acc = med*sample_rate*BLOCK_SIZE_LIGHT-get_field(C_sampling,C_sampling_field_bits,med);
- if(acc<i) {
- if(med==start) break;
- start=med;
- }
- else {
- if(end==0) break;
- end = med-1;
- }
- }
- acc = get_field(C_sampling,C_sampling_field_bits,start);
- while(start<C_len-1 && acc+sample_rate*BLOCK_SIZE_LIGHT==get_field(C_sampling,C_sampling_field_bits,start+1)) {
- start++;
- acc +=sample_rate*BLOCK_SIZE_LIGHT;
- }
- acc = start*sample_rate*BLOCK_SIZE_LIGHT-acc;
- pos = (start)*sample_rate;
- uint pos_O = get_field(O_pos,O_pos_field_bits,start);
- // Sequential search over C
- uint s = 0;
- for(;pos<C_len;pos++) {
- s = get_field(C,C_field_bits,pos);
- if(acc+BLOCK_SIZE_LIGHT-s>=i) break;
- pos_O += E->get_log2binomial(BLOCK_SIZE_LIGHT,s);
- acc += BLOCK_SIZE_LIGHT-s;
- }
- pos = (pos)*BLOCK_SIZE_LIGHT;
- // Search inside the block
-
- while(acc<i) {
- uint new_posO = pos_O+E->get_log2binomial(BLOCK_SIZE_LIGHT,s);
- uint block = E->short_bitmap(s,get_var_field(O,pos_O,new_posO-1));
- pos_O = new_posO;
- new_posO = 0;
- while(acc<i && new_posO<BLOCK_SIZE_LIGHT) {
- pos++;new_posO++;
- acc += (((block&1)==0)?1:0);
- block = block/2;
- }
- }
- pos--;
- assert(acc==i);
- assert(rank0(pos)==i);
- assert(!access(pos));
- return pos;
-}
-
-uint static_bitsequence_rrr02_light::select1(uint i) {
- uint C_len = len/BLOCK_SIZE_LIGHT + (len%BLOCK_SIZE_LIGHT!=0);
- uint C_field_bits = bits(BLOCK_SIZE_LIGHT);
- uint C_sampling_len = C_len/sample_rate+2;
- uint C_sampling_field_bits = bits(ones);
- uint O_pos_field_bits = bits(O_bits_len);
- if(i==0) return -1;
- if(i>ones) return len;
- // Search over partial sums
- uint start=0;
- uint end=C_sampling_len-1;
- uint med, acc=0, pos;
- while(start<end-1) {
- med = (start+end)/2;
- acc = get_field(C_sampling,C_sampling_field_bits,med);
- if(acc<i) {
- if(med==start) break;
- start=med;
- }
- else {
- if(end==0) break;
- end = med-1;
- }
- }
- acc = get_field(C_sampling,C_sampling_field_bits,start);
- while(start<C_len-1 && acc==get_field(C_sampling,C_sampling_field_bits,start+1)) start++;
- pos = (start)*sample_rate;
- uint pos_O = get_field(O_pos,O_pos_field_bits,start);
- acc = get_field(C_sampling,C_sampling_field_bits,start);
- // Sequential search over C
- uint s = 0;
- for(;pos<C_len;pos++) {
- s = get_field(C,C_field_bits,pos);
- if(acc+s>=i) break;
- pos_O += E->get_log2binomial(BLOCK_SIZE_LIGHT,s);
- acc += s;
- }
- pos = (pos)*BLOCK_SIZE_LIGHT;
- //cout << "pos=" << pos << endl;
- // Search inside the block
- while(acc<i) {
- uint new_posO = pos_O+E->get_log2binomial(BLOCK_SIZE_LIGHT,s);
- uint block = E->short_bitmap(s,get_var_field(O,pos_O,new_posO-1));
- pos_O = new_posO;
- new_posO = 0;
- while(acc<i && new_posO<BLOCK_SIZE_LIGHT) {
- pos++;new_posO++;
- acc += (((block&1)!=0)?1:0);
- block = block/2;
- }
- //cout << "i=" << i << " len=" << len << " ones=" << ones << " pos=" << pos << " acc=" << acc << " rank=" << rank1(pos) << endl;
- }
- pos--;
- assert(acc==i);
- assert(rank1(pos)==i);
- assert(access(pos));
- return pos;
-}
-
-uint static_bitsequence_rrr02_light::size() {
- VARS_NEEDED
- /*cout << "RRR02 SIZE: " << endl;
- cout << "Default: " << 9*sizeof(uint)+sizeof(uint*)*4 << endl;
- cout << "Cs: " << uint_len(C_len,C_field_bits)*sizeof(uint) << endl;
- cout << "Os: " << O_len*sizeof(uint) << endl;
- cout << "CSamp: " << uint_len(C_sampling_len,C_sampling_field_bits)*sizeof(uint) << endl;
- cout << "OSamp: " << uint_len(O_pos_len,O_pos_field_bits)*sizeof(uint) << endl;
- cout << "E: " << E->size() << endl;*/
- uint sum = sizeof(uint)*8;//sizeof(static_bitsequence_rrr02_light);
- sum += uint_len(C_len,C_field_bits)*sizeof(uint);
- sum += O_len*sizeof(uint);
- sum += uint_len(C_sampling_len,C_sampling_field_bits)*sizeof(uint);
- sum += uint_len(O_pos_len,O_pos_field_bits)*sizeof(uint);
- //sum += E->size();
- return sum;
-}
-
-static_bitsequence_rrr02_light::~static_bitsequence_rrr02_light() {
- if(C!=NULL) delete [] C;
- if(O!=NULL) delete [] O;
- if(C_sampling!=NULL) delete [] C_sampling;
- if(O_pos!=NULL) delete [] O_pos;
- E = E->unuse();
-}
-
-int static_bitsequence_rrr02_light::save(FILE * fp) {
- uint C_len = len/BLOCK_SIZE_LIGHT + (len%BLOCK_SIZE_LIGHT!=0);
- uint C_field_bits = bits(BLOCK_SIZE_LIGHT);
- uint O_len = uint_len(1,O_bits_len);
- uint wr = RRR02_LIGHT_HDR;
- wr = fwrite(&wr,sizeof(uint),1,fp);
- wr += fwrite(&len,sizeof(uint),1,fp);
- wr += fwrite(&ones,sizeof(uint),1,fp);
- wr += fwrite(&O_bits_len,sizeof(uint),1,fp);
- wr += fwrite(&sample_rate,sizeof(uint),1,fp);
- if(wr!=5) return -1;
- wr = fwrite(C,sizeof(uint),uint_len(C_len,C_field_bits),fp);
- if(wr!=uint_len(C_len,C_field_bits)) return -1;
- wr = fwrite(O,sizeof(uint),O_len,fp);
- if(wr!=O_len) return -1;
- return 0;
-}
-
-static_bitsequence_rrr02_light * static_bitsequence_rrr02_light::load(FILE * fp) {
- static_bitsequence_rrr02_light * ret = new static_bitsequence_rrr02_light();
- uint rd = 0, type;
- rd += fread(&type,sizeof(uint),1,fp);
- rd += fread(&ret->len,sizeof(uint),1,fp);
- rd += fread(&ret->ones,sizeof(uint),1,fp);
- rd += fread(&ret->O_bits_len,sizeof(uint),1,fp);
- rd += fread(&ret->sample_rate,sizeof(uint),1,fp);
- uint C_len = ret->len/BLOCK_SIZE_LIGHT + (ret->len%BLOCK_SIZE_LIGHT!=0);
- uint C_field_bits = bits(BLOCK_SIZE_LIGHT);
- uint O_len = uint_len(1,ret->O_bits_len);
- if(rd!=5 || type!=RRR02_LIGHT_HDR) {
- delete ret;
- return NULL;
- }
- ret->C = new uint[uint_len(C_len,C_field_bits)];
- rd = fread(ret->C,sizeof(uint),uint_len(C_len,C_field_bits),fp);
- if(rd!=uint_len(C_len,C_field_bits)) {
- ret->C=NULL;
- delete ret;
- return NULL;
- }
- ret->O = new uint[O_len];
- rd = fread(ret->O,sizeof(uint),O_len,fp);
- if(rd!=O_len) {
- ret->O=NULL;
- delete ret;
- return NULL;
- }
- ret->create_sampling(ret->sample_rate);
- return ret;
-}
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