perm loadPerm(ifstream & f) {
uint aux;
perm P;
uint v;
P = new struct sperm; //(struct sperm*) malloc(sizeof(struct sperm));
P->nelems = loadValue<uint>(f);
P->nbits = bits(P->nelems-1);
aux = uint_len(P->nelems,P->nbits);
P->elems = loadValue<uint>(f,aux);
v = loadValue<uint>(f);
if (v) {
P->bmap = BitSequence::load(f);
}
else P->bmap = NULL;
P->nbwdptrs = loadValue<uint>(f);
aux = uint_len(P->nbwdptrs,P->nbits);
P->bwdptrs = loadValue<uint>(f,aux);
P->t = loadValue<uint>(f);
return P;
}
void BitSequenceRRR::create_sampling(uint sample_rate) {
this->sample_rate = sample_rate;
// Sampling for C
C_sampling_len = C_len/sample_rate+2;
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)
O_pos_len = C_len/sample_rate+1;
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,get_field(C,C_field_bits,i));
}
}
uint savePerm(const perm P, ofstream & f) {
uint aux;
uint v;
saveValue(f,P->nelems);
saveValue(f,P->elems,uint_len(P->nelems,P->nbits));
aux = ((P->nelems+W-1)/W);
if (P->bmap) {
v=1;
saveValue(f,v);
P->bmap->save(f);
}
else {
v=0;
saveValue(f,v);
}
saveValue(f,P->nbwdptrs);
aux = uint_len(P->nbwdptrs,P->nbits);
saveValue(f,P->bwdptrs,aux);
saveValue(f,P->t);
return 0;
}
BitSequenceRG::BitSequenceRG(const BitString & bs, uint _factor) {
/*cout << "*****" << endl;
cout << bitarray << endl;
cout << _n << endl;
cout << _factor << endl; */
const uint * bitarray = bs.getData();
size_t _n = bs.getLength();
if(_factor==0) exit(-1);
data=new uint[_n/W+1];
for(size_t i=0;i<uint_len(_n,1);i++)
data[i] = bitarray[i];
for(size_t i=uint_len(_n,1);i<_n/W+1;i++)
data[i] = 0;
//this->owner = true;
this->n=_n;
uint lgn=bits(n-1);
this->factor=_factor;
if (_factor==0) this->factor=lgn;
else this->factor=_factor;
b=32;
s=b*this->factor;
integers = n/W+1;
BuildRank();
this->length = n;
this->ones = rank1(n-1);
}
size_t BitSequenceRRR::getSize() const
{
// we consider E to be free (64K shared among all the RRR02 bitmaps)
size_t sum = sizeof(BitSequenceRRR);
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);
return sum;
}
perm loadPerm(FILE *f) {
uint aux;
perm P;
uint v;
P = new struct sperm; //(struct sperm*) malloc(sizeof(struct sperm));
if (fread(&P->nelems,sizeof(uint),1,f) != 1) {
fprintf(stderr,"Error: Cannot read Permutation from file\n");
exit(1);
}
P->nbits = bits(P->nelems-1);
aux = uint_len(P->nelems,P->nbits);
P->elems = new uint[aux]; //(uint *)malloc(aux*sizeof(uint));
if (fread(P->elems,sizeof(uint),aux,f) != aux) {
fprintf(stderr,"Error: Cannot read Permutation from file\n");
exit(1);
}
if (fread(&v,sizeof(uint),1,f) != 1) {
fprintf(stderr,"Error: Cannot read Permutation from file\n");
exit(1);
}
if (v) {
P->bmap = static_bitsequence::load(f);
}
else P->bmap = NULL;
if (fread(&P->nbwdptrs,sizeof(uint),1,f) != 1) {
fprintf(stderr,"Error: Cannot read Permutation from file\n");
exit(1);
}
aux = uint_len(P->nbwdptrs,P->nbits);
P->bwdptrs = new uint[aux]; //(uint*) malloc(aux*sizeof(uint));
if (fread(P->bwdptrs,sizeof(uint),aux,f) != aux) {
fprintf(stderr,"Error: Cannot read Permutation from file\n");
exit(1);
}
if (fread(&P->t,sizeof(uint),1,f) != 1) {
fprintf(stderr,"Error: Cannot read Permutation from file\n");
exit(1);
}
return P;
}
uint savePerm(perm P, FILE *f) {
uint aux;
uint v;
if (fwrite(&P->nelems,sizeof(uint),1,f) != 1) {
fprintf(stderr,"Error: Cannot write Permutation on file\n");
exit(1);
}
aux = uint_len(P->nelems,P->nbits);
if (fwrite(P->elems,sizeof(uint),aux,f) != aux) {
fprintf(stderr,"Error: Cannot write Permutation on file\n");
exit(1);
}
aux = ((P->nelems+W-1)/W);
if (P->bmap) {
v=1;
if (fwrite(&v,sizeof(uint),1,f) != 1) {
fprintf(stderr,"Error: Cannot write Permutation on file\n");
exit(1);
}
P->bmap->save(f);
}
else {
v=0;
if (fwrite(&v,sizeof(uint),1,f) != 1) {
fprintf(stderr,"Error: Cannot write Permutation on file\n");
exit(1);
}
}
if (fwrite(&P->nbwdptrs,sizeof(uint),1,f) != 1) {
fprintf(stderr,"Error: Cannot write Permutation on file\n");
exit(1);
}
aux = uint_len(P->nbwdptrs,P->nbits);
if (fwrite(P->bwdptrs,sizeof(uint),aux,f) != aux) {
fprintf(stderr,"Error: Cannot write Permutation on file\n");
exit(1);
}
if (fwrite(&P->t,sizeof(uint),1,f) != 1) {
fprintf(stderr,"Error: Cannot write Permutation on file\n");
exit(1);
}
return 0;
}
BitSequenceSDArray::BitSequenceSDArray(const BitString & bs) {
uint * tmp_seq = new uint[uint_len(bs.getLength(),1)+1];
ones = 0;
for(uint i=0;i<uint_len(bs.getLength(),1)+1;i++)
tmp_seq[i] = 0;
for(uint i=0;i<bs.getLength();i++)
if(bs[i]) {
__setbit(tmp_seq,i,1);
ones++;
}
if(ones)
selects3_construct(&sd,bs.getLength(),tmp_seq);
this->length = bs.getLength();
delete [] tmp_seq;
}
BitSequenceSDArray::BitSequenceSDArray(uint * buff, size_t len) {
uint * tmp_seq = new uint[uint_len(len,1)+1];
ones = 0;
for(uint i=0;i<uint_len(len,1)+1;i++)
tmp_seq[i] = 0;
for(uint i=0;i<len;i++)
if(bitget(buff,i)) {
__setbit(tmp_seq,i,1);
ones++;
}
if(ones)
selects3_construct(&sd,len,tmp_seq);
this->length = len;
delete [] tmp_seq;
}
void Array::initData() {
bitsPerItem = bits(maxValue);
uintLength = uint_len(length,bitsPerItem);
data = new uint[uintLength];
for(size_t i=0;i<uintLength;i++)
data[i] = 0;
}
BitSequenceRRR * BitSequenceRRR::load(ifstream & f) {
BitSequenceRRR * ret = NULL;
try
{
ret = new BitSequenceRRR();
uint type = loadValue<uint>(f);
// TODO:throw an exception!
if(type!=RRR02_HDR) {
abort();
}
ret->length = loadValue<size_t>(f);
//cout << ret->length << endl;
ret->ones = loadValue<size_t>(f);
//cout << ret->ones << endl;
ret->C_len = loadValue<uint>(f);
//cout << ret->C_len << endl;
ret->C_field_bits = loadValue<uint>(f);
//cout << ret->C_field_bits << endl;
ret->O_len = loadValue<uint>(f);
//cout << ret->O_len << endl;
ret->O_bits_len = loadValue<uint>(f);
//cout << ret->O_bits_len << endl;
ret->sample_rate = loadValue<uint>(f);
//cout << ret->sample_rate << endl;
//ret->length = loadValue<uint>(f);
ret->C = loadValue<uint>(f,uint_len(ret->C_len,ret->C_field_bits));
ret->O = loadValue<uint>(f,ret->O_len);
ret->create_sampling(ret->sample_rate);
return ret;
}
catch(exception e) {
delete ret;
}
return NULL;
}
static_bitsequence_sdarray::static_bitsequence_sdarray(uint * buff, uint len) {
uint * tmp_seq = new uint[uint_len(len,1)+1];
ones = 0;
for(uint i=0;i<uint_len(len,1)+1;i++)
tmp_seq[i] = 0;
for(uint i=0;i<len;i++)
if(bitget(buff,i)) {
__setbit(tmp_seq,i,1);
ones++;
}
if(ones)
selects3_construct(&sd,len,tmp_seq);
this->len = len;
//sd.lasti=(uint)-3;
//this->ones = sd.m;
delete [] tmp_seq;
}
BitSequenceRGK::BitSequenceRGK(Builder builder) {
BitString &bs = *builder.bs_;
uint _factor = builder.factor_;
select1sampling = builder.sonesamp_;
select0sampling = builder.szerosamp_;
fastselect0 = builder.fastselect0_;
fastselect1 = builder.fastselect1_;
const uint *bitarray = bs.getData();
size_t _n = bs.getLength();
if (_factor == 0) exit(-1);
data = new uint[_n / W + 1];
for (size_t i = 0; i < uint_len(_n, 1); i++)
data[i] = bitarray[i];
for (size_t i = uint_len(_n, 1); i < _n / W + 1; i++)
data[i] = 0;
//this->owner = true;
this->n = _n;
uint lgn = bits(n - 1);
this->factor = _factor;
if (_factor == 0) this->factor = lgn;
else this->factor = _factor;
b = 32;
s = b * this->factor;
integers = n / W + 1;
BuildRank();
this->length = n;
this->ones = rank1(n - 1);
if (fastselect1) {
// cout << "entered here" << endl;
this->Stones = new uint[ones / select1sampling + 1];
Stones[0] = 0;
for (size_t i = 0; i <= ones; i += select1sampling) {
if (i == 0) continue;
Stones[i / select1sampling] = this->select1_s(i);
}
}
if (fastselect0) {
this->Stzero = new uint[(n - ones) / select0sampling + 1];
Stzero[0] = 0;
for (size_t i = 0; i <= (n - ones); i += select0sampling) {
if (i == 0) continue;
Stzero[i / select0sampling] = this->select0_s((i));
}
}
}
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]);
}
sigma++;
uint * X_bitmap = new uint[uint_len(1+chunk_length+sigma,1)];
assert(X_bitmap!=NULL);
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[uint_len(pi_blen,chunk_length)];
assert(pi!=NULL);
for(uint i=0; i<uint_len(pi_blen,chunk_length); i++) pi[i] = 0;
uint X_pos = 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<counter[c+1]; i++) {
bitset(X_bitmap, X_pos);
X_pos++;
}
counter[c+1]+=counter[c];
}
X_pos++;
for(uint i=0; i<chunk_length; i++) {
set_field(pi, pi_blen,counter[sequence[i]], i);
counter[sequence[i]]++;
}
//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);
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->len = chunk_length;
delete [] counter;
}
BitSequenceRGK::BitSequenceRGK(uint *bitarray, size_t _n, uint _factor, uint selectsampling) {
if (_factor == 0) exit(-1);
data = new uint[_n / W + 1];
for (size_t i = 0; i < uint_len(_n, 1); i++)
data[i] = bitarray[i];
for (size_t i = uint_len(_n, 1); i < _n / W + 1; i++)
data[i] = 0;
//this->owner = true;
this->n = _n;
uint lgn = bits(n - 1);
this->factor = _factor;
if (_factor == 0) this->factor = lgn;
else this->factor = _factor;
b = 32;
s = b * this->factor;
integers = n / W + 1;
BuildRank();
this->length = n;
this->ones = rank1(n - 1);
fastselect0 = true;
fastselect1 = true;
select1sampling = selectsampling;
select0sampling = selectsampling;
if (fastselect1) {
// cout << "entered here" << endl;
this->Stones = new uint[ones / select1sampling + 1];
Stones[0] = 0;
for (size_t i = 0; i <= ones; i += select1sampling) {
if (i == 0) continue;
Stones[i / select1sampling] = this->select1_s(i);
}
}
if (fastselect0) {
this->Stzero = new uint[(n - ones) / select0sampling + 1];
Stzero[0] = 0;
for (size_t i = 0; i <= (n - ones); i += select0sampling) {
if (i == 0) continue;
Stzero[i / select0sampling] = this->select0_s((i));
}
}
}
BitmapsSequence::BitmapsSequence(const Array &a, Mapper * am, BitSequenceBuilder * bsb, bool keepsSequence) : Sequence(0) {
bsb->use();
length = a.getLength();
this->keepsSequence = keepsSequence;
//cout << "length=" << length << endl;
sigma = a.getMax()+1;
//cout << "sigma=" << sigma << endl;
this->am = am;
am->use();
if (keepsSequence) {
seq = new Array(a.getLength(), sigma - 1);
for (uint i = 0; i < a.getLength(); i++)
seq->setField(i, am->map(a.getField(i)));
}
uint * occ = new uint[sigma+1];
for(uint i=0;i<=sigma;i++) occ[i] = 0;
for(uint i=0;i<length;i++) occ[am->map(a[i])+1]++;
for(uint i=1;i<sigma;i++) occ[i] += occ[i-1];
uint * pos = new uint[length];
for(uint i=0;i<length;i++) pos[i] = 0;
for(uint i=0;i<length;i++) pos[occ[am->map(a[i])]++]=i;
bitmaps = new BitSequence*[sigma];
uint * bm = new uint[uint_len(length,1)];
uint pp=0;
for(uint i=0;i<sigma;i++) {
for(uint j=0;j<uint_len(length,1);j++)
bm[j]=0;
while(pp<occ[i]) {
bitset(bm,pos[pp]);
pp++;
}
//cout << "build " << bm << " len=" << length << " i=" << i << endl;
bitmaps[i] = bsb->build(bm,length);
}
delete [] bm;
delete [] occ;
delete [] pos;
bsb->unuse();
}
BitmapsSequence::BitmapsSequence(uint * seq, size_t n, Mapper * am, BitSequenceBuilder * bsb, bool keepsSequence) : Sequence(n) {
bsb->use();
sigma = 0;
this->keepsSequence = keepsSequence;
//length = n;
this->am = am;
am->use();
for(uint i=0;i<n;i++) sigma=max(sigma,am->map(seq[i]));
sigma++;
if (keepsSequence) {
this->seq = new Array(n, sigma - 1);
for (uint i = 0; i < n; i++)
this->seq->setField(i, am->map(seq[i]));
}
uint * occ = new uint[sigma+1];
for(uint i=0;i<=sigma;i++) occ[i] = 0;
for(uint i=0;i<n;i++) occ[am->map(seq[i])+1]++;
for(uint i=1;i<sigma;i++) occ[i] += occ[i-1];
uint * pos = new uint[n];
for(uint i=0;i<n;i++) pos[i] = 0;
for(uint i=0;i<n;i++) pos[occ[am->map(seq[i])]++]=i;
bitmaps = new BitSequence*[sigma];
uint * bm = new uint[uint_len(n,1)];
uint pp=0;
for(uint i=0;i<sigma;i++) {
for(uint j=0;j<uint_len(n,1);j++)
bm[j]=0;
while(pp<occ[i]) {
bitset(bm,pos[pp]);
pp++;
}
bitmaps[i] = bsb->build(bm,length);
}
delete [] bm;
delete [] occ;
delete [] pos;
bsb->unuse();
}
void BitSequenceRRR::save(ofstream & f) const
{
uint wr = RRR02_HDR;
saveValue(f,wr);
saveValue(f,length);
saveValue(f,ones);
saveValue(f,C_len);
saveValue(f,C_field_bits);
saveValue(f,O_len);
saveValue(f,O_bits_len);
saveValue(f,sample_rate);
saveValue(f,C,uint_len(C_len,C_field_bits));
saveValue(f,O,O_len);
}
void BitSequenceRRR::build(const uint * bitseq, size_t len, uint sample_rate) {
ones = 0;
this->length = len;
if(E==NULL) E = new table_offset(BLOCK_SIZE);
E->use();
// Table C
C_len = len/BLOCK_SIZE + (len%BLOCK_SIZE!=0);
C_field_bits = bits(BLOCK_SIZE);
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,min((uint)len-1,(i+1)*BLOCK_SIZE-1)));
assert(value<=BLOCK_SIZE);
set_field(C,C_field_bits,i,value);
ones += value;
O_bits_len += E->get_log2binomial(BLOCK_SIZE,value);
}
// Table O
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,min((uint)len-1,(i+1)*BLOCK_SIZE-1));
set_var_field(O,O_pos,O_pos+E->get_log2binomial(BLOCK_SIZE,popcount(value))-1,E->compute_offset((ushort)value));
O_pos += E->get_log2binomial(BLOCK_SIZE,popcount(value));
}
C_sampling = NULL;
this->O_pos = NULL;
create_sampling(sample_rate);
}
void BitSequenceRRR::save(ofstream & f) const
{
/*cout << "===================" << endl;
cout << "length = " << length << endl;
cout << "ones = " << ones << endl;
cout << "C_len = " << C_len << endl;
cout << "C_field_bits = " << C_field_bits << endl;
cout << "O_len = " << O_len << endl;
cout << "O_bits_len = " << O_bits_len << endl;
cout << "sample_rate = " << sample_rate << endl;
cout << "C_alen = " << uint_len(C_len,C_field_bits) << endl;
cout << "O_alen = " << O_len << endl;*/
uint wr = RRR02_HDR;
saveValue(f,wr);
saveValue(f,length);
saveValue(f,ones);
saveValue(f,C_len);
saveValue(f,C_field_bits);
saveValue(f,O_len);
saveValue(f,O_bits_len);
saveValue(f,sample_rate);
saveValue(f,C,uint_len(C_len,C_field_bits));
saveValue(f,O,O_len);
}
uint sizeofPerm(perm P) {
return sizeof(struct sperm) +
((uint_len(P->nelems,P->nbits))*sizeof(uint)) +
((P->bmap)?(P->bmap->size()):0) +
((uint_len(P->nbwdptrs,P->nbits))*sizeof(uint));
}
perm createPerm(uint *elems, uint nelems, uint t, static_bitsequence_builder * bmb) {
perm P;
uint *b, *baux, nextelem, i, j, bptr,
aux, antbptr,nbwdptrs, elem,nbits, firstelem, cyclesize;
auxbwd *auxbwdptr;
P = new struct sperm;
P->elems = elems;
P->nelems = nelems;
P->nbits = bits(nelems-1);
nbits = bits(nelems-1);
P->t = t;
if (t==1) {
P->bwdptrs = new uint[uint_len(nelems,nbits)];
assert(P->bwdptrs!=NULL);
P->nbwdptrs = nelems;
for (i=0; i<nelems; i++) {
uint bg = get_field(elems, nbits, i);
assert(bg<nelems);
set_field(P->bwdptrs, nbits, bg, i);
}
P->bmap = NULL;
}
else {
auxbwdptr = new auxbwd[(t+((int)ceil((double)nelems/t)))];
assert(auxbwdptr!=NULL);
b = new uint[uint_len(nelems,1)];
for(i=0;i<uint_len(nelems,1);i++)
b[i]=0;
assert(b!=NULL);
baux = new uint[uint_len(nelems,1)];
for(i=0;i<uint_len(nelems,1);i++)
baux[i] = 0;
assert(baux!=NULL);
nbwdptrs = 0;
for (i = 0; i < nelems; i++) {
if (bitget(baux,i) == 0) {
nextelem = j = bptr = antbptr = i;
aux = 0;
bitset(baux, j);
cyclesize = 0;
firstelem = j;
while ((elem=get_field(elems,nbits,j)) != nextelem) {
j = elem;
bitset(baux, j);
aux++;
if (aux >= t) {
auxbwdptr[nbwdptrs].key = j;
auxbwdptr[nbwdptrs++].pointer = bptr;
antbptr = bptr;
bptr = j;
aux = 0;
bitset(b, j);
}
cyclesize++;
}
if (cyclesize >= t) {
auxbwdptr[nbwdptrs].key = nextelem;
auxbwdptr[nbwdptrs++].pointer = bptr;
bitset(b, nextelem);
}
}
}
qsort(auxbwdptr, nbwdptrs, sizeof(auxbwd), &compare);
aux = uint_len(nbwdptrs,P->nbits);
P->bwdptrs = new uint[aux];
assert(P->bwdptrs!=NULL);
for(i=0;i<aux;i++) P->bwdptrs[i] = 0;
P->nbwdptrs = nbwdptrs;
for (i = 0; i < nbwdptrs; i++) {
set_field(P->bwdptrs, nbits, i, auxbwdptr[i].pointer);
//if(i<5)
// printf(" %d ",get_field(P->bwdptrs,nbits,i));
}
//printf("\n");
P->bmap = bmb->build(b, nelems);
//delete [] P->bmap;
delete [] b;
delete [] (baux);
delete [] (auxbwdptr);
}
return P;
}
size_t BitSequenceRG::SpaceRequirementInBits() const
{
return uint_len(n,1)*sizeof(uint)*8+(n/s)*sizeof(uint)*8 +sizeof(BitSequenceRG)*8;
}