this->am = am;
am->use();
for(uint i=0;i<n;i++) sigma=max(sigma,am->map(seq[i]));
- bitmaps = new static_bitsequence*[++sigma];
- uint ** bm = new uint*[sigma];
+ sigma++;
+ 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 static_bitsequence*[sigma];
+ uint * bm = new uint[uint_len(n,1)];
+ uint pp=0;
for(uint i=0;i<sigma;i++) {
- bm[i] = new uint[uint_len(len,1)];
- for(uint j=0;j<uint_len(len,1);j++)
- bm[i][j] = 0;
+ for(uint j=0;j<uint_len(n,1);j++) bm[j]=0;
+ while(pp<occ[i]) {
+ bitset(bm,pos[pp]);
+ pp++;
+ }
+ bitmaps[i] = bmb->build(bm,len);
}
- for(uint i=0;i<n;i++)
- bitset(bm[am->map(seq[i])],i);
- for(uint i=0;i<sigma;i++)
- bitmaps[i] = bmb->build(bm[i],len);
- for(uint i=0;i<sigma;i++)
- delete [] bm[i];
delete [] bm;
+ delete [] occ;
+ delete [] pos;
}
static_sequence_bs::static_sequence_bs() {