void User::calculate_gc(const int width, const int lookahead)
{
if(Tn < 1) return;
double * tar_tseries = new double[(width+lookahead+1) * K];
double * src_tseries = new double[(width+lookahead+1) * K];
for(std::map<int, std::map<User *, int> *>::iterator iter = neighbors.begin(); iter != neighbors.end(); iter++)
{
int t = iter->first;
std::map<User *, int> * neighbors_t = iter->second;
std::map<User *, double> * neighbors_gc_t = neighbors_gc[t];
for(std::map<User *, int>::iterator iter2 = neighbors_t->begin(); iter2 != neighbors_t->end(); iter2++)
{
User * tar = iter2->first;
(*neighbors_gc_t)[tar] = calculate_gc(tar, t, width, lookahead, src_tseries, tar_tseries);
}
}
delete [] src_tseries;
delete [] tar_tseries;
}
double *gt_encseq_get_gc(const GtEncseq *encseq,
bool with_special,
bool calculate,
GT_UNUSED GtError *err)
{
GtEncseqReader *reader;
GtAlphabet *alphabet;
double *gc_content;
/* unit = file or sequence depending on per_file */
unsigned long char_idx, totallength, max_unit,
seq_idx = 0,
nextsep = 0,
at_count = 0,
gc_count = 0,
default_count = 0;
bool is_mirrored_encseq;
GtUchar acgt[8], current_c;
alphabet = gt_encseq_alphabet(encseq);
gt_assert(gt_alphabet_is_dna(alphabet));
gt_alphabet_encode_seq(alphabet, acgt,
"aAtTcCgG", 8UL);
totallength = gt_encseq_total_length(encseq);
reader = gt_encseq_create_reader_with_readmode(encseq,
GT_READMODE_FORWARD,
0);
is_mirrored_encseq = gt_encseq_is_mirrored(encseq);
if (is_mirrored_encseq)
{
max_unit = GT_DIV2(gt_encseq_num_of_sequences(encseq));
gc_content = gt_calloc((size_t) GT_MULT2(max_unit), sizeof (double));
}
else
{
max_unit = gt_encseq_num_of_sequences(encseq);
gc_content = gt_calloc((size_t) max_unit, sizeof (double));
}
nextsep = gt_encseq_seqstartpos(encseq, seq_idx) +
gt_encseq_seqlength(encseq, seq_idx);
for (char_idx = 0; char_idx < totallength; char_idx++)
{
if (nextsep == char_idx)
{
if (calculate)
{
calculate_gc(encseq,
gc_content,
with_special,
seq_idx,
gc_count,
at_count);
}
else
{
gc_content[seq_idx] = (double) gc_count;
}
seq_idx++;
nextsep = gt_encseq_seqstartpos(encseq, seq_idx) +
gt_encseq_seqlength(encseq, seq_idx);
gt_encseq_reader_reinit_with_readmode(reader,
encseq,
GT_READMODE_FORWARD,
char_idx + 1UL);
gc_count = at_count = default_count = 0UL;
continue;
}
current_c = gt_encseq_reader_next_encoded_char(reader);
if (current_c == acgt[0] ||
current_c == acgt[1] ||
current_c == acgt[2] ||
current_c == acgt[3])
{
at_count++;
}
else
{
if (current_c == acgt[4] ||
current_c == acgt[5] ||
current_c == acgt[6] ||
current_c == acgt[7])
{
gc_count++;
}
else
{
default_count++;
}
}
}
if (calculate)
{
calculate_gc(encseq,
gc_content,
with_special,
seq_idx,
gc_count,
at_count);
}
else
{
gc_content[seq_idx] = (double) gc_count;
}
gt_encseq_reader_delete(reader);
if (is_mirrored_encseq)
{
unsigned long double_max_unit = GT_MULT2(max_unit);
for (seq_idx = 0; seq_idx < max_unit; seq_idx++)
{
gc_content[double_max_unit - seq_idx - 1] =
gc_content[seq_idx];
}
}
return gc_content;
}
