//------------------------------------------------------------------------------
void CheckDuplicates( const vector< string > & input,
const string & infmt,
const CWinMaskUtil::CIdSet * ids,
const CWinMaskUtil::CIdSet * exclude_ids )
{
typedef vector< string >::const_iterator input_iterator;
dup_lookup_table table;
CRef<CObjectManager> om(CObjectManager::GetInstance());
for( input_iterator i( input.begin() ); i != input.end(); ++i )
{
Uint4 seqnum( 0 );
for(CWinMaskUtil::CInputBioseq_CI bs_iter(*i, infmt); bs_iter; ++bs_iter)
{
CBioseq_Handle bsh = *bs_iter;
if( CWinMaskUtil::consider( bsh, ids, exclude_ids ) )
{
TSeqPos data_len = bsh.GetBioseqLength();
if( data_len < MIN_SEQ_LENGTH )
continue;
string id;
sequence::GetId(bsh, sequence::eGetId_Best)
.GetSeqId()->GetLabel(&id);
data_len -= SAMPLE_SKIP;
tracker track( table, id );
string index;
CSeqVector data =
bsh.GetSeqVector(CBioseq_Handle::eCoding_Iupac);
for( TSeqPos i = 0; i < data_len; ++i )
{
index.erase();
data.GetSeqData(i, i + SAMPLE_LENGTH, index);
const dup_lookup_table::sample * sample( table[index] );
if( sample != 0 )
track( index, seqnum, i, sample->begin(), sample->end() );
}
table.add_seq_info( id, data );
++seqnum;
}
}
}
}
void CNucProp::CountNmers(CSeqVector& seqvec, int n, vector<int>& table)
{
TSeqPos len = seqvec.size();
table.resize(NumberOfNmers(n));
// clear table
for (int i = 0; i < NumberOfNmers(n); i++) {
table[i] = 0;
}
string seq_string;
seqvec.GetSeqData(0, len, seq_string);
const char *seq;
seq = seq_string.data();
for (TSeqPos i = 0; i <= len-n; ++i) {
int nmerint = Nmer2Int(seq+i, n);
if (nmerint >= 0) { // if no ambiguity chars
table[nmerint]++;
}
}
}
void CSimpleOM::GetIupac(string& result, const CSeq_id& id, ENa_strand strand)
{
CSeqVector vec = GetSeqVector(id, strand);
vec.SetIupacCoding();
vec.GetSeqData(0, vec.size(), result);
}
void CSimpleOM::GetIupac(string& result, TGi gi, ENa_strand strand)
{
CSeqVector vec = GetSeqVector(gi, strand);
vec.SetIupacCoding();
vec.GetSeqData(0, vec.size(), result);
}
