//----------------------------------------------------------------------------
// CTmTxKey::transid
// Construct a transid from the key and return it.
//----------------------------------------------------------------------------
TM_Txid_Internal CTmTxKey::transid()
{
TM_Txid_Internal lv_transid;
memset(&lv_transid, 0, sizeof(lv_transid));
lv_transid.iv_node = node();
lv_transid.iv_seq_num = seqnum();
lv_transid.iv_incarnation_num = gv_tm_info.incarnation_num();
return lv_transid;
} //transid
//------------------------------------------------------------------------------
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;
}
}
}
}
