static void UnpackSeqEntry(CSeq_entry& seqEntry, SequenceSet *parent, SequenceSet::SequenceList& seqlist)
{
if (seqEntry.IsSeq()) {
const Sequence *sequence = new Sequence(parent, seqEntry.SetSeq());
if (!sequence || !sequence->identifier)
FATALMSG("Can't create Sequence object, aborting...");
seqlist.push_back(sequence);
} else { // Bioseq-set
UnpackSeqSet(seqEntry.SetSet(), parent, seqlist);
}
}
void SequenceSet::UnpackSeqEntry(const CSeq_entry& seqEntry)
{
if (seqEntry.IsSeq()) {
const Sequence *sequence = new Sequence(seqEntry.GetSeq());
if (!sequence || sequence->Status() != CAV_SUCCESS) {
status = sequence->Status();
return;
}
sequences.push_back(sequence);
} else { // Bioseq-set
UnpackSeqSet(seqEntry.GetSet());
}
}
void SequenceTable::addSequences(CSeq_entry& seqEntry)
{
if (seqEntry.IsSet())
{
list< CRef< CSeq_entry > >& seqSet = seqEntry.SetSet().SetSeq_set();
list< CRef< CSeq_entry > >::iterator it = seqSet.begin();
for (; it != seqSet.end(); it++)
addSequences(*(*it));
}
else
{
CRef< CBioseq > bioseq(&(seqEntry.SetSeq()));
addSequence(bioseq);
}
}
/**\internal
**\brief Get a FASTA formatted id string (the first available) from the
** CSeq_entry structure.
**
**\param entry sequence description structure
**\return the first id string corresponding to entry
**/
static const string GetIdString( const CSeq_entry & entry )
{
CRef<CObjectManager> om(CObjectManager::GetInstance());
const CBioseq & seq = entry.GetSeq();
CRef<CScope> scope(new CScope(*om));
CSeq_entry_Handle seh = scope->AddTopLevelSeqEntry(
const_cast< CSeq_entry & >( entry ) );
return CWinMaskSeqTitle::GetId( seh, seq );
/*
list< CRef< CSeq_id > > idlist = seq.GetId();
if( idlist.empty() )
return "???";
else
{
CNcbiOstrstream os;
(*idlist.begin())->WriteAsFasta( os );
return CNcbiOstrstreamToString(os);
}
*/
}
