void SequenceSet::UnpackSeqSet(const CBioseq_set& bss)
{
CBioseq_set::TSeq_set::const_iterator q, qe = bss.GetSeq_set().end();
for (q=bss.GetSeq_set().begin(); q!=qe; ++q) {
if (q->GetObject().IsSeq()) {
// only store amino acid or nucleotide sequences
if (q->GetObject().GetSeq().GetInst().GetMol() != CSeq_inst::eMol_aa &&
q->GetObject().GetSeq().GetInst().GetMol() != CSeq_inst::eMol_dna &&
q->GetObject().GetSeq().GetInst().GetMol() != CSeq_inst::eMol_rna &&
q->GetObject().GetSeq().GetInst().GetMol() != CSeq_inst::eMol_na)
continue;
const Sequence *sequence = new Sequence(q->GetObject().GetSeq());
if (!sequence || sequence->Status() != CAV_SUCCESS) {
status = sequence->Status();
return;
}
sequences.push_back(sequence);
} else { // Bioseq-set
UnpackSeqSet(q->GetObject().GetSet());
}
}
}
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());
}
}
static void UnpackSeqSet(CBioseq_set& bss, SequenceSet *parent, SequenceSet::SequenceList& seqlist)
{
CBioseq_set::TSeq_set::iterator q, qe = bss.SetSeq_set().end();
for (q=bss.SetSeq_set().begin(); q!=qe; ++q) {
if (q->GetObject().IsSeq()) {
// only store amino acid or nucleotide sequences
if (q->GetObject().GetSeq().GetInst().GetMol() != CSeq_inst::eMol_aa &&
q->GetObject().GetSeq().GetInst().GetMol() != CSeq_inst::eMol_dna &&
q->GetObject().GetSeq().GetInst().GetMol() != CSeq_inst::eMol_rna &&
q->GetObject().GetSeq().GetInst().GetMol() != CSeq_inst::eMol_na)
continue;
const Sequence *sequence = new Sequence(parent, q->GetObject().SetSeq());
if (!sequence || !sequence->identifier)
FATALMSG("Can't create Sequence object, aborting...");
seqlist.push_back(sequence);
} else { // Bioseq-set
UnpackSeqSet(q->GetObject().SetSet(), parent, seqlist);
}
}
}
