/// Converts a list of Bioseqs into a TSeqLocVector. All Bioseqs are added to
/// the same CScope object
/// @param subjects Bioseqs to convert
static TSeqLocVector
s_ConvertBioseqs2TSeqLocVector(const CBlast4_subject::TSequences& subjects)
{
TSeqLocVector retval;
CRef<CScope> subj_scope(new CScope(*CObjectManager::GetInstance()));
ITERATE(CBlast4_subject::TSequences, bioseq, subjects) {
subj_scope->AddBioseq(**bioseq);
CRef<CSeq_id> seqid = FindBestChoice((*bioseq)->GetId(),
CSeq_id::BestRank);
const TSeqPos length = (*bioseq)->GetInst().GetLength();
CRef<CSeq_loc> sl(new CSeq_loc(*seqid, 0, length-1));
retval.push_back(SSeqLoc(sl, subj_scope));
}
void GetSequenceLengthAndId(const blast::IBlastSeqInfoSrc * seqinfo_src,
int oid,
CRef<CSeq_id> & seqid,
TSeqPos * length)
{
_ASSERT(length);
list<CRef<CSeq_id> > seqid_list = seqinfo_src->GetId(oid);
CRef<CSeq_id> id = FindBestChoice(seqid_list, CSeq_id::BestRank);
if (id.NotEmpty()) {
seqid.Reset(new CSeq_id);
SerialAssign(*seqid, *id);
}
*length = seqinfo_src->GetLength(oid);
return;
}
CRef<CSeq_loc>
CBlastFastaInputSource::x_FastaToSeqLoc(CRef<objects::CSeq_loc>& lcase_mask,
CScope& scope)
{
static const TSeqRange kEmptyRange(TSeqRange::GetEmpty());
CRef<CBlastScopeSource> query_scope_source;
if (m_Config.GetLowercaseMask())
lcase_mask = m_InputReader->SaveMask();
CRef<CSeq_entry> seq_entry(m_InputReader->ReadOneSeq());
if (lcase_mask) {
if (lcase_mask->Which() != CSeq_loc::e_not_set) {
lcase_mask->SetStrand(eNa_strand_plus);
}
_ASSERT(lcase_mask->GetStrand() == eNa_strand_plus ||
lcase_mask->GetStrand() == eNa_strand_unknown);
}
_ASSERT(seq_entry.NotEmpty());
scope.AddTopLevelSeqEntry(*seq_entry);
CTypeConstIterator<CBioseq> itr(ConstBegin(*seq_entry));
CRef<CSeq_loc> retval(new CSeq_loc());
if ( !blast::HasRawSequenceData(*itr) ) {
CBlastInputReader* blast_reader =
dynamic_cast<CBlastInputReader*>(m_InputReader.get());
_ASSERT(blast_reader);
CRef<CBlastScopeSource> query_scope_source =
blast_reader->GetQueryScopeSource();
query_scope_source->AddDataLoaders(CRef<CScope>(&scope));
}
if (m_ReadProteins && itr->IsNa()) {
NCBI_THROW(CInputException, eSequenceMismatch,
"Nucleotide FASTA provided for protein sequence");
} else if ( !m_ReadProteins && itr->IsAa() ) {
NCBI_THROW(CInputException, eSequenceMismatch,
"Protein FASTA provided for nucleotide sequence");
}
// set strand
if (m_Config.GetStrand() == eNa_strand_other ||
m_Config.GetStrand() == eNa_strand_unknown) {
if (m_ReadProteins)
retval->SetInt().SetStrand(eNa_strand_unknown);
else
retval->SetInt().SetStrand(eNa_strand_both);
} else {
if (m_ReadProteins) {
NCBI_THROW(CInputException, eInvalidStrand,
"Cannot assign nucleotide strand to protein sequence");
}
retval->SetInt().SetStrand(m_Config.GetStrand());
}
// sanity checks for the range
const TSeqPos from = m_Config.GetRange().GetFrom() == kEmptyRange.GetFrom()
? 0 : m_Config.GetRange().GetFrom();
const TSeqPos to = m_Config.GetRange().GetTo() == kEmptyRange.GetTo()
? 0 : m_Config.GetRange().GetTo();
// Get the sequence length
const TSeqPos seqlen = seq_entry->GetSeq().GetInst().GetLength();
//if (seqlen == 0) {
// NCBI_THROW(CInputException, eEmptyUserInput,
// "Query contains no sequence data");
//}
_ASSERT(seqlen != numeric_limits<TSeqPos>::max());
if (to > 0 && to < from) {
NCBI_THROW(CInputException, eInvalidRange,
"Invalid sequence range");
}
if (from > seqlen) {
NCBI_THROW(CInputException, eInvalidRange,
"Invalid from coordinate (greater than sequence length)");
}
// N.B.: if the to coordinate is greater than or equal to the sequence
// length, we fix that silently
// set sequence range
retval->SetInt().SetFrom(from);
retval->SetInt().SetTo((to > 0 && to < seqlen) ? to : (seqlen-1));
// set ID
retval->SetInt().SetId().Assign(*FindBestChoice(itr->GetId(), CSeq_id::BestRank));
return retval;
}
