CRef<CSeq_interval>
CSpliced_exon::CreateRowSeq_interval(CSeq_align::TDim row,
const CSpliced_seg& seg) const
{
CRef<CSeq_interval> ret;
ret.Reset(new CSeq_interval);
TSeqRange range = GetRowSeq_range(row, false);
ret->SetFrom(range.GetFrom());
ret->SetTo(range.GetTo());
if (row == 0) {
if ( IsSetProduct_id() ) {
ret->SetId().Assign(GetProduct_id());
}
else if ( seg.IsSetProduct_id() ) {
ret->SetId().Assign(seg.GetProduct_id());
}
else {
NCBI_THROW(CSeqalignException, eInvalidAlignment,
"CSpliced_exon::CreateRowSeq_interval() - "
"missing product id.");
}
if ( IsSetProduct_strand() ) {
ret->SetStrand(GetProduct_strand());
}
else if ( seg.IsSetProduct_strand() ) {
ret->SetStrand(seg.GetProduct_strand());
}
}
else if (row == 1) {
// Genomic
if ( IsSetGenomic_id() ) {
ret->SetId().Assign(GetGenomic_id());
}
else if ( seg.IsSetGenomic_id() ) {
ret->SetId().Assign(seg.GetGenomic_id());
}
else {
NCBI_THROW(CSeqalignException, eInvalidAlignment, "CSpliced_exon::CreateRowSeq_interval() - "
"missing genomic id.");
}
if ( IsSetGenomic_strand() ) {
ret->SetStrand(GetGenomic_strand());
}
else if ( seg.IsSetGenomic_strand() ) {
ret->SetStrand(seg.GetGenomic_strand());
}
}
return ret;
}
void x_ValidatePssmVsGi129295(CConstRef<CSeq_align> sa) {
BOOST_REQUIRE(sa->GetSegs().IsDenseg());
const CDense_seg & denseg = sa->GetSegs().GetDenseg();
// Validate the first (and only) HSP, which is a self hit
const TSeqRange hsp(0, 231);
TSeqRange hsp1_query = denseg.GetSeqRange(0);
TSeqRange hsp1_subj = denseg.GetSeqRange(1);
BOOST_REQUIRE_EQUAL(hsp.GetFrom(), hsp1_query.GetFrom());
BOOST_REQUIRE_EQUAL(hsp.GetTo(), hsp1_query.GetTo());
BOOST_REQUIRE_EQUAL(hsp.GetFrom(), hsp1_subj.GetFrom());
BOOST_REQUIRE_EQUAL(hsp.GetTo(), hsp1_subj.GetTo());
}
CRef<objects::CBioseq>
SeqLocToBioseq(const objects::CSeq_loc& loc, objects::CScope& scope)
{
CRef<CBioseq> bioseq;
if ( !loc.GetId() ) {
return bioseq;
}
// Build a Seq-entry for the query Seq-loc
CBioseq_Handle handle = scope.GetBioseqHandle(*loc.GetId());
if( !handle ){
return bioseq;
}
bioseq.Reset( new CBioseq() );
// add an ID for our sequence
CRef<CSeq_id> id(new CSeq_id());
id->Assign(*handle.GetSeqId());
bioseq->SetId().push_back(id);
// a title
CRef<CSeqdesc> title( new CSeqdesc() );
string title_str;
id -> GetLabel(&title_str );
title_str += ": ";
loc.GetLabel( &title_str );
title->SetTitle( title_str );
bioseq->SetDescr().Set().push_back( title );
///
/// create the seq-inst
/// we can play some games here
///
CSeq_inst& inst = bioseq->SetInst();
if (handle.IsAa()) {
inst.SetMol(CSeq_inst::eMol_aa);
} else {
inst.SetMol(CSeq_inst::eMol_na);
}
bool process_whole = false;
if (loc.IsWhole()) {
process_whole = true;
} else if (loc.IsInt()) {
TSeqRange range = loc.GetTotalRange();
if (range.GetFrom() == 0 && range.GetTo() == handle.GetBioseqLength() - 1) {
/// it's whole
process_whole = true;
}
}
/// BLAST now handles delta-seqs correctly, so we can submit this
/// as a delta-seq
if (process_whole) {
/// just encode the whole sequence
CSeqVector vec(loc, scope, CBioseq_Handle::eCoding_Iupac);
string seq_string;
vec.GetSeqData(0, vec.size(), seq_string);
inst.SetRepr(CSeq_inst::eRepr_raw);
inst.SetLength(seq_string.size());
if (vec.IsProtein()) {
inst.SetMol(CSeq_inst::eMol_aa);
inst.SetSeq_data().SetIupacaa().Set().swap(seq_string);
} else {
inst.SetMol(CSeq_inst::eMol_na);
inst.SetSeq_data().SetIupacna().Set().swap(seq_string);
CSeqportUtil::Pack(&inst.SetSeq_data());
}
} else {
inst.SetRepr(CSeq_inst::eRepr_delta);
inst.SetLength(handle.GetBioseqLength());
CDelta_ext& ext = inst.SetExt().SetDelta();
///
/// create a delta sequence
///
//const CSeq_id& id = sequence::GetId(loc, &scope);
//ENa_strand strand = sequence::GetStrand(loc, &scope);
TSeqRange range = loc.GetTotalRange();
/// first segment: gap out to initial start of seq-loc
if (range.GetFrom() != 0) {
ext.AddLiteral(range.GetFrom());
}
CSeq_loc_CI loc_iter(loc);
if (loc_iter) {
TSeqRange prev = loc_iter.GetRange();
ENa_strand strand = loc_iter.GetStrand();
do {
/// encode a literal for the included bases
CRef<CSeq_loc> sl =
handle.GetRangeSeq_loc(prev.GetFrom(), prev.GetTo(), strand);
CSeqVector vec(*sl, scope, CBioseq_Handle::eCoding_Iupac);
string seq_string;
vec.GetSeqData(0, vec.size(), seq_string);
ext.AddLiteral(seq_string,
(vec.IsProtein() ? CSeq_inst::eMol_aa : CSeq_inst::eMol_na));
/// skip to the next segment
/// we may need to include a gap
++loc_iter;
if (loc_iter) {
TSeqRange next = loc_iter.GetRange();
ext.AddLiteral(next.GetFrom() - prev.GetTo());
prev = next;
strand = loc_iter.GetStrand();
}
}
while (loc_iter);
/// gap at the end
if (prev.GetTo() < handle.GetBioseqLength() - 1) {
ext.AddLiteral(handle.GetBioseqLength() - prev.GetTo() - 1);
}
}
}
return bioseq;
}
CSeqLocInfo(objects::CSeq_id& id, TSeqRange& range, int frame)
: m_Interval(new objects::CSeq_interval(id, range.GetFrom(),
range.GetToOpen()))
{ SetFrame(frame); }