SCompartmentData(const CSeq_align_set &compartment)
: num_alignments(compartment.Get().size())
{
CSeq_align align;
align.SetSegs().SetDisc(const_cast<CSeq_align_set &>(compartment));
query_range = align.GetSeqRange(0);
subject_range = align.GetSeqRange(1);
}
int CTestCompartApplication::Run(void)
{
// Get arguments
const CArgs& args = GetArgs();
CRef<CObjectManager> om(CObjectManager::GetInstance());
CGBDataLoader::RegisterInObjectManager(*om);
CRef<CScope> scope(new CScope(*om));
scope->AddDefaults();
list< CRef<CSeq_align> > aligns;
{{
CNcbiIstream& istr = args["i"].AsInputFile();
auto_ptr<CObjectIStream> is
(CObjectIStream::Open(eSerial_AsnText, istr));
while ( !is->EndOfData() ) {
CRef<CSeq_align> align(new CSeq_align);
*is >> *align;
aligns.push_back(align);
}
}}
CNcbiOstream& ostr = args["o"].AsOutputFile();
TCompartOptions opts = fCompart_Defaults;
if (args["allow-intersect"]) {
opts |= fCompart_AllowIntersections;
}
if (args["allow-intersect-query"]) {
opts |= fCompart_AllowIntersectionsQuery;
}
if (args["allow-intersect-subject"]) {
opts |= fCompart_AllowIntersectionsSubject;
}
if (args["allow-intersect-both"]) {
opts |= fCompart_AllowIntersectionsBoth;
}
list< CRef<CSeq_align_set> > compartments;
FindCompartments(aligns, compartments, opts);
LOG_POST(Error << "input alignments: " << aligns.size());
LOG_POST(Error << "output compartments: " << compartments.size());
size_t count = 0;
NON_CONST_ITERATE (list< CRef<CSeq_align_set> >, i, compartments) {
++count;
CSeq_align align;
align.SetSegs().SetDisc(**i);
TSeqRange r1 = align.GetSeqRange(0);
TSeqRange r2 = align.GetSeqRange(1);
CSeq_id_Handle id1 = CSeq_id_Handle::GetHandle(align.GetSeq_id(0));
CSeq_id_Handle id2 = CSeq_id_Handle::GetHandle(align.GetSeq_id(1));
LOG_POST(Error << "compartment " << count << ":");
LOG_POST(Error << " query = " << id1 << " (" << r1.GetFrom() + 1 << ".." << r1.GetTo() + 1 << ")");
LOG_POST(Error << " subject = " << id2 << " (" << r2.GetFrom() + 1 << ".." << r2.GetTo() + 1 << ")");
LOG_POST(Error << " alignments = " << (*i)->Get().size());
string title("Compartment ");
title += NStr::NumericToString(count);
CSeq_annot annot;
annot.SetNameDesc(title);
annot.SetTitleDesc(title);
annot.SetData().SetAlign() = (*i)->Get();
ostr << MSerial_AsnText << annot;
}
CAlignSort::SSortKey
CAlignSort::SAlignExtractor::operator()(const CSeq_align& align)
{
SSortKey key;
ITERATE (vector<string>, iter, key_toks) {
SSortKey::TItem item;
if (NStr::EqualNocase(*iter, "query")) {
CSeq_id_Handle idh =
CSeq_id_Handle::GetHandle(align.GetSeq_id(0));
idh = sequence::GetId(idh, *scope,
sequence::eGetId_Canonical);
item.first = idh.GetSeqId()->AsFastaString();
}
else if (NStr::EqualNocase(*iter, "subject")) {
CSeq_id_Handle idh =
CSeq_id_Handle::GetHandle(align.GetSeq_id(1));
idh = sequence::GetId(idh, *scope,
sequence::eGetId_Canonical);
item.first = idh.GetSeqId()->AsFastaString();
}
else if (NStr::EqualNocase(*iter, "query_start")) {
item.second = align.GetSeqStart(0);
}
else if (NStr::EqualNocase(*iter, "subject_start")) {
item.second = align.GetSeqStart(1);
}
else if (NStr::EqualNocase(*iter, "query_end")) {
item.second = align.GetSeqStop(0);
}
else if (NStr::EqualNocase(*iter, "subject_end")) {
item.second = align.GetSeqStop(1);
}
else if (NStr::EqualNocase(*iter, "query_strand")) {
item.second = align.GetSeqStrand(0);
}
else if (NStr::EqualNocase(*iter, "subject_strand")) {
item.second = align.GetSeqStrand(1);
}
else if (NStr::EqualNocase(*iter, "query_align_len")) {
item.second = align.GetSeqRange(0).GetLength();
}
else if (NStr::EqualNocase(*iter, "subject_align_len")) {
item.second = align.GetSeqRange(1).GetLength();
}
else if (NStr::EqualNocase(*iter, "query_traceback")) {
CScoreBuilder builder;
item.first = builder.GetTraceback(*scope, align, 0);
}
else if (NStr::EqualNocase(*iter, "subject_traceback")) {
CScoreBuilder builder;
item.first = builder.GetTraceback(*scope, align, 1);
}
else {
/// assume it is a score
CScoreLookup lookup;
lookup.SetScope(*scope);
item.second = lookup.GetScore(align, *iter);
}
key.items.push_back(item);
}