NCBI C++ ToolKit
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#include <ncbi_pch.hpp>
#include <corelib/ncbiapp.hpp>
#include <corelib/ncbienv.hpp>
#include <corelib/ncbiargs.hpp>
#include <algorithm>
#include <corelib/ncbistre.hpp>
#include <serial/objostr.hpp>
#include <serial/serial.hpp>
#include <algo/align/util/blast_tabular.hpp>
#include <algo/align/util/hit_comparator.hpp>
#include <algo/align/util/compartment_finder.hpp>
#include <algo/align/prosplign/compartments.hpp>
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Classes | |
class | CCompartApplication |
Functions | |
USING_SCOPE (prosplign) | |
void | PrintCompartments (int &last_id, const string &query, const string &subj, const TCompartmentStructs &compartments, ostream &ostr) |
void | DoCompartments (const CSplign::THitRefs &one_query_subj_pair_hitrefs, const CCompartOptions &compart_options, bool hits, int &last_id, const string &query, const string &subj) |
string | GetSeqIdString (const CSeq_id &id) |
int | PdbBadRank (const CRef< CSeq_id > &id) |
int | main (int argc, const char *argv[]) |
Variables | |
USING_NCBI_SCOPE | |
void DoCompartments | ( | const CSplign::THitRefs & | one_query_subj_pair_hitrefs, |
const CCompartOptions & | compart_options, | ||
bool | hits, | ||
int & | last_id, | ||
const string & | query, | ||
const string & | subj | ||
) |
Definition at line 73 of file compartp.cpp.
References CreateCompartmentAccessor(), FormatAsAsn(), CCompartmentAccessor< THit >::GetFirst(), CCompartmentAccessor< THit >::GetNext(), ITERATE, MakeCompartments(), NULL, PrintCompartments(), and query.
Referenced by CCompartApplication::Run().
Definition at line 100 of file compartp.cpp.
Referenced by BlastXML_FormatReport(), BOOST_AUTO_TEST_CASE(), CFastaIdValidate::CheckIDLength(), CDisplaySeqalign::DisplaySeqalign(), CSeqUtils::GetAccessionPlacementsMsec(), UpdateViewer::ImportStructure(), IAlignRowHandle::IsConsensus(), CCompartApplication::Run(), s_BlastXMLAddIteration(), s_SetBlastXMLSearch(), CSearch< LEGACY, NHITS >::SetResult(), and CWriteDB_Impl::x_CookSequence().
Definition at line 151 of file compartp.cpp.
References CNcbiApplicationAPI::AppMain(), eDiagFilter_All, and SetDiagFilter().
Definition at line 105 of file compartp.cpp.
References CSeq_id::FastaAARank(), CSeq_id_Base::IsPdb(), and kMax_Int.
Referenced by CCompartApplication::Run().
void PrintCompartments | ( | int & | last_id, |
const string & | query, | ||
const string & | subj, | ||
const TCompartmentStructs & | compartments, | ||
ostream & | ostr | ||
) |
Definition at line 64 of file compartp.cpp.
References i, ITERATE, and query.
Referenced by DoCompartments().
USING_SCOPE | ( | prosplign | ) |
USING_NCBI_SCOPE |
Definition at line 19 of file compartp.cpp.