compartp.cpp File Reference

#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>

Include dependency graph for compartp.cpp:

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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

Function Documentation

DoCompartments()

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().

GetSeqIdString()

string GetSeqIdString

(

const CSeq_id &

id

)

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().

main()

int main	(	int	argc,
		const char *	argv[]
	)

Definition at line 151 of file compartp.cpp.

References CNcbiApplicationAPI::AppMain(), eDiagFilter_All, and SetDiagFilter().

PdbBadRank()

int PdbBadRank

(

const CRef< CSeq_id > &

id

)

Definition at line 105 of file compartp.cpp.

References CSeq_id::FastaAARank(), CSeq_id_Base::IsPdb(), and kMax_Int.

Referenced by CCompartApplication::Run().

PrintCompartments()

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()

USING_SCOPE

(

prosplign

)

Variable Documentation

USING_NCBI_SCOPE

USING_NCBI_SCOPE

Definition at line 19 of file compartp.cpp.