#include <ncbi_pch.hpp>
#include <algo/sequence/cpg.hpp>
#include <corelib/ncbiapp.hpp>
#include <corelib/ncbiargs.hpp>
#include <corelib/ncbienv.hpp>
#include <objmgr/object_manager.hpp>
#include <objtools/data_loaders/genbank/gbloader.hpp>
#include <objmgr/scope.hpp>
#include <objmgr/seq_vector.hpp>

Include dependency graph for cpgdemo.cpp:

Go to the SVN repository for this file.

Classes
class	CCpGDemoApp

Functions
	USING_SCOPE (objects)

CNcbiOstream &	operator<< (CNcbiOstream &o, SCpGIsland i)

int	ScanForCpGs (const string &acc, CScope &scope, const CArgs &args)

int	ScanForCpGs (istream &infile, const CArgs &args)

int	main (int argc, char **argv)

Variables
	USING_NCBI_SCOPE

Function Documentation

◆ main()

int main	(	int	argc,
		char **	argv
	)

Definition at line 247 of file cpgdemo.cpp.

References CNcbiApplicationAPI::AppMain(), eDS_Default, and NULL.

◆ operator<<()

CNcbiOstream& operator<<	(	CNcbiOstream &	o,
		SCpGIsland	i
	)

Definition at line 95 of file cpgdemo.cpp.

References i, and len.

◆ ScanForCpGs() [1/2]

int ScanForCpGs	(	const string &	acc,
		CScope &	scope,
		const CArgs &	args
	)

Definition at line 109 of file cpgdemo.cpp.

References CBioseq_Handle::eCoding_Iupac, CScope::GetBioseqHandle(), CCpGIslands::GetIsles(), CSeqVector::GetSeqData(), CBioseq_Handle::GetSeqVector(), i, ITERATE, CCpGIslands::MergeIslesWithin(), CRef< C, Locker >::Reset(), CSeqVector::size(), and CException::what().

Referenced by CCpGDemoApp::Run().

◆ ScanForCpGs() [2/2]

int ScanForCpGs	(	istream &	infile,
		const CArgs &	args
	)

Definition at line 151 of file cpgdemo.cpp.

References Critical(), ERR_POST, CCpGIslands::GetIsles(), i, infile, ITERATE, max(), and CCpGIslands::MergeIslesWithin().

◆ USING_SCOPE()

USING_SCOPE ( objects )

Variable Documentation

◆ USING_NCBI_SCOPE

USING_NCBI_SCOPE

Definition at line 45 of file cpgdemo.cpp.

Classes

Functions

Variables