src/algo/sequence/demo/cpgdemo.cpp File Reference

#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 source code of 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

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Function Documentation

int main (  int  argc, char **  argv )

Definition at line 247 of file cpgdemo.cpp. References CNcbiApplication::AppMain(), eDS_Default, and theApp.

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

Definition at line 95 of file cpgdemo.cpp. References len, SCpGIsland::m_C, SCpGIsland::m_CG, SCpGIsland::m_G, SCpGIsland::m_Start, and SCpGIsland::m_Stop.

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

Definition at line 151 of file cpgdemo.cpp. References ERR_POST, and ITERATE.

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(), CSeqVector::GetSeqData(), CBioseq_Handle::GetSeqVector(), ITERATE, CRef< C, Locker >::Reset(), CSeqVector::size(), and CException::what(). Referenced by CCpGDemoApp::Run().

USING_SCOPE (  objects   )

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Variable Documentation

USING_NCBI_SCOPE

Definition at line 45 of file cpgdemo.cpp.

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