CTLSContigHandler Class Reference

Search Toolkit Book for CTLSContigHandler

Inheritance diagram for CTLSContigHandler:

Collaboration diagram for CTLSContigHandler:

Public Member Functions
	CTLSContigHandler ()
virtual	~CTLSContigHandler ()
virtual void	ProcessBioseq (CBioseq_Handle bh)
const string &	GetConsensus ()
void	SetConsensus (const string &consensus)
Public Member Functions inherited from CTLSHandler
	CTLSHandler ()
virtual	~CTLSHandler ()
void	OpenInputFile (const string &filename, bool binary)
void	OpenOutputFile (const string &filename, bool binary)
void	ProcessAsnInput (void)
void	ProcessSeqSubmit (void)
void	ProcessSeqEntry (void)
void	ProcessSet (void)
void	ProcessSeqEntry (CRef< CSeq_entry > se)
CRef< CBioseq_set >	ReadBioseqSet (void)
CRef< CSeq_entry >	ReadSeqEntry (void)
void	StreamFile (const string &infile, const string &outfile, bool binary)

Public Attributes
bool	first = true

Protected Attributes
string	m_Consensus
bool	m_CalculateConsensus
Protected Attributes inherited from CTLSHandler
CRef< CObjectManager >	m_ObjMgr
unique_ptr< CObjectIStream >	m_In
unique_ptr< CObjectOStream >	m_Out

Additional Inherited Members
Protected Member Functions inherited from CTLSHandler
CRef< CScope >	BuildScope (void)

Detailed Description

Definition at line 255 of file tls.cpp.

Constructor & Destructor Documentation

CTLSContigHandler()

CTLSContigHandler::CTLSContigHandler ( )

inline

Definition at line 258 of file tls.cpp.

~CTLSContigHandler()

virtual CTLSContigHandler::~CTLSContigHandler ( )

inlinevirtual

Definition at line 259 of file tls.cpp.

Member Function Documentation

GetConsensus()

const string& CTLSContigHandler::GetConsensus ( )

inline

Definition at line 262 of file tls.cpp.

ProcessBioseq()

void CTLSContigHandler::ProcessBioseq ( CBioseq_Handle  bh )

virtual

Reimplemented from CTLSHandler.

Definition at line 272 of file tls.cpp.

References first(), GenerateTargetedLocusName(), GetTargetedLocusNameConsensus(), NStr::IsBlank(), and SetTargetedLocusName().

SetConsensus()

void CTLSContigHandler::SetConsensus ( const string &  consensus )

inline

Definition at line 263 of file tls.cpp.

Member Data Documentation

first

bool CTLSContigHandler::first = true

Definition at line 264 of file tls.cpp.

m_CalculateConsensus

bool CTLSContigHandler::m_CalculateConsensus

protected

Definition at line 268 of file tls.cpp.

m_Consensus

string CTLSContigHandler::m_Consensus

protected

Definition at line 267 of file tls.cpp.

---

The documentation for this class was generated from the following file:

• src/app/tls/tls.cpp