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CBasicFastaWrapper Class Reference

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Concrete implementations of the CFastaIOWrapper virtual class. More...

#include <algo/structure/cd_utils/cuReadFastaWrapper.hpp>

+ Inheritance diagram for CBasicFastaWrapper:
+ Collaboration diagram for CBasicFastaWrapper:

Public Member Functions

 CBasicFastaWrapper (TReadFastaFlags fastaFlags, bool cacheRawFasta)
 
virtual ~CBasicFastaWrapper ()
 
bool ReadAsSeqEntry (CNcbiIstream &iStream, CRef< CSeq_entry > &seqEntry)
 
virtual bool ReadFile (CNcbiIstream &iStream)
 
void SetFastaFlags (TReadFastaFlags flagsToSet)
 
void UnsetFastaFlags (TReadFastaFlags flagsToUnset)
 
- Public Member Functions inherited from CFastaIOWrapper
 CFastaIOWrapper (bool cacheRawString=false)
 
virtual ~CFastaIOWrapper ()
 
virtual bool Write (CNcbiOstream &ostream)
 
virtual unsigned int GetNumRead () const
 
virtual string GetActiveDefline (unsigned int index) const
 
virtual string GetActiveSequence (unsigned int index, bool removeWhitespace=true) const
 
virtual string GetRawDefline (unsigned int index) const
 
virtual string GetRawSequence (unsigned int index, bool removeWhitespace=true) const
 
bool HasSeqEntry () const
 
const CRef< CSeq_entry > & GetSeqEntry () const
 
virtual stringGetActiveFastaString ()
 
const stringGetRawFastaString ()
 
void ClearActiveFasta ()
 
void ResetActiveFasta ()
 
string GetError ()
 
bool IsUseBioseqSet () const
 
void SetUseBioseqSet (bool useBioseqSet)
 

Protected Attributes

TReadFastaFlags m_readFastaFlags
 
- Protected Attributes inherited from CFastaIOWrapper
bool m_cacheRawFasta
 
string m_rawFastaString
 
string m_activeFastaString
 
string m_error
 
bool m_useBioseqSet
 
CRef< CSeq_entrym_seqEntry
 

Additional Inherited Members

- Protected Member Functions inherited from CFastaIOWrapper
string GetSubstring (const string &s, unsigned int index, bool isDefline) const
 
- Static Protected Attributes inherited from CFastaIOWrapper
static const char gt = '>'
 
static const char nl = '\n'
 

Detailed Description

Concrete implementations of the CFastaIOWrapper virtual class.

Definition at line 131 of file cuReadFastaWrapper.hpp.

Constructor & Destructor Documentation

◆ CBasicFastaWrapper()

CBasicFastaWrapper::CBasicFastaWrapper ( TReadFastaFlags  fastaFlags,
bool  cacheRawFasta 
)
inline

◆ ~CBasicFastaWrapper()

virtual CBasicFastaWrapper::~CBasicFastaWrapper ( )
inlinevirtual

Definition at line 140 of file cuReadFastaWrapper.hpp.

Member Function Documentation

◆ ReadAsSeqEntry()

bool CBasicFastaWrapper::ReadAsSeqEntry ( CNcbiIstream iStream,
CRef< CSeq_entry > &  seqEntry 
)

◆ ReadFile()

bool CBasicFastaWrapper::ReadFile ( CNcbiIstream iStream)
virtual

◆ SetFastaFlags()

void CBasicFastaWrapper::SetFastaFlags ( TReadFastaFlags  flagsToSet)
inline

Definition at line 155 of file cuReadFastaWrapper.hpp.

References m_readFastaFlags.

Referenced by CCdFromFasta::ImportAlignmentData().

◆ UnsetFastaFlags()

void CBasicFastaWrapper::UnsetFastaFlags ( TReadFastaFlags  flagsToUnset)
inline

Definition at line 158 of file cuReadFastaWrapper.hpp.

References m_readFastaFlags.

Member Data Documentation

◆ m_readFastaFlags

TReadFastaFlags CBasicFastaWrapper::m_readFastaFlags
protected

The documentation for this class was generated from the following files:
Modified on Sun Jul 14 04:59:00 2024 by modify_doxy.py rev. 669887