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NCBI C++ ToolKit: include/algo/structure/cd_utils/cuReadFastaWrapper.hpp Source File

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35 #ifndef CU_FASTA_IO_WRAPPER__HPP 36 #define CU_FASTA_IO_WRAPPER__HPP 51 static const char gt

;

52 static const char nl

;

57

m_cacheRawFasta = cacheRawString;

58

m_rawFastaString =

""

;

59

m_activeFastaString =

""

;

60

m_useBioseqSet =

true

;

68

ostream << m_activeFastaString;

69 return

(m_activeFastaString.length() > 0);

74 virtual unsigned int

GetNumRead()

const

;

75 virtual string

GetActiveDefline(

unsigned int

index)

const

;

76 virtual string

GetActiveSequence(

unsigned int

index,

bool

removeWhitespace =

true

)

const

;

77 virtual string

GetRawDefline(

unsigned int

index)

const

;

78 virtual string

GetRawSequence(

unsigned int

index,

bool

removeWhitespace =

true

)

const

;

87 return

m_activeFastaString;

92 return

m_rawFastaString;

100

m_activeFastaString = m_rawFastaString;

121 string

GetSubstring(

const string

& s,

unsigned int

index,

bool

isDefline)

const

;

136

m_readFastaFlags = fastaFlags;

156

m_readFastaFlags |= flagsToSet;

159

m_readFastaFlags &= (0xFFFFFFFF^flagsToUnset);

Concrete implementations of the CFastaIOWrapper virtual class.

virtual ~CBasicFastaWrapper()

TReadFastaFlags m_readFastaFlags

void SetFastaFlags(TReadFastaFlags flagsToSet)

void UnsetFastaFlags(TReadFastaFlags flagsToUnset)

CBasicFastaWrapper(TReadFastaFlags fastaFlags, bool cacheRawFasta)

string m_activeFastaString

const string & GetRawFastaString()

virtual string & GetActiveFastaString()

const CRef< CSeq_entry > & GetSeqEntry() const

virtual ~CFastaIOWrapper()

virtual bool Write(CNcbiOstream &ostream)

CFastaIOWrapper(bool cacheRawString=false)

void SetUseBioseqSet(bool useBioseqSet)

virtual bool ReadFile(CNcbiIstream &iStream)=0

CRef< CSeq_entry > m_seqEntry

bool IsUseBioseqSet() const

Include a standard set of the NCBI C++ Toolkit most basic headers.

Operators to edit gaps in sequences.

CFastaReader::TFlags TReadFastaFlags

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

#define NCBI_CDUTILS_EXPORT

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