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NCBI C++ ToolKit: src/algo/structure/cd_utils/cuReadFastaWrapper.cpp Source File

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User-defined methods of the data storage class.

TReadFastaFlags m_readFastaFlags

virtual bool ReadFile(CNcbiIstream &iStream)

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

string m_activeFastaString

virtual unsigned int GetNumRead() const

virtual string GetActiveSequence(unsigned int index, bool removeWhitespace=true) const

virtual string GetActiveDefline(unsigned int index) const

string GetSubstring(const string &s, unsigned int index, bool isDefline) const

virtual string GetRawDefline(unsigned int index) const

virtual string GetRawSequence(unsigned int index, bool removeWhitespace=true) const

CRef< CSeq_entry > m_seqEntry

Base class for reading FASTA sequences.

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

Simple implementation of ILineReader for i(o)streams.

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

string RemoveWhitespace_CJL(const string &s)

EDiagSev SetDiagPostLevel(EDiagSev post_sev=eDiag_Error)

Set the threshold severity for posting the messages.

EDiagSev

Severity level for the posted diagnostics.

@ eDiag_Error

Error message.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

CRef< CSeq_entry > ReadSet(int max_seqs=kMax_Int, ILineErrorListener *pMessageListener=nullptr)

Read multiple sequences (by default, as many as are available.)

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

#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::istream CNcbiIstream

Portable alias for istream.

NCBI_NS_STD::string::size_type SIZE_TYPE

TSet & SetSet(void)

Select the variant.

const TSet & GetSet(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

bool IsSet(void) const

Check if variant Set is selected.

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

void Select(E_Choice index, EResetVariant reset=eDoResetVariant)

Select the requested variant if needed.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

The NCBI C++/STL use hints.

NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.

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