Search Toolkit Book for CMaskWriterFasta

Output filter to write masked data in fasta format. More...

#include <objtools/seqmasks_io/mask_writer_fasta.hpp>

Inheritance diagram for CMaskWriterFasta:

Collaboration diagram for CMaskWriterFasta:

Public Member Functions
	CMaskWriterFasta (CNcbiOstream &arg_os, bool hard_masking=false)
	Object constructor. More...

virtual	~CMaskWriterFasta ()
	Object destructor. More...

virtual void	Print (objects::CBioseq_Handle &bsh, const TMaskList &mask, bool parsed_id=false)
	Output masked sequence data. More...

Public Member Functions inherited from CMaskWriter
	CMaskWriter (CNcbiOstream &arg_os)
	Object constructor. More...

virtual	~CMaskWriter ()
	Object destructor. More...

Private Attributes
bool	m_HardMasking

Additional Inherited Members
Public Types inherited from CMaskWriter
typedef pair< TSeqPos, TSeqPos >	TMaskedInterval
	Type representing a masked interval within a sequence. More...

typedef vector< TMaskedInterval >	TMaskList
	A type representing the total of masking information about a sequence. More...

Protected Member Functions inherited from CMaskWriter
virtual void	PrintId (objects::CBioseq_Handle &bsh, bool parsed_id)
	Output of the sequence id. More...

virtual string	IdToString (objects::CBioseq_Handle &bsh, bool parsed_id)
	Convert the sequence id to a string. More...

Protected Attributes inherited from CMaskWriter
CNcbiOstream &	os
	the standard C++ ostream object More...

Detailed Description

Output filter to write masked data in fasta format.

In the output the sequence ids are preserved. The masked portions of sequences are printed in lower case letters.

Definition at line 47 of file mask_writer_fasta.hpp.

Constructor & Destructor Documentation

◆ CMaskWriterFasta()

CMaskWriterFasta::CMaskWriterFasta	(	CNcbiOstream &	arg_os,
		bool	hard_masking = `false`
	)

inline

Object constructor.

Parameters

arg_os the output stream used to initialize the base class instance.

Definition at line 58 of file mask_writer_fasta.hpp.

◆ ~CMaskWriterFasta()

virtual CMaskWriterFasta::~CMaskWriterFasta ( )

inlinevirtual

Object destructor.

Definition at line 65 of file mask_writer_fasta.hpp.

Member Function Documentation

◆ Print()

void CMaskWriterFasta::Print	(	objects::CBioseq_Handle &	bsh,
		const TMaskList &	mask,
		bool	parsed_id = `false`
	)

virtual

Output masked sequence data.

Parameters

bsh	the bioseq handle
mask	the resulting list of masked intervals
parsed_id	bioseq id was parsed by CMaskReader.

Implements CMaskWriter.

Definition at line 46 of file mask_writer_fasta.cpp.

References data, CBioseq_Handle::eCoding_Iupac, i, letter(), m_HardMasking, mask, CMaskWriter::os, CMaskWriter::PrintId(), and tolower().

Member Data Documentation

◆ m_HardMasking

bool CMaskWriterFasta::m_HardMasking

private

Definition at line 79 of file mask_writer_fasta.hpp.

Referenced by Print().

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

include/objtools/seqmasks_io/mask_writer_fasta.hpp
src/objtools/seqmasks_io/mask_writer_fasta.cpp

Public Member Functions

Private Attributes

Additional Inherited Members