NCBI C++ ToolKit
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CMaskWriterFasta Class Reference

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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, TSeqPosTMaskedInterval
 Type representing a masked interval within a sequence. More...
 
typedef vector< TMaskedIntervalTMaskList
 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
CNcbiOstreamos
 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_osthe 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
bshthe bioseq handle
maskthe resulting list of masked intervals
parsed_idbioseq 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:
Modified on Sun Apr 14 05:28:59 2024 by modify_doxy.py rev. 669887