Search Toolkit Book for CMaskWriterInt

Output filter to print masked sequences as sets of intervals. More...

#include <objtools/seqmasks_io/mask_writer_int.hpp>

Inheritance diagram for CMaskWriterInt:

Collaboration diagram for CMaskWriterInt:

Public Member Functions
	CMaskWriterInt (CNcbiOstream &arg_os)
	Object constructor. More...

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

virtual void	Print (objects::CBioseq_Handle &bsh, const TMaskList &mask, bool parsed_id=false)
	Send the masking data to the output stream. More...

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

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

Static Public Member Functions
static void	PrintMasks (CNcbiOstream &os, const TMaskList &mask)
	Print masks only. More...

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 print masked sequences as sets of intervals.

Masking data for each new sequence in the file starts with a fasta stile id. Then each contiguous interval of masked sequence starting at position 'start' and ending at position 'end' it is printed on a separate line [start] - [end].

Definition at line 51 of file mask_writer_int.hpp.

Constructor & Destructor Documentation

◆ CMaskWriterInt()

CMaskWriterInt::CMaskWriterInt ( CNcbiOstream & arg_os )

inline

Object constructor.

Parameters

arg_os output stream used to initialize the base class instance

Definition at line 62 of file mask_writer_int.hpp.

◆ ~CMaskWriterInt()

virtual CMaskWriterInt::~CMaskWriterInt ( )

inlinevirtual

Object destructor.

Definition at line 69 of file mask_writer_int.hpp.

Member Function Documentation

◆ Print()

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

virtual

Send the masking data to the output stream.

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 40 of file mask_writer_int.cpp.

References mask, CMaskWriter::os, CMaskWriter::PrintId(), and PrintMasks().

◆ PrintMasks()

void CMaskWriterInt::PrintMasks	(	CNcbiOstream &	os,
		const TMaskList &	mask
	)

static

Print masks only.

Definition at line 49 of file mask_writer_int.cpp.

References i, ITERATE, mask, and CMaskWriter::os.

Referenced by CMaskWriterBlastDbMaskInfo::Print(), and Print().

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

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

Public Member Functions

Static Public Member Functions