NCBI C++ ToolKit
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CMaskWriterInt Class Reference

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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, 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 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_osoutput 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
bshthe bioseq handle
maskthe resulting list of masked intervals
parsed_idbioseq 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:
Modified on Tue Apr 16 20:09:37 2024 by modify_doxy.py rev. 669887