NCBI C++ ToolKit
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CMaskWriterTabular Class Reference

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

#include <objtools/seqmasks_io/mask_writer_tab.hpp>

+ Inheritance diagram for CMaskWriterTabular:
+ Collaboration diagram for CMaskWriterTabular:

Public Member Functions

 CMaskWriterTabular (CNcbiOstream &arg_os)
 Object constructor. More...
virtual ~CMaskWriterTabular ()
 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...

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
 the standard C++ ostream object More...

Detailed Description

Output filter to print masked sequences as sets of intervals one per line.

Masking data for each new sequence in the file starts with a fasta style id and is followed by a range indicating the masked sequence starting at position 'start' and ending at position 'end', each field is separated by a tab character (i.e.: [id]\t[start]\t[end])

Definition at line 51 of file mask_writer_tab.hpp.

Constructor & Destructor Documentation

◆ CMaskWriterTabular()

CMaskWriterTabular::CMaskWriterTabular ( CNcbiOstream arg_os)

Object constructor.

arg_osoutput stream used to initialize the base class instance

Definition at line 62 of file mask_writer_tab.hpp.

◆ ~CMaskWriterTabular()

virtual CMaskWriterTabular::~CMaskWriterTabular ( )

Object destructor.

Definition at line 69 of file mask_writer_tab.hpp.

Member Function Documentation

◆ Print()

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

Send the masking data to the output stream.

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_tab.cpp.

References i, CMaskWriter::IdToString(), ITERATE, mask, and CMaskWriter::os.

The documentation for this class was generated from the following files:
Modified on Wed Apr 17 13:08:15 2024 by rev. 669887