bpp-seq-omics  2.2.0
Public Member Functions | Protected Member Functions | Protected Attributes | Private Member Functions | Private Attributes | List of all members
bpp::MafParser Class Reference

MAF file parser. More...

#include <Bpp/Seq/Io/Maf/MafParser.h>

+ Inheritance diagram for bpp::MafParser:
+ Collaboration diagram for bpp::MafParser:

Public Member Functions

 MafParser (std::istream *stream, bool parseMask=false)
 
void addIterationListener (IterationListener *listener)
 
MafBlock * nextBlock () throw (Exception)
 Get the next available alignment block. More...
 
bool isVerbose () const
 
void setVerbose (bool yn)
 

Protected Member Functions

virtual void fireIterationStartSignal_ ()
 
virtual void fireIterationMoveSignal_ (const MafBlock &currentBlock)
 
virtual void fireIterationStopSignal_ ()
 

Protected Attributes

std::vector< IterationListener * > iterationListeners_
 
bool started_
 
bool verbose_
 

Private Member Functions

 MafParser (const MafParser &maf)
 
MafParser & operator= (const MafParser &maf)
 
MafBlock * analyseCurrentBlock_ () throw (Exception)
 

Private Attributes

std::istream * stream_
 
bool mask_
 
CaseMaskedAlphabet cmAlphabet_
 
bool firstBlock_
 

Detailed Description

MAF file parser.

This class parses synteny blocks from Maf file.

The MAF format is documented on the UCSC Genome Browser website: http://genome.ucsc.edu/FAQ/FAQformat.html#format5

Author
Julien Dutheil

Definition at line 61 of file MafParser.h.

Constructor & Destructor Documentation

◆ MafParser() [1/2]

bpp::MafParser::MafParser ( std::istream *  stream,
bool  parseMask = false 
)
inline

Definition at line 71 of file MafParser.h.

◆ MafParser() [2/2]

bpp::MafParser::MafParser ( const MafParser &  maf)
inlineprivate

Definition at line 76 of file MafParser.h.

Member Function Documentation

◆ addIterationListener()

void bpp::AbstractMafIterator::addIterationListener ( IterationListener *  listener)
inlinevirtualinherited

Implements bpp::MafIterator.

Definition at line 99 of file MafIterator.h.

◆ analyseCurrentBlock_()

MafBlock * MafParser::analyseCurrentBlock_ ( )
throw (Exception
)
privatevirtual

Implements bpp::AbstractMafIterator.

Definition at line 49 of file MafParser.cpp.

References bpp::MafBlock::addSequence(), bpp::MafSequence::getGenomicSize(), bpp::MafBlock::setPass(), and bpp::MafBlock::setScore().

◆ fireIterationMoveSignal_()

void AbstractMafIterator::fireIterationMoveSignal_ ( const MafBlock &  currentBlock)
protectedvirtualinherited

Definition at line 57 of file MafIterator.cpp.

◆ fireIterationStartSignal_()

void AbstractMafIterator::fireIterationStartSignal_ ( )
protectedvirtualinherited

Definition at line 51 of file MafIterator.cpp.

◆ fireIterationStopSignal_()

void AbstractMafIterator::fireIterationStopSignal_ ( )
protectedvirtualinherited

Definition at line 63 of file MafIterator.cpp.

◆ isVerbose()

bool bpp::AbstractMafIterator::isVerbose ( ) const
inlinevirtualinherited

Implements bpp::MafIterator.

Definition at line 116 of file MafIterator.h.

◆ nextBlock()

MafBlock* bpp::AbstractMafIterator::nextBlock ( )
throw (Exception
)
inlinevirtualinherited

Get the next available alignment block.

Returns
A maf alignment block, or a null pointer if no more block is available.

Implements bpp::MafIterator.

Definition at line 103 of file MafIterator.h.

◆ operator=()

MafParser& bpp::MafParser::operator= ( const MafParser &  maf)
inlineprivate

Definition at line 77 of file MafParser.h.

References firstBlock_, mask_, and stream_.

◆ setVerbose()

void bpp::AbstractMafIterator::setVerbose ( bool  yn)
inlinevirtualinherited

Implements bpp::MafIterator.

Definition at line 117 of file MafIterator.h.

Member Data Documentation

◆ cmAlphabet_

CaseMaskedAlphabet bpp::MafParser::cmAlphabet_
private

Definition at line 67 of file MafParser.h.

◆ firstBlock_

bool bpp::MafParser::firstBlock_
private

Definition at line 68 of file MafParser.h.

Referenced by operator=().

◆ iterationListeners_

std::vector<IterationListener*> bpp::AbstractMafIterator::iterationListeners_
protectedinherited

Definition at line 89 of file MafIterator.h.

◆ mask_

bool bpp::MafParser::mask_
private

Definition at line 66 of file MafParser.h.

Referenced by operator=().

◆ started_

bool bpp::AbstractMafIterator::started_
protectedinherited

Definition at line 90 of file MafIterator.h.

◆ stream_

std::istream* bpp::MafParser::stream_
private

Definition at line 65 of file MafParser.h.

Referenced by operator=().

◆ verbose_

bool bpp::AbstractMafIterator::verbose_
protectedinherited

Definition at line 91 of file MafIterator.h.

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