bpp::AbstractMafIterator Class Reference

Partial implementation of the MafIterator interface. More...

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

Inheritance diagram for bpp::AbstractMafIterator:

Collaboration diagram for bpp::AbstractMafIterator:

Public Member Functions
	AbstractMafIterator ()
virtual	~AbstractMafIterator ()
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 MafBlock *	analyseCurrentBlock_ ()=0
virtual void	fireIterationStartSignal_ ()
virtual void	fireIterationMoveSignal_ (const MafBlock &currentBlock)
virtual void	fireIterationStopSignal_ ()

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

Detailed Description

Partial implementation of the MafIterator interface.

This implements the listener parts.

Definition at line 85 of file MafIterator.h.

Constructor & Destructor Documentation

AbstractMafIterator()

bpp::AbstractMafIterator::AbstractMafIterator ( )

inline

Definition at line 94 of file MafIterator.h.

~AbstractMafIterator()

virtual bpp::AbstractMafIterator::~AbstractMafIterator ( )

inlinevirtual

Definition at line 96 of file MafIterator.h.

Member Function Documentation

addIterationListener()

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

inlinevirtual

Implements bpp::MafIterator.

Definition at line 99 of file MafIterator.h.

analyseCurrentBlock_()

virtual MafBlock* bpp::AbstractMafIterator::analyseCurrentBlock_ ( )

protectedpure virtual

Implemented in bpp::MafIteratorSynchronizer, bpp::TrashIteratorAdapter, bpp::AlignmentFilter2MafIterator, bpp::OutputAlignmentMafIterator, bpp::BlockMergerMafIterator, bpp::AlignmentFilterMafIterator, bpp::SequenceFilterMafIterator, bpp::EntropyFilterMafIterator, bpp::OrphanSequenceFilterMafIterator, bpp::SequenceStatisticsMafIterator, bpp::FeatureExtractor, bpp::VcfOutputMafIterator, bpp::FeatureFilterMafIterator, bpp::CoordinatesOutputMafIterator, bpp::MaskFilterMafIterator, bpp::QualityFilterMafIterator, bpp::DuplicateFilterMafIterator, bpp::ConcatenateMafIterator, bpp::ChromosomeMafIterator, bpp::OutputMafIterator, bpp::SequenceStreamToMafIterator, bpp::MafParser, bpp::WindowSplitMafIterator, bpp::FullGapFilterMafIterator, bpp::BlockLengthMafIterator, and bpp::BlockSizeMafIterator.

fireIterationMoveSignal_()

void AbstractMafIterator::fireIterationMoveSignal_ ( const MafBlock &  currentBlock )

protectedvirtual

Definition at line 57 of file MafIterator.cpp.

fireIterationStartSignal_()

void AbstractMafIterator::fireIterationStartSignal_ ( )

protectedvirtual

Definition at line 51 of file MafIterator.cpp.

fireIterationStopSignal_()

void AbstractMafIterator::fireIterationStopSignal_ ( )

protectedvirtual

Definition at line 63 of file MafIterator.cpp.

isVerbose()

bool bpp::AbstractMafIterator::isVerbose ( ) const

inlinevirtual

Implements bpp::MafIterator.

Definition at line 116 of file MafIterator.h.

nextBlock()

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

inlinevirtual

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.

setVerbose()

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

inlinevirtual

Implements bpp::MafIterator.

Definition at line 117 of file MafIterator.h.

Member Data Documentation

iterationListeners_

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

protected

Definition at line 89 of file MafIterator.h.

started_

bool bpp::AbstractMafIterator::started_

protected

Definition at line 90 of file MafIterator.h.

verbose_

bool bpp::AbstractMafIterator::verbose_

protected

Definition at line 91 of file MafIterator.h.

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

• Bpp/Seq/Io/Maf/MafIterator.h
• Bpp/Seq/Io/Maf/MafIterator.cpp