bpp::MafIteratorSynchronizer Class Reference

This special iterator synchronizes two adaptors. More...

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

Inheritance diagram for bpp::MafIteratorSynchronizer:

Collaboration diagram for bpp::MafIteratorSynchronizer:

Public Member Functions
	MafIteratorSynchronizer (MafIterator *primaryIterator, MafIterator *secondaryIterator)
void	setLogStream (std::shared_ptr< OutputStream > logstream)
void	addIterationListener (IterationListener *listener)
MafBlock *	nextBlock ()
	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
MafIterator *	iterator_
MafBlock *	currentBlock_
std::shared_ptr< OutputStream >	logstream_
std::vector< IterationListener * >	iterationListeners_
bool	started_
bool	verbose_

Private Member Functions
	MafIteratorSynchronizer (const MafIteratorSynchronizer &iterator)
MafIteratorSynchronizer &	operator= (const MafIteratorSynchronizer &iterator)
MafBlock *	analyseCurrentBlock_ ()

Private Attributes
MafIterator *	secondaryIterator_

Detailed Description

This special iterator synchronizes two adaptors.

It takes as input a main iterator and a secondary one. The nextBlock method of the secondary iterator will be called immediately after the one of the primary one. The resulting block of the main iterator will be forwarded, while the one of the secondary iterator will be destroyed.

Definition at line 216 of file MafIterator.h.

Constructor & Destructor Documentation

MafIteratorSynchronizer() [1/2]

bpp::MafIteratorSynchronizer::MafIteratorSynchronizer ( MafIterator *  primaryIterator, MafIterator *  secondaryIterator  )

inline

Definition at line 223 of file MafIterator.h.

MafIteratorSynchronizer() [2/2]

bpp::MafIteratorSynchronizer::MafIteratorSynchronizer ( const MafIteratorSynchronizer &  iterator )

inlineprivate

Definition at line 228 of file MafIterator.h.

Member Function Documentation

addIterationListener()

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

inlinevirtualinherited

Implements bpp::MafIterator.

Definition at line 99 of file MafIterator.h.

References bpp::AbstractMafIterator::iterationListeners_.

analyseCurrentBlock_()

MafBlock* bpp::MafIteratorSynchronizer::analyseCurrentBlock_ ( )

inlineprivatevirtual

Implements bpp::AbstractMafIterator.

Definition at line 241 of file MafIterator.h.

References bpp::AbstractFilterMafIterator::currentBlock_, bpp::AbstractFilterMafIterator::iterator_, bpp::MafIterator::nextBlock(), and secondaryIterator_.

fireIterationMoveSignal_()

void AbstractMafIterator::fireIterationMoveSignal_ ( const MafBlock &  currentBlock )

protectedvirtualinherited

Definition at line 57 of file MafIterator.cpp.

Referenced by bpp::AbstractMafIterator::nextBlock().

fireIterationStartSignal_()

void AbstractMafIterator::fireIterationStartSignal_ ( )

protectedvirtualinherited

Definition at line 51 of file MafIterator.cpp.

Referenced by bpp::AbstractMafIterator::nextBlock().

fireIterationStopSignal_()

void AbstractMafIterator::fireIterationStopSignal_ ( )

protectedvirtualinherited

Definition at line 63 of file MafIterator.cpp.

Referenced by bpp::AbstractMafIterator::nextBlock().

isVerbose()

bool bpp::AbstractMafIterator::isVerbose ( ) const

inlinevirtualinherited

Implements bpp::MafIterator.

Definition at line 116 of file MafIterator.h.

References bpp::AbstractMafIterator::verbose_.

nextBlock()

MafBlock* bpp::AbstractMafIterator::nextBlock ( )

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.

References bpp::AbstractMafIterator::analyseCurrentBlock_(), bpp::AbstractMafIterator::fireIterationMoveSignal_(), bpp::AbstractMafIterator::fireIterationStartSignal_(), bpp::AbstractMafIterator::fireIterationStopSignal_(), and bpp::AbstractMafIterator::started_.

operator=()

MafIteratorSynchronizer& bpp::MafIteratorSynchronizer::operator= ( const MafIteratorSynchronizer &  iterator )

inlineprivate

Definition at line 233 of file MafIterator.h.

References secondaryIterator_.

setLogStream()

void bpp::AbstractFilterMafIterator::setLogStream ( std::shared_ptr< OutputStream >  logstream )

inlineinherited

Definition at line 178 of file MafIterator.h.

References bpp::AbstractFilterMafIterator::logstream_.

setVerbose()

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

inlinevirtualinherited

Implements bpp::MafIterator.

Definition at line 117 of file MafIterator.h.

References bpp::AbstractMafIterator::verbose_.

Member Data Documentation

currentBlock_

MafBlock* bpp::AbstractFilterMafIterator::currentBlock_

protectedinherited

Definition at line 154 of file MafIterator.h.

Referenced by bpp::BlockLengthMafIterator::analyseCurrentBlock_(), bpp::BlockSizeMafIterator::analyseCurrentBlock_(), analyseCurrentBlock_(), bpp::MsmcOutputMafIterator::analyseCurrentBlock_(), bpp::OrderFilterMafIterator::analyseCurrentBlock_(), bpp::OutputMafIterator::analyseCurrentBlock_(), bpp::PlinkOutputMafIterator::analyseCurrentBlock_(), bpp::SequenceStatisticsMafIterator::analyseCurrentBlock_(), bpp::TableOutputMafIterator::analyseCurrentBlock_(), bpp::VcfOutputMafIterator::analyseCurrentBlock_(), and bpp::AbstractFilterMafIterator::operator=().

iterationListeners_

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

protectedinherited

Definition at line 89 of file MafIterator.h.

Referenced by bpp::AbstractMafIterator::addIterationListener().

iterator_

MafIterator* bpp::AbstractFilterMafIterator::iterator_

protectedinherited

Definition at line 153 of file MafIterator.h.

Referenced by bpp::BlockLengthMafIterator::analyseCurrentBlock_(), bpp::BlockSizeMafIterator::analyseCurrentBlock_(), analyseCurrentBlock_(), bpp::MsmcOutputMafIterator::analyseCurrentBlock_(), bpp::OrderFilterMafIterator::analyseCurrentBlock_(), bpp::OutputMafIterator::analyseCurrentBlock_(), bpp::PlinkOutputMafIterator::analyseCurrentBlock_(), bpp::SequenceStatisticsMafIterator::analyseCurrentBlock_(), bpp::TableOutputMafIterator::analyseCurrentBlock_(), bpp::VcfOutputMafIterator::analyseCurrentBlock_(), and bpp::AbstractFilterMafIterator::operator=().

logstream_

std::shared_ptr<OutputStream> bpp::AbstractFilterMafIterator::logstream_

protectedinherited

Definition at line 155 of file MafIterator.h.

Referenced by bpp::BlockLengthMafIterator::analyseCurrentBlock_(), bpp::BlockSizeMafIterator::analyseCurrentBlock_(), bpp::AbstractFilterMafIterator::operator=(), and bpp::AbstractFilterMafIterator::setLogStream().

secondaryIterator_

MafIterator* bpp::MafIteratorSynchronizer::secondaryIterator_

private

Definition at line 220 of file MafIterator.h.

Referenced by analyseCurrentBlock_(), and operator=().

started_

bool bpp::AbstractMafIterator::started_

protectedinherited

Definition at line 90 of file MafIterator.h.

Referenced by bpp::AbstractMafIterator::nextBlock().

verbose_

bool bpp::AbstractMafIterator::verbose_

protectedinherited

Definition at line 91 of file MafIterator.h.

Referenced by bpp::AbstractMafIterator::isVerbose(), and bpp::AbstractMafIterator::setVerbose().

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

• Bpp/Seq/Io/Maf/MafIterator.h