bpp::AbstractFilterMafIterator Class Reference

Helper class for developping filter for maf blocks. More...

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

Inheritance diagram for bpp::AbstractFilterMafIterator:

Collaboration diagram for bpp::AbstractFilterMafIterator:

Public Member Functions
	AbstractFilterMafIterator (MafIterator *iterator)
void	setLogStream (OutputStream *logstream)
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
MafIterator *	iterator_
MafBlock *	currentBlock_
OutputStream *	logstream_
std::vector< IterationListener * >	iterationListeners_
bool	started_
bool	verbose_

Private Member Functions
	AbstractFilterMafIterator (const AbstractFilterMafIterator &it)
AbstractFilterMafIterator &	operator= (const AbstractFilterMafIterator &it)

Detailed Description

Helper class for developping filter for maf blocks.

Definition at line 149 of file MafIterator.h.

Constructor & Destructor Documentation

AbstractFilterMafIterator() [1/2]

bpp::AbstractFilterMafIterator::AbstractFilterMafIterator ( MafIterator *  iterator )

inline

Definition at line 158 of file MafIterator.h.

AbstractFilterMafIterator() [2/2]

bpp::AbstractFilterMafIterator::AbstractFilterMafIterator ( const AbstractFilterMafIterator &  it )

inlineprivate

Definition at line 164 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.

analyseCurrentBlock_()

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

protectedpure virtualinherited

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 )

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=()

AbstractFilterMafIterator& bpp::AbstractFilterMafIterator::operator= ( const AbstractFilterMafIterator &  it )

inlineprivate

Definition at line 169 of file MafIterator.h.

References iterator_, and logstream_.

setLogStream()

void bpp::AbstractFilterMafIterator::setLogStream ( OutputStream *  logstream )

inline

Definition at line 178 of file MafIterator.h.

setVerbose()

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

inlinevirtualinherited

Implements bpp::MafIterator.

Definition at line 117 of file MafIterator.h.

Member Data Documentation

currentBlock_

MafBlock* bpp::AbstractFilterMafIterator::currentBlock_

protected

Definition at line 154 of file MafIterator.h.

Referenced by bpp::BlockLengthMafIterator::analyseCurrentBlock_(), bpp::BlockSizeMafIterator::analyseCurrentBlock_(), bpp::OutputMafIterator::analyseCurrentBlock_(), bpp::VcfOutputMafIterator::analyseCurrentBlock_(), and bpp::SequenceStatisticsMafIterator::analyseCurrentBlock_().

iterationListeners_

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

protectedinherited

Definition at line 89 of file MafIterator.h.

iterator_

MafIterator* bpp::AbstractFilterMafIterator::iterator_

protected

Definition at line 153 of file MafIterator.h.

Referenced by bpp::BlockLengthMafIterator::analyseCurrentBlock_(), bpp::BlockSizeMafIterator::analyseCurrentBlock_(), bpp::OutputMafIterator::analyseCurrentBlock_(), bpp::VcfOutputMafIterator::analyseCurrentBlock_(), bpp::SequenceStatisticsMafIterator::analyseCurrentBlock_(), and operator=().

logstream_

OutputStream* bpp::AbstractFilterMafIterator::logstream_

protected

Definition at line 155 of file MafIterator.h.

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

started_

bool bpp::AbstractMafIterator::started_

protectedinherited

Definition at line 90 of file MafIterator.h.

verbose_

bool bpp::AbstractMafIterator::verbose_

protectedinherited

Definition at line 91 of file MafIterator.h.

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

• Bpp/Seq/Io/Maf/MafIterator.h