Filter maf blocks highly divergent regions. More...

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

Inheritance diagram for bpp::EntropyFilterMafIterator:

Collaboration diagram for bpp::EntropyFilterMafIterator:

Public Member Functions
	EntropyFilterMafIterator (MafIterator *iterator, const std::vector< std::string > &species, unsigned int windowSize, unsigned int step, double maxEnt, unsigned int maxPos, bool keepTrashedBlocks, bool missingAsGap, bool ignoreGaps)

MafBlock *	nextRemovedBlock () throw (Exception)
	Get the next available removed alignment block. More...

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 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
MafBlock *	analyseCurrentBlock_ () throw (Exception)

Private Attributes
std::vector< std::string >	species_

unsigned int	windowSize_

unsigned int	step_

double	maxEnt_

unsigned int	maxPos_

std::deque< MafBlock * >	blockBuffer_

std::deque< MafBlock * >	trashBuffer_

std::deque< unsigned int >	window_

bool	keepTrashedBlocks_

bool	missingAsGap_

bool	ignoreGaps_

Detailed Description

Filter maf blocks highly divergent regions.

This iterators takes two parameters: g=maxEnt and n=maxPos. Windows with more than n positions with a entropy higher than maxEnt will be discarded. In addition, consecutives patterns are only counted once. In case a sequence from the list is missing, it can be either ignored or counted as a full sequence of gaps.

Definition at line 59 of file EntropyFilterMafIterator.h.

Constructor & Destructor Documentation

◆ EntropyFilterMafIterator()

bpp::EntropyFilterMafIterator::EntropyFilterMafIterator	(	MafIterator *	iterator,
		const std::vector< std::string > &	species,
		unsigned int	windowSize,
		unsigned int	step,
		double	maxEnt,
		unsigned int	maxPos,
		bool	keepTrashedBlocks,
		bool	missingAsGap,
		bool	ignoreGaps
	)

inline

Definition at line 77 of file EntropyFilterMafIterator.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 * EntropyFilterMafIterator::analyseCurrentBlock_	(		)
throw	(	Exception
	)

privatevirtual

Implements bpp::AbstractMafIterator.

Definition at line 50 of file EntropyFilterMafIterator.cpp.

References bpp::MafBlock::addSequence(), bpp::MafBlock::getDescription(), bpp::MafBlock::getNumberOfSequences(), bpp::MafBlock::getNumberOfSites(), bpp::MafBlock::getPass(), bpp::MafBlock::getScore(), bpp::MafBlock::getSequence(), bpp::MafBlock::getSequenceForSpecies(), bpp::MafBlock::getSpeciesList(), bpp::MafBlock::hasSequenceForSpecies(), bpp::MafBlock::setPass(), bpp::MafBlock::setScore(), and bpp::MafSequence::subSequence().

◆ 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.

◆ nextRemovedBlock()

MafBlock* bpp::EntropyFilterMafIterator::nextRemovedBlock	(		)
throw	(	Exception
	)

inlinevirtual

Get the next available removed alignment block.

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

Implements bpp::MafTrashIterator.

Definition at line 93 of file EntropyFilterMafIterator.h.

References trashBuffer_.

◆ setLogStream()

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

inlineinherited

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

◆ blockBuffer_

std::deque<MafBlock*> bpp::EntropyFilterMafIterator::blockBuffer_

private

Definition at line 69 of file EntropyFilterMafIterator.h.

◆ currentBlock_

MafBlock* bpp::AbstractFilterMafIterator::currentBlock_

protectedinherited

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_().

◆ ignoreGaps_

bool bpp::EntropyFilterMafIterator::ignoreGaps_

private

Definition at line 74 of file EntropyFilterMafIterator.h.

◆ iterationListeners_

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

protectedinherited

Definition at line 89 of file MafIterator.h.

◆ iterator_

MafIterator* bpp::AbstractFilterMafIterator::iterator_

protectedinherited

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 bpp::AbstractFilterMafIterator::operator=().

◆ keepTrashedBlocks_

bool bpp::EntropyFilterMafIterator::keepTrashedBlocks_

private

Definition at line 72 of file EntropyFilterMafIterator.h.

◆ logstream_

OutputStream* bpp::AbstractFilterMafIterator::logstream_

protectedinherited

Definition at line 155 of file MafIterator.h.

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

◆ maxEnt_

double bpp::EntropyFilterMafIterator::maxEnt_

private

Definition at line 67 of file EntropyFilterMafIterator.h.

◆ maxPos_

unsigned int bpp::EntropyFilterMafIterator::maxPos_

private

Definition at line 68 of file EntropyFilterMafIterator.h.

◆ missingAsGap_

bool bpp::EntropyFilterMafIterator::missingAsGap_

private

Definition at line 73 of file EntropyFilterMafIterator.h.

◆ species_

std::vector<std::string> bpp::EntropyFilterMafIterator::species_

private

Definition at line 64 of file EntropyFilterMafIterator.h.

◆ started_

bool bpp::AbstractMafIterator::started_

protectedinherited

Definition at line 90 of file MafIterator.h.

◆ step_

unsigned int bpp::EntropyFilterMafIterator::step_

private

Definition at line 66 of file EntropyFilterMafIterator.h.

◆ trashBuffer_

std::deque<MafBlock*> bpp::EntropyFilterMafIterator::trashBuffer_

private

Definition at line 70 of file EntropyFilterMafIterator.h.

Referenced by nextRemovedBlock().

◆ verbose_

bool bpp::AbstractMafIterator::verbose_

protectedinherited

Definition at line 91 of file MafIterator.h.

◆ window_

std::deque<unsigned int> bpp::EntropyFilterMafIterator::window_

private

Definition at line 71 of file EntropyFilterMafIterator.h.

◆ windowSize_

unsigned int bpp::EntropyFilterMafIterator::windowSize_

private

Definition at line 65 of file EntropyFilterMafIterator.h.

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

Bpp/Seq/Io/Maf/EntropyFilterMafIterator.h
Bpp/Seq/Io/Maf/EntropyFilterMafIterator.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ EntropyFilterMafIterator()

Member Function Documentation

◆ addIterationListener()

◆ analyseCurrentBlock_()

◆ fireIterationMoveSignal_()

◆ fireIterationStartSignal_()

◆ fireIterationStopSignal_()

◆ isVerbose()

◆ nextBlock()

◆ nextRemovedBlock()

◆ setLogStream()

◆ setVerbose()

Member Data Documentation

◆ blockBuffer_

◆ currentBlock_

◆ ignoreGaps_

◆ iterationListeners_

◆ iterator_

◆ keepTrashedBlocks_

◆ logstream_

◆ maxEnt_

◆ maxPos_

◆ missingAsGap_

◆ species_

◆ started_

◆ step_

◆ trashBuffer_

◆ verbose_

◆ window_

◆ windowSize_