Filter maf blocks to remove ambiguously aligned or non-informative regions. More...

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

Inheritance diagram for bpp::AlignmentFilterMafIterator:

Collaboration diagram for bpp::AlignmentFilterMafIterator:

Public Member Functions
	AlignmentFilterMafIterator (MafIterator *iterator, const std::vector< std::string > &species, unsigned int windowSize, unsigned int step, unsigned int maxGap, double maxEnt, bool keepTrashedBlocks, bool missingAsGap)
	Create a new AlignmentFilterMafIterator with absolute thresholds. More...

	AlignmentFilterMafIterator (MafIterator *iterator, const std::vector< std::string > &species, unsigned int windowSize, unsigned int step, double maxPropGap, double maxEnt, bool keepTrashedBlocks, bool missingAsGap)
	Create a new AlignmentFilterMafIterator with relative thresholds. More...

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

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
MafBlock *	analyseCurrentBlock_ ()

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

unsigned int	windowSize_

unsigned int	step_

unsigned int	maxGap_

double	maxPropGap_

double	maxEnt_

std::deque< MafBlock * >	blockBuffer_

std::deque< MafBlock * >	trashBuffer_

std::deque< std::vector< int > >	window_

bool	keepTrashedBlocks_

bool	missingAsGap_

bool	relative_

Detailed Description

Filter maf blocks to remove ambiguously aligned or non-informative regions.

Regions with a too high proportion of gaps, unknown character or high entropy in a set of species will be removed, and blocks adjusted accordingly.

The total entropy of a window is defined as $\frac{\sum_i {E(5)}_i}{w}$ where is the shannon entropy of site i, computed using a logarithm of base 5, and w is the window size. As a result, the total entropy is normalized so that it falls between 0 and 1. A logarithm of base 5 is used to account for the fact that gaps are considered as a state.

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 63 of file AlignmentFilterMafIterator.h.

Constructor & Destructor Documentation

◆ AlignmentFilterMafIterator() [1/2]

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

inline

Create a new AlignmentFilterMafIterator with absolute thresholds.

Parameters

iterator	Input iterator
species	Selection of species on which filtering criteria are applied. Results of filtering will be applied to all species.
windowSize	Size of the sliding window (nt).
step	Step by which windows are moved (nt).
maxGap	Maximum number of gaps allowed in the window.
maxEnt	Maximum entropy allowed in the window.
keepTrashedBlocks	Removed windows are kept as separate blocks.
missingAsGap	Add missing species as gap sequences where needed.

Definition at line 96 of file AlignmentFilterMafIterator.h.

◆ AlignmentFilterMafIterator() [2/2]

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

inline

Create a new AlignmentFilterMafIterator with relative thresholds.

Parameters

iterator	Input iterator
species	Selection of species on which filtering criteria are applied. Results of filtering will be applied to all species.
windowSize	Size of the sliding window (nt).
step	Step by which windows are moved (nt).
maxPropGap	Maximum proportion of gaps allowed in the window.
maxEnt	Maximum entropy allowed in the window.
keepTrashedBlocks	Removed windows are kept as separate blocks.
missingAsGap	Add missing species as gap sequences where needed.