bpp::AlignmentFilter2MafIterator Class Reference

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

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

Inheritance diagram for bpp::AlignmentFilter2MafIterator:

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Collaboration diagram for bpp::AlignmentFilter2MafIterator:

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List of all members.

Public Member Functions
	AlignmentFilter2MafIterator (MafIterator *iterator, const std::vector< std::string > &species, unsigned int windowSize, unsigned int step, unsigned int maxGap, unsigned int maxPos, bool keepTrashedBlocks)
MafBlock *	nextBlock () throw (Exception)
	Get the next available alignment block.
MafBlock *	nextRemovedBlock () throw (Exception)
	Get the next available removed alignment block.
void	setLogStream (OutputStream *logstream)
bool	verbose () const
void	verbose (bool yn)
Protected Attributes
MafIterator *	iterator_
OutputStream *	logstream_
bool	verbose_
Private Attributes
std::vector< std::string >	species_
unsigned int	windowSize_
unsigned int	step_
unsigned int	maxGap_
unsigned int	maxPos_
std::deque< MafBlock * >	blockBuffer_
std::deque< MafBlock * >	trashBuffer_
std::deque< std::vector< bool > >	window_
bool	keepTrashedBlocks_

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Detailed Description

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

This iterators offers a different algorithm than AlignmentFilterMafIterator. It takes two parameters: g=maxGap and n=maxPos. windows with at more than n positions containing each of them more than g=maxPos gaps will be discarded. In addition, consecutives patterns are only counted once.

Definition at line 668 of file MafIterator.h.

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Constructor & Destructor Documentation

bpp::AlignmentFilter2MafIterator::AlignmentFilter2MafIterator	(	MafIterator *	iterator,
		const std::vector< std::string > &	species,
		unsigned int	windowSize,
		unsigned int	step,
		unsigned int	maxGap,
		unsigned int	maxPos,
		bool	keepTrashedBlocks
	)			[inline]

Definition at line 684 of file MafIterator.h.

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Member Function Documentation

MafBlock * AlignmentFilter2MafIterator::nextBlock

(

)

throw (Exception) [virtual]

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 554 of file MafIterator.cpp.

References bpp::MafBlock::addSequence(), blockBuffer_, bpp::ApplicationTools::displayGauge(), bpp::ApplicationTools::displayTask(), bpp::ApplicationTools::displayTaskDone(), bpp::AlphabetTools::DNA_ALPHABET, bpp::OutputStream::endLine(), bpp::EdSymbolList::getContent(), bpp::MafBlock::getDescription(), bpp::AbstractAlphabet::getGapCharacterCode(), bpp::MafBlock::getNumberOfSequences(), bpp::MafBlock::getNumberOfSites(), bpp::MafBlock::getPass(), bpp::MafBlock::getScore(), bpp::MafBlock::getSequence(), bpp::MafBlock::getSequenceForSpecies(), bpp::NucleicAlphabet::getUnknownCharacterCode(), bpp::AbstractFilterMafIterator::iterator_, keepTrashedBlocks_, bpp::AbstractFilterMafIterator::logstream_, maxGap_, maxPos_, bpp::ApplicationTools::message, bpp::MafIterator::nextBlock(), bpp::MafBlock::setPass(), bpp::MafBlock::setScore(), species_, step_, bpp::MafSequence::subSequence(), trashBuffer_, bpp::AbstractFilterMafIterator::verbose_, window_, and windowSize_.

MafBlock* bpp::AlignmentFilter2MafIterator::nextRemovedBlock

(

)

throw (Exception) [inline, virtual]

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 700 of file MafIterator.h.

void bpp::AbstractFilterMafIterator::setLogStream

(

OutputStream *

logstream

)

[inline, inherited]

Definition at line 341 of file MafIterator.h.

void bpp::AbstractFilterMafIterator::verbose

(

bool

yn

)

[inline, inherited]

Definition at line 343 of file MafIterator.h.

bool bpp::AbstractFilterMafIterator::verbose

(

)

const [inline, inherited]

Definition at line 342 of file MafIterator.h.

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Member Data Documentation

std::deque<MafBlock*> bpp::AlignmentFilter2MafIterator::blockBuffer_ [private]

Definition at line 678 of file MafIterator.h.

Referenced by nextBlock().

MafIterator* bpp::AbstractFilterMafIterator::iterator_ [protected, inherited]

Definition at line 323 of file MafIterator.h.

Referenced by bpp::FeatureExtractor::nextBlock(), bpp::FeatureFilterMafIterator::nextBlock(), bpp::PairwiseSequenceStatisticsMafIterator::nextBlock(), bpp::SequenceStatisticsMafIterator::nextBlock(), bpp::QualityFilterMafIterator::nextBlock(), bpp::MaskFilterMafIterator::nextBlock(), nextBlock(), bpp::AlignmentFilterMafIterator::nextBlock(), bpp::FullGapFilterMafIterator::nextBlock(), bpp::BlockMergerMafIterator::nextBlock(), bpp::DuplicateFilterMafIterator::nextBlock(), bpp::ChromosomeMafIterator::nextBlock(), bpp::SequenceFilterMafIterator::nextBlock(), and bpp::AbstractFilterMafIterator::operator=().

bool bpp::AlignmentFilter2MafIterator::keepTrashedBlocks_ [private]

Definition at line 681 of file MafIterator.h.

Referenced by nextBlock().

OutputStream* bpp::AbstractFilterMafIterator::logstream_ [protected, inherited]

Definition at line 324 of file MafIterator.h.

Referenced by bpp::FeatureExtractor::nextBlock(), bpp::FeatureFilterMafIterator::nextBlock(), bpp::QualityFilterMafIterator::nextBlock(), bpp::MaskFilterMafIterator::nextBlock(), nextBlock(), bpp::AlignmentFilterMafIterator::nextBlock(), bpp::FullGapFilterMafIterator::nextBlock(), bpp::BlockMergerMafIterator::nextBlock(), bpp::DuplicateFilterMafIterator::nextBlock(), bpp::ChromosomeMafIterator::nextBlock(), bpp::SequenceFilterMafIterator::nextBlock(), and bpp::AbstractFilterMafIterator::operator=().

unsigned int bpp::AlignmentFilter2MafIterator::maxGap_ [private]

Definition at line 676 of file MafIterator.h.

Referenced by nextBlock().

unsigned int bpp::AlignmentFilter2MafIterator::maxPos_ [private]

Definition at line 677 of file MafIterator.h.

Referenced by nextBlock().

std::vector<std::string> bpp::AlignmentFilter2MafIterator::species_ [private]

Definition at line 673 of file MafIterator.h.

Referenced by nextBlock().

unsigned int bpp::AlignmentFilter2MafIterator::step_ [private]

Definition at line 675 of file MafIterator.h.

Referenced by nextBlock().

std::deque<MafBlock*> bpp::AlignmentFilter2MafIterator::trashBuffer_ [private]

Definition at line 679 of file MafIterator.h.

Referenced by nextBlock().

bool bpp::AbstractFilterMafIterator::verbose_ [protected, inherited]

Definition at line 325 of file MafIterator.h.

Referenced by bpp::FeatureExtractor::nextBlock(), bpp::FeatureFilterMafIterator::nextBlock(), bpp::QualityFilterMafIterator::nextBlock(), bpp::MaskFilterMafIterator::nextBlock(), nextBlock(), bpp::AlignmentFilterMafIterator::nextBlock(), bpp::FullGapFilterMafIterator::nextBlock(), and bpp::AbstractFilterMafIterator::operator=().

std::deque< std::vector<bool> > bpp::AlignmentFilter2MafIterator::window_ [private]

Definition at line 680 of file MafIterator.h.

Referenced by nextBlock().

unsigned int bpp::AlignmentFilter2MafIterator::windowSize_ [private]

Definition at line 674 of file MafIterator.h.

Referenced by nextBlock().

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

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