Merge blocks if some of their sequences are contiguous. More...

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

Inheritance diagram for bpp::BlockMergerMafIterator:

Collaboration diagram for bpp::BlockMergerMafIterator:

Public Member Functions
	BlockMergerMafIterator (MafIterator *iterator, const std::vector< std::string > &species, unsigned int maxDist=0, bool renameChimericChromosomes=false)

void	ignoreChromosome (const std::string &chr)

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
	BlockMergerMafIterator (const BlockMergerMafIterator &iterator)

BlockMergerMafIterator &	operator= (const BlockMergerMafIterator &iterator)

MafBlock *	analyseCurrentBlock_ ()

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

MafBlock *	incomingBlock_

std::vector< std::string >	ignoreChrs_

unsigned int	maxDist_

bool	renameChimericChromosomes_

std::map< std::string, unsigned int >	chimericChromosomeCounts_

Detailed Description

Merge blocks if some of their sequences are contiguous.

The user specifies the focus species. Sequences that are not in this set will be automatically merged and their coordinates removed. The scores, if any, will be averaged for the block, weighted by the corresponding block sizes. The pass value will be removed if it is different for the two blocks. It is possible to define a maximum distance for the merging. Setting a distance of zero implies that the blocks have to be exactly contiguous. Alternatively, the appropriate number of 'N' will be inserted in all species. All species however have to be distant of the exact same amount.

Definition at line 63 of file BlockMergerMafIterator.h.

Constructor & Destructor Documentation

◆ BlockMergerMafIterator() [1/2]

bpp::BlockMergerMafIterator::BlockMergerMafIterator	(	MafIterator *	iterator,
		const std::vector< std::string > &	species,
		unsigned int	maxDist = `0`,
		bool	renameChimericChromosomes = `false`
	)

inline

Definition at line 75 of file BlockMergerMafIterator.h.

References incomingBlock_, and bpp::MafIterator::nextBlock().

◆ BlockMergerMafIterator() [2/2]

bpp::BlockMergerMafIterator::BlockMergerMafIterator ( const BlockMergerMafIterator & iterator )

inlineprivate

Definition at line 88 of file BlockMergerMafIterator.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 * BlockMergerMafIterator::analyseCurrentBlock_ ( )

privatevirtual

Implements bpp::AbstractMafIterator.

Definition at line 50 of file BlockMergerMafIterator.cpp.

References bpp::MafBlock::addSequence(), bpp::VectorTools::contains(), bpp::AlphabetTools::DNA_ALPHABET, bpp::MafSequence::getChromosome(), bpp::MafSequence::getSrcSize(), bpp::MafSequence::getStrand(), bpp::MafSequence::hasCoordinates(), bpp::MafBlock::setPass(), bpp::MafBlock::setScore(), bpp::MafSequence::start(), bpp::MafSequence::stop(), bpp::TextTools::toString(), bpp::VectorTools::unique(), and bpp::VectorTools::vectorUnion().

◆ 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().

◆ ignoreChromosome()

void bpp::BlockMergerMafIterator::ignoreChromosome ( const std::string & chr )

inline

brief Add a chromosome that should be ignored to the list.

Parameters

chr	The name of the chromosome to be ignored.

Definition at line 114 of file BlockMergerMafIterator.h.

References ignoreChrs_.

◆ 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=()

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

inlineprivate

Definition at line 98 of file BlockMergerMafIterator.h.

References chimericChromosomeCounts_, ignoreChrs_, incomingBlock_, maxDist_, renameChimericChromosomes_, and species_.

◆ 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

◆ chimericChromosomeCounts_

std::map<std::string, unsigned int> bpp::BlockMergerMafIterator::chimericChromosomeCounts_

private

Definition at line 72 of file BlockMergerMafIterator.h.

Referenced by operator=().

◆ currentBlock_

MafBlock* bpp::AbstractFilterMafIterator::currentBlock_

protectedinherited

Definition at line 154 of file MafIterator.h.

◆ ignoreChrs_

std::vector<std::string> bpp::BlockMergerMafIterator::ignoreChrs_

private

Definition at line 69 of file BlockMergerMafIterator.h.

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

◆ incomingBlock_

MafBlock* bpp::BlockMergerMafIterator::incomingBlock_

private

Definition at line 68 of file BlockMergerMafIterator.h.

Referenced by BlockMergerMafIterator(), and 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.

◆ 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().

◆ maxDist_

unsigned int bpp::BlockMergerMafIterator::maxDist_

private

Definition at line 70 of file BlockMergerMafIterator.h.

Referenced by operator=().

◆ renameChimericChromosomes_

bool bpp::BlockMergerMafIterator::renameChimericChromosomes_

private

Definition at line 71 of file BlockMergerMafIterator.h.

Referenced by operator=().

◆ species_

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

private

Definition at line 67 of file BlockMergerMafIterator.h.

Referenced by 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().

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

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

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ BlockMergerMafIterator() [1/2]

◆ BlockMergerMafIterator() [2/2]

Member Function Documentation

◆ addIterationListener()

◆ analyseCurrentBlock_()

◆ fireIterationMoveSignal_()

◆ fireIterationStartSignal_()

◆ fireIterationStopSignal_()

◆ ignoreChromosome()

◆ isVerbose()

◆ nextBlock()

◆ operator=()

◆ setLogStream()

◆ setVerbose()

Member Data Documentation

◆ chimericChromosomeCounts_

◆ currentBlock_

◆ ignoreChrs_

◆ incomingBlock_

◆ iterationListeners_

◆ iterator_

◆ logstream_

◆ maxDist_

◆ renameChimericChromosomes_

◆ species_

◆ started_

◆ verbose_