This iterator check that blocks are ordered according to a reference sequence. More...

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

Inheritance diagram for bpp::OrderFilterMafIterator:

Collaboration diagram for bpp::OrderFilterMafIterator:

Public Member Functions
	OrderFilterMafIterator (MafIterator *iterator, const std::string &reference, bool unsortedBlockDiscarded=true, bool unsortedBlockThrowsException=false, bool overlappingBlockDiscarded=true, bool overlappingBlockThrowsException=false)
	Build a new OrderFilterMafIterator object. More...

MafBlock *	analyseCurrentBlock_ ()

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
	OrderFilterMafIterator (const OrderFilterMafIterator &iterator)

OrderFilterMafIterator &	operator= (const OrderFilterMafIterator &iterator)

bool	parseBlock_ (const MafBlock &block)

Private Attributes
std::string	refSpecies_

std::string	currentChr_

size_t	previousBlockStart_

size_t	previousBlockStop_

bool	unsortedBlockDiscarded_

bool	unsortedBlockThrowsException_

bool	overlappingBlockDiscarded_

bool	overlappingBlockThrowsException_

Detailed Description

This iterator check that blocks are ordered according to a reference sequence.

The occurrence of overlapping or unordered blocks result in an error message. Alternatively, conflicting blocks can be discarded.

Definition at line 58 of file OrderFilterMafIterator.h.

Constructor & Destructor Documentation

◆ OrderFilterMafIterator() [1/2]

bpp::OrderFilterMafIterator::OrderFilterMafIterator	(	MafIterator *	iterator,
		const std::string &	reference,
		bool	unsortedBlockDiscarded = `true`,
		bool	unsortedBlockThrowsException = `false`,
		bool	overlappingBlockDiscarded = `true`,
		bool	overlappingBlockThrowsException = `false`
	)

inline

Build a new OrderFilterMafIterator object.

Parameters

iterator	The input iterator.
reference	The species to use as a reference for coordinates.
unsortedBlockDiscarded	Tell is unsorted blocks should be discarded
unsortedBlockThrowsException	Tell is unsorted blocks should throw an exception
overlappingBlockDiscarded	Tell is overlapping blocks should be discarded
overlappingBlockThrowsException	Tell is overlapping blocks should throw an exception

Definition at line 82 of file OrderFilterMafIterator.h.

◆ OrderFilterMafIterator() [2/2]

bpp::OrderFilterMafIterator::OrderFilterMafIterator ( const OrderFilterMafIterator & iterator )

inlineprivate

Definition at line 100 of file OrderFilterMafIterator.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* bpp::OrderFilterMafIterator::analyseCurrentBlock_ ( )

inlinevirtual

Implements bpp::AbstractMafIterator.

Definition at line 127 of file OrderFilterMafIterator.h.

References bpp::AbstractFilterMafIterator::currentBlock_, bpp::AbstractFilterMafIterator::iterator_, bpp::MafIterator::nextBlock(), and parseBlock_().

◆ 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().

◆ 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=()

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

inlineprivate

Definition at line 112 of file OrderFilterMafIterator.h.

References currentChr_, overlappingBlockDiscarded_, overlappingBlockThrowsException_, previousBlockStart_, previousBlockStop_, refSpecies_, unsortedBlockDiscarded_, and unsortedBlockThrowsException_.

◆ parseBlock_()

bool OrderFilterMafIterator::parseBlock_ ( const MafBlock & block )

private

Definition at line 57 of file OrderFilterMafIterator.cpp.

References bpp::MafSequence::getChromosome(), bpp::MafSequence::getDescription(), bpp::MafBlock::getSequenceForSpecies(), bpp::MafBlock::hasSequenceForSpecies(), bpp::MafSequence::start(), bpp::MafSequence::stop(), and bpp::TextTools::toString().

Referenced by analyseCurrentBlock_().

◆ 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

◆ currentBlock_

MafBlock* bpp::AbstractFilterMafIterator::currentBlock_

protectedinherited

Definition at line 154 of file MafIterator.h.

◆ currentChr_

std::string bpp::OrderFilterMafIterator::currentChr_

private

Definition at line 63 of file OrderFilterMafIterator.h.

Referenced by 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().

◆ overlappingBlockDiscarded_

bool bpp::OrderFilterMafIterator::overlappingBlockDiscarded_

private

Definition at line 68 of file OrderFilterMafIterator.h.

Referenced by operator=().

◆ overlappingBlockThrowsException_

bool bpp::OrderFilterMafIterator::overlappingBlockThrowsException_

private

Definition at line 69 of file OrderFilterMafIterator.h.

Referenced by operator=().

◆ previousBlockStart_

size_t bpp::OrderFilterMafIterator::previousBlockStart_

private

Definition at line 64 of file OrderFilterMafIterator.h.

Referenced by operator=().

◆ previousBlockStop_

size_t bpp::OrderFilterMafIterator::previousBlockStop_

private

Definition at line 65 of file OrderFilterMafIterator.h.

Referenced by operator=().

◆ refSpecies_

std::string bpp::OrderFilterMafIterator::refSpecies_

private

Definition at line 62 of file OrderFilterMafIterator.h.

Referenced by operator=().

◆ started_

bool bpp::AbstractMafIterator::started_

protectedinherited

Definition at line 90 of file MafIterator.h.

Referenced by bpp::AbstractMafIterator::nextBlock().

◆ unsortedBlockDiscarded_

bool bpp::OrderFilterMafIterator::unsortedBlockDiscarded_

private

Definition at line 66 of file OrderFilterMafIterator.h.

Referenced by operator=().

◆ unsortedBlockThrowsException_

bool bpp::OrderFilterMafIterator::unsortedBlockThrowsException_

private

Definition at line 67 of file OrderFilterMafIterator.h.

Referenced by operator=().

◆ 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/OrderFilterMafIterator.h
Bpp/Seq/Io/Maf/OrderFilterMafIterator.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ OrderFilterMafIterator() [1/2]

◆ OrderFilterMafIterator() [2/2]

Member Function Documentation

◆ addIterationListener()

◆ analyseCurrentBlock_()

◆ fireIterationMoveSignal_()

◆ fireIterationStartSignal_()

◆ fireIterationStopSignal_()

◆ isVerbose()

◆ nextBlock()

◆ operator=()

◆ parseBlock_()

◆ setLogStream()

◆ setVerbose()

Member Data Documentation

◆ currentBlock_

◆ currentChr_

◆ iterationListeners_

◆ iterator_

◆ logstream_

◆ overlappingBlockDiscarded_

◆ overlappingBlockThrowsException_

◆ previousBlockStart_

◆ previousBlockStop_

◆ refSpecies_

◆ started_

◆ unsortedBlockDiscarded_

◆ unsortedBlockThrowsException_

◆ verbose_