This iterator forward the iterator given as input after having printed its content to an alignment file. The syntax for ENSEMBL meta data is used. More...

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

Inheritance diagram for bpp::OutputAlignmentMafIterator:

Collaboration diagram for bpp::OutputAlignmentMafIterator:

Public Member Functions
	OutputAlignmentMafIterator (MafIterator iterator, std::ostream out, OAlignment *writer, bool mask=true)
	Creates a new OutputAlignmentMafIterator object. More...

	OutputAlignmentMafIterator (MafIterator iterator, const std::string &file, OAlignment writer, bool mask=true)
	Creates a new OutputAlignmentMafIterator object. More...

	~OutputAlignmentMafIterator ()

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
	OutputAlignmentMafIterator (const OutputAlignmentMafIterator &iterator)

OutputAlignmentMafIterator &	operator= (const OutputAlignmentMafIterator &iterator)

MafBlock *	analyseCurrentBlock_ () throw (Exception)

void	writeBlock (std::ostream &out, const MafBlock &block) const

Private Attributes
std::ostream *	output_

std::string	file_

bool	mask_

std::auto_ptr< OAlignment >	writer_

unsigned int	currentBlockIndex_

Detailed Description

This iterator forward the iterator given as input after having printed its content to an alignment file. The syntax for ENSEMBL meta data is used.

Definition at line 59 of file OutputAlignmentMafIterator.h.

Constructor & Destructor Documentation

◆ OutputAlignmentMafIterator() [1/3]

bpp::OutputAlignmentMafIterator::OutputAlignmentMafIterator	(	MafIterator *	iterator,
		std::ostream *	out,
		OAlignment *	writer,
		bool	mask = `true`
	)

inline

Creates a new OutputAlignmentMafIterator object.

All block will be printed as separate alignment, yet one after the other on the stream. Be aware that not all format will recognize the resulting file as a multiple alignment file (Mase and Clustal will for instance, not Fasta).

Parameters

iterator	The input iterator
out	A pointer toward the output stream. The stream will not be own by this instance, and will not be copied neither destroyed.
writer	A pointer toward an alignment writer object which specifies the format to use when writing sequences. The underlying object will be own by this instance, and destroyed when this object is deleted.
mask	Tell if sequences should be printed masked (if applicable).

Definition at line 81 of file OutputAlignmentMafIterator.h.

◆ OutputAlignmentMafIterator() [2/3]

bpp::OutputAlignmentMafIterator::OutputAlignmentMafIterator	(	MafIterator *	iterator,
		const std::string &	file,
		OAlignment *	writer,
		bool	mask = `true`
	)

inline

Creates a new OutputAlignmentMafIterator object.

All block will be printed as separate alignment, yet one after the other on the stream. Be aware that not all format will recognize the resulting file as a multiple alignment file (Mase and Clustal will for instance, not Fasta).

Parameters

iterator	The input iterator
file	A string describing the path to the output files. Each block will be written to a distinct file. If "file" is a fixed string, it will only contain the last block. Using the i code in the file name allows to generate one file per block, i denoting the block index.
writer	A pointer toward an alignment writer object which specifies the format to use when writing sequences. The underlying object will be own by this instance, and destroyed when this object is deleted.
mask	Tell if sequences should be printed masked (if applicable).

Definition at line 100 of file OutputAlignmentMafIterator.h.

◆ ~OutputAlignmentMafIterator()

bpp::OutputAlignmentMafIterator::~OutputAlignmentMafIterator ( )

inline

Definition at line 107 of file OutputAlignmentMafIterator.h.

◆ OutputAlignmentMafIterator() [3/3]

bpp::OutputAlignmentMafIterator::OutputAlignmentMafIterator ( const OutputAlignmentMafIterator & iterator )

inlineprivate

Definition at line 110 of file OutputAlignmentMafIterator.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 * OutputAlignmentMafIterator::analyseCurrentBlock_	(		)
throw	(	Exception
	)

privatevirtual

Implements bpp::AbstractMafIterator.

Definition at line 53 of file OutputAlignmentMafIterator.cpp.

◆ 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.

◆ operator=()

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

inlineprivate

Definition at line 119 of file OutputAlignmentMafIterator.h.

References currentBlockIndex_, file_, mask_, output_, and writer_.

◆ 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.

◆ writeBlock()

void OutputAlignmentMafIterator::writeBlock	(	std::ostream &	out,
		const MafBlock &	block
	)		const

private

Definition at line 69 of file OutputAlignmentMafIterator.cpp.

References bpp::MafBlock::getAlignment(), bpp::MafSequence::getChromosome(), bpp::MafBlock::getSequence(), bpp::MafSequence::getSpecies(), bpp::MafSequence::getStrand(), bpp::MafSequence::hasCoordinates(), bpp::MafSequence::start(), and bpp::MafSequence::stop().

Member Data Documentation

◆ 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_().

◆ currentBlockIndex_

unsigned int bpp::OutputAlignmentMafIterator::currentBlockIndex_

private

Definition at line 67 of file OutputAlignmentMafIterator.h.

Referenced by operator=().

◆ file_

std::string bpp::OutputAlignmentMafIterator::file_

private

Definition at line 64 of file OutputAlignmentMafIterator.h.

Referenced by operator=().

◆ 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=().

◆ 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=().

◆ mask_

bool bpp::OutputAlignmentMafIterator::mask_

private

Definition at line 65 of file OutputAlignmentMafIterator.h.

Referenced by operator=().

◆ output_

std::ostream* bpp::OutputAlignmentMafIterator::output_

private

Definition at line 63 of file OutputAlignmentMafIterator.h.

Referenced by operator=().

◆ started_

bool bpp::AbstractMafIterator::started_

protectedinherited

Definition at line 90 of file MafIterator.h.

◆ verbose_

bool bpp::AbstractMafIterator::verbose_

protectedinherited

Definition at line 91 of file MafIterator.h.

◆ writer_

std::auto_ptr<OAlignment> bpp::OutputAlignmentMafIterator::writer_

private

Definition at line 66 of file OutputAlignmentMafIterator.h.

Referenced by operator=().

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

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

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ OutputAlignmentMafIterator() [1/3]

◆ OutputAlignmentMafIterator() [2/3]

◆ ~OutputAlignmentMafIterator()

◆ OutputAlignmentMafIterator() [3/3]

Member Function Documentation

◆ addIterationListener()

◆ analyseCurrentBlock_()

◆ fireIterationMoveSignal_()

◆ fireIterationStartSignal_()

◆ fireIterationStopSignal_()

◆ isVerbose()

◆ nextBlock()

◆ operator=()

◆ setLogStream()

◆ setVerbose()

◆ writeBlock()

Member Data Documentation

◆ currentBlock_

◆ currentBlockIndex_

◆ file_

◆ iterationListeners_

◆ iterator_

◆ logstream_

◆ mask_

◆ output_

◆ started_

◆ verbose_

◆ writer_