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, bool outputCoordinates=true, bool addLDHatHeader=false, const std::string &reference="")
	Creates a new OutputAlignmentMafIterator object. More...

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

	~OutputAlignmentMafIterator ()

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
	OutputAlignmentMafIterator (const OutputAlignmentMafIterator &iterator)

OutputAlignmentMafIterator &	operator= (const OutputAlignmentMafIterator &iterator)

MafBlock *	analyseCurrentBlock_ ()

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

Private Attributes
std::ostream *	output_

std::string	file_

bool	mask_

bool	outputCoordinates_

bool	addLDHatHeader_

std::unique_ptr< OAlignment >	writer_

unsigned int	currentBlockIndex_

std::string	refSpecies_

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`,
		bool	outputCoordinates = `true`,
		bool	addLDHatHeader = `false`,
		const std::string &	reference = `""`
	)

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).
outputCoordinates	Tell if coordinates should be written in sequence headers, if any.
addLDHatHeader	Tell if first line of file should contain number and lenght of sequences (for instance for use with LDhat/convert).
reference	[optional] specify a reference species which can be used to configure file names (for instance using coordinates information).

Definition at line 88 of file OutputAlignmentMafIterator.h.

◆ OutputAlignmentMafIterator() [2/3]

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

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).
outputCoordinates	Tell if coordinates should be written in sequence headers, if any.
addLDHatHeader	Tell if first line of file should contain number and lenght of sequences (for instance for use with LDhat/convert).
reference	[optional] specify a reference species which can be used to configure file names (for instance using coordinates information).