bpp::CoordinatesOutputMafIterator Class Reference

Output each sequence coordinates for each block. More...

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

Inheritance diagram for bpp::CoordinatesOutputMafIterator:

Collaboration diagram for bpp::CoordinatesOutputMafIterator:

Public Member Functions
	CoordinatesOutputMafIterator (MafIterator *iterator, std::ostream *out, const std::vector< std::string > &species)
	Creates a new CoordinatesOutputMafIterator object. More...
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
	CoordinatesOutputMafIterator (const CoordinatesOutputMafIterator &iterator)
CoordinatesOutputMafIterator &	operator= (const CoordinatesOutputMafIterator &iterator)
void	writeHeader_ (std::ostream &out) const
MafBlock *	analyseCurrentBlock_ () throw (Exception)

Private Attributes
std::ostream *	output_
std::vector< std::string >	species_

Detailed Description

Output each sequence coordinates for each block.

The set of species for which coordinates are output is provided as argument. The current implementation outputs results as a table to a file. Later implementation may involve a dedicated data structure for other application usage (file indexing and so one).

Definition at line 58 of file CoordinatesOutputMafIterator.h.

Constructor & Destructor Documentation

CoordinatesOutputMafIterator() [1/2]

bpp::CoordinatesOutputMafIterator::CoordinatesOutputMafIterator ( MafIterator *  iterator, std::ostream *  out, const std::vector< std::string > &  species  )

inline

Creates a new CoordinatesOutputMafIterator object.

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.
species	A vector of species names for which coordinates should be output. In case of missing species for one block, NA will be produced.

Definition at line 73 of file CoordinatesOutputMafIterator.h.

References output_, and writeHeader_().

CoordinatesOutputMafIterator() [2/2]

bpp::CoordinatesOutputMafIterator::CoordinatesOutputMafIterator ( const CoordinatesOutputMafIterator &  iterator )

inlineprivate

Definition at line 81 of file CoordinatesOutputMafIterator.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 * CoordinatesOutputMafIterator::analyseCurrentBlock_ ( ) throw ( Exception )

privatevirtual

Implements bpp::AbstractMafIterator.

Definition at line 55 of file CoordinatesOutputMafIterator.cpp.

References bpp::MafBlock::getSequencesForSpecies().

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=()

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

inlineprivate

Definition at line 87 of file CoordinatesOutputMafIterator.h.

References output_, and species_.

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.

writeHeader_()

void CoordinatesOutputMafIterator::writeHeader_ ( std::ostream &  out ) const

private

Definition at line 45 of file CoordinatesOutputMafIterator.cpp.

Referenced by CoordinatesOutputMafIterator().

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_().

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=().

output_

std::ostream* bpp::CoordinatesOutputMafIterator::output_

private

Definition at line 62 of file CoordinatesOutputMafIterator.h.

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

species_

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

private

Definition at line 63 of file CoordinatesOutputMafIterator.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.

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

• Bpp/Seq/Io/Maf/CoordinatesOutputMafIterator.h
• Bpp/Seq/Io/Maf/CoordinatesOutputMafIterator.cpp