bpp::ConcatenateMafIterator Class Reference

Concatenate blocks up to a certain size. More...

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

Inheritance diagram for bpp::ConcatenateMafIterator:

Collaboration diagram for bpp::ConcatenateMafIterator:

Public Member Functions
	ConcatenateMafIterator (MafIterator *iterator, unsigned int minimumSize)
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
	ConcatenateMafIterator (const ConcatenateMafIterator &iterator)
ConcatenateMafIterator &	operator= (const ConcatenateMafIterator &iterator)
MafBlock *	analyseCurrentBlock_ () throw (Exception)

Private Attributes
MafBlock *	incomingBlock_
unsigned int	minimumSize_

Detailed Description

Concatenate blocks up to a certain size.

Blocks are appended regardless of their coordinates, to form concatenated blocks of at least a given number of positions. 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 blocks.

Definition at line 59 of file ConcatenateMafIterator.h.

Constructor & Destructor Documentation

ConcatenateMafIterator() [1/2]

bpp::ConcatenateMafIterator::ConcatenateMafIterator ( MafIterator *  iterator, unsigned int  minimumSize  )

inline

Definition at line 67 of file ConcatenateMafIterator.h.

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

ConcatenateMafIterator() [2/2]

bpp::ConcatenateMafIterator::ConcatenateMafIterator ( const ConcatenateMafIterator &  iterator )

inlineprivate

Definition at line 76 of file ConcatenateMafIterator.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 * ConcatenateMafIterator::analyseCurrentBlock_ ( ) throw ( Exception )

privatevirtual

Implements bpp::AbstractMafIterator.

Definition at line 50 of file ConcatenateMafIterator.cpp.

References bpp::MafBlock::addSequence(), bpp::MafSequence::getChromosome(), bpp::MafSequence::getDescription(), bpp::MafBlock::getSpeciesList(), bpp::MafSequence::getStrand(), bpp::MafSequence::removeCoordinates(), bpp::MafSequence::setChromosome(), bpp::MafSequence::setName(), bpp::MafBlock::setPass(), bpp::MafBlock::setScore(), and bpp::MafSequence::setStrand().

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=()

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

inlineprivate

Definition at line 82 of file ConcatenateMafIterator.h.

References incomingBlock_, and minimumSize_.

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.

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_().

incomingBlock_

MafBlock* bpp::ConcatenateMafIterator::incomingBlock_

private

Definition at line 63 of file ConcatenateMafIterator.h.

Referenced by ConcatenateMafIterator(), and 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=().

minimumSize_

unsigned int bpp::ConcatenateMafIterator::minimumSize_

private

Definition at line 64 of file ConcatenateMafIterator.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/ConcatenateMafIterator.h
• Bpp/Seq/Io/Maf/ConcatenateMafIterator.cpp