bpp::WindowSplitMafIterator Class Reference

Splits block into windows of given sizes. More...

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

Inheritance diagram for bpp::WindowSplitMafIterator:

Collaboration diagram for bpp::WindowSplitMafIterator:

Public Member Functions
	WindowSplitMafIterator (MafIterator *iterator, unsigned int windowSize, short splitOption=CENTER) throw (Exception)
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)

Static Public Attributes
static const short	RAGGED_LEFT = 0
static const short	RAGGED_RIGHT = 1
static const short	CENTER = 2
static const short	ADJUST = 3

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
MafBlock *	analyseCurrentBlock_ () throw (Exception)

Private Attributes
unsigned int	windowSize_
short	align_
std::deque< MafBlock * >	blockBuffer_

Detailed Description

Splits block into windows of given sizes.

Definition at line 55 of file WindowSplitMafIterator.h.

Constructor & Destructor Documentation

WindowSplitMafIterator()

bpp::WindowSplitMafIterator::WindowSplitMafIterator ( MafIterator *  iterator, unsigned int  windowSize, short  splitOption = CENTER  ) throw ( Exception )

inline

Definition at line 70 of file WindowSplitMafIterator.h.

References ADJUST, CENTER, RAGGED_LEFT, and RAGGED_RIGHT.

Member Function Documentation

addIterationListener()

void bpp::AbstractMafIterator::addIterationListener ( IterationListener *  listener )

inlinevirtualinherited

Implements bpp::MafIterator.

Definition at line 99 of file MafIterator.h.

analyseCurrentBlock_()

MafBlock * WindowSplitMafIterator::analyseCurrentBlock_ ( ) throw ( Exception )

privatevirtual

Implements bpp::AbstractMafIterator.

Definition at line 55 of file WindowSplitMafIterator.cpp.

References bpp::MafBlock::addSequence(), bpp::MafBlock::getNumberOfSequences(), bpp::MafBlock::getNumberOfSites(), bpp::MafBlock::getPass(), bpp::MafBlock::getScore(), bpp::MafBlock::getSequence(), bpp::MafBlock::setPass(), bpp::MafBlock::setScore(), and bpp::MafSequence::subSequence().

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.

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

ADJUST

const short WindowSplitMafIterator::ADJUST = 3

static

Definition at line 67 of file WindowSplitMafIterator.h.

Referenced by WindowSplitMafIterator().

align_

short bpp::WindowSplitMafIterator::align_

private

Definition at line 60 of file WindowSplitMafIterator.h.

blockBuffer_

std::deque<MafBlock*> bpp::WindowSplitMafIterator::blockBuffer_

private

Definition at line 61 of file WindowSplitMafIterator.h.

CENTER

const short WindowSplitMafIterator::CENTER = 2

static

Definition at line 66 of file WindowSplitMafIterator.h.

Referenced by WindowSplitMafIterator().

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=().

RAGGED_LEFT

const short WindowSplitMafIterator::RAGGED_LEFT = 0

static

Definition at line 64 of file WindowSplitMafIterator.h.

Referenced by WindowSplitMafIterator().

RAGGED_RIGHT

const short WindowSplitMafIterator::RAGGED_RIGHT = 1

static

Definition at line 65 of file WindowSplitMafIterator.h.

Referenced by WindowSplitMafIterator().

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.

windowSize_

unsigned int bpp::WindowSplitMafIterator::windowSize_

private

Definition at line 59 of file WindowSplitMafIterator.h.

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

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