bpp::DuplicateFilterMafIterator Class Reference

Filter maf blocks to remove duplicated blocks, according to a reference sequence). More...

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

Inheritance diagram for bpp::DuplicateFilterMafIterator:

Collaboration diagram for bpp::DuplicateFilterMafIterator:

Public Member Functions
	DuplicateFilterMafIterator (MafIterator *iterator, const std::string &reference)
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
	DuplicateFilterMafIterator (const DuplicateFilterMafIterator &iterator)
DuplicateFilterMafIterator &	operator= (const DuplicateFilterMafIterator &iterator)
MafBlock *	analyseCurrentBlock_ () throw (Exception)

Private Attributes
std::string	ref_
std::map< std::string, std::map< char, std::map< size_t, std::map< size_t, size_t > > > >	blocks_

Detailed Description

Filter maf blocks to remove duplicated blocks, according to a reference sequence).

Definition at line 55 of file DuplicateFilterMafIterator.h.

Constructor & Destructor Documentation

DuplicateFilterMafIterator() [1/2]

bpp::DuplicateFilterMafIterator::DuplicateFilterMafIterator ( MafIterator *  iterator, const std::string &  reference  )

inline

Parameters

iterator	The input iterator.
reference	The reference species name.

Definition at line 70 of file DuplicateFilterMafIterator.h.

DuplicateFilterMafIterator() [2/2]

bpp::DuplicateFilterMafIterator::DuplicateFilterMafIterator ( const DuplicateFilterMafIterator &  iterator )

inlineprivate

Definition at line 77 of file DuplicateFilterMafIterator.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 * DuplicateFilterMafIterator::analyseCurrentBlock_ ( ) throw ( Exception )

privatevirtual

Implements bpp::AbstractMafIterator.

Definition at line 50 of file DuplicateFilterMafIterator.cpp.

References bpp::MafBlock::getSequence(), and bpp::MafSequence::getSpecies().

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=()

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

inlineprivate

Definition at line 83 of file DuplicateFilterMafIterator.h.

References blocks_, and ref_.

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

blocks_

std::map< std::string, std::map< char, std::map< size_t, std::map< size_t, size_t > > > > bpp::DuplicateFilterMafIterator::blocks_

private

Contains the list of 'seen' block, as [chr][strand][start][stop]

Definition at line 63 of file DuplicateFilterMafIterator.h.

Referenced by operator=().

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=().

ref_

std::string bpp::DuplicateFilterMafIterator::ref_

private

Definition at line 59 of file DuplicateFilterMafIterator.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/DuplicateFilterMafIterator.h
• Bpp/Seq/Io/Maf/DuplicateFilterMafIterator.cpp