bpp::DuplicateFilterMafIterator Class Reference

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

#include <Bpp/Seq/Io/MafIterator.h>

Inheritance diagram for bpp::DuplicateFilterMafIterator:

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Collaboration diagram for bpp::DuplicateFilterMafIterator:

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List of all members.

Public Member Functions
	DuplicateFilterMafIterator (MafIterator *iterator, const std::string &reference)
MafBlock *	nextBlock () throw (Exception)
	Get the next available alignment block.
void	setLogStream (OutputStream *logstream)
bool	verbose () const
void	verbose (bool yn)
Protected Attributes
MafIterator *	iterator_
OutputStream *	logstream_
bool	verbose_
Private Member Functions
	DuplicateFilterMafIterator (const DuplicateFilterMafIterator &iterator)
DuplicateFilterMafIterator &	operator= (const DuplicateFilterMafIterator &iterator)
Private Attributes
std::string	ref_
std::map< std::string, std::map< char, std::map < unsigned int, std::map < unsigned int, unsigned int > > > >	blocks_
MafBlock *	currentBlock_

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Detailed Description

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

Definition at line 482 of file MafIterator.h.

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Constructor & Destructor Documentation

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

Parameters:

	iterator	The input iterator.
	reference	The reference species name.

Definition at line 498 of file MafIterator.h.

bpp::DuplicateFilterMafIterator::DuplicateFilterMafIterator

(

const DuplicateFilterMafIterator &

iterator

)

[inline, private]

Definition at line 506 of file MafIterator.h.

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Member Function Documentation

MafBlock * DuplicateFilterMafIterator::nextBlock

(

)

throw (Exception) [virtual]

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 164 of file MafIterator.cpp.

References blocks_, currentBlock_, bpp::MafSequence::getChromosome(), bpp::MafBlock::getNumberOfSequences(), bpp::MafBlock::getSequence(), bpp::MafSequence::getSpecies(), bpp::MafSequence::getStrand(), bpp::AbstractFilterMafIterator::iterator_, bpp::AbstractFilterMafIterator::logstream_, bpp::MafIterator::nextBlock(), ref_, bpp::MafSequence::start(), and bpp::MafSequence::stop().

DuplicateFilterMafIterator& bpp::DuplicateFilterMafIterator::operator=

(

const DuplicateFilterMafIterator &

iterator

)

[inline, private]

Definition at line 513 of file MafIterator.h.

References blocks_, and ref_.

void bpp::AbstractFilterMafIterator::setLogStream

(

OutputStream *

logstream

)

[inline, inherited]

Definition at line 341 of file MafIterator.h.

void bpp::AbstractFilterMafIterator::verbose

(

bool

yn

)

[inline, inherited]

Definition at line 343 of file MafIterator.h.

bool bpp::AbstractFilterMafIterator::verbose

(

)

const [inline, inherited]

Definition at line 342 of file MafIterator.h.

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Member Data Documentation

std::map< std::string, std::map< char, std::map< unsigned int, std::map< unsigned int, unsigned int > > > > bpp::DuplicateFilterMafIterator::blocks_ [private]

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

Definition at line 490 of file MafIterator.h.

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

MafBlock* bpp::DuplicateFilterMafIterator::currentBlock_ [private]

Definition at line 491 of file MafIterator.h.

Referenced by nextBlock().

MafIterator* bpp::AbstractFilterMafIterator::iterator_ [protected, inherited]

Definition at line 323 of file MafIterator.h.

Referenced by bpp::FeatureExtractor::nextBlock(), bpp::FeatureFilterMafIterator::nextBlock(), bpp::PairwiseSequenceStatisticsMafIterator::nextBlock(), bpp::SequenceStatisticsMafIterator::nextBlock(), bpp::QualityFilterMafIterator::nextBlock(), bpp::MaskFilterMafIterator::nextBlock(), bpp::AlignmentFilter2MafIterator::nextBlock(), bpp::AlignmentFilterMafIterator::nextBlock(), bpp::FullGapFilterMafIterator::nextBlock(), bpp::BlockMergerMafIterator::nextBlock(), nextBlock(), bpp::ChromosomeMafIterator::nextBlock(), bpp::SequenceFilterMafIterator::nextBlock(), and bpp::AbstractFilterMafIterator::operator=().

OutputStream* bpp::AbstractFilterMafIterator::logstream_ [protected, inherited]

Definition at line 324 of file MafIterator.h.

Referenced by bpp::FeatureExtractor::nextBlock(), bpp::FeatureFilterMafIterator::nextBlock(), bpp::QualityFilterMafIterator::nextBlock(), bpp::MaskFilterMafIterator::nextBlock(), bpp::AlignmentFilter2MafIterator::nextBlock(), bpp::AlignmentFilterMafIterator::nextBlock(), bpp::FullGapFilterMafIterator::nextBlock(), bpp::BlockMergerMafIterator::nextBlock(), nextBlock(), bpp::ChromosomeMafIterator::nextBlock(), bpp::SequenceFilterMafIterator::nextBlock(), and bpp::AbstractFilterMafIterator::operator=().

std::string bpp::DuplicateFilterMafIterator::ref_ [private]

Definition at line 486 of file MafIterator.h.

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

bool bpp::AbstractFilterMafIterator::verbose_ [protected, inherited]

Definition at line 325 of file MafIterator.h.

Referenced by bpp::FeatureExtractor::nextBlock(), bpp::FeatureFilterMafIterator::nextBlock(), bpp::QualityFilterMafIterator::nextBlock(), bpp::MaskFilterMafIterator::nextBlock(), bpp::AlignmentFilter2MafIterator::nextBlock(), bpp::AlignmentFilterMafIterator::nextBlock(), bpp::FullGapFilterMafIterator::nextBlock(), and bpp::AbstractFilterMafIterator::operator=().

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

• Bpp/Seq/Io/MafIterator.h
• Bpp/Seq/Io/MafIterator.cpp