bpp::SequenceFilterMafIterator Class Reference

Filter maf blocks to keep a subset of sequences, given their name. this filter can also be used to filter block which contain a certain set of sequences. More...

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

Inheritance diagram for bpp::SequenceFilterMafIterator:

Collaboration diagram for bpp::SequenceFilterMafIterator:

Public Member Functions
	SequenceFilterMafIterator (MafIterator *iterator, const std::vector< std::string > &species, bool strict=false, bool keep=false, bool rmDuplicates=false)
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
	SequenceFilterMafIterator (const SequenceFilterMafIterator &iterator)
SequenceFilterMafIterator &	operator= (const SequenceFilterMafIterator &iterator)
MafBlock *	analyseCurrentBlock_ () throw (Exception)

Private Attributes
std::vector< std::string >	species_
bool	strict_
bool	keep_
bool	rmDuplicates_

Detailed Description

Filter maf blocks to keep a subset of sequences, given their name. this filter can also be used to filter block which contain a certain set of sequences.

Typical usage:

• strict=yes, keep=no: extract the species from the list, only if all of them are present in a block.
• strict=no, keep=no: extract the species from the list, at least the one which are there.
• strict=yes, keep=yes: filter blocks to retain only the ones that contain at least all species from the list. Blocks that are empty after the filtering are removed.

Definition at line 62 of file SequenceFilterMafIterator.h.

Constructor & Destructor Documentation

SequenceFilterMafIterator() [1/2]

bpp::SequenceFilterMafIterator::SequenceFilterMafIterator ( MafIterator *  iterator, const std::vector< std::string > &  species, bool  strict = false, bool  keep = false, bool  rmDuplicates = false  )

inline

Parameters

iterator	The input iterator.
species	The list of species names to be retained.
strict	If true, then block that do not contain all species will be discarded.
keep	If true, sequences not in the selection will be kept.
rmDuplicates	If true, block that contain more than one instance for at least one species will be discarded.

Definition at line 79 of file SequenceFilterMafIterator.h.

SequenceFilterMafIterator() [2/2]

bpp::SequenceFilterMafIterator::SequenceFilterMafIterator ( const SequenceFilterMafIterator &  iterator )

inlineprivate

Definition at line 88 of file SequenceFilterMafIterator.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 * SequenceFilterMafIterator::analyseCurrentBlock_ ( ) throw ( Exception )

privatevirtual

Implements bpp::AbstractMafIterator.

Definition at line 50 of file SequenceFilterMafIterator.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=()

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

inlineprivate

Definition at line 96 of file SequenceFilterMafIterator.h.

References keep_, rmDuplicates_, species_, and strict_.

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_().

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=().

keep_

bool bpp::SequenceFilterMafIterator::keep_

private

Definition at line 68 of file SequenceFilterMafIterator.h.

Referenced by 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=().

rmDuplicates_

bool bpp::SequenceFilterMafIterator::rmDuplicates_

private

Definition at line 69 of file SequenceFilterMafIterator.h.

Referenced by operator=().

species_

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

private

Definition at line 66 of file SequenceFilterMafIterator.h.

Referenced by operator=().

started_

bool bpp::AbstractMafIterator::started_

protectedinherited

Definition at line 90 of file MafIterator.h.

strict_

bool bpp::SequenceFilterMafIterator::strict_

private

Definition at line 67 of file SequenceFilterMafIterator.h.

Referenced by operator=().

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