bpp-seq-omics  2.4.1
Public Member Functions | Protected Member Functions | Protected Attributes | Private Member Functions | Private Attributes | List of all members
bpp::QualityFilterMafIterator Class Reference

Filter maf blocks to remove regions with low quality. More...

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

+ Inheritance diagram for bpp::QualityFilterMafIterator:
+ Collaboration diagram for bpp::QualityFilterMafIterator:

Public Member Functions

 QualityFilterMafIterator (MafIterator *iterator, const std::vector< std::string > &species, unsigned int windowSize, unsigned int step, unsigned int minQual, bool keepTrashedBlocks)
 
MafBlock * nextRemovedBlock ()
 Get the next available removed alignment block. More...
 
void setLogStream (std::shared_ptr< OutputStream > logstream)
 
void addIterationListener (IterationListener *listener)
 
MafBlock * nextBlock ()
 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_
 
std::shared_ptr< OutputStream > logstream_
 
std::vector< IterationListener * > iterationListeners_
 
bool started_
 
bool verbose_
 

Private Member Functions

MafBlock * analyseCurrentBlock_ ()
 

Private Attributes

std::vector< std::string > species_
 
unsigned int windowSize_
 
unsigned int step_
 
unsigned int minQual_
 
std::deque< MafBlock * > blockBuffer_
 
std::deque< MafBlock * > trashBuffer_
 
std::deque< std::vector< int > > window_
 
bool keepTrashedBlocks_
 

Detailed Description

Filter maf blocks to remove regions with low quality.

Regions with a too low average quality in a set of species will be removed, and blocks adjusted accordingly.

Definition at line 58 of file QualityFilterMafIterator.h.

Constructor & Destructor Documentation

◆ QualityFilterMafIterator()

bpp::QualityFilterMafIterator::QualityFilterMafIterator ( MafIterator *  iterator,
const std::vector< std::string > &  species,
unsigned int  windowSize,
unsigned int  step,
unsigned int  minQual,
bool  keepTrashedBlocks 
)
inline

Definition at line 73 of file QualityFilterMafIterator.h.

Member Function Documentation

◆ addIterationListener()

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

Implements bpp::MafIterator.

Definition at line 99 of file MafIterator.h.

References bpp::AbstractMafIterator::iterationListeners_.

◆ analyseCurrentBlock_()

MafBlock * QualityFilterMafIterator::analyseCurrentBlock_ ( )
privatevirtual

Implements bpp::AbstractMafIterator.

Definition at line 53 of file QualityFilterMafIterator.cpp.

References bpp::MafBlock::addSequence(), bpp::ApplicationTools::displayGauge(), bpp::ApplicationTools::displayTask(), bpp::ApplicationTools::displayTaskDone(), bpp::SequenceWithAnnotation::getAnnotation(), bpp::MafBlock::getNumberOfSequences(), bpp::MafBlock::getNumberOfSites(), bpp::MafBlock::getPass(), bpp::MafBlock::getScore(), bpp::SequenceQuality::getScores(), bpp::MafBlock::getSequence(), bpp::MafBlock::getSequenceForSpecies(), bpp::SequenceWithAnnotation::hasAnnotation(), bpp::ApplicationTools::message, bpp::SequenceQuality::QUALITY_SCORE, bpp::MafBlock::setPass(), bpp::MafBlock::setScore(), bpp::SequenceWithAnnotation::size(), and bpp::MafSequence::subSequence().

◆ fireIterationMoveSignal_()

void AbstractMafIterator::fireIterationMoveSignal_ ( const MafBlock &  currentBlock)
protectedvirtualinherited

Definition at line 57 of file MafIterator.cpp.

Referenced by bpp::AbstractMafIterator::nextBlock().

◆ fireIterationStartSignal_()

void AbstractMafIterator::fireIterationStartSignal_ ( )
protectedvirtualinherited

Definition at line 51 of file MafIterator.cpp.

Referenced by bpp::AbstractMafIterator::nextBlock().

◆ fireIterationStopSignal_()

void AbstractMafIterator::fireIterationStopSignal_ ( )
protectedvirtualinherited

Definition at line 63 of file MafIterator.cpp.

Referenced by bpp::AbstractMafIterator::nextBlock().

◆ isVerbose()

bool bpp::AbstractMafIterator::isVerbose ( ) const
inlinevirtualinherited

Implements bpp::MafIterator.

Definition at line 116 of file MafIterator.h.

References bpp::AbstractMafIterator::verbose_.

◆ nextBlock()

MafBlock* bpp::AbstractMafIterator::nextBlock ( )
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.

References bpp::AbstractMafIterator::analyseCurrentBlock_(), bpp::AbstractMafIterator::fireIterationMoveSignal_(), bpp::AbstractMafIterator::fireIterationStartSignal_(), bpp::AbstractMafIterator::fireIterationStopSignal_(), and bpp::AbstractMafIterator::started_.

◆ nextRemovedBlock()

MafBlock* bpp::QualityFilterMafIterator::nextRemovedBlock ( )
inlinevirtual

Get the next available removed alignment block.

Returns
A maf alignment block, or a null pointer if no more block is available.

Implements bpp::MafTrashIterator.

Definition at line 86 of file QualityFilterMafIterator.h.

References trashBuffer_.

◆ setLogStream()

void bpp::AbstractFilterMafIterator::setLogStream ( std::shared_ptr< OutputStream >  logstream)
inlineinherited

Definition at line 178 of file MafIterator.h.

References bpp::AbstractFilterMafIterator::logstream_.

◆ setVerbose()

void bpp::AbstractMafIterator::setVerbose ( bool  yn)
inlinevirtualinherited

Implements bpp::MafIterator.

Definition at line 117 of file MafIterator.h.

References bpp::AbstractMafIterator::verbose_.

Member Data Documentation

◆ blockBuffer_

std::deque<MafBlock*> bpp::QualityFilterMafIterator::blockBuffer_
private

Definition at line 67 of file QualityFilterMafIterator.h.

◆ currentBlock_

MafBlock* bpp::AbstractFilterMafIterator::currentBlock_
protectedinherited

Definition at line 154 of file MafIterator.h.

Referenced by bpp::BlockLengthMafIterator::analyseCurrentBlock_(), bpp::BlockSizeMafIterator::analyseCurrentBlock_(), bpp::MafIteratorSynchronizer::analyseCurrentBlock_(), bpp::MsmcOutputMafIterator::analyseCurrentBlock_(), bpp::OrderFilterMafIterator::analyseCurrentBlock_(), bpp::OutputMafIterator::analyseCurrentBlock_(), bpp::PlinkOutputMafIterator::analyseCurrentBlock_(), bpp::SequenceStatisticsMafIterator::analyseCurrentBlock_(), bpp::TableOutputMafIterator::analyseCurrentBlock_(), bpp::VcfOutputMafIterator::analyseCurrentBlock_(), and bpp::AbstractFilterMafIterator::operator=().

◆ iterationListeners_

std::vector<IterationListener*> bpp::AbstractMafIterator::iterationListeners_
protectedinherited

Definition at line 89 of file MafIterator.h.

Referenced by bpp::AbstractMafIterator::addIterationListener().

◆ iterator_

MafIterator* bpp::AbstractFilterMafIterator::iterator_
protectedinherited

Definition at line 153 of file MafIterator.h.

Referenced by bpp::BlockLengthMafIterator::analyseCurrentBlock_(), bpp::BlockSizeMafIterator::analyseCurrentBlock_(), bpp::MafIteratorSynchronizer::analyseCurrentBlock_(), bpp::MsmcOutputMafIterator::analyseCurrentBlock_(), bpp::OrderFilterMafIterator::analyseCurrentBlock_(), bpp::OutputMafIterator::analyseCurrentBlock_(), bpp::PlinkOutputMafIterator::analyseCurrentBlock_(), bpp::SequenceStatisticsMafIterator::analyseCurrentBlock_(), bpp::TableOutputMafIterator::analyseCurrentBlock_(), bpp::VcfOutputMafIterator::analyseCurrentBlock_(), and bpp::AbstractFilterMafIterator::operator=().

◆ keepTrashedBlocks_

bool bpp::QualityFilterMafIterator::keepTrashedBlocks_
private

Definition at line 70 of file QualityFilterMafIterator.h.

◆ logstream_

std::shared_ptr<OutputStream> bpp::AbstractFilterMafIterator::logstream_
protectedinherited

Definition at line 155 of file MafIterator.h.

Referenced by bpp::BlockLengthMafIterator::analyseCurrentBlock_(), bpp::BlockSizeMafIterator::analyseCurrentBlock_(), bpp::AbstractFilterMafIterator::operator=(), and bpp::AbstractFilterMafIterator::setLogStream().

◆ minQual_

unsigned int bpp::QualityFilterMafIterator::minQual_
private

Definition at line 66 of file QualityFilterMafIterator.h.

◆ species_

std::vector<std::string> bpp::QualityFilterMafIterator::species_
private

Definition at line 63 of file QualityFilterMafIterator.h.

◆ started_

bool bpp::AbstractMafIterator::started_
protectedinherited

Definition at line 90 of file MafIterator.h.

Referenced by bpp::AbstractMafIterator::nextBlock().

◆ step_

unsigned int bpp::QualityFilterMafIterator::step_
private

Definition at line 65 of file QualityFilterMafIterator.h.

◆ trashBuffer_

std::deque<MafBlock*> bpp::QualityFilterMafIterator::trashBuffer_
private

Definition at line 68 of file QualityFilterMafIterator.h.

Referenced by nextRemovedBlock().

◆ verbose_

bool bpp::AbstractMafIterator::verbose_
protectedinherited

Definition at line 91 of file MafIterator.h.

Referenced by bpp::AbstractMafIterator::isVerbose(), and bpp::AbstractMafIterator::setVerbose().

◆ window_

std::deque< std::vector<int> > bpp::QualityFilterMafIterator::window_
private

Definition at line 69 of file QualityFilterMafIterator.h.

◆ windowSize_

unsigned int bpp::QualityFilterMafIterator::windowSize_
private

Definition at line 64 of file QualityFilterMafIterator.h.

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