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

Remove from alignment all positions that fall within any feature from a list given as a SequenceFeatureSet object. More...

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

+ Inheritance diagram for bpp::FeatureFilterMafIterator:
+ Collaboration diagram for bpp::FeatureFilterMafIterator:

Public Member Functions

 FeatureFilterMafIterator (MafIterator *iterator, const std::string &refSpecies, const SequenceFeatureSet &features, 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::string refSpecies_
 
std::deque< MafBlock * > blockBuffer_
 
std::deque< MafBlock * > trashBuffer_
 
bool keepTrashedBlocks_
 
std::map< std::string, MultiRange< size_t > > ranges_
 

Detailed Description

Remove from alignment all positions that fall within any feature from a list given as a SequenceFeatureSet object.

Removed regions are outputed as a trash iterator.

Definition at line 57 of file FeatureFilterMafIterator.h.

Constructor & Destructor Documentation

◆ FeatureFilterMafIterator()

bpp::FeatureFilterMafIterator::FeatureFilterMafIterator ( MafIterator *  iterator,
const std::string &  refSpecies,
const SequenceFeatureSet &  features,
bool  keepTrashedBlocks 
)
inline

Definition at line 69 of file FeatureFilterMafIterator.h.

References bpp::SequenceFeatureSet::fillRangeCollectionForSequence(), bpp::SequenceFeatureSet::getSequences(), and ranges_.

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 * FeatureFilterMafIterator::analyseCurrentBlock_ ( )
privatevirtual

Implements bpp::AbstractMafIterator.

Definition at line 50 of file FeatureFilterMafIterator.cpp.

References bpp::MafBlock::addSequence(), bpp::ApplicationTools::displayGauge(), bpp::ApplicationTools::displayTask(), bpp::ApplicationTools::displayTaskDone(), bpp::SequenceWithAnnotation::getAlphabet(), bpp::MultiRange< class >::getBounds(), bpp::MafSequence::getChromosome(), bpp::MafBlock::getDescription(), bpp::MafSequence::getDescription(), bpp::Alphabet::getGapCharacterCode(), bpp::MafBlock::getNumberOfSequences(), bpp::MafBlock::getNumberOfSites(), bpp::MafBlock::getPass(), bpp::MafSequence::getRange(), bpp::MafBlock::getScore(), bpp::MafBlock::getSequence(), bpp::MafBlock::getSequenceForSpecies(), bpp::MafSequence::getSrcSize(), bpp::MafSequence::getStrand(), bpp::MafBlock::hasSequenceForSpecies(), bpp::MultiRange< class >::isEmpty(), bpp::ApplicationTools::message, bpp::VectorTools::print(), bpp::MultiRange< class >::restrictTo(), bpp::MafBlock::setPass(), bpp::MafBlock::setScore(), bpp::SequenceWithAnnotation::size(), bpp::MafSequence::start(), bpp::MafSequence::stop(), bpp::MafSequence::subSequence(), and bpp::TextTools::toString().

◆ 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::FeatureFilterMafIterator::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 89 of file FeatureFilterMafIterator.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::FeatureFilterMafIterator::blockBuffer_
private

Definition at line 63 of file FeatureFilterMafIterator.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::FeatureFilterMafIterator::keepTrashedBlocks_
private

Definition at line 65 of file FeatureFilterMafIterator.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().

◆ ranges_

std::map<std::string, MultiRange<size_t> > bpp::FeatureFilterMafIterator::ranges_
private

Definition at line 66 of file FeatureFilterMafIterator.h.

Referenced by FeatureFilterMafIterator().

◆ refSpecies_

std::string bpp::FeatureFilterMafIterator::refSpecies_
private

Definition at line 62 of file FeatureFilterMafIterator.h.

◆ started_

bool bpp::AbstractMafIterator::started_
protectedinherited

Definition at line 90 of file MafIterator.h.

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

◆ trashBuffer_

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

Definition at line 64 of file FeatureFilterMafIterator.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().

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