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

Filter maf blocks to keep a the ones which display a specified combination of species. More...

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

+ Inheritance diagram for bpp::OrphanSequenceFilterMafIterator:
+ Collaboration diagram for bpp::OrphanSequenceFilterMafIterator:

Public Member Functions

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

 OrphanSequenceFilterMafIterator (const OrphanSequenceFilterMafIterator &iterator)
 
OrphanSequenceFilterMafIterator & operator= (const OrphanSequenceFilterMafIterator &iterator)
 
MafBlock * analyseCurrentBlock_ ()
 

Private Attributes

std::vector< std::string > species_
 
bool strict_
 
bool rmDuplicates_
 

Detailed Description

Filter maf blocks to keep a the ones which display a specified combination of species.

This filter is typically used to retrieve "orphan" sequences, that is sequences only present in one (set of) species.

Definition at line 57 of file OrphanSequenceFilterMafIterator.h.

Constructor & Destructor Documentation

◆ OrphanSequenceFilterMafIterator() [1/2]

bpp::OrphanSequenceFilterMafIterator::OrphanSequenceFilterMafIterator ( MafIterator *  iterator,
const std::vector< std::string > &  species,
bool  strict = false,
bool  keep = false,
bool  rmDuplicates = false 
)
inline
Parameters
iteratorThe input iterator.
speciesThe list of species names to be retained.
strictIf true, then block that do not contain all of the specified species will be discarded.
keepIf true, then additional species sequences will be kept.
rmDuplicatesIf true, block that contain more than one instance for at least one species will be discarded.

Definition at line 73 of file OrphanSequenceFilterMafIterator.h.

◆ OrphanSequenceFilterMafIterator() [2/2]

bpp::OrphanSequenceFilterMafIterator::OrphanSequenceFilterMafIterator ( const OrphanSequenceFilterMafIterator &  iterator)
inlineprivate

Definition at line 85 of file OrphanSequenceFilterMafIterator.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 * OrphanSequenceFilterMafIterator::analyseCurrentBlock_ ( )
privatevirtual

Implements bpp::AbstractMafIterator.

Definition at line 50 of file OrphanSequenceFilterMafIterator.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.

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_.

◆ operator=()

OrphanSequenceFilterMafIterator& bpp::OrphanSequenceFilterMafIterator::operator= ( const OrphanSequenceFilterMafIterator &  iterator)
inlineprivate

Definition at line 92 of file OrphanSequenceFilterMafIterator.h.

References rmDuplicates_, species_, and strict_.

◆ 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

◆ 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=().

◆ 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().

◆ rmDuplicates_

bool bpp::OrphanSequenceFilterMafIterator::rmDuplicates_
private

Definition at line 63 of file OrphanSequenceFilterMafIterator.h.

Referenced by operator=().

◆ species_

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

Definition at line 61 of file OrphanSequenceFilterMafIterator.h.

Referenced by operator=().

◆ started_

bool bpp::AbstractMafIterator::started_
protectedinherited

Definition at line 90 of file MafIterator.h.

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

◆ strict_

bool bpp::OrphanSequenceFilterMafIterator::strict_
private

Definition at line 62 of file OrphanSequenceFilterMafIterator.h.

Referenced by operator=().

◆ 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: