bpp-seq-omics  2.4.1
Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
bpp::AbstractMafIterator Class Referenceabstract

Partial implementation of the MafIterator interface. More...

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

+ Inheritance diagram for bpp::AbstractMafIterator:
+ Collaboration diagram for bpp::AbstractMafIterator:

Public Member Functions

 AbstractMafIterator ()
 
virtual ~AbstractMafIterator ()
 
void addIterationListener (IterationListener *listener)
 
MafBlock * nextBlock ()
 Get the next available alignment block. More...
 
bool isVerbose () const
 
void setVerbose (bool yn)
 

Protected Member Functions

virtual MafBlock * analyseCurrentBlock_ ()=0
 
virtual void fireIterationStartSignal_ ()
 
virtual void fireIterationMoveSignal_ (const MafBlock &currentBlock)
 
virtual void fireIterationStopSignal_ ()
 

Protected Attributes

std::vector< IterationListener * > iterationListeners_
 
bool started_
 
bool verbose_
 

Detailed Description

Partial implementation of the MafIterator interface.

This implements the listener parts.

Definition at line 85 of file MafIterator.h.

Constructor & Destructor Documentation

◆ AbstractMafIterator()

bpp::AbstractMafIterator::AbstractMafIterator ( )
inline

Definition at line 94 of file MafIterator.h.

◆ ~AbstractMafIterator()

virtual bpp::AbstractMafIterator::~AbstractMafIterator ( )
inlinevirtual

Definition at line 96 of file MafIterator.h.

Member Function Documentation

◆ addIterationListener()

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

Implements bpp::MafIterator.

Definition at line 99 of file MafIterator.h.

References iterationListeners_.

◆ analyseCurrentBlock_()

virtual MafBlock* bpp::AbstractMafIterator::analyseCurrentBlock_ ( )
protectedpure virtual

Implemented in bpp::WindowSplitMafIterator, bpp::VcfOutputMafIterator, bpp::TableOutputMafIterator, bpp::SequenceStreamToMafIterator, bpp::SequenceStatisticsMafIterator, bpp::SequenceLDhotOutputMafIterator, bpp::SequenceFilterMafIterator, bpp::RemoveEmptySequencesMafIterator, bpp::QualityFilterMafIterator, bpp::PlinkOutputMafIterator, bpp::OutputMafIterator, bpp::OutputAlignmentMafIterator, bpp::OrphanSequenceFilterMafIterator, bpp::OrderFilterMafIterator, bpp::MsmcOutputMafIterator, bpp::MaskFilterMafIterator, bpp::MafParser, bpp::MafIteratorSynchronizer, bpp::TrashIteratorAdapter, bpp::FullGapFilterMafIterator, bpp::FeatureFilterMafIterator, bpp::FeatureExtractorMafIterator, bpp::EntropyFilterMafIterator, bpp::DuplicateFilterMafIterator, bpp::CoordinateTranslatorMafIterator, bpp::CoordinatesOutputMafIterator, bpp::ConcatenateMafIterator, bpp::ChromosomeMafIterator, bpp::BlockSizeMafIterator, bpp::BlockMergerMafIterator, bpp::BlockLengthMafIterator, bpp::AlignmentFilter2MafIterator, and bpp::AlignmentFilterMafIterator.

Referenced by nextBlock().

◆ fireIterationMoveSignal_()

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

Definition at line 57 of file MafIterator.cpp.

Referenced by nextBlock().

◆ fireIterationStartSignal_()

void AbstractMafIterator::fireIterationStartSignal_ ( )
protectedvirtual

Definition at line 51 of file MafIterator.cpp.

Referenced by nextBlock().

◆ fireIterationStopSignal_()

void AbstractMafIterator::fireIterationStopSignal_ ( )
protectedvirtual

Definition at line 63 of file MafIterator.cpp.

Referenced by nextBlock().

◆ isVerbose()

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

Implements bpp::MafIterator.

Definition at line 116 of file MafIterator.h.

References verbose_.

◆ nextBlock()

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

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 analyseCurrentBlock_(), fireIterationMoveSignal_(), fireIterationStartSignal_(), fireIterationStopSignal_(), and started_.

◆ setVerbose()

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

Implements bpp::MafIterator.

Definition at line 117 of file MafIterator.h.

References verbose_.

Member Data Documentation

◆ iterationListeners_

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

Definition at line 89 of file MafIterator.h.

Referenced by addIterationListener().

◆ started_

bool bpp::AbstractMafIterator::started_
protected

Definition at line 90 of file MafIterator.h.

Referenced by nextBlock().

◆ verbose_

bool bpp::AbstractMafIterator::verbose_
protected

Definition at line 91 of file MafIterator.h.

Referenced by isVerbose(), and setVerbose().

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