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

Concatenate blocks up to a certain size. More...

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

+ Inheritance diagram for bpp::ConcatenateMafIterator:
+ Collaboration diagram for bpp::ConcatenateMafIterator:

Public Member Functions

 ConcatenateMafIterator (MafIterator *iterator, unsigned int minimumSize, std::string refSpecies="")
 
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

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

Private Attributes

MafBlock * incomingBlock_
 
unsigned int minimumSize_
 
std::string refSpecies_
 

Detailed Description

Concatenate blocks up to a certain size.

Blocks are appended regardless of their coordinates, to form concatenated blocks of at least a given number of positions. The scores, if any, will be averaged for the block, weighted by the corresponding block sizes. The pass value will be removed if it is different for the blocks. If a reference species is given, only block with identical chr tag will be concatenated.

Definition at line 60 of file ConcatenateMafIterator.h.

Constructor & Destructor Documentation

◆ ConcatenateMafIterator() [1/2]

bpp::ConcatenateMafIterator::ConcatenateMafIterator ( MafIterator *  iterator,
unsigned int  minimumSize,
std::string  refSpecies = "" 
)
inline

Definition at line 69 of file ConcatenateMafIterator.h.

References incomingBlock_, and bpp::MafIterator::nextBlock().

◆ ConcatenateMafIterator() [2/2]

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

Definition at line 79 of file ConcatenateMafIterator.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 * ConcatenateMafIterator::analyseCurrentBlock_ ( )
privatevirtual

Implements bpp::AbstractMafIterator.

Definition at line 53 of file ConcatenateMafIterator.cpp.

References bpp::MafBlock::addSequence(), count(), bpp::ApplicationTools::displayMessage(), bpp::ApplicationTools::displayUnlimitedGauge(), bpp::MafBlock::setPass(), bpp::MafBlock::setScore(), bpp::VectorTools::unique(), and bpp::VectorTools::vectorUnion().

◆ 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=()

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

Definition at line 86 of file ConcatenateMafIterator.h.

References incomingBlock_, minimumSize_, and refSpecies_.

◆ 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=().

◆ incomingBlock_

MafBlock* bpp::ConcatenateMafIterator::incomingBlock_
private

Definition at line 64 of file ConcatenateMafIterator.h.

Referenced by ConcatenateMafIterator(), and 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().

◆ minimumSize_

unsigned int bpp::ConcatenateMafIterator::minimumSize_
private

Definition at line 65 of file ConcatenateMafIterator.h.

Referenced by operator=().

◆ refSpecies_

std::string bpp::ConcatenateMafIterator::refSpecies_
private

Definition at line 66 of file ConcatenateMafIterator.h.

Referenced by operator=().

◆ started_

bool bpp::AbstractMafIterator::started_
protectedinherited

Definition at line 90 of file MafIterator.h.

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

◆ 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: