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

This iterator forward the iterator given as input after having printed its content to a file. More...

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

+ Inheritance diagram for bpp::OutputMafIterator:
+ Collaboration diagram for bpp::OutputMafIterator:

Public Member Functions

 OutputMafIterator (MafIterator *iterator, std::ostream *out, bool mask=true)
 
MafBlock * analyseCurrentBlock_ ()
 
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

 OutputMafIterator (const OutputMafIterator &iterator)
 
OutputMafIterator & operator= (const OutputMafIterator &iterator)
 
void writeHeader (std::ostream &out) const
 
void writeBlock (std::ostream &out, const MafBlock &block) const
 

Private Attributes

std::ostream * output_
 
bool mask_
 

Detailed Description

This iterator forward the iterator given as input after having printed its content to a file.

Definition at line 55 of file OutputMafIterator.h.

Constructor & Destructor Documentation

◆ OutputMafIterator() [1/2]

bpp::OutputMafIterator::OutputMafIterator ( MafIterator *  iterator,
std::ostream *  out,
bool  mask = true 
)
inline

Definition at line 63 of file OutputMafIterator.h.

References output_, and writeHeader().

◆ OutputMafIterator() [2/2]

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

Definition at line 71 of file OutputMafIterator.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* bpp::OutputMafIterator::analyseCurrentBlock_ ( )
inlinevirtual

Implements bpp::AbstractMafIterator.

Definition at line 86 of file OutputMafIterator.h.

References bpp::AbstractFilterMafIterator::currentBlock_, bpp::AbstractFilterMafIterator::iterator_, bpp::MafIterator::nextBlock(), output_, and writeBlock().

◆ 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=()

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

Definition at line 77 of file OutputMafIterator.h.

References mask_, and output_.

◆ 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_.

◆ writeBlock()

void OutputMafIterator::writeBlock ( std::ostream &  out,
const MafBlock &  block 
) const
private

Definition at line 60 of file OutputMafIterator.cpp.

References bpp::SequenceWithAnnotation::getAnnotation(), bpp::MafSequence::getGenomicSize(), bpp::SequenceWithAnnotation::getName(), bpp::MafBlock::getNumberOfSequences(), bpp::MafBlock::getPass(), bpp::MafBlock::getScore(), bpp::MafBlock::getSequence(), bpp::MafSequence::getSrcSize(), bpp::MafSequence::getStrand(), bpp::SequenceWithAnnotation::hasAnnotation(), bpp::MafSequence::hasCoordinates(), bpp::SequenceMask::MASK, bpp::SequenceQuality::QUALITY_SCORE, bpp::TextTools::resizeLeft(), bpp::TextTools::resizeRight(), bpp::SequenceWithAnnotation::size(), bpp::MafSequence::start(), bpp::SequenceWithAnnotation::toString(), and bpp::TextTools::toString().

Referenced by analyseCurrentBlock_().

◆ writeHeader()

void OutputMafIterator::writeHeader ( std::ostream &  out) const
private

Definition at line 54 of file OutputMafIterator.cpp.

Referenced by OutputMafIterator().

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_(), 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_(), 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().

◆ mask_

bool bpp::OutputMafIterator::mask_
private

Definition at line 60 of file OutputMafIterator.h.

Referenced by operator=().

◆ output_

std::ostream* bpp::OutputMafIterator::output_
private

Definition at line 59 of file OutputMafIterator.h.

Referenced by analyseCurrentBlock_(), operator=(), and OutputMafIterator().

◆ 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: