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

A MafIterator built from a sequence stream. More...

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

+ Inheritance diagram for bpp::SequenceStreamToMafIterator:
+ Collaboration diagram for bpp::SequenceStreamToMafIterator:

Public Member Functions

 SequenceStreamToMafIterator (ISequenceStream *seqStream, std::istream *stream, bool parseMask=false, bool zeroBasedCoordinates=true)
 
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

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

Private Member Functions

 SequenceStreamToMafIterator (const SequenceStreamToMafIterator &ss2mi)
 
SequenceStreamToMafIterator & operator= (const SequenceStreamToMafIterator &ss2mi)
 
MafBlock * analyseCurrentBlock_ ()
 

Private Attributes

std::unique_ptr< ISequenceStream > seqStream_
 
std::istream * stream_
 
bool zeroBasedCoords_
 
bool firstBlock_
 

Detailed Description

A MafIterator built from a sequence stream.

Each block will contain one sequence from the original file.

Author
Julien Dutheil

Definition at line 60 of file SequenceStreamToMafIterator.h.

Constructor & Destructor Documentation

◆ SequenceStreamToMafIterator() [1/2]

bpp::SequenceStreamToMafIterator::SequenceStreamToMafIterator ( ISequenceStream *  seqStream,
std::istream *  stream,
bool  parseMask = false,
bool  zeroBasedCoordinates = true 
)
inline

Definition at line 70 of file SequenceStreamToMafIterator.h.

◆ SequenceStreamToMafIterator() [2/2]

bpp::SequenceStreamToMafIterator::SequenceStreamToMafIterator ( const SequenceStreamToMafIterator &  ss2mi)
inlineprivate

Definition at line 75 of file SequenceStreamToMafIterator.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 * SequenceStreamToMafIterator::analyseCurrentBlock_ ( )
privatevirtual

Implements bpp::AbstractMafIterator.

Definition at line 47 of file SequenceStreamToMafIterator.cpp.

References bpp::SequenceWithAnnotation::getName(), bpp::StringTokenizer::nextToken(), bpp::StringTokenizer::numberOfRemainingTokens(), bpp::MafSequence::setName(), bpp::MafSequence::setStart(), bpp::MafSequence::setStrand(), and bpp::SequenceWithAnnotation::size().

◆ 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=()

SequenceStreamToMafIterator& bpp::SequenceStreamToMafIterator::operator= ( const SequenceStreamToMafIterator &  ss2mi)
inlineprivate

Definition at line 77 of file SequenceStreamToMafIterator.h.

References firstBlock_, seqStream_, stream_, and zeroBasedCoords_.

◆ 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

◆ firstBlock_

bool bpp::SequenceStreamToMafIterator::firstBlock_
private

Definition at line 67 of file SequenceStreamToMafIterator.h.

Referenced by operator=().

◆ iterationListeners_

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

Definition at line 89 of file MafIterator.h.

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

◆ seqStream_

std::unique_ptr<ISequenceStream> bpp::SequenceStreamToMafIterator::seqStream_
private

Definition at line 64 of file SequenceStreamToMafIterator.h.

Referenced by operator=().

◆ started_

bool bpp::AbstractMafIterator::started_
protectedinherited

Definition at line 90 of file MafIterator.h.

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

◆ stream_

std::istream* bpp::SequenceStreamToMafIterator::stream_
private

Definition at line 65 of file SequenceStreamToMafIterator.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().

◆ zeroBasedCoords_

bool bpp::SequenceStreamToMafIterator::zeroBasedCoords_
private

Definition at line 66 of file SequenceStreamToMafIterator.h.

Referenced by operator=().

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