bpp::CoreSequence Class Reference

The core sequence interface. More...

#include <Bpp/Seq/CoreSequence.h>

Inheritance diagram for bpp::CoreSequence:

Collaboration diagram for bpp::CoreSequence:

Public Member Functions
	CoreSequence ()
virtual	~CoreSequence ()
CoreSequence *	clone () const =0
virtual const Comments &	getComments () const =0
	Get the comments. More...
virtual void	setComments (const Comments &comments)=0
	Set the comments. More...
virtual void	clearComments ()=0
	Clear the comments. More...
Setting/getting the name of the sequence.
virtual const std::string &	getName () const =0
	Get the name of this sequence. More...
virtual void	setName (const std::string &name)=0
	Set the name of this sequence. More...
Adjusting the size of the sequence.
virtual void	setToSizeR (size_t newSize)=0
	Set up the size of a sequence from the right side. More...
virtual void	setToSizeL (size_t newSize)=0
	Set up the size of a sequence from the left side. More...

Detailed Description

The core sequence interface.

This interface specifies the 'core' functionality of a sequence, that is, an ordered set of states, a name and some meta data (comments).

Definition at line 63 of file CoreSequence.h.

Constructor & Destructor Documentation

CoreSequence()

bpp::CoreSequence::CoreSequence ( )

inline

Definition at line 67 of file CoreSequence.h.

~CoreSequence()

virtual bpp::CoreSequence::~CoreSequence ( )

inlinevirtual

Definition at line 69 of file CoreSequence.h.

Member Function Documentation

clearComments()

virtual void bpp::CoreSequence::clearComments ( )

pure virtual

Clear the comments.

Implemented in bpp::SequenceWithQuality, bpp::SequenceWithAnnotation, bpp::BasicSequence, and bpp::BasicProbabilisticSequence.

clone()

CoreSequence* bpp::CoreSequence::clone ( ) const

pure virtual

Implements bpp::Clonable.

Implemented in bpp::Sequence, bpp::ProbabilisticSequence, bpp::AbstractSequenceSymbolList< T >, bpp::CoreSequenceSymbolList< T >, bpp::AbstractCoreSequence, bpp::SequenceWithQuality, bpp::SequenceWithAnnotation, bpp::BasicSequence, and bpp::BasicProbabilisticSequence.

getComments()

virtual const Comments& bpp::CoreSequence::getComments ( ) const

pure virtual

Get the comments.

Returns

The comments.

Implemented in bpp::SequenceWithQuality, bpp::SequenceWithAnnotation, and bpp::AbstractCoreSequence.

Referenced by bpp::VectorProbabilisticSiteContainer::addSequence(), bpp::VectorSiteContainer::addSequence(), bpp::AllelicAlphabet::convertFromStateAlphabet(), bpp::SequenceWithAnnotationTools::createMaskAnnotation(), bpp::AbstractProbabilisticSequenceContainer::getComments(), bpp::AbstractSequenceContainer::getComments(), bpp::VectorProbabilisticSequenceContainer::getComments(), bpp::AbstractCoreSequence::operator=(), bpp::SequenceWithAnnotation::operator=(), bpp::NucleicAcidsReplication::reverse(), bpp::AbstractReverseTransliterator::reverse(), bpp::SequenceTools::RNYslice(), bpp::SequenceTools::subseq(), bpp::NucleicAcidsReplication::translate(), bpp::AbstractTransliterator::translate(), bpp::Pasta::writeSequence(), and bpp::Fasta::writeSequence().

getName()

virtual const std::string& bpp::CoreSequence::getName ( ) const

pure virtual

Get the name of this sequence.

Returns

This sequence name.

Implemented in bpp::SequenceWithAnnotation, and bpp::AbstractCoreSequence.

Referenced by bpp::VectorProbabilisticSequenceContainer::addSequence(), bpp::VectorProbabilisticSiteContainer::addSequence(), bpp::VectorSequenceContainer::addSequence(), bpp::VectorSiteContainer::addSequence(), bpp::SequenceTools::combineSequences(), bpp::SequenceTools::concatenate(), bpp::AllelicAlphabet::convertFromStateAlphabet(), bpp::SequenceWithAnnotationTools::createMaskAnnotation(), bpp::VectorSequenceContainer::deleteSequenceByName(), bpp::AbstractProbabilisticSequenceContainer::getName(), bpp::AbstractSequenceContainer::getName(), bpp::VectorProbabilisticSequenceContainer::getName(), bpp::SequenceTools::getPutativeHaplotypes(), bpp::VectorSequenceContainer::getSequenceByName(), bpp::AbstractCoreSequence::operator=(), bpp::SequenceWithAnnotation::operator=(), bpp::VectorSequenceContainer::removeSequenceByName(), bpp::CodonAlphabet::reverse(), bpp::WordAlphabet::reverse(), bpp::NucleicAcidsReplication::reverse(), bpp::AbstractReverseTransliterator::reverse(), bpp::SequenceTools::RNYslice(), bpp::VectorProbabilisticSiteContainer::setSequence(), bpp::VectorProbabilisticSequenceContainer::setSequence(), bpp::VectorSiteContainer::setSequence(), bpp::VectorSequenceContainer::setSequence(), bpp::SequenceTools::subseq(), bpp::SequenceTools::subtractHaplotype(), bpp::NucleicAcidsReplication::translate(), bpp::AbstractTransliterator::translate(), bpp::CodonAlphabet::translate(), bpp::WordAlphabet::translate(), bpp::Clustal::writeAlignment(), bpp::Pasta::writeSequence(), and bpp::Fasta::writeSequence().

setComments()

virtual void bpp::CoreSequence::setComments ( const Comments &  comments )

pure virtual

Set the comments.

Parameters

comments

The new comments.

Implemented in bpp::SequenceWithQuality, bpp::SequenceWithAnnotation, and bpp::AbstractCoreSequence.

Referenced by bpp::Pasta::nextSequence(), bpp::Fasta::nextSequence(), bpp::VectorProbabilisticSequenceContainer::setComments(), bpp::VectorSequenceContainer::setComments(), and bpp::SequenceTools::subseq().

setName()

virtual void bpp::CoreSequence::setName ( const std::string &  name )

pure virtual

Set the name of this sequence.

Parameters

name	The new name of the sequence.

Implemented in bpp::SequenceWithAnnotation, and bpp::AbstractCoreSequence.

Referenced by bpp::SequenceTools::getPutativeHaplotypes(), bpp::Pasta::nextSequence(), bpp::Fasta::nextSequence(), bpp::PhredPoly::nextSequence(), bpp::PhredPhd::nextSequence(), bpp::VectorProbabilisticSequenceContainer::setSequenceNames(), bpp::VectorSequenceContainer::setSequenceNames(), and bpp::SequenceTools::subseq().

setToSizeL()

virtual void bpp::CoreSequence::setToSizeL ( size_t  newSize )

pure virtual

Set up the size of a sequence from the left side.

All new characters are filled with gaps. If the specified size is < to the sequence size, the sequence will be truncated.

Parameters

newSize

The new size of the sequence.

Implemented in bpp::SequenceWithAnnotation, bpp::BasicSequence, and bpp::BasicProbabilisticSequence.

setToSizeR()

virtual void bpp::CoreSequence::setToSizeR ( size_t  newSize )

pure virtual

Set up the size of a sequence from the right side.

All new characters are filled with gaps. If the specified size is < to the sequence size, the sequence will be truncated.

Parameters

newSize

The new size of the sequence.

Implemented in bpp::SequenceWithAnnotation, bpp::BasicSequence, and bpp::BasicProbabilisticSequence.

Referenced by bpp::SequenceTools::concatenate().

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

• Bpp/Seq/CoreSequence.h