bpp::CoreSymbolList< T > Class Template Reference

The CoreSymbolList interface. More...

#include <Bpp/Seq/CoreSymbolList.h>

Inheritance diagram for bpp::CoreSymbolList< T >:

Collaboration diagram for bpp::CoreSymbolList< T >:

Public Member Functions
virtual	~CoreSymbolList ()
virtual const Alphabet *	getAlphabet () const =0
	Get the alphabet associated to the list. More...
virtual size_t	size () const =0
	Get the number of elements in the list. More...
virtual std::string	toString () const =0
	Convert the list as a string. More...
virtual double	getStateValueAt (size_t siteIndex, int state) const
virtual double	operator() (size_t siteIndex, int state) const
The Clonable interface
CoreSymbolList *	clone () const =0
Acting on the content of the list.
virtual void	setContent (const std::vector< T > &list)=0
	Set the whole content of the list. More...
virtual const std::vector< T > &	getContent () const =0
Edition methods.
virtual void	addElement (const T &c)=0
	Add a character to the end of the list. More...
virtual void	addElement (size_t pos, const T &c)=0
	Add a character at a certain position in the list. More...
virtual void	setElement (size_t pos, const T &c)=0
	Set the element at position 'pos' to character 'c'. More...
virtual const T &	getElement (size_t pos) const =0
	Get the element at position 'pos' as a character. More...
Provide direct access to the list content.
Warning These operators allow you to modifiy the list content. No alphabet checking is performed for your modifications, so use with care, or consider using the setContent() method.
virtual const T &	getValue (size_t pos) const =0
	checked access to a character in list. More...
virtual const T &	operator[] (size_t pos) const =0
	Operator [] overloaded for quick access to a character in list. More...
virtual T &	operator[] (size_t pos)=0
	Operator [] overloaded for quick access to a character in list. More...
Edition methods.
virtual void	deleteElement (size_t pos)=0
	Remove the element at position 'pos'. More...
virtual void	deleteElements (size_t pos, size_t len)=0
	Remove the elements at position 'pos'. More...
Provide direct access to the list content.
Warning These operators allow you to modifiy the list content. No alphabet checking is performed for your modifications, so use with care, or consider using the setContent() method.
virtual void	shuffle ()=0
	Randomly shuffle the content of the list, with linear complexity. More...

Detailed Description

template<class T>
class bpp::CoreSymbolList< T >

The CoreSymbolList interface.

Definition at line 167 of file CoreSymbolList.h.

Constructor & Destructor Documentation

~CoreSymbolList()

template<class T >

virtual bpp::CoreSymbolList< T >::~CoreSymbolList ( )

inlinevirtual

Definition at line 180 of file CoreSymbolList.h.

Member Function Documentation

addElement() [1/2]

template<class T >

virtual void bpp::CoreSymbolList< T >::addElement ( const T &  c )

pure virtual

Add a character to the end of the list.

Parameters

c	The character to add.

Implemented in bpp::EdSymbolList< T >, bpp::SymbolList< T >, and bpp::BasicProbabilisticSymbolList.

Referenced by bpp::AlignedSequenceContainer::addSite(), bpp::SequenceTools::getPutativeHaplotypes(), bpp::AbstractReverseTransliterator::reverse(), and bpp::AbstractTransliterator::translate().

addElement() [2/2]

template<class T >

virtual void bpp::CoreSymbolList< T >::addElement ( size_t  pos, const T &  c  )

pure virtual

Add a character at a certain position in the list.

Parameters

pos	The postion where to insert the element.
c	The character to add.

Implemented in bpp::EdSymbolList< T >, bpp::SymbolList< T >, and bpp::BasicProbabilisticSymbolList.

clone()

template<class T >

CoreSymbolList* bpp::CoreSymbolList< T >::clone ( ) const

pure virtual

Implements bpp::CruxSymbolList.

Implemented in bpp::SymbolList< int >, bpp::SymbolList< T >, bpp::Sequence, bpp::ProbabilisticSymbolList, bpp::ProbabilisticSequence, bpp::EdCoreSymbolList< T >, bpp::AbstractSequenceSymbolList< T >, bpp::CoreSequenceSymbolList< T >, bpp::EdSymbolList< T >, bpp::EdSymbolList< int >, bpp::Site, bpp::SequenceWithQuality, bpp::SequenceWithAnnotation, bpp::BasicSequence, bpp::BasicProbabilisticSymbolList, bpp::ProbabilisticSite, bpp::BasicProbabilisticSequence, bpp::EdIntSymbolList, and bpp::BasicIntSymbolList.

deleteElement()

virtual void bpp::CruxSymbolList::deleteElement ( size_t  pos )

pure virtualinherited

Remove the element at position 'pos'.

Parameters

pos	The position of the element to remove.

Implemented in bpp::EdSymbolList< T >, bpp::EdSymbolList< int >, bpp::SymbolList< T >, bpp::SymbolList< int >, and bpp::BasicProbabilisticSymbolList.

Referenced by bpp::AlignedSequenceContainer::deleteSite(), bpp::SequenceTools::getCDS(), bpp::SequenceTools::removeGaps(), bpp::VectorSiteContainer::removeSequence(), bpp::AlignedSequenceContainer::removeSite(), and bpp::SequenceTools::removeStops().

deleteElements()

virtual void bpp::CruxSymbolList::deleteElements ( size_t  pos, size_t  len  )

pure virtualinherited

Remove the elements at position 'pos'.

Parameters

pos	The position of the first element to remove.
len	The length of the region to remove.

Implemented in bpp::EdSymbolList< T >, bpp::EdSymbolList< int >, bpp::SymbolList< T >, bpp::SymbolList< int >, and bpp::BasicProbabilisticSymbolList.

Referenced by bpp::AlignedSequenceContainer::deleteSites().

getAlphabet()

virtual const Alphabet* bpp::CruxSymbolList::getAlphabet ( ) const

pure virtualinherited

Get the alphabet associated to the list.

Returns

A const pointer to the alphabet.

See also

Alphabet class.

Implemented in bpp::SymbolList< T >, bpp::SymbolList< int >, and bpp::BasicProbabilisticSymbolList.

Referenced by bpp::VectorProbabilisticSequenceContainer::addSequence(), bpp::VectorProbabilisticSiteContainer::addSequence(), bpp::VectorSequenceContainer::addSequence(), bpp::VectorSiteContainer::addSequence(), bpp::CompressedVectorSiteContainer::addSite(), bpp::AlignedSequenceContainer::addSite(), bpp::VectorSiteContainer::addSite(), bpp::SiteContainerTools::alignNW(), bpp::BasicSequence::append(), bpp::SequenceWithAnnotation::append(), bpp::SequenceTools::areSequencesIdentical(), bpp::SymbolListTools::areSymbolListsIdentical(), bpp::SequenceTools::bowkerTest(), bpp::SymbolListTools::changeGapsToUnknownCharacters(), bpp::SymbolListTools::changeUnresolvedCharactersToGaps(), bpp::SequenceTools::combineSequences(), bpp::SequenceTools::complement(), bpp::SiteContainerTools::computeSimilarity(), bpp::SequenceTools::concatenate(), bpp::SequenceWithAnnotationTools::createMaskAnnotation(), bpp::SequenceTools::findFirstOf(), bpp::CodonSiteTools::fixedDifferences(), bpp::CodonSiteTools::generateCodonSiteWithoutRareVariant(), bpp::SequenceTools::getCDS(), bpp::GeneticCode::getCodingSequence(), bpp::SequenceTools::getComplement(), bpp::SymbolListTools::getCounts(), bpp::SymbolListTools::getGCContent(), bpp::SequenceTools::getNumberOfCompleteSites(), bpp::SymbolListTools::getNumberOfDistinctPositions(), bpp::SymbolListTools::getNumberOfPositionsWithoutGap(), bpp::SequenceTools::getNumberOfSites(), bpp::SequenceTools::getNumberOfUnresolvedSites(), bpp::SequenceTools::getPercentIdentity(), bpp::SequenceTools::getPutativeHaplotypes(), bpp::SequenceTools::getSequenceWithCompleteSites(), bpp::SequenceTools::getSequenceWithoutGaps(), bpp::SequenceTools::getSequenceWithoutStops(), bpp::SymbolListTools::hasGap(), bpp::CodonSiteTools::hasGapOrStop(), bpp::CodonSiteTools::hasStop(), bpp::SymbolListTools::hasUnknown(), bpp::SymbolListTools::hasUnresolved(), bpp::SequenceTools::invertComplement(), bpp::SymbolListTools::isComplete(), bpp::SymbolListTools::isConstant(), bpp::SymbolListTools::isGapOnly(), bpp::SymbolListTools::isGapOrUnresolvedOnly(), bpp::CodonSiteTools::isMonoSitePolymorphic(), bpp::CodonSiteTools::isSynonymousPolymorphic(), bpp::SymbolListTools::jointEntropy(), bpp::CodonSiteTools::meanNumberOfSynonymousPositions(), bpp::SymbolListTools::mutualInformation(), bpp::Pasta::nextSequence(), bpp::PhredPoly::nextSequence(), bpp::SymbolListTools::numberOfGaps(), bpp::CodonSiteTools::numberOfNonSynonymousSubstitutions(), bpp::CodonSiteTools::numberOfSubstitutions(), bpp::SymbolListTools::numberOfUnresolved(), bpp::SymbolList< T >::operator=(), bpp::BasicProbabilisticSymbolList::operator=(), bpp::CodonSiteTools::piNonSynonymous(), bpp::CodonSiteTools::piSynonymous(), bpp::SequenceTools::removeGaps(), bpp::SequenceTools::removeStops(), bpp::SequenceTools::replaceStopsWithGaps(), bpp::WordAlphabet::reverse(), bpp::NucleicAcidsReplication::reverse(), bpp::AbstractReverseTransliterator::reverse(), bpp::SequenceTools::reverseTranscript(), bpp::SequenceTools::RNYslice(), bpp::VectorProbabilisticSiteContainer::setSequence(), bpp::VectorProbabilisticSequenceContainer::setSequence(), bpp::VectorSiteContainer::setSequence(), bpp::VectorSequenceContainer::setSequence(), bpp::AlignedSequenceContainer::setSite(), bpp::CompressedVectorSiteContainer::setSite(), bpp::VectorSiteContainer::setSite(), bpp::SequenceTools::subseq(), bpp::SequenceTools::subtractHaplotype(), bpp::SequenceTools::transcript(), bpp::NucleicAcidsReplication::translate(), bpp::AbstractTransliterator::translate(), bpp::WordAlphabet::translate(), bpp::SiteContainerTools::translateAlignment(), bpp::SymbolListTools::variabilityShannon(), and bpp::Pasta::writeSequence().

getContent()

template<class T >

virtual const std::vector<T>& bpp::CoreSymbolList< T >::getContent ( ) const

pure virtual

Implemented in bpp::ProbabilisticSequence, bpp::SymbolList< T >, bpp::SymbolList< int >, bpp::BasicProbabilisticSymbolList, and bpp::BasicProbabilisticSequence.

Referenced by bpp::SequenceWithQualityTools::concatenate(), bpp::SequenceWithQualityTools::invert(), bpp::BasicProbabilisticSymbolList::operator=(), bpp::BasicSequence::operator=(), and bpp::SequenceWithAnnotation::operator=().

getElement()

template<class T >

virtual const T& bpp::CoreSymbolList< T >::getElement ( size_t  pos ) const

pure virtual

Get the element at position 'pos' as a character.

Parameters

pos	The position of the character to retrieve.

Implemented in bpp::SymbolList< T >, bpp::SymbolList< int >, and bpp::BasicProbabilisticSymbolList.

getStateValueAt()

virtual double bpp::CruxSymbolList::getStateValueAt ( size_t  siteIndex, int  state  ) const

inlinevirtualinherited

Reimplemented in bpp::BasicProbabilisticSymbolList, bpp::BasicIntSymbolList, and bpp::EdCoreSymbolList< T >.

Definition at line 147 of file CoreSymbolList.h.

Referenced by bpp::VectorProbabilisticSiteContainer::addSequence(), bpp::BasicProbabilisticSymbolList::BasicProbabilisticSymbolList(), bpp::VectorProbabilisticSequenceContainer::getStateValueAt(), bpp::VectorSequenceContainer::getStateValueAt(), bpp::EdCoreSymbolList< T >::getStateValueAt(), and bpp::Pasta::writeSequence().

getValue()

template<class T >

virtual const T& bpp::CoreSymbolList< T >::getValue ( size_t  pos ) const

pure virtual

checked access to a character in list.

Parameters

pos	The position to retrieve.

Returns

The T value of character at position pos.

Implemented in bpp::SymbolList< T >, bpp::SymbolList< int >, and bpp::BasicProbabilisticSymbolList.

Referenced by bpp::VectorSiteContainer::addSequence(), bpp::SequenceTools::combineSequences(), bpp::SequenceTools::complement(), bpp::SequenceTools::findFirstOf(), bpp::SymbolListTools::getGCContent(), bpp::SequenceTools::getPercentIdentity(), bpp::SequenceTools::invert(), bpp::SequenceTools::invertComplement(), bpp::NucleicAcidsReplication::reverse(), bpp::AbstractReverseTransliterator::reverse(), bpp::VectorProbabilisticSiteContainer::setSequence(), bpp::VectorSiteContainer::setSequence(), bpp::SequenceTools::subtractHaplotype(), bpp::NucleicAcidsReplication::translate(), and bpp::AbstractTransliterator::translate().

operator()()

virtual double bpp::CruxSymbolList::operator() ( size_t  siteIndex, int  state  ) const

inlinevirtualinherited

Reimplemented in bpp::BasicProbabilisticSymbolList, bpp::BasicIntSymbolList, and bpp::EdCoreSymbolList< T >.

Definition at line 154 of file CoreSymbolList.h.

Referenced by bpp::EdCoreSymbolList< T >::operator()().

operator[]() [1/2]

template<class T >

virtual const T& bpp::CoreSymbolList< T >::operator[] ( size_t  pos ) const

pure virtual

Operator [] overloaded for quick access to a character in list.

Parameters

pos	The position to retrieve.

Returns

The T value of character at position pos.

Implemented in bpp::SymbolList< T >, bpp::SymbolList< int >, and bpp::BasicProbabilisticSymbolList.

operator[]() [2/2]

template<class T >

virtual T& bpp::CoreSymbolList< T >::operator[] ( size_t  pos )

pure virtual

Operator [] overloaded for quick access to a character in list.

Parameters

pos	The position to retrieve.

Returns

The T value of character at position pos.

Implemented in bpp::SymbolList< T >, bpp::SymbolList< int >, and bpp::BasicProbabilisticSymbolList.

setContent()

template<class T >

virtual void bpp::CoreSymbolList< T >::setContent ( const std::vector< T > &  list )

pure virtual

Set the whole content of the list.

Parameters

list	The new content of the list.

See also

The list constructor for information about the way lists are internaly stored.

Implemented in bpp::EdSymbolList< T >, bpp::SymbolList< T >, and bpp::BasicProbabilisticSymbolList.

Referenced by bpp::Pasta::nextSequence().

setElement()

template<class T >

virtual void bpp::CoreSymbolList< T >::setElement ( size_t  pos, const T &  c  )

pure virtual

Set the element at position 'pos' to character 'c'.

Parameters

pos	The position of the character to set.
c	The value of the element.

Implemented in bpp::EdSymbolList< T >, bpp::SymbolList< T >, and bpp::BasicProbabilisticSymbolList.

Referenced by bpp::SequenceTools::complement(), bpp::SequenceTools::invert(), bpp::SequenceTools::invertComplement(), bpp::SequenceTools::replaceStopsWithGaps(), and bpp::AlignedSequenceContainer::setSite().

shuffle()

virtual void bpp::CruxSymbolList::shuffle ( )

pure virtualinherited

Randomly shuffle the content of the list, with linear complexity.

Implemented in bpp::SymbolList< T >, bpp::SymbolList< int >, and bpp::BasicProbabilisticSymbolList.

size()

virtual size_t bpp::CruxSymbolList::size ( ) const

pure virtualinherited

Get the number of elements in the list.

Returns

The number of sites in the list.

Implemented in bpp::SymbolList< T >, bpp::SymbolList< int >, and bpp::BasicProbabilisticSymbolList.

Referenced by bpp::VectorProbabilisticSiteContainer::addSequence(), bpp::AlignedSequenceContainer::addSequence(), bpp::VectorSiteContainer::addSequence(), bpp::CompressedVectorSiteContainer::addSite(), bpp::AlignedSequenceContainer::addSite(), bpp::VectorSiteContainer::addSite(), bpp::AlignedSequenceContainer::AlignedSequenceContainer(), bpp::BasicSequence::append(), bpp::SequenceWithAnnotation::append(), bpp::SequenceTools::areSequencesIdentical(), bpp::SymbolListTools::areSymbolListsIdentical(), bpp::SequenceTools::bowkerTest(), bpp::SymbolListTools::changeGapsToUnknownCharacters(), bpp::SymbolListTools::changeUnresolvedCharactersToGaps(), bpp::AlignedSequenceContainer::checkSize_(), bpp::SequenceTools::combineSequences(), bpp::SequenceTools::complement(), bpp::SiteContainerTools::computeSimilarity(), bpp::SequenceTools::concatenate(), bpp::SequenceWithAnnotationTools::createMaskAnnotation(), bpp::SequenceTools::findFirstOf(), bpp::CodonSiteTools::fixedDifferences(), bpp::CodonSiteTools::generateCodonSiteWithoutRareVariant(), bpp::SiteContainerTools::getAlignmentPositions(), bpp::SequenceTools::getCDS(), bpp::GeneticCode::getCodingSequence(), bpp::SequenceContainerTools::getCodonPosition(), bpp::SymbolListTools::getCounts(), bpp::SequenceContainerTools::getCounts(), bpp::SymbolListTools::getFrequencies(), bpp::SequenceContainerTools::getFrequencies(), bpp::SymbolListTools::getGCContent(), bpp::SymbolListTools::getMajorAllele(), bpp::SymbolListTools::getMajorAlleleFrequency(), bpp::SymbolListTools::getMinorAllele(), bpp::SymbolListTools::getMinorAlleleFrequency(), bpp::SequenceTools::getNumberOfCompleteSites(), bpp::SymbolListTools::getNumberOfDistinctCharacters(), bpp::SymbolListTools::getNumberOfDistinctPositions(), bpp::SymbolListTools::getNumberOfPositionsWithoutGap(), bpp::SequenceTools::getNumberOfSites(), bpp::SequenceTools::getNumberOfUnresolvedSites(), bpp::SequenceTools::getPercentIdentity(), bpp::SequenceTools::getPutativeHaplotypes(), bpp::SiteContainerTools::getSequencePositions(), bpp::SequenceTools::getSequenceWithCompleteSites(), bpp::SequenceTools::getSequenceWithoutGaps(), bpp::SequenceTools::getSequenceWithoutStops(), bpp::CompressedVectorSiteContainer::getSiteIndex_(), bpp::VectorProbabilisticSequenceContainer::getStateValueAt(), bpp::VectorSequenceContainer::getStateValueAt(), bpp::CodonAlphabet::getWord(), bpp::WordAlphabet::getWord(), bpp::SymbolListTools::hasGap(), bpp::CodonSiteTools::hasGapOrStop(), bpp::SimpleSequencePositionIterator::hasMorePositions(), bpp::SymbolListTools::hasSingleton(), bpp::CodonSiteTools::hasStop(), bpp::SymbolListTools::hasUnknown(), bpp::SymbolListTools::hasUnresolved(), bpp::SymbolListTools::heterozygosity(), bpp::SequenceMask::init(), bpp::SequenceQuality::init(), bpp::SequenceTools::invert(), bpp::SequenceTools::invertComplement(), bpp::SymbolListTools::isComplete(), bpp::SymbolListTools::isConstant(), bpp::SymbolListTools::isDoubleton(), bpp::CodonSiteTools::isFourFoldDegenerated(), bpp::SymbolListTools::isGapOnly(), bpp::SymbolListTools::isGapOrUnresolvedOnly(), bpp::CodonSiteTools::isMonoSitePolymorphic(), bpp::SymbolListTools::isParsimonyInformativeSite(), bpp::CodonSiteTools::isSynonymousPolymorphic(), bpp::SymbolListTools::isTriplet(), bpp::SymbolListTools::jointEntropy(), bpp::CodonSiteTools::meanNumberOfSynonymousPositions(), bpp::SymbolListTools::mutualInformation(), bpp::SymbolListTools::numberOfGaps(), bpp::CodonSiteTools::numberOfNonSynonymousSubstitutions(), bpp::CodonSiteTools::numberOfSubstitutions(), bpp::SymbolListTools::numberOfUnresolved(), bpp::SymbolList< T >::operator=(), operator==(), bpp::CodonSiteTools::piNonSynonymous(), bpp::CodonSiteTools::piSynonymous(), bpp::SequenceTools::removeGaps(), bpp::SequenceTools::removeStops(), bpp::SequenceTools::replaceStopsWithGaps(), bpp::SiteContainerTools::resolveDottedAlignment(), bpp::CodonAlphabet::reverse(), bpp::WordAlphabet::reverse(), bpp::NucleicAcidsReplication::reverse(), bpp::AbstractReverseTransliterator::reverse(), bpp::SequenceTools::RNYslice(), bpp::SequenceContainerTools::sequencesHaveTheSameLength(), bpp::SequenceWalker::SequenceWalker(), bpp::VectorProbabilisticSiteContainer::setSequence(), bpp::VectorSiteContainer::setSequence(), bpp::AlignedSequenceContainer::setSequence(), bpp::AlignedSequenceContainer::setSite(), bpp::CompressedVectorSiteContainer::setSite(), bpp::VectorSiteContainer::setSite(), bpp::SequenceTools::subseq(), bpp::SequenceTools::subtractHaplotype(), bpp::SymbolList< T >::SymbolList(), bpp::NucleicAcidsReplication::translate(), bpp::AbstractTransliterator::translate(), bpp::CodonAlphabet::translate(), bpp::WordAlphabet::translate(), bpp::SiteContainerTools::translateAlignment(), bpp::SymbolListTools::variabilityFactorial(), bpp::SymbolListTools::variabilityShannon(), bpp::Phylip::writeInterleaved(), bpp::Fasta::writeSequence(), bpp::Pasta::writeSequence(), and bpp::Phylip::writeSequential().

toString()

virtual std::string bpp::CruxSymbolList::toString ( ) const

pure virtualinherited

Convert the list as a string.

This method is useful for dumping a list to a file or to the screen for display.

Returns

The whole list as a string.

Implemented in bpp::SymbolList< T >, bpp::SymbolList< int >, bpp::BasicSequence, bpp::BasicProbabilisticSymbolList, bpp::EdIntSymbolList, and bpp::BasicIntSymbolList.

Referenced by bpp::SequenceWithAnnotationTools::createMaskAnnotation(), bpp::AbstractProbabilisticSequenceContainer::toString(), bpp::AbstractSequenceContainer::toString(), bpp::VectorProbabilisticSequenceContainer::toString(), bpp::Clustal::writeAlignment(), and bpp::Stockholm::writeAlignment().

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

• Bpp/Seq/CoreSymbolList.h