bpp::CruxSymbolListSite Class Reference

The CruxSymbolListSite interface, from CoreSite and CruxSymbolList. More...

#include <Bpp/Seq/CruxSymbolListSite.h>

Inheritance diagram for bpp::CruxSymbolListSite:

Collaboration diagram for bpp::CruxSymbolListSite:

Public Member Functions
virtual	~CruxSymbolListSite ()
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
CruxSymbolListSite *	clone () const =0
Setting/getting the position of the site.
virtual int	getPosition () const =0
	Get the position of this site. More...
virtual void	setPosition (int position)=0
	Set the position of this site. 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

The CruxSymbolListSite interface, from CoreSite and CruxSymbolList.

Definition at line 55 of file CruxSymbolListSite.h.

Constructor & Destructor Documentation

~CruxSymbolListSite()

virtual bpp::CruxSymbolListSite::~CruxSymbolListSite ( )

inlinevirtual

Definition at line 69 of file CruxSymbolListSite.h.

Member Function Documentation

clone()

CruxSymbolListSite* bpp::CruxSymbolListSite::clone ( ) const

pure virtual

Implements bpp::CoreSite.

Implemented in bpp::Site, and bpp::ProbabilisticSite.

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().

getPosition()

virtual int bpp::CoreSite::getPosition ( ) const

pure virtualinherited

Get the position of this site.

Returns

The position of this site.

Implemented in bpp::AbstractCoreSite.

Referenced by bpp::AbstractCoreSite::operator=().

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().

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()().

setPosition()

virtual void bpp::CoreSite::setPosition ( int  position )

pure virtualinherited

Set the position of this site.

Parameters

position

The new position of the site.

Implemented in bpp::AbstractCoreSite.

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/CruxSymbolListSite.h