bpp Namespace Reference

This alphabet is used to deal NumericAlphabet. More...

Namespaces
	BrentOneDimension
	Graph
	IntegerTools
	NewtonBacktrackOneDimension
	PowellMultiDimensions
	StatTools
	TextTools
	VectorTools

Classes
class	DownhillSimplexMethod
class	AssociationGraphObserver
class	AssociationGraphImplObserver
class	GoldenSectionSearch
class	AbstractDiscreteDistribution
class	AbstractColorSet
class	AbstractFontManager
class	AbstractGraphicDevice
class	AbstractHmmLikelihood
class	AbstractHmmTransitionMatrix
class	AbstractNumericalDerivative
class	AbstractOptimizationStopCondition
class	AbstractOptimizer
class	AbstractOutputStream
class	AbstractParameterAliasable
class	AbstractParametrizable
class	AdaptiveKernelDensityEstimation
class	AliasParameterListener
class	ApplicationTools
class	AssociationDAGraphImplObserver
class	AssociationDAGraphObserver
class	AssociationTreeGraphImplObserver
class	AssociationTreeGraphObserver
class	AttributesTools
class	AutoCorrelationTransitionMatrix
class	AutoParameter
class	BackupListener
class	BadIntegerException
class	BadNumberException
class	BadSizeException
class	BetaDiscreteDistribution
class	BfgsMultiDimensions
class	BinaryOperator
class	BppApplication
class	BppBoolean
class	BppDouble
class	BppInteger
class	BppNotANumber
class	BppNumberI
class	BppODiscreteDistributionFormat
class	BppOParametrizableFormat
class	BppString
class	BppUnsignedInteger
class	BppVector
class	Bracket
class	BracketPoint
class	BrentOneDimension
class	Clonable
class	ColMatrix
class	ColorManager
class	ColorSet
class	ColorTools
class	ComputationTree
class	ConjugateGradientMultiDimensions
class	ConstantDistribution
class	ConstantOperator
class	ConstraintException
class	ConstraintInterface
class	ContingencyTableGenerator
class	ContingencyTableTest
class	CoordsTools
class	CorrespondenceAnalysis
class	DAGraph
class	DAGraphImpl
class	DataTable
class	DefaultColorSet
class	DimensionException
class	DirectionFunction
class	DirichletDiscreteDistribution
class	DiscreteDistributionInterface
class	DualityDiagram
class	DuplicatedTableColumnNameException
class	DuplicatedTableRowNameException
class	DvipsColorSet
class	EdgesIteratorClass
class	EdgesIteratorClass< Graph::ALLGRAPHITER, is_const >
class	EdgesIteratorClass< Graph::INCOMINGNEIGHBORITER, is_const >
class	EdgesIteratorClass< Graph::OUTGOINGNEIGHBORITER, is_const >
class	EigenValue
class	ElementNotFoundException
class	EmptyVectorException
class	Exception
class	ExponentialDiscreteDistribution
class	FileTools
class	FirstOrderDerivable
class	FirstOrderDerivableWrapper
class	FivePointsNumericalDerivative
class	Font
class	FontManager
class	FullHmmTransitionMatrix
class	FunctionInterface
class	FunctionOperator
class	FunctionStopCondition
class	FunctionTools
class	FunctionWrapper
class	GammaDiscreteDistribution
class	GaussianDiscreteDistribution
class	GlobalGraph
class	Graph
class	GraphicDevice
class	GraphObserver
class	HmmBadStateException
class	HmmEmissionProbabilities
class	HmmLikelihood
class	HmmStateAlphabet
class	HmmTransitionMatrix
class	HmmUnvalidAlphabetException
class	IDiscreteDistribution
class	IndexOutOfBoundsException
class	InfinityDerivableFirstOrderWrapper
class	InfinityDerivableSecondOrderWrapper
class	InfinityFunctionWrapper
class	IntervalConstraint
class	IntervalTransformedParameter
class	InvariantMixedDiscreteDistribution
class	IoDiscreteDistribution
class	IoDiscreteDistributionFactory
class	IOException
class	IOFormat
class	IOParametrizable
class	KeyvalException
class	KeyvalTools
class	LinearMatrix
class	LogsumHmmLikelihood
class	LowMemoryRescaledHmmLikelihood
class	LUDecomposition
class	MapTools
class	MathOperator
class	Matrix
class	MatrixTools
class	MetaOptimizer
class	MetaOptimizerInfos
class	MixtureOfDiscreteDistributions
class	MolscriptColorSet
class	MultipleDiscreteDistribution
class	MultiRange
class	NegativeOperator
class	NeighborIteratorClass
class	NestedStringTokenizer
class	NewtonBacktrackOneDimension
class	NewtonOneDimension
class	NodesIteratorClass
class	NodesIteratorClass< Graph::ALLGRAPHITER, is_const >
class	NodesIteratorClass< Graph::INCOMINGNEIGHBORITER, is_const >
class	NodesIteratorClass< Graph::OUTGOINGNEIGHBORITER, is_const >
class	NoTableColumnNamesException
class	NoTableRowNamesException
class	NotImplementedException
class	NullOutputStream
class	NullPointerException
class	Number
class	NumberFormatException
class	NumCalcApplicationTools
class	NumConstants
class	NumTools
class	ODiscreteDistribution
class	OneDimensionOptimizationTools
class	OParametrizable
class	Operator
class	OptimizationEvent
class	OptimizationListener
class	OptimizationStopCondition
class	OptimizerInterface
class	OrderedSimplex
class	OutOfRangeException
class	OutputStream
class	Parameter
class	ParameterAliasable
class	ParameterAliasableAdapter
class	ParameterEvent
class	ParameterException
class	ParameterGrid
class	ParameterList
class	ParameterListener
class	ParameterNotFoundException
class	ParametersStopCondition
class	Parametrizable
class	ParametrizableAdapter
class	ParametrizableCollection
class	PgfGraphicDevice
class	PlaceboTransformedParameter
class	Point2D
class	PowellMultiDimensions
class	PrincipalComponentAnalysis
class	RandomTools
class	Range
class	RangeCollection
class	rangeComp_
class	RangeSet
class	RColorSet
class	ReparametrizationDerivableFirstOrderWrapper
class	ReparametrizationDerivableSecondOrderWrapper
class	ReparametrizationFunctionWrapper
class	RescaledHmmLikelihood
class	RGBColor
class	RowMatrix
class	RTransformedParameter
class	SecondOrderDerivable
class	SecondOrderDerivableWrapper
class	SimpleDiscreteDistribution
class	SimpleMultiDimensions
class	SimpleNewtonMultiDimensions
class	Simplex
class	StateChangedEvent
class	StateListener
class	StatTest
class	StatTools
class	StdErr
class	StdOut
class	StdStr
class	StlOutputStream
class	StlOutputStreamWrapper
class	StringTokenizer
class	SvgGraphicDevice
class	Table
class	TableColumnNameNotFoundException
class	TableColumnNamesException
class	TableNameNotFoundException
class	TableRowNameNotFoundException
class	TableRowNamesException
class	TestFunction
class	ThreePointsNumericalDerivative
class	TransformedParameter
class	TreeGraph
class	TreeGraphImpl
class	TruncatedExponentialDiscreteDistribution
class	TwoPointsNumericalDerivative
class	UniformDiscreteDistribution
class	UnvalidFlagException
class	VectorException
class	VectorTools
class	XFigColorManager
class	XFigGraphicDevice
class	XFigLaTeXFontManager
class	XFigPostscriptFontManager
class	ZeroDivisionException
class	AbstractAlphabet
	A partial implementation of the Alphabet interface. More...
class	AllelicAlphabet
	The base class for allelic alphabets. More...
class	Alphabet
	The Alphabet interface. More...
class	AlphabetException
	The alphabet exception base class. More...
class	BadCharException
	An alphabet exception thrown when trying to specify a bad char to the alphabet. More...
class	BadIntException
	An alphabet exception thrown when trying to specify a bad int to the alphabet. More...
class	AlphabetMismatchException
	Exception thrown when two alphabets do not match. More...
class	CharStateNotSupportedException
	Exception thrown in case no character is available for a certain state in an alphabet. More...
class	AlphabetNumericState
	States that do have a double value. More...
class	AlphabetState
	This is the base class to describe states in an Alphabet. More...
class	AlphabetTools
	Utilitary functions dealing with alphabets. More...
class	BinaryAlphabet
	The BinaryAlphabet class, letters are 0 and 1. More...
class	CaseMaskedAlphabet
	Case-sensitive letter alphabet. More...
class	CodonAlphabet
	Codon alphabet class. More...
class	DefaultAlphabet
	The DefaultAlphabet class. More...
class	DNA
	This alphabet is used to deal with DNA sequences. More...
class	IntegerAlphabet
	The Integer Alphabet class, letters are from 0 to a given number, MAX. More...
class	LetterAlphabet
	Specialized partial implementation of Alphabet using single letters. More...
class	LexicalAlphabet
	Alphabet made of given words. More...
class	NucleicAlphabet
	The abstract base class for nucleic alphabets. More...
class	NucleicAlphabetState
	This is the base class to describe states in a NucleicAlphabet. More...
class	NumericAlphabet
class	ProteicAlphabet
	This alphabet is used to deal with proteins. More...
class	ProteicAlphabetState
	This is the base class to describe states in a ProteicAlphabet. More...
class	RNA
	This alphabet is used to deal with RNA sequences. More...
class	RNY
class	CoreWordAlphabet
	The interface class for word alphabets. More...
class	WordAlphabet
	The base class for word alphabets. More...
class	AAChargeIndex
	Charge of each amino acid. More...
class	AAChenGuHuangHydrophobicityIndex
	Hydrophobicity of each amino acid, according to Table 1 in Chen, Gu and Huang, BMC Bioinformatics 2006. More...
class	AAChouFasmanAHelixIndex
	A-Helix score for the Chou-Fasman algorithm of secondary structure prediction, according to http://prowl.rockefeller.edu/aainfo/chou.htm. More...
class	AAChouFasmanBSheetIndex
	B-sheet score for the Chou-Fasman algorithm of secondary structure prediction, according to http://prowl.rockefeller.edu/aainfo/chou.htm. More...
class	AAChouFasmanTurnIndex
	Turn score for the Chou-Fasman algorithm of secondary structure prediction, according to http://prowl.rockefeller.edu/aainfo/chou.htm. More...
class	AAIndex1Entry
	Create a AlphabetIndex1 object from an AAIndex2 entry. More...
class	AAIndex2Entry
	Create a AlphabetIndex2 object from an AAIndex2 entry. More...
class	AAMassIndex
	Mass (dalton) of each amino acid, according to http://www.imb-jena.de/IMAGE_AA.html. More...
class	AASEA1030Index
	Percentage of amino acids having a Solvent Exposed Area between 10 and 30 Angström^2 for each type of amino acid, according to http://prowl.rockefeller.edu/aainfo/access.htm. More...
class	AASEAInf10Index
	Percentage of amino acids having a Solvent Exposed Area below 10 Angström^2 for each type of amino acid, according to http://prowl.rockefeller.edu/aainfo/access.htm. More...
class	AASEASup30Index
	Percentage of amino acids having a Solvent Exposed Area above 30 Angström^2 for each type of amino acid, according to http://prowl.rockefeller.edu/aainfo/access.htm. More...
class	AASurfaceIndex
	Surface (Angström^2) of each amino acid, according to http://www.imb-jena.de/IMAGE_AA.html. More...
class	AAVolumeIndex
	Volume (Angström^3) of each amino acid, according to http://www.imb-jena.de/IMAGE_AA.html (Note: original webpage is not available anymore) More...
class	AlphabetIndex1
	One dimensionnal alphabet index interface. More...
class	ProteicAlphabetIndex1
class	AlphabetIndex2
	Two dimensionnal alphabet index interface. More...
class	ProteicAlphabetIndex2
	Virtual AlphabetIndex2 for proteic alphabet. More...
class	BLOSUM50
	BLOSUM 50 Substitution Matrix. More...
class	CodonFromProteicAlphabetIndex1
	AlphabetIndex1 for codon based on ProteicAlphabetIndex1. More...
class	CodonFromProteicAlphabetIndex2
class	DefaultNucleotideScore
	Default Substitution Matrix for nucleotide alignments. More...
class	GranthamAAChemicalDistance
	Grantham (1974) Amino-Acid chemical distance. More...
class	GranthamAAPolarityIndex
	Polarity index used in Grantham (1974). More...
class	GranthamAAVolumeIndex
	Volume index used in Grantham (1974). More...
class	KD_AAHydropathyIndex
	Hydropathy index defined in Kyte & Doolitle (1982). More...
class	KleinAANetChargeIndex
	Charge of each amino acid. More...
class	MiyataAAChemicalDistance
	Miyata et al. (1979) Amino-Acid chemical distance. More...
class	SimpleIndexDistance
	Simple dissimilarity distance. More...
class	SimpleScore
	Simple Substitution Matrix, with match and mismatch penalties. More...
class	UserAlphabetIndex1
	Alphabet index given by user. More...
class	UserAlphabetIndex2
	Alphabet index given by user. More...
class	BppSequenceApplication
class	SequenceApplicationTools
	This class provides some common tools for applications. More...
class	CodonSiteTools
	Utilitary functions for codon sites. More...
class	Commentable
class	SimpleCommentable
class	AbstractTemplateSequenceContainer
	Partial implementation of the SequenceContainer interface. More...
class	TemplateAlignedSequenceContainer
	The AlignedSequencesContainer class. More...
class	TemplateAlignmentDataInterface
	The Container of Aligned Values interface. More...
class	CompressedVectorSiteContainer
	A low memory, yet restricted, version of the VectorSiteContainer class. More...
class	MappedNamedContainer
	MappedNamedContainer class. More...
class	NamedContainerInterface
	A Container template for objects that are accessible through names. More...
class	PositionedContainerInterface
	The PositionedContainer interface. More...
class	PositionedNamedContainerInterface
	The template PositionedNamedContainer interface, that links position & name containers. More...
class	TemplateSequenceContainerInterface
	The SequenceContainer interface. More...
class	SwitchDeleter
class	SequenceNotFoundException
	Exception thrown when a sequence is not found The sequence not found exception base class. More...
class	EmptyContainerException
	Exception thrown when an empty container is found. More...
class	SequenceContainerTools
	Utilitary methods dealing with sequence containers. More...
class	TemplateSequenceDataInterface
	The SequenceData interface. More...
class	SequencedValuesContainer
class	TemplateSiteContainerInterface
	The SiteContainer interface. More...
class	SiteNotFoundException
	The site not found exception base class. More...
class	AbstractTemplateSiteContainerIterator
	Partial implementation of the SiteIterator interface, allowing to loop over a site container. More...
class	SimpleTemplateSiteContainerIterator
	Loop over all sites in a SiteContainer. More...
class	NoGapTemplateSiteContainerIterator
	Loop over all sites without gaps in a SiteContainer. More...
class	CompleteTemplateSiteContainerIterator
	Loop over all complete sites in a SiteContainer (i.e. sites without gap and unresolved characters). More...
class	SiteContainerTools
	Some utililitary methods to deal with site containers. More...
class	VectorMappedContainer
	The template VectorMappedContainer class. More...
class	VectorPositionedContainer
	The template VectorPositionedContainer class. More...
class	TemplateVectorSequenceContainer
	The VectorSequenceContainer class. More...
class	TemplateVectorSiteContainer
	The VectorSiteContainer class. More...
class	CoreSequenceInterface
	The core sequence interface. More...
class	AbstractCoreSequence
	A partial implementation of the CoreSequence interface. More...
class	CoreSiteInterface
	The core site interface. More...
class	AbstractCoreSite
	A partial implementation of the CoreSite interface. More...
class	CruxSymbolListInterface
	The CruxSymbolList interface. More...
class	TemplateCoreSymbolListInterface
	The CoreSymbolList interface. More...
class	CoreSymbolListEditionEvent
class	CoreSymbolListInsertionEvent
class	CoreSymbolListDeletionEvent
class	CoreSymbolListSubstitutionEvent
class	CoreSymbolListListener
class	TemplateEventDrivenCoreSymbolListInterface
	Interface for event-driven CoreSymbolList objects. More...
class	DistanceMatrix
	A Matrix class to store phylogenetic distances. More...
class	DNAToRNA
	Reverse iterator to convert RNA to DNA. More...
class	AscidianMitochondrialGeneticCode
	This class implements the ascidian mitochondrial genetic code as describe on the NCBI web site: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG13. More...
class	CiliateNuclearGeneticCode
	This class implements the mold, protozoan, and coelenterate mitochondrial code and the Mycoplasma/Spiroplasma code as describe on the NCBI website: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG4. More...
class	EchinodermMitochondrialGeneticCode
	This class implements the Echinoderm and Faltworms Mitochondrial genetic code as describe on the NCBI website: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG9. More...
class	StopCodonException
	Exception thrown when a stop codon is found. More...
class	GeneticCode
	Partial implementation of the Transliterator interface for genetic code object. More...
class	InvertebrateMitochondrialGeneticCode
	This class implements the Invertebrate Mitochondrial genetic code as describe on the NCBI website: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG5. More...
class	MoldMitochondrialGeneticCode
	This class implements the mold, protozoan, and coelenterate mitochondrial code and the Mycoplasma/Spiroplasma code as describe on the NCBI website: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG4. More...
class	StandardGeneticCode
	This class implements the standard genetic code as describe on the NCBI web site: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG1. More...
class	VertebrateMitochondrialGeneticCode
	This class implements the vertebrate mitochondrial genetic code as describe on the NCBI web site: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG2. More...
class	YeastMitochondrialGeneticCode
	This class implements the Invertebrate Mitochondrial genetic code as describe on the NCBI website: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG3. More...
class	IntSymbolListInterface
	The specific IntSymbolList interface. More...
class	IntSymbolList
	A basic IntSymbolList object. More...
class	EventDrivenIntSymbolList
	A event-driven IntSymbolList object. More...
class	AbstractIAlignment
	Partial implementation of the IAlignment interface, dedicated to alignment readers. More...
class	AbstractIAlignment2
	Partial implementation of the IAlignment and ISequence interface, dedicated to alignment readers. More...
class	AbstractIProbabilisticAlignment
class	AbstractIProbabilisticAlignment2
class	AbstractISequence
	Partial implementation of the ISequence interface. More...
class	AbstractIProbabilisticSequence
	Partial implementation of the IProbabilisticSequence interface. More...
class	AbstractOAlignment
	Partial implementation of the OAlignment interface. More...
class	AbstractOProbabilisticAlignment
	Partial implementation of the OProbabilisticAlignment interface. More...
class	AbstractOSequence
	Partial implementation of the OSequence interface. More...
class	AbstractOSequence2
	Partial implementation of the OAlignment interface. More...
class	AbstractOProbabilisticSequence
	Partial implementation of the OProbabilisticSequence interface. More...
class	AbstractOProbabilisticSequence2
	Partial implementation of the OProbabilisticAlignment interface. More...
class	BppOAlignmentReaderFormat
	Sequence I/O in BppO format. More...
class	BppOAlignmentWriterFormat
	Sequence I/O in BppO format. More...
class	BppOAlphabetIndex1Format
	AlphabetIndex1 I/O in BppO format. More...
class	BppOAlphabetIndex2Format
	AlphabetIndex2 I/O in BppO format. More...
class	BppOSequenceReaderFormat
	Sequence I/O in BppO format. More...
class	BppOSequenceStreamReaderFormat
	Sequence I/O in BppO format. More...
class	BppOSequenceWriterFormat
	Sequence I/O in BppO format. More...
class	Clustal
	The clustal sequence file format. More...
class	DCSE
	Support for the Dedicated Comparative Sequence Editor format. More...
class	Fasta
	The fasta sequence file format. More...
class	GenBank
	The GenBank sequence file format. More...
class	IODistanceMatrix
	General interface for distance matrix I/O. More...
class	IDistanceMatrix
	General interface for distance matrix readers. More...
class	ODistanceMatrix
	General interface for distance matrix writers. More...
class	AbstractIDistanceMatrix
	Partial implementation of the IDistanceMatrix interface. More...
class	AbstractODistanceMatrix
	Partial implementation of the ODistanceMatrix interface. More...
class	IODistanceMatrixFactory
	Utilitary class for creating distance matrix readers and writers. More...
class	IOSequence
	The IOSequence interface. More...
class	IOProbabilisticSequence
	The IOProbabislisticSequence interface. More...
class	IoSequenceFactory
	Utilitary class for creating sequence readers and writers. More...
class	IOSequenceStream
	The IOSequenceStream interface. More...
class	ISequence
	The ISequence interface. More...
class	IAlignment
	The IAlignment interface. More...
class	IProbabilisticSequence
	The IProbabilisticSequence interface. More...
class	IProbabilisticAlignment
	The IProbabilisticSequence interface. More...
class	TemplateISequenceStream
	The ISequenceStream interface. More...
class	MaseHeader
	A class to store information from the header of Mase files. More...
class	Mase
	The mase sequence file format. More...
class	MaseTools
	Utilitary methods that deal with the Mase format. More...
class	NexusIOSequence
	The Nexus format reader for sequences. More...
class	NexusTools
	Tools for parsing Nexus files. More...
class	OSequence
	The OSequence interface. More...
class	OAlignment
	The OAlignment interface. More...
class	OProbabilisticSequence
	The OProbabilisticSequence interface. More...
class	OProbabilisticAlignment
	The OProbabilisticAlignment interface. More...
class	TemplateOSequenceStream
	The OSequenceStream interface. More...
class	Pasta
	The Pasta sequence file format. More...
class	PhredPhd
	The phd sequence file format from phred software. More...
class	PhredPoly
	The poly sequence file format from phred software. More...
class	Phylip
	The Phylip & co format. More...
class	PhylipDistanceMatrixFormat
	Distance matrix I/O in Phylip format. More...
class	SequenceFileIndex
	Index to retrieve Sequence in a file. More...
class	Stockholm
	The Stockholm alignment file format. More...
class	TemplateStreamSequenceIterator
	A sequence iterator based on a sequence stream. More...
class	NucleicAcidsReplication
	Replication between to nucleic acids. More...
class	ProbabilisticSequenceInterface
	The probabilistic sequence interface. More...
class	ProbabilisticSequence
	A basic implementation of the ProbabilisticSequence interface. More...
class	ProbabilisticSiteInterface
	The ProbabilisticSite interface. More...
class	ProbabilisticSite
class	ProbabilisticSymbolListInterface
	The ProbabilisticSymbolList interface. More...
class	ProbabilisticSymbolList
	ProbabilisticSymbolList object. More...
class	SequenceInterface
	The sequence interface. More...
class	Sequence
	A basic implementation of the Sequence interface. More...
class	SequenceException
	The sequence exception base class. More...
class	EmptySequenceException
	Exception thrown when a sequence is found to be empty and it should not. More...
class	SequenceWithGapException
	Exception thrown when a sequence is found to have gap and it should not. More...
class	SequenceNotAlignedException
	Exception thrown when a sequence is not align with others. More...
class	TemplateSequenceIteratorInterface
	Generic sequence iterator interface, allowing to loop over sequences. More...
class	SequencePositionIterator
	Loop over a Sequence. More...
class	AbstractSequencePositionIterator
	Partial implementation of the SequencePositionIterator interface. More...
class	SimpleSequencePositionIterator
	Loop over all positions in a Sequence. More...
class	BowkerTest
	Bowker's homogeneity test results class. More...
class	SequenceTools
	SequenceTools static class. More...
class	SequenceWalker
	A helper class to easily convert coordinates between sequence and alignments. More...
class	SequenceAnnotation
	Interface for sequence annotations. More...
class	SequenceWithAnnotation
	An implementation of the Sequence interface that supports annotation. More...
class	SequenceMask
class	SequenceWithAnnotationTools
	The SequenceWithAnnotationTools static class. More...
class	SequenceQuality
	The SequenceQuality class. More...
class	SequenceWithQuality
	A SequenceWithAnnotation class with quality scores attached. More...
class	SequenceWithQualityTools
	The SequenceWithQualityTools static class. More...
class	SiteInterface
	The site interface. More...
class	Site
	The Site class. More...
class	SiteException
	The site exception base class. More...
class	EmptySiteException
	Exception sent when a empty site is found. More...
class	SiteWithGapException
	Exception sent when a site containing gap is found. More...
class	TemplateSiteIteratorInterface
	Generic site iterator interface, allowing to loop over sites. More...
class	SiteTools
	Utilitary methods dealing with sites. More...
class	StringSequenceTools
	Utilitary methods working on raw string objects. More...
class	AbstractTemplateSymbolList
	A partial implementation of a SymbolList object. More...
class	AbstractTemplateEventDrivenSymbolList
	A partial implementation of a EventDrivenSymbolList object. More...
class	SymbolListTools
	Utilitary functions dealing with both sites and sequences. More...
class	TransliteratorInterface
	This interface is used when translating a sequence from an alphabet to another: it gives the translation rules, eg: RNA -> DNA. More...
class	ReverseTransliteratorInterface
	The same as previous, but can perform the reverse translation, eg: RNA -> DNA and DNA -> RNA;. More...
class	AbstractTransliterator
	Partial implementation of the Transliterator interface. More...
class	AbstractReverseTransliterator
	Partial implementation of the ReverseTransliterator interface. More...

Typedefs
typedef AssociationDAGraphImplObserver< N, E, DAGlobalGraph >	AssociationDAGlobalGraphObserver
typedef AssociationGraphImplObserver< N, E, GlobalGraph >	AssociationGlobalGraphObserver
typedef AssociationTreeGraphImplObserver< N, E, TreeGlobalGraph >	AssociationTreeGlobalGraphObserver
typedef DAGraphImpl< GlobalGraph >	DAGlobalGraph
typedef TreeGraphImpl< GlobalGraph >	TreeGlobalGraph
typedef std::vector< std::complex< double > >	Vcomplex
typedef std::vector< Vcomplex >	VVcomplex
typedef std::vector< VVcomplex >	VVVcomplex
typedef std::vector< std::complex< long double > >	Vlcomplex
typedef std::vector< Vlcomplex >	VVlcomplex
typedef std::vector< VVlcomplex >	VVVlcomplex
typedef std::vector< double >	Vdouble
typedef std::vector< Vdouble >	VVdouble
typedef std::vector< VVdouble >	VVVdouble
typedef std::vector< VVVdouble >	VVVVdouble
typedef std::vector< long double >	Vldouble
typedef std::vector< Vldouble >	VVldouble
typedef std::vector< VVldouble >	VVVldouble
typedef std::vector< VVVldouble >	VVVVldouble
typedef std::vector< int >	Vint
typedef std::vector< Vint >	VVint
typedef std::vector< VVint >	VVVint
typedef std::vector< VVVint >	VVVVint
typedef std::vector< unsigned int >	Vuint
typedef std::vector< Vuint >	VVuint
typedef std::vector< VVuint >	VVVuint
typedef std::vector< VVVuint >	VVVVuint
typedef std::vector< std::string >	Comments
	Declaration of Comments type. More...
using	AlignedSequenceContainer = TemplateAlignedSequenceContainer< Sequence, Site >
using	ProbabilisticAlignedSequenceContainer = TemplateAlignedSequenceContainer< ProbabilisticSequence, ProbabilisticSite >
using	AlignmentDataInterface = TemplateAlignmentDataInterface< std::string >
using	SequenceContainerInterface = TemplateSequenceContainerInterface< Sequence >
using	ProbabilisticSequenceContainerInterface = TemplateSequenceContainerInterface< ProbabilisticSequence >
using	SequenceSelection = std::vector< size_t >
using	SiteSelection = std::vector< size_t >
using	SequenceDataInterface = TemplateSequenceDataInterface< std::string >
using	SiteContainerInterface = TemplateSiteContainerInterface< Site, Sequence, std::string >
using	ProbabilisticSiteContainerInterface = TemplateSiteContainerInterface< ProbabilisticSite, ProbabilisticSequence, std::string >
using	SimpleSiteContainerIterator = SimpleTemplateSiteContainerIterator< Site, Sequence, std::string >
using	SimpleProbabilisticSiteContainerIterator = SimpleTemplateSiteContainerIterator< ProbabilisticSite, ProbabilisticSequence, std::string >
using	VectorSequenceContainer = TemplateVectorSequenceContainer< Sequence >
using	ProbabilisticVectorSequenceContainer = TemplateVectorSequenceContainer< ProbabilisticSequence >
using	VectorSiteContainer = TemplateVectorSiteContainer< Site, Sequence >
using	ProbabilisticVectorSiteContainer = TemplateVectorSiteContainer< ProbabilisticSite, ProbabilisticSequence >
using	IntCoreSymbolListInterface = TemplateCoreSymbolListInterface< int >
using	ProbabilisticCoreSymbolListInterface = TemplateCoreSymbolListInterface< std::vector< double > >
using	IntEventDrivenCoreSymbolListInterface = TemplateEventDrivenCoreSymbolListInterface< int >
using	ProbabilisticEventDrivenCoreSymbolListInterface = TemplateEventDrivenCoreSymbolListInterface< std::vector< double > >
typedef CoreSymbolListListener< int >	IntSymbolListListener
typedef CoreSymbolListEditionEvent< int >	IntSymbolListEditionEvent
typedef CoreSymbolListInsertionEvent< int >	IntSymbolListInsertionEvent
typedef CoreSymbolListDeletionEvent< int >	IntSymbolListDeletionEvent
typedef CoreSymbolListSubstitutionEvent< int >	IntSymbolListSubstitutionEvent
using	ISequenceStream = TemplateISequenceStream< Sequence >
using	ISequenceWithQualityStream = TemplateISequenceStream< SequenceWithQuality >
using	IProbabilisticSequenceStream = TemplateISequenceStream< ProbabilisticSequence >
using	OSequenceStream = TemplateOSequenceStream< Sequence >
using	OSequenceWithQualityStream = TemplateOSequenceStream< SequenceWithQuality >
using	OProbabilisticSequenceStream = TemplateOSequenceStream< ProbabilisticSequence >

Functions
std::ostream &	operator<< (std::ostream &out, const BppBoolean &s)
std::ostream &	operator<< (std::ostream &out, const BppString &s)
bool	operator== (const Matrix< Scalar > &m1, const Matrix< Scalar > &m2)
std::vector< T >	operator+ (const std::vector< T > &v1, const std::vector< T > &v2)
std::vector< T >	operator- (const std::vector< T > &v1, const std::vector< T > &v2)
std::vector< T >	operator* (const std::vector< T > &v1, const std::vector< T > &v2)
std::vector< T >	operator/ (const std::vector< T > &v1, const std::vector< T > &v2)
std::vector< T >	operator+ (const std::vector< T > &v1, const C &c)
std::vector< T >	operator+ (const C &c, const std::vector< T > &v1)
std::vector< T >	operator- (const std::vector< T > &v1, const C &c)
std::vector< T >	operator- (const C &c, const std::vector< T > &v1)
std::vector< T >	operator* (const std::vector< T > &v1, const C &c)
std::vector< T >	operator* (const C &c, const std::vector< T > &v1)
std::vector< T >	operator/ (const std::vector< T > &v1, const C &c)
std::vector< T >	operator/ (const C &c, const std::vector< T > &v1)
void	operator+= (std::vector< T > &v1, const std::vector< T > &v2)
void	operator-= (std::vector< T > &v1, const std::vector< T > &v2)
void	operator*= (std::vector< T > &v1, const std::vector< T > &v2)
void	operator/= (std::vector< T > &v1, const std::vector< T > &v2)
void	operator&= (std::vector< T > &v1, const C &c)
void	operator+= (std::vector< T > &v1, const C &c)
void	operator-= (std::vector< T > &v1, const C &c)
void	operator*= (std::vector< T > &v1, const C &c)
void	operator/= (std::vector< T > &v1, const C &c)

Detailed Description

This alphabet is used to deal NumericAlphabet.

This alphabet is used to deal quotiented triplet RNY + combinations with "-".

Author

Laurent Guéguen

More explicitly, a quotiented triplet RNY is defined on the alphabet

.

Triplet "---" is the only triplet defined as gap. Other triplets with "-" are defined as unresolved.

Author

Laurent Guéguen

Typedef Documentation

AlignedSequenceContainer

using bpp::AlignedSequenceContainer = typedef TemplateAlignedSequenceContainer<Sequence, Site>

Definition at line 577 of file AlignedSequenceContainer.h.

AlignmentDataInterface

using bpp::AlignmentDataInterface = typedef TemplateAlignmentDataInterface<std::string>

Definition at line 77 of file AlignmentData.h.

Comments

typedef std::vector<std::string> bpp::Comments

Declaration of Comments type.

Comments are defined as a std::vector of std::strings to allow the later creation of a full Comments class.

Definition at line 21 of file Commentable.h.

IntCoreSymbolListInterface

using bpp::IntCoreSymbolListInterface = typedef TemplateCoreSymbolListInterface<int>

Definition at line 251 of file CoreSymbolList.h.

IntEventDrivenCoreSymbolListInterface

using bpp::IntEventDrivenCoreSymbolListInterface = typedef TemplateEventDrivenCoreSymbolListInterface<int>

Definition at line 442 of file CoreSymbolList.h.

IntSymbolListDeletionEvent

typedef CoreSymbolListDeletionEvent<int> bpp::IntSymbolListDeletionEvent

Definition at line 230 of file IntSymbolList.h.

IntSymbolListEditionEvent

typedef CoreSymbolListEditionEvent<int> bpp::IntSymbolListEditionEvent

Definition at line 226 of file IntSymbolList.h.

IntSymbolListInsertionEvent

typedef CoreSymbolListInsertionEvent<int> bpp::IntSymbolListInsertionEvent

Definition at line 228 of file IntSymbolList.h.

IntSymbolListListener

typedef CoreSymbolListListener<int> bpp::IntSymbolListListener

Definition at line 224 of file IntSymbolList.h.

IntSymbolListSubstitutionEvent

typedef CoreSymbolListSubstitutionEvent<int> bpp::IntSymbolListSubstitutionEvent

Definition at line 232 of file IntSymbolList.h.

IProbabilisticSequenceStream

using bpp::IProbabilisticSequenceStream = typedef TemplateISequenceStream<ProbabilisticSequence>

Definition at line 48 of file ISequenceStream.h.

ISequenceStream

using bpp::ISequenceStream = typedef TemplateISequenceStream<Sequence>

Definition at line 46 of file ISequenceStream.h.

ISequenceWithQualityStream

using bpp::ISequenceWithQualityStream = typedef TemplateISequenceStream<SequenceWithQuality>

Definition at line 47 of file ISequenceStream.h.

OProbabilisticSequenceStream

using bpp::OProbabilisticSequenceStream = typedef TemplateOSequenceStream<ProbabilisticSequence>

Definition at line 46 of file OSequenceStream.h.

OSequenceStream

using bpp::OSequenceStream = typedef TemplateOSequenceStream<Sequence>

Definition at line 44 of file OSequenceStream.h.

OSequenceWithQualityStream

using bpp::OSequenceWithQualityStream = typedef TemplateOSequenceStream<SequenceWithQuality>

Definition at line 45 of file OSequenceStream.h.

ProbabilisticAlignedSequenceContainer

using bpp::ProbabilisticAlignedSequenceContainer = typedef TemplateAlignedSequenceContainer<ProbabilisticSequence, ProbabilisticSite>

Definition at line 578 of file AlignedSequenceContainer.h.

ProbabilisticCoreSymbolListInterface

using bpp::ProbabilisticCoreSymbolListInterface = typedef TemplateCoreSymbolListInterface< std::vector<double> >

Definition at line 252 of file CoreSymbolList.h.

ProbabilisticEventDrivenCoreSymbolListInterface

using bpp::ProbabilisticEventDrivenCoreSymbolListInterface = typedef TemplateEventDrivenCoreSymbolListInterface< std::vector<double> >

Definition at line 443 of file CoreSymbolList.h.

ProbabilisticSequenceContainerInterface

using bpp::ProbabilisticSequenceContainerInterface = typedef TemplateSequenceContainerInterface<ProbabilisticSequence>

Definition at line 184 of file SequenceContainer.h.

ProbabilisticSiteContainerInterface

using bpp::ProbabilisticSiteContainerInterface = typedef TemplateSiteContainerInterface<ProbabilisticSite, ProbabilisticSequence, std::string>

Definition at line 123 of file SiteContainer.h.

ProbabilisticVectorSequenceContainer

using bpp::ProbabilisticVectorSequenceContainer = typedef TemplateVectorSequenceContainer<ProbabilisticSequence>

Definition at line 395 of file VectorSequenceContainer.h.

ProbabilisticVectorSiteContainer

using bpp::ProbabilisticVectorSiteContainer = typedef TemplateVectorSiteContainer<ProbabilisticSite, ProbabilisticSequence>

Definition at line 825 of file VectorSiteContainer.h.

SequenceContainerInterface

using bpp::SequenceContainerInterface = typedef TemplateSequenceContainerInterface<Sequence>

Definition at line 183 of file SequenceContainer.h.

SequenceDataInterface

using bpp::SequenceDataInterface = typedef TemplateSequenceDataInterface<std::string>

Definition at line 233 of file SequenceData.h.

SequenceSelection

using bpp::SequenceSelection = typedef std::vector<size_t>

Definition at line 23 of file SequenceContainerTools.h.

SimpleProbabilisticSiteContainerIterator

using bpp::SimpleProbabilisticSiteContainerIterator = typedef SimpleTemplateSiteContainerIterator<ProbabilisticSite, ProbabilisticSequence, std::string>

Definition at line 86 of file SiteContainerIterator.h.

SimpleSiteContainerIterator

using bpp::SimpleSiteContainerIterator = typedef SimpleTemplateSiteContainerIterator<Site, Sequence, std::string>

Definition at line 85 of file SiteContainerIterator.h.

SiteContainerInterface

using bpp::SiteContainerInterface = typedef TemplateSiteContainerInterface<Site, Sequence, std::string>

Definition at line 122 of file SiteContainer.h.

SiteSelection

typedef std::vector< size_t > bpp::SiteSelection

Definition at line 24 of file SequenceContainerTools.h.

VectorSequenceContainer

using bpp::VectorSequenceContainer = typedef TemplateVectorSequenceContainer<Sequence>

Definition at line 394 of file VectorSequenceContainer.h.

VectorSiteContainer

using bpp::VectorSiteContainer = typedef TemplateVectorSiteContainer<Site, Sequence>

Definition at line 824 of file VectorSiteContainer.h.