bpp Namespace Reference

Namespaces
	BrentOneDimension
	Graph
	IntegerTools
	NewtonBacktrackOneDimension
	PowellMultiDimensions
	StatTools
	TextTools
	VectorTools

Classes
class	DownhillSimplexMethod
class	AssociationGraphObserver
class	AssociationGraphImplObserver
class	GoldenSectionSearch
class	AbstractDiscreteDistribution
class	Fasta
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	Constraint
class	ConstraintException
class	ContingencyTableGenerator
class	ContingencyTableTest
class	CoordsTools
class	CorrespondenceAnalysis
class	DAGraph
class	DAGraphImpl
class	DataTable
class	DefaultColorSet
class	DerivableFirstOrder
class	DerivableFirstOrderWrapper
class	DerivableSecondOrder
class	DerivableSecondOrderWrapper
class	DimensionException
class	DirectionFunction
class	DirichletDiscreteDistribution
class	DiscreteDistribution
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	FivePointsNumericalDerivative
class	Font
class	FontManager
class	FullHmmTransitionMatrix
class	Function
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	Optimizer
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	RandomFactory
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	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	Uniform01K
class	Uniform01QD
class	Uniform01WH
class	UniformDiscreteDistribution
class	UnvalidFlagException
class	VectorException
class	VectorTools
class	XFigColorManager
class	XFigGraphicDevice
class	XFigLaTeXFontManager
class	XFigPostscriptFontManager
class	ZeroDivisionException
class	AAChargeIndex
class	AAChenGuHuangHydrophobicityIndex
class	AAChouFasmanAHelixIndex
class	AAChouFasmanBSheetIndex
class	AAChouFasmanTurnIndex
class	AAIndex1Entry
class	AAIndex2Entry
class	AAMassIndex
class	AASEA1030Index
class	AASEAInf10Index
class	AASEASup30Index
class	AASurfaceIndex
class	AAVolumeIndex
class	AbstractAlphabet
class	AbstractCoreSequence
class	AbstractCoreSite
class	AbstractIAlignment
class	AbstractIProbabilisticAlignment
class	AbstractISequence
class	AbstractOAlignment
class	AbstractOProbabilisticAlignment
class	AbstractOSequence
class	AbstractProbabilisticSequenceContainer
class	AbstractReverseTransliterator
class	AbstractSequenceContainer
class	AbstractSequenceContainerIterator
class	AbstractSequencePositionIterator
class	AbstractSequenceSymbolList
class	AbstractSiteContainerIterator
class	AbstractTransliterator
class	AbstractValuesContainer
class	AlignedSequenceContainer
class	AlignedValuesContainer
class	Alphabet
class	AlphabetException
class	AlphabetIndex1
class	AlphabetIndex2
class	AlphabetMismatchException
class	AlphabetNumericState
class	AlphabetState
class	AlphabetTools
class	AscidianMitochondrialGeneticCode
class	BadCharException
class	BadIntException
class	BasicIntSymbolList
class	BasicProbabilisticSequence
class	BasicProbabilisticSymbolList
class	BasicSequence
class	BinaryAlphabet
class	BLOSUM50
class	BowkerTest
class	BppOAlignmentReaderFormat
class	BppOAlignmentWriterFormat
class	BppOAlphabetIndex1Format
class	BppOAlphabetIndex2Format
class	BppOSequenceReaderFormat
class	BppOSequenceStreamReaderFormat
class	BppOSequenceWriterFormat
class	BppSequenceApplication
class	CaseMaskedAlphabet
class	CharStateNotSupportedException
class	CiliateNuclearGeneticCode
class	Clustal
class	CodonAlphabet
class	CodonFromProteicAlphabetIndex1
class	CodonFromProteicAlphabetIndex2
class	CodonSiteTools
class	Commentable
class	CompleteSiteContainerIterator
class	CompressedVectorSiteContainer
class	ConstSequenceIterator
class	ConstSequenceWithQualityIterator
class	ConstSiteIterator
class	CoreSequence
class	CoreSequenceSymbolList
class	CoreSite
class	CoreSymbolList
class	CoreSymbolListDeletionEvent
class	CoreSymbolListEditionEvent
class	CoreSymbolListInsertionEvent
class	CoreSymbolListListener
class	CoreSymbolListSubstitutionEvent
class	CoreWordAlphabet
class	CruxSymbolList
class	CruxSymbolListSite
class	DCSE
class	DefaultAlphabet
class	DefaultNucleotideScore
class	DistanceMatrix
class	DNA
class	DNAToRNA
class	EchinodermMitochondrialGeneticCode
class	EdCoreSymbolList
class	EdIntSymbolList
class	EdSymbolList
class	EmptyContainerException
class	EmptySequenceException
class	EmptySiteException
class	GenBank
class	GeneticCode
class	GranthamAAChemicalDistance
class	GranthamAAPolarityIndex
class	GranthamAAVolumeIndex
class	IAlignment
class	IntegerAlphabet
class	IntSymbolList
class	InvertebrateMitochondrialGeneticCode
class	IOProbabilisticSequence
class	IOSequence
class	IoSequenceFactory
class	IOSequenceStream
class	IProbabilisticAlignment
class	IProbabilisticSequence
class	ISequence
class	ISequenceStream
class	KD_AAHydropathyIndex
class	KleinAANetChargeIndex
class	LetterAlphabet
class	LexicalAlphabet
class	MappedNamedContainer
class	MapSequenceContainer
class	Mase
class	MaseHeader
class	MaseTools
class	MiyataAAChemicalDistance
class	MoldMitochondrialGeneticCode
class	NamedContainer
class	NexusIOSequence
class	NexusTools
class	NoGapSiteContainerIterator
class	NucleicAcidsReplication
class	NucleicAlphabet
class	NucleicAlphabetState
class	NumericAlphabet
class	OAlignment
class	OProbabilisticAlignment
class	OProbabilisticSequence
class	OrderedSequenceContainer
class	OrderedValuesContainer
class	OSequence
class	OSequenceStream
class	Pasta
class	PhredPhd
class	PhredPoly
class	Phylip
class	PositionedContainer
class	PositionedNamedContainer
class	ProbabilisticSequenceContainer
class	ProbabilisticSite
class	ProbabilisticSiteContainer
class	ProbabilisticSymbolList
class	ProteicAlphabet
class	ProteicAlphabetIndex1
class	ProteicAlphabetIndex2
class	ProteicAlphabetState
class	ReverseTransliterator
class	RNA
class	RNY
class	Sequence
class	SequenceAnnotation
class	SequenceApplicationTools
class	SequenceContainer
class	SequenceContainerTools
class	SequencedValuesContainer
class	SequenceException
class	SequenceFileIndex
class	SequenceIterator
class	SequenceMask
class	SequenceNotAlignedException
class	SequenceNotFoundException
class	SequencePositionIterator
class	SequenceQuality
class	SequenceTools
class	SequenceWalker
class	SequenceWithAnnotation
class	SequenceWithAnnotationTools
class	SequenceWithGapException
class	SequenceWithQuality
class	SequenceWithQualityIterator
class	SequenceWithQualityTools
class	SimpleIndexDistance
class	SimpleScore
class	SimpleSequenceContainerIterator
class	SimpleSequencePositionIterator
class	SimpleSiteContainerIterator
class	Site
class	SiteContainer
class	SiteContainerTools
class	SiteException
class	SiteIterator
class	SiteNotFoundException
class	SiteTools
class	SiteWithGapException
class	StandardGeneticCode
class	Stockholm
class	StopCodonException
class	StreamSequenceIterator
class	StreamSequenceWithQualityIterator
class	StringSequenceTools
class	SymbolList
class	SymbolListTools
class	Transliterator
class	UserAlphabetIndex1
class	UserAlphabetIndex2
class	VectorMappedContainer
class	VectorPositionedContainer
class	VectorProbabilisticSiteContainer
class	VectorSequenceContainer
class	VectorSiteContainer
class	VertebrateMitochondrialGeneticCode
class	WordAlphabet
class	YeastMitochondrialGeneticCode
class	AlleleInfo
	The AlleleInfo interface. More...
class	BasicAlleleInfo
	The BasicAlleleInfo class. More...
class	BiAlleleMonolocusGenotype
	The BiAlleleMonolocusGenotype class. More...
class	AnalyzedLoci
	The AnalyzedLoci class. More...
class	AnalyzedSequences
	The AnalyzedSequences class. More...
class	DataSet
	The DataSet class. More...
class	DataSetTools
	A set of tools for DataSet. More...
class	Date
	The Date class. More...
class	Group
	The Group class. More...
class	Individual
	The Individual class. More...
class	AbstractIDataSet
	Partial implementation of the DataSet Input interface. More...
class	AbstractODataSet
	Partial implementation of the DataSet Output interface. More...
class	DarwinDon
	The Darwin .don output format for popgenlib. More...
class	DarwinVarSingle
	The Darwin .don output format for popgenlib. More...
class	GeneMapperCsvExport
	The GeneMapperCsvExport input format for popgenlib. More...
class	Genepop
	The Genepop input format for popgenlib. More...
class	Genetix
	The Genetix input format for popgenlib. More...
class	IDataSet
	The IDataSet interface. More...
class	IODataSet
	Interface for input/ouput with DataSet. More...
class	ODataSet
	The ODataSet interface. More...
class	PopgenlibIO
	The native I/O format for popgenlib. More...
class	Locality
	The Locality class. More...
class	MultiSeqIndividual
class	BadIdentifierException
	The BadIdentifierException class. More...
class	LocusNotFoundException
	The LocusNotFoundException class. More...
class	AlleleNotFoundException
	The AlleleNotFoundException class. More...
class	LocalityNotFoundException
	The LocalityNotFoundException class. More...
class	IndividualNotFoundException
	The IndividualNotFoundException class. More...
class	GroupNotFoundException
	The GroupNotFoundException class. More...
class	LocusInfo
	The LocusInfo class. More...
class	MonoAlleleMonolocusGenotype
	The MonoAlleleMonolocusGenotype class. More...
class	MonolocusGenotype
	The MonolocusGenotype virtual class. More...
class	MonolocusGenotypeTools
	The MonolocusGenotypeTools static class. More...
class	MultiAlleleMonolocusGenotype
	The MultiAlleleMonolocusGenotype class. More...
class	MultilocusGenotype
	The MultilocusGenotype class. More...
class	MultilocusGenotypeStatistics
	The MultilocusGenotypeStatistics class. More...
class	PolymorphismMultiGContainer
	The PolymorphismMultiGContainer class. More...
class	PolymorphismMultiGContainerTools
	Tools for PolymorphismMultiGContainer. More...
class	PolymorphismSequenceContainer
	The PolymorphismSequenceContainer class. More...
class	PolymorphismSequenceContainerTools
	Utilitary function to manipulate PolymorphismSequenceContainer. More...
class	SequenceStatistics
	Static class providing methods to compute statistics on sequences data. 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
typedef std::vector< size_t >	SequenceSelection
typedef std::vector< size_t >	SiteSelection
typedef CoreSymbolList< int >	IntCoreSymbolList
typedef CoreSymbolList< std::vector< double > >	ProbaCoreSymbolList
typedef CoreSequenceSymbolList< int >	IntCoreSequenceSymbolList
typedef CoreSequenceSymbolList< std::vector< double > >	ProbaCoreSequenceSymbolList
typedef AbstractSequenceSymbolList< int >	intAbstractSequenceSymbolList
typedef AbstractSequenceSymbolList< std::vector< double > >	probaAbstractSequenceSymbolList
typedef CoreSymbolListListener< int >	IntSymbolListListener
typedef CoreSymbolListEditionEvent< int >	IntSymbolListEditionEvent
typedef CoreSymbolListInsertionEvent< int >	IntSymbolListInsertionEvent
typedef CoreSymbolListDeletionEvent< int >	IntSymbolListDeletionEvent
typedef CoreSymbolListSubstitutionEvent< int >	IntSymbolListSubstitutionEvent
typedef ProbaCoreSequenceSymbolList	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)
bool	operator== (const Site &site1, const Site &site2)
bool	operator< (const Site &site1, const Site &site2)