Namespaces
	BrentOneDimension

	Graph

	IntegerTools

	NewtonBacktrackOneDimension

	PowellMultiDimensions

	StatTools

	TextTools

	VectorTools

Classes
class	DownhillSimplexMethod

class	AssociationGraphObserver

class	AssociationGraphImplObserver

class	GoldenSectionSearch

class	AbstractDiscreteDistribution

class	AllelicAlphabet

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	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	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	AbstractIAlignment2

class	AbstractIDistanceMatrix

class	AbstractIProbabilisticAlignment

class	AbstractIProbabilisticAlignment2

class	AbstractIProbabilisticSequence

class	AbstractISequence

class	AbstractOAlignment

class	AbstractODistanceMatrix

class	AbstractOProbabilisticAlignment

class	AbstractOProbabilisticSequence

class	AbstractOProbabilisticSequence2

class	AbstractOSequence

class	AbstractOSequence2

class	AbstractReverseTransliterator

class	AbstractSequencePositionIterator

class	AbstractTemplateEventDrivenSymbolList

class	AbstractTemplateSequenceContainer

class	AbstractTemplateSiteContainerIterator

class	AbstractTemplateSymbolList

class	AbstractTransliterator

class	Alphabet

class	AlphabetException

class	AlphabetIndex1

class	AlphabetIndex2

class	AlphabetMismatchException

class	AlphabetNumericState

class	AlphabetState

class	AlphabetTools

class	AscidianMitochondrialGeneticCode

class	BadCharException

class	BadIntException

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	CompleteTemplateSiteContainerIterator

class	CompressedVectorSiteContainer

class	CoreSequenceInterface

class	CoreSiteInterface

class	CoreSymbolListDeletionEvent

class	CoreSymbolListEditionEvent

class	CoreSymbolListInsertionEvent

class	CoreSymbolListListener

class	CoreSymbolListSubstitutionEvent

class	CoreWordAlphabet

class	CruxSymbolListInterface

class	DCSE

class	DefaultAlphabet

class	DefaultNucleotideScore

class	DistanceMatrix

class	DNA

class	DNAToRNA

class	EchinodermMitochondrialGeneticCode

class	EmptyContainerException

class	EmptySequenceException

class	EmptySiteException

class	EventDrivenIntSymbolList

class	GenBank

class	GeneticCode

class	GranthamAAChemicalDistance

class	GranthamAAPolarityIndex

class	GranthamAAVolumeIndex

class	IAlignment

class	IDistanceMatrix

class	IntegerAlphabet

class	IntSymbolList

class	IntSymbolListInterface

class	InvertebrateMitochondrialGeneticCode

class	IODistanceMatrix

class	IODistanceMatrixFactory

class	IOProbabilisticSequence

class	IOSequence

class	IoSequenceFactory

class	IOSequenceStream

class	IProbabilisticAlignment

class	IProbabilisticSequence

class	ISequence

class	KD_AAHydropathyIndex

class	KleinAANetChargeIndex

class	LetterAlphabet

class	LexicalAlphabet

class	MappedNamedContainer

class	Mase

class	MaseHeader

class	MaseTools

class	MiyataAAChemicalDistance

class	MoldMitochondrialGeneticCode

class	NamedContainerInterface

class	NexusIOSequence

class	NexusTools

class	NoGapTemplateSiteContainerIterator

class	NucleicAcidsReplication

class	NucleicAlphabet

class	NucleicAlphabetState

class	NumericAlphabet

class	OAlignment

class	ODistanceMatrix

class	OProbabilisticAlignment

class	OProbabilisticSequence

class	OSequence

class	Pasta

class	PhredPhd

class	PhredPoly

class	Phylip

class	PhylipDistanceMatrixFormat

class	PositionedContainerInterface

class	PositionedNamedContainerInterface

class	ProbabilisticSequence

class	ProbabilisticSequenceInterface

class	ProbabilisticSite

class	ProbabilisticSiteInterface

class	ProbabilisticSymbolList

class	ProbabilisticSymbolListInterface

class	ProteicAlphabet

class	ProteicAlphabetIndex1

class	ProteicAlphabetIndex2

class	ProteicAlphabetState

class	ReverseTransliteratorInterface

class	RNA

class	RNY

class	Sequence

class	SequenceAnnotation

class	SequenceApplicationTools

class	SequenceContainerTools

class	SequencedValuesContainer

class	SequenceException

class	SequenceFileIndex

class	SequenceInterface

class	SequenceMask

class	SequenceNotAlignedException

class	SequenceNotFoundException

class	SequencePositionIterator

class	SequenceQuality

class	SequenceTools

class	SequenceWalker

class	SequenceWithAnnotation

class	SequenceWithAnnotationTools

class	SequenceWithGapException

class	SequenceWithQuality

class	SequenceWithQualityTools

class	SimpleCommentable

class	SimpleIndexDistance

class	SimpleScore

class	SimpleSequencePositionIterator

class	SimpleTemplateSiteContainerIterator

class	Site

class	SiteContainerTools

class	SiteException

class	SiteInterface

class	SiteNotFoundException

class	SiteTools

class	SiteWithGapException

class	StandardGeneticCode

class	Stockholm

class	StopCodonException

class	StringSequenceTools

class	SwitchDeleter

class	SymbolListTools

class	TemplateAlignedSequenceContainer

class	TemplateAlignmentDataInterface

class	TemplateCoreSymbolListInterface

class	TemplateEventDrivenCoreSymbolListInterface

class	TemplateISequenceStream

class	TemplateOSequenceStream

class	TemplateSequenceContainerInterface

class	TemplateSequenceDataInterface

class	TemplateSequenceIteratorInterface

class	TemplateSiteContainerInterface

class	TemplateSiteIteratorInterface

class	TemplateStreamSequenceIterator

class	TemplateVectorSequenceContainer

class	TemplateVectorSiteContainer

class	TransliteratorInterface

class	UserAlphabetIndex1

class	UserAlphabetIndex2

class	VectorMappedContainer

class	VectorPositionedContainer

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	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/output 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	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	MonolocusGenotypeInterface
	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 TemplateAlignedSequenceContainer< Sequence, Site >	AlignedSequenceContainer

typedef TemplateAlignedSequenceContainer< ProbabilisticSequence, ProbabilisticSite >	ProbabilisticAlignedSequenceContainer

typedef TemplateAlignmentDataInterface< std::string >	AlignmentDataInterface

typedef TemplateSequenceContainerInterface< Sequence >	SequenceContainerInterface

typedef TemplateSequenceContainerInterface< ProbabilisticSequence >	ProbabilisticSequenceContainerInterface

typedef std::vector< size_t >	SequenceSelection

typedef std::vector< size_t >	SiteSelection

typedef TemplateSequenceDataInterface< std::string >	SequenceDataInterface

typedef TemplateSiteContainerInterface< Site, Sequence, std::string >	SiteContainerInterface

typedef TemplateSiteContainerInterface< ProbabilisticSite, ProbabilisticSequence, std::string >	ProbabilisticSiteContainerInterface

typedef SimpleTemplateSiteContainerIterator< Site, Sequence, std::string >	SimpleSiteContainerIterator

typedef SimpleTemplateSiteContainerIterator< ProbabilisticSite, ProbabilisticSequence, std::string >	SimpleProbabilisticSiteContainerIterator

typedef TemplateVectorSequenceContainer< Sequence >	VectorSequenceContainer

typedef TemplateVectorSequenceContainer< ProbabilisticSequence >	ProbabilisticVectorSequenceContainer

typedef TemplateVectorSiteContainer< Site, Sequence >	VectorSiteContainer

typedef TemplateVectorSiteContainer< ProbabilisticSite, ProbabilisticSequence >	ProbabilisticVectorSiteContainer

typedef TemplateCoreSymbolListInterface< int >	IntCoreSymbolListInterface

typedef TemplateCoreSymbolListInterface< std::vector< double > >	ProbabilisticCoreSymbolListInterface

typedef TemplateEventDrivenCoreSymbolListInterface< int >	IntEventDrivenCoreSymbolListInterface

typedef TemplateEventDrivenCoreSymbolListInterface< std::vector< double > >	ProbabilisticEventDrivenCoreSymbolListInterface

typedef CoreSymbolListListener< int >	IntSymbolListListener

typedef CoreSymbolListEditionEvent< int >	IntSymbolListEditionEvent

typedef CoreSymbolListInsertionEvent< int >	IntSymbolListInsertionEvent

typedef CoreSymbolListDeletionEvent< int >	IntSymbolListDeletionEvent

typedef CoreSymbolListSubstitutionEvent< int >	IntSymbolListSubstitutionEvent

typedef TemplateISequenceStream< Sequence >	ISequenceStream

typedef TemplateISequenceStream< SequenceWithQuality >	ISequenceWithQualityStream

typedef TemplateISequenceStream< ProbabilisticSequence >	IProbabilisticSequenceStream

typedef TemplateOSequenceStream< Sequence >	OSequenceStream

typedef TemplateOSequenceStream< SequenceWithQuality >	OSequenceWithQualityStream

typedef TemplateOSequenceStream< ProbabilisticSequence >	OProbabilisticSequenceStream

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

using	CompleteSiteContainerIterator = CompleteTemplateSiteContainerIterator< Site, Sequence, std::string >

using	NoGapSiteContainerIterator = NoGapTemplateSiteContainerIterator< Site, Sequence, std::string >

using	ConstSiteIterator = TemplateSiteIteratorInterface< const Site >

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)