bpp-phyl  2.4.0
bpp Namespace Reference

Namespaces

 BrentOneDimension
 
 Graph
 
 IntegerTools
 
 NewtonBacktrackOneDimension
 
 PowellMultiDimensions
 
 StatTools
 
 TextTools
 
 VectorTools
 

Classes

class  AAChargeIndex
 
class  AAChenGuHuangHydrophobicityIndex
 
class  AAChouFasmanAHelixIndex
 
class  AAChouFasmanBSheetIndex
 
class  AAChouFasmanTurnIndex
 
class  AAExteriorSubstitutionRegister
 Indexes only substitutions between amino-acids. Groups are distinguished by their direction. More...
 
class  AAIndex1Entry
 
class  AAIndex2Entry
 
class  AAInteriorSubstitutionRegister
 Indexes only intra amino-acid substitutions. Every group represents a substitutions for the same amino acid. Met and Trp are not taken into account due their non-degenerescence. More...
 
class  AAMassIndex
 
class  AASEA1030Index
 
class  AASEAInf10Index
 
class  AASEASup30Index
 
class  AASurfaceIndex
 
class  AAVolumeIndex
 
class  AbstractAgglomerativeDistanceMethod
 Partial implementation of the AgglomerativeDistanceMethod interface. More...
 
class  AbstractAlphabet
 
class  AbstractBiblioMixedSubstitutionModel
 Abstract class for mixture models based on the bibliography. More...
 
class  AbstractBiblioSubstitutionModel
 Partial implementation of the SubstitutionModel interface for models that are set for matching the bibliography, and are only defined through a link to a "real" model. More...
 
class  AbstractCodonAAFitnessSubstitutionModel
 Abstract class for modelling of ratios of substitution rates between codons, whatever they are synonymous or not. More...
 
class  AbstractCodonAARateSubstitutionModel
 Abstract class for modelling of non-synonymous and synonymous substitution rates in codon models, given an amino acid rate matrix (from a shared_ptr model). More...
 
class  AbstractCodonBGCSubstitutionModel
 Abstract class for modelling of non-synonymous and synonymous substitution rates in codon models, with gBGC. More...
 
class  AbstractCodonCpGSubstitutionModel
 Abstract class for modelling of CpG -> CpA or TpG (symetric) hypermutability substitution rate inside codons. Note that the neihbouring effects between codons are not considered. More...
 
class  AbstractCodonDistanceSubstitutionModel
 Abstract class for modelling of non-synonymous and synonymous substitution rates in codon models. More...
 
class  AbstractCodonFitnessSubstitutionModel
 Abstract class for modelling of ratios of substitution rates between codons, whatever they are synonymous or not. More...
 
class  AbstractCodonFrequenciesSubstitutionModel
 Abstract Class for substitution models on codons parametrized by frequencies. More...
 
class  AbstractCodonPhaseFrequenciesSubstitutionModel
 Abstract Class for substitution models on codons parametrized by a frequency. More...
 
class  AbstractCodonSubstitutionModel
 Abstract class for substitution models on codons. More...
 
class  AbstractColorSet
 
class  AbstractCoreSequence
 
class  AbstractCoreSite
 
class  AbstractDendrogramPlot
 Basic implementation of dendrogram plots. More...
 
class  AbstractDiscreteDistribution
 
class  AbstractDiscreteRatesAcrossSitesTreeLikelihood
 Partial implementation of the DiscreteRatesAcrossSitesTreeLikelihood interface. More...
 
class  AbstractFontManager
 
class  AbstractFrequenciesSet
 Basic implementation of the FrequenciesSet interface. More...
 
class  AbstractFromSubstitutionModelTransitionModel
 Virtual class of a Transition Model related to a given SubstitutionModel. More...
 
class  AbstractGraphicDevice
 
class  AbstractHmmLikelihood
 
class  AbstractHmmTransitionMatrix
 
class  AbstractHomogeneousTreeLikelihood
 Partial implementation for homogeneous model of the TreeLikelihood interface. More...
 
class  AbstractIAlignment
 
class  AbstractIDistanceMatrix
 Partial implementation of the IDistanceMatrix interface. More...
 
class  AbstractIMultiTree
 Partial implementation of the IMultiTree interface. More...
 
class  AbstractISequence
 
class  AbstractITree
 Partial implementation of the ITree interface. More...
 
class  AbstractKroneckerCodonSubstitutionModel
 Abstract class for substitution models on codons allowing multiple substitutions. More...
 
class  AbstractKroneckerWordSubstitutionModel
 Abstract Kronecker Word Model. More...
 
class  AbstractMapping
 Partial implementation of the mapping interface. More...
 
class  AbstractMixedSubstitutionModel
 Partial implementation for Mixed Substitution models, defined as a mixture of "simple" substitution models. Each model has a specific probability and rate, with the constraint that the expectation (on the distribution of the models) of the rate of all the models equals one. More...
 
class  AbstractMutationProcess
 Partial implmentation of the MutationProcess interface. More...
 
class  AbstractNonHomogeneousTreeLikelihood
 Partial implementation for branch non-homogeneous models of the TreeLikelihood interface. More...
 
class  AbstractNucleotideSubstitutionModel
 Specialisation abstract class for nucleotide substitution model. More...
 
class  AbstractNumericalDerivative
 
class  AbstractOAlignment
 
class  AbstractODistanceMatrix
 Partial implementation of the ODistanceMatrix interface. More...
 
class  AbstractOMultiTree
 Partial implementation of the OTree interface. More...
 
class  AbstractOptimizationStopCondition
 
class  AbstractOptimizer
 
class  AbstractOSequence
 
class  AbstractOTree
 Partial implementation of the OTree interface. More...
 
class  AbstractOutputStream
 
class  AbstractParameterAliasable
 
class  AbstractParametrizable
 
class  AbstractProteinSubstitutionModel
 Specialisation abstract class for protein substitution model. More...
 
class  AbstractReverseTransliterator
 
class  AbstractReversibleNucleotideSubstitutionModel
 Specialisation abstract class for reversible nucleotide substitution model. More...
 
class  AbstractReversibleProteinSubstitutionModel
 Specialisation abstract class for reversible protein substitution model. More...
 
class  AbstractReversibleSubstitutionModel
 Partial implementation of the ReversibleSubstitutionModel interface. More...
 
class  AbstractReward
 Basic implementation of the the Reward interface. More...
 
class  AbstractRewardMapping
 Partial implementation of the reward mapping interface. More...
 
class  AbstractSequenceContainer
 
class  AbstractSequenceContainerIterator
 
class  AbstractSequencePositionIterator
 
class  AbstractSiteContainerIterator
 
class  AbstractStateMap
 A convenience partial implementation of the StateMap interface. More...
 
class  AbstractSubstitutionCount
 Basic implementation of the the SubstitutionCount interface. More...
 
class  AbstractSubstitutionMapping
 Partial implementation of the substitution mapping interface. More...
 
class  AbstractSubstitutionModel
 Partial implementation of the SubstitutionModel interface. More...
 
class  AbstractSubstitutionRegister
 
class  AbstractTotallyWrappedModel
 
class  AbstractTotallyWrappedSubstitutionModel
 
class  AbstractTransliterator
 
class  AbstractTreeDrawing
 Partial implementation of the TreeDrawing interface. More...
 
class  AbstractTreeLikelihood
 Partial implementation of the TreeLikelihood interface. More...
 
class  AbstractTreeLikelihoodData
 Partial implementation of the TreeLikelihoodData interface. More...
 
class  AbstractTreeParsimonyData
 Partial implementation of the TreeParsimonyData interface. More...
 
class  AbstractTreeParsimonyScore
 Partial implementation of the TreeParsimonyScore interface. More...
 
class  AbstractWeightedSubstitutionCount
 Partial implementation of the WeightedSubstitutionCount interface. More...
 
class  AbstractWordFrequenciesSet
 
class  AbstractWordSubstitutionModel
 Abstract Basal class for words of substitution models. More...
 
class  AbstractWrappedModel
 Abstract class of Wrapping model class, where all methods are redirected from getModel(). More...
 
class  AbstractWrappedSubstitutionModel
 
class  AdaptiveKernelDensityEstimation
 
class  AgglomerativeDistanceMethod
 Interface for agglomerative distance methods. More...
 
class  AliasParameterListener
 
class  AlignedSequenceContainer
 
class  Alphabet
 
class  AlphabetException
 
class  AlphabetIndex1
 
class  AlphabetIndex2
 
class  AlphabetMismatchException
 
class  AlphabetNumericState
 
class  AlphabetState
 
class  AlphabetTools
 
class  AncestralStateReconstruction
 Interface for ancestral states reconstruction methods. More...
 
class  AnonymousSubstitutionModel
 
class  ApplicationTools
 
class  AscidianMitochondrialGeneticCode
 
class  AssociationDAGraphImplObserver
 
class  AssociationDAGraphObserver
 
class  AssociationGraphImplObserver
 
class  AssociationGraphObserver
 
class  AssociationTreeGraphImplObserver
 
class  AssociationTreeGraphObserver
 
class  AttributesTools
 
class  AutoCorrelationTransitionMatrix
 
class  AutoParameter
 
class  BackupListener
 
class  BadCharException
 
class  BadIntegerException
 
class  BadIntException
 
class  BadNumberException
 
class  BadSizeException
 
class  BasicSequence
 
class  BasicSymbolList
 
class  BasicTreeDrawingDisplayControler
 Easy tune of tree drawings display, a basic implementation: More...
 
class  BetaDiscreteDistribution
 
class  BfgsMultiDimensions
 
class  BinaryAlphabet
 
class  BinaryOperator
 
class  BinarySubstitutionModel
 The Model on two states. More...
 
class  BioNJ
 The BioNJ distance method. More...
 
class  BipartitionList
 This class deals with the bipartitions defined by trees. More...
 
class  BipartitionTools
 This class provides tools related to the BipartitionList class. More...
 
class  BLOSUM50
 
class  BootstrapValuesTreeDrawingListener
 A TreeDrawingListener implementation that write the bootstrap values of inner nodes. More...
 
class  BowkerTest
 
class  BppApplication
 
class  BppBoolean
 
class  BppDouble
 
class  BppInteger
 
class  BppNotANumber
 
class  BppNumberI
 
class  BppOAlignmentReaderFormat
 
class  BppOAlignmentWriterFormat
 
class  BppOAlphabetIndex1Format
 
class  BppOAlphabetIndex2Format
 
class  BppODiscreteDistributionFormat
 
class  BppOFrequenciesSetFormat
 Frequencies set I/O in BppO format. More...
 
class  BppOMultiTreeReaderFormat
 Tree I/O in BppO format. More...
 
class  BppOMultiTreeWriterFormat
 Tree I/O in BppO format. More...
 
class  BppOParametrizableFormat
 
class  BppORateDistributionFormat
 Rate Distribution I/O in BppO format. More...
 
class  BppOSequenceReaderFormat
 
class  BppOSequenceStreamReaderFormat
 
class  BppOSequenceWriterFormat
 
class  BppOSubstitutionModelFormat
 Substitution model I/O in BppO format. More...
 
class  BppOTransitionModelFormat
 Transition model I/O in BppO format. More...
 
class  BppOTreeReaderFormat
 Tree I/O in BppO format. More...
 
class  BppOTreeWriterFormat
 Tree I/O in BppO format. More...
 
class  BppString
 
class  BppUnsignedInteger
 
class  BppVector
 
class  Bracket
 
class  BracketPoint
 
class  BranchLengthsTreeDrawingListener
 A TreeDrawingListener implementation that write the branch lengths of inner nodes. More...
 
class  BranchLikelihood
 Compute likelihood for a 4-tree. More...
 
class  BrentOneDimension
 
class  CanonicalStateMap
 This class implements a state map where all resolved states are modeled. More...
 
class  CaseMaskedAlphabet
 
class  CategorySubstitutionRegister
 The CategorySubstitutionRegisters. More...
 
class  CharStateNotSupportedException
 
class  CladogramDrawBranchEvent
 
class  CladogramPlot
 Cladogram representation of trees. More...
 
class  ClockTreeLikelihood
 Interface for likelihood computation with a global clock. More...
 
class  Clonable
 
class  Clustal
 
class  ClusterInfos
 
class  Coala
 The Coala branch-heterogeneous amino-acid substitution model. More...
 
class  CoalaCore
 This class is the core class inherited by the Coala class. COaLA is a branch-heterogeneous amino-acid substitution model. More...
 
class  CodonAdHocSubstitutionModel
 Class for substitution models of codons with several layers of codon models. More...
 
class  CodonAlphabet
 
class  CodonDistanceFrequenciesSubstitutionModel
 Class for asynonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic models. More...
 
class  CodonDistancePhaseFrequenciesSubstitutionModel
 Class for asynonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic basic models. More...
 
class  CodonDistanceSubstitutionModel
 Class for substitution models of codons with non-synonymous/synonymous ratios of substitution rates defined through a distance between amino-acids. More...
 
class  CodonFrequenciesSet
 Parametrize a set of state frequencies for codons. More...
 
class  CodonFromIndependentFrequenciesSet
 the Frequencies in codons are the product of Independent Frequencies in letters with the frequencies of stop codons set to zero. More...
 
class  CodonFromUniqueFrequenciesSet
 the Frequencies in codons are the product of the frequencies for a unique FrequenciesSet in letters, with the frequencies of stop codons set to zero. More...
 
class  CodonReversibleSubstitutionModel
 Abstract class for reversible codon models. More...
 
class  CodonSiteTools
 
class  CodonSubstitutionModel
 
class  ColMatrix
 
class  ColorManager
 
class  ColorSet
 
class  ColorTools
 
class  CompleteSiteContainerIterator
 
class  CompleteSubstitutionRegister
 Completion of a given substitution register to consider all substitutions. The new substitutions are considered in an additional type. More...
 
class  ComprehensiveSubstitutionRegister
 Distinguishes all types of substitutions. More...
 
class  CompressedVectorSiteContainer
 
class  ComputationTree
 
class  ConjugateGradientMultiDimensions
 
class  ConstantDistribution
 
class  ConstantOperator
 
class  ConstantRateDistribution
 
class  Constraint
 
class  ConstraintException
 
class  ConstSequenceIterator
 
class  ConstSequenceWithQualityIterator
 
class  ConstSiteIterator
 
class  ContingencyTableGenerator
 
class  ContingencyTableTest
 
class  CoordsTools
 
class  CoreCodonSubstitutionModel
 Abstract classes for codon models. More...
 
class  CoreSequence
 
class  CoreSite
 
class  CoreWordAlphabet
 
class  CorrespondenceAnalysis
 
class  Cursor
 Data structure describing a plotting direction. More...
 
class  DAGraph
 
class  DAGraphImpl
 
class  DataTable
 
class  DCSE
 
class  DecompositionMethods
 Methods useful for analytical substitution count and rewards using the eigen decomposition method. More...
 
class  DecompositionReward
 Analytical reward using the eigen decomposition method. More...
 
class  DecompositionSubstitutionCount
 Analytical substitution count using the eigen decomposition method. More...
 
class  DefaultAlphabet
 
class  DefaultColorSet
 
class  DefaultNucleotideScore
 
class  DerivableFirstOrder
 
class  DerivableFirstOrderWrapper
 
class  DerivableSecondOrder
 
class  DerivableSecondOrderWrapper
 
class  DetailedSiteSimulator
 This interface adds the dSimulate method to the SiteSimulator interface. More...
 
class  DimensionException
 
class  DirectionFunction
 
class  DirichletDiscreteDistribution
 
class  DiscreteDistribution
 
class  DiscreteRatesAcrossSitesClockTreeLikelihood
 Interface for likelihood computation with a global clock and rate across sites variation. More...
 
class  DiscreteRatesAcrossSitesTreeLikelihood
 Interface for rate across sites (RAS) implementation. More...
 
class  DistanceEstimation
 Estimate a distance matrix from sequence data, according to a given model. More...
 
class  DistanceMatrix
 
class  DistanceMethod
 General interface for distance-based phylogenetic reconstruction methods. More...
 
class  DNA
 
class  DNAToRNA
 
class  DnDsSubstitutionRegister
 Distinguishes synonymous from non-synonymous substitutions. More...
 
class  DownhillSimplexMethod
 
class  DRASDRTreeLikelihoodData
 Likelihood data structure for rate across sites models, using a double-recursive algorithm. More...
 
class  DRASDRTreeLikelihoodLeafData
 Likelihood data structure for a leaf. More...
 
class  DRASDRTreeLikelihoodNodeData
 Likelihood data structure for a node. More...
 
class  DRASRTreeLikelihoodData
 discrete Rate Across Sites, (simple) Recursive likelihood data structure. More...
 
class  DRASRTreeLikelihoodNodeData
 Likelihood data structure for a node. More...
 
class  DrawBranchEvent
 Event class used by TreeDrawing classes. More...
 
class  DrawIBranchEvent
 Event class that uses INode object (more efficient than relying on nodes id, but less generic). More...
 
class  DrawINodeEvent
 Event class that uses INode object (more efficient than relying on nodes id, but less generic). More...
 
class  DrawNodeEvent
 Event class used by TreeDrawing classes. More...
 
class  DrawTreeEvent
 Event class used by TreeDrawing classes. More...
 
class  DRHomogeneousMixedTreeLikelihood
 A class to compute the average of several DRHomogeneousTreeLikelihood defined from a Mixed Substitution Model. More...
 
class  DRHomogeneousTreeLikelihood
 This class implements the likelihood computation for a tree using the double-recursive algorithm. More...
 
class  DRNonHomogeneousTreeLikelihood
 This class implements the likelihood computation for a tree using the double-recursive algorithm, allowing for non-homogeneous models of substitutions. More...
 
class  DRTreeLikelihood
 Interface for double-recursive (DR) implementation of the likelihood computation. More...
 
class  DRTreeLikelihoodTools
 Utilitary methods dealing with objects implementing the DRTreeLikelihood interface. More...
 
class  DRTreeParsimonyData
 Parsimony data structure for double-recursive (DR) algorithm. More...
 
class  DRTreeParsimonyLeafData
 Parsimony data structure for a leaf. More...
 
class  DRTreeParsimonyNodeData
 Parsimony data structure for a node. More...
 
class  DRTreeParsimonyScore
 Double recursive implementation of interface TreeParsimonyScore. More...
 
class  DSO78
 The Dayhoff, Schwartz and Orcutt substitution model for proteins. More...
 
class  DualityDiagram
 
class  DuplicatedTableColumnNameException
 
class  DuplicatedTableRowNameException
 
class  DvipsColorSet
 
class  EchinodermMitochondrialGeneticCode
 
class  EdgesIteratorClass
 
class  EdgesIteratorClass< Graph::ALLGRAPHITER, is_const >
 
class  EdgesIteratorClass< Graph::INCOMINGNEIGHBORITER, is_const >
 
class  EdgesIteratorClass< Graph::OUTGOINGNEIGHBORITER, is_const >
 
class  EdSymbolList
 
class  EigenValue
 
class  ElementNotFoundException
 
class  EmptyContainerException
 
class  EmptySequenceException
 
class  EmptySiteException
 
class  EmptyVectorException
 
class  Exception
 
class  ExponentialDiscreteDistribution
 
class  ExponentialDiscreteRateDistribution
 
class  F84
 The Felsenstein (1984) substitution model for nucleotides. More...
 
class  Fasta
 
class  FileTools
 
class  FivePointsNumericalDerivative
 
class  FixedCodonFrequenciesSet
 FrequenciesSet useful for homogeneous and stationary models, codon implementation. More...
 
class  FixedFrequenciesSet
 FrequenciesSet useful for homogeneous and stationary models. More...
 
class  FixedNucleotideFrequenciesSet
 FrequenciesSet useful for homogeneous and stationary models, nucleotide implementation. More...
 
class  FixedProteinFrequenciesSet
 FrequenciesSet useful for homogeneous and stationary models, protein implementation. More...
 
class  Font
 
class  FontManager
 
class  FrequenciesSet
 
class  FromMixtureSubstitutionModel
 Model taken from a SubModel of a Mixture of SubstitutionModels. More...
 
class  FromModelFrequenciesSet
 FrequenciesSet to be used with a Markov-modulated substitution model. More...
 
class  FullCodonFrequenciesSet
 A generic FrequenciesSet for Full Codon alphabets. More...
 
class  FullFrequenciesSet
 A generic FrequenciesSet allowing for the estimation of all frequencies. More...
 
class  FullHmmTransitionMatrix
 
class  FullNucleotideFrequenciesSet
 Nucleotide FrequenciesSet using three independent parameters (theta, theta1, theta2) to modelize the four frequencies: More...
 
class  FullPerAACodonFrequenciesSet
 FrequenciesSet integrating ProteinFrequenciesSet inside CodonFrequenciesSet. In this case, FrequencieSet defined inside each amino acid is parametrized as a FullFrequenciesSet. Hence there are 61-20=41 parameters in addition of the parameters of the ProteinFrequenciesSet. More...
 
class  FullProteinFrequenciesSet
 Protein FrequenciesSet using 19 independent parameters to model the 20 frequencies. More...
 
class  Function
 
class  FunctionOperator
 
class  FunctionStopCondition
 
class  FunctionTools
 
class  FunctionWrapper
 
class  G2001
 Galtier's 2001 covarion model. More...
 
class  GammaDiscreteDistribution
 
class  GammaDiscreteRateDistribution
 
class  GaussianDiscreteDistribution
 
class  GaussianDiscreteRateDistribution
 
class  gBGC
 gBGC model. More...
 
class  GCFrequenciesSet
 Nucleotide FrequenciesSet using only one parameter, the GC content. More...
 
class  GCSubstitutionRegister
 Distinguishes AT<->GC from GC<->AT. More...
 
class  GCSynonymousSubstitutionRegister
 Distinguishes AT->GC vs GC->AT inside synonymous substitutions on third codon position. More...
 
class  GenBank
 
class  GeneralSubstitutionRegister
 Sets a Register based on a matrix of integers. If M is the matrix, M[i,j] is the number of the substitution type from i to j, or 0 if there is no substitution type from i to j. More...
 
class  GeneticCode
 
class  GlobalClockTreeLikelihoodFunctionWrapper
 
class  GlobalGraph
 
class  GoldenSectionSearch
 
class  GranthamAAChemicalDistance
 
class  GranthamAAPolarityIndex
 
class  GranthamAAVolumeIndex
 
class  Graph
 
class  GraphicDevice
 
class  GraphObserver
 
class  GTR
 The General Time-Reversible substitution model for nucleotides. More...
 
class  GY94
 The Goldman and Yang (1994) substitution model for codons. More...
 
class  HierarchicalClustering
 Hierarchical clustering. More...
 
class  HKY85
 The Hasegawa M, Kishino H and Yano T (1985) substitution model for nucleotides. More...
 
class  HmmBadStateException
 
class  HmmEmissionProbabilities
 
class  HmmLikelihood
 
class  HmmStateAlphabet
 
class  HmmTransitionMatrix
 
class  HmmUnvalidAlphabetException
 
class  HomogeneousSequenceSimulator
 Site and sequences simulation under homogeneous models. More...
 
class  HomogeneousTreeLikelihood
 Specialization of the TreeLikelihood interface for the Homogeneous case. More...
 
class  IAlignment
 
class  IDiscreteDistribution
 
class  IDistanceMatrix
 General interface for distance matrix readers. More...
 
class  IFrequenciesSet
 General interface for distance matrix readers. More...
 
class  IMultiTree
 General interface for multiple trees readers. More...
 
class  IndexOutOfBoundsException
 
class  InfinityDerivableFirstOrderWrapper
 
class  InfinityDerivableSecondOrderWrapper
 
class  InfinityFunctionWrapper
 
class  InMixedSubstitutionModel
 SubModel taken from a MixedSubstitutionModel, kept in the context of the MixedSubstitutionModel (see FromMixtureSubstitutionModel for an out of context subModel). So "rate" and "scale" are set for the MixedSubstitutionModel. More...
 
class  IntegerAlphabet
 
class  IntervalConstraint
 
class  IntervalTransformedParameter
 
class  InvariantMixedDiscreteDistribution
 
class  InvertebrateMitochondrialGeneticCode
 
class  IoDiscreteDistribution
 
class  IoDiscreteDistributionFactory
 
class  IODistanceMatrix
 General interface for distance matrix I/O. More...
 
class  IODistanceMatrixFactory
 Utilitary class for creating distance matrix readers and writers. More...
 
class  IOException
 
class  IOFormat
 
class  IoFrequenciesSet
 General interface for model I/O. More...
 
class  IOFrequenciesSetFactory
 Utilitary class for creating frequencies set readers and writers. More...
 
class  IOPairedSiteLikelihoods
 Base class for I/O on paired-site likelihoods. More...
 
class  IOParametrizable
 
class  IOPhymlPairedSiteLikelihoods
 This class provides input for the Phyml paired-site likelihoods format. More...
 
class  IOSequence
 
class  IoSequenceFactory
 
class  IOSequenceStream
 
class  IoSubstitutionModel
 General interface for model I/O. More...
 
class  IOSubstitutionModelFactory
 Utilitary class for creating substitution model readers and writers. More...
 
class  IOTree
 General interface for tree I/O. More...
 
class  IOTreeFactory
 Utilitary class for creating tree readers and writers. More...
 
class  IOTreepuzzlePairedSiteLikelihoods
 This class provides I/O for the Tree-Puzzle/RAxML (phylip-like) paired-site likelihoods format. More...
 
class  ISequence
 
class  ISequenceStream
 
class  ISubstitutionModel
 General interface for distance matrix readers. More...
 
class  ITree
 General interface for tree readers. More...
 
class  JCnuc
 The Jukes-Cantor substitution model for nucleotides. More...
 
class  JCprot
 The Jukes-Cantor substitution model for proteins. More...
 
class  JTT92
 The Jones, Taylor and Thornton substitution model for proteins. More...
 
class  K80
 The Kimura 2-rates substitution model for nucleotides. More...
 
class  KCM
 The general multiple substitution model for codons, from Zaheri & al, 2014. More...
 
class  KeyvalException
 
class  KeyvalTools
 
class  KleinAANetChargeIndex
 
class  KrKcSubstitutionRegister
 Count conservative and radical amino-acid substitutions. More...
 
class  KroneckerCodonDistanceFrequenciesSubstitutionModel
 Class for non-synonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic models, with allowed multiple substitutions. More...
 
class  KroneckerCodonDistanceSubstitutionModel
 Class for non-synonymous substitution models on codons with parameterized nucleotidic models, with allowed multiple substitutions. More...
 
class  KroneckerWordSubstitutionModel
 Basal class for words of substitution models with multiple substitutions. More...
 
class  L95
 The no-strand bias substitution model for nucleotides, from Lobry 1995. The point of this model is that the substitution rate from a nucleotide N towards another M is the same as the rate from the complement of N towards the complement of M. Note that this model is not reversible. More...
 
class  LabelCollapsedNodesTreeDrawingListener
 A TreeDrawingListener implementation that label the collapsed nodes. More...
 
class  LabelInnerNodesTreeDrawingListener
 A TreeDrawingListener implementation that write the names of inner nodes. More...
 
class  LabelSubstitutionCount
 Labelling substitution count. More...
 
class  LaplaceSubstitutionCount
 Laplace estimate of the substitution count. More...
 
class  LeafNamesTreeDrawingListener
 A TreeDrawingListener implementation that write leaf names. More...
 
class  LetterAlphabet
 
class  LexicalAlphabet
 
class  LG08
 The Le and Gascuel substitution model for proteins. More...
 
class  LG10_EX_EHO
 The Le and Gascuel (2010) EX_EHO substitution model for proteins. More...
 
class  LGL08_CAT
 The Le et al (2008) CAT substitution model for proteins. More...
 
class  LinearMatrix
 
class  LLG08_EHO
 The Le et al (2008) EH0 substitution model for proteins. More...
 
class  LLG08_EX2
 The Le et al (2008) EX2 substitution model for proteins. More...
 
class  LLG08_EX3
 The Le et al (2008) EX3 substitution model for proteins. More...
 
class  LLG08_UL2
 The Le et al (2008) UL2 substitution model for proteins. More...
 
class  LLG08_UL3
 The Le et al (2008) UL3 substitution model for proteins. More...
 
class  LogsumHmmLikelihood
 
class  LowMemoryRescaledHmmLikelihood
 
class  LUDecomposition
 
class  Mapping
 General interface for storing mapping data. More...
 
class  MapSequenceContainer
 
class  MapTools
 
class  MarginalAncestralStateReconstruction
 Likelihood ancestral states reconstruction: marginal method. More...
 
class  MarkovModulatedFrequenciesSet
 FrequenciesSet to be used with a Markov-modulated substitution model. More...
 
class  MarkovModulatedStateMap
 This class implements a state map for Markov modulated models. More...
 
class  MarkovModulatedSubstitutionModel
 Partial implementation of the Markov-modulated class of substitution models. More...
 
class  Mase
 
class  MaseHeader
 
class  MaseTools
 
class  MathOperator
 
class  Matrix
 
class  MatrixTools
 
class  MetaOptimizer
 
class  MetaOptimizerInfos
 
class  MG94
 The Muse and Gaut (1994) substitution model for codons. More...
 
class  MixedSubstitutionModel
 Interface for Substitution models, defined as a mixture of "simple" substitution models. More...
 
class  MixedSubstitutionModelSet
 Substitution models manager for Mixed Substitution Models. This class inherits from SubstitutionModelSet. More...
 
class  MixtureOfASubstitutionModel
 Substitution models defined as a mixture of nested substitution models. More...
 
class  MixtureOfDiscreteDistributions
 
class  MixtureOfSubstitutionModels
 Substitution models defined as a mixture of several substitution models. More...
 
class  MiyataAAChemicalDistance
 
class  ModelList
 A list of models, for building a WordSubstitutionModel. More...
 
class  MoldMitochondrialGeneticCode
 
class  MolscriptColorSet
 
class  MultipleDiscreteDistribution
 
class  MultiRange
 
class  MutationPath
 This class is used by MutationProcess to store detailed results of simulations. More...
 
class  MutationProcess
 Interface for simulations. More...
 
class  MvaFrequenciesSet
 A frequencies set used to estimate frequencies at the root with the COaLA model. Frequencies at the root are optimized in the same way than the equlibrium frequencies on branches. Hyperparameters are used, which represent positions along the principal axes obtained from a preliminary Correspondence Analysis. From the optimized positions, the 20 frequencies are calculated. More...
 
class  NaiveSubstitutionCount
 Naive substitution count. More...
 
class  NaNListener
 A listener which capture NaN function values and throw an exception in case this happens. More...
 
class  NegativeOperator
 
class  NeighborIteratorClass
 
class  NeighborJoining
 The neighbor joining distance method. More...
 
class  NestedStringTokenizer
 
class  Newick
 The so-called 'newick' parenthetic format. More...
 
class  NewtonBacktrackOneDimension
 
class  NewtonOneDimension
 
class  NexusIOSequence
 
class  NexusIOTree
 a simple parser for reading trees from a Nexus file. More...
 
class  NexusTools
 
class  Nhx
 The so-called 'Nhx - New Hampshire eXtended' parenthetic format. More...
 
class  NNIHomogeneousTreeLikelihood
 This class adds support for NNI topology estimation to the DRHomogeneousTreeLikelihood class. More...
 
class  NNISearchable
 Interface for Nearest Neighbor Interchanges algorithms. More...
 
class  NNITopologyListener
 Listener used internally by the optimizeTreeNNI method. More...
 
class  NNITopologyListener2
 Listener used internally by the optimizeTreeNNI2 method. More...
 
class  NNITopologySearch
 NNI topology search method. More...
 
class  Node
 The phylogenetic node class. More...
 
class  NodeException
 General exception thrown when something is wrong with a particular node. More...
 
class  NodeNotFoundException
 Exception thrown when something is wrong with a particular node. More...
 
class  NodePException
 General exception thrown when something is wrong with a particular node. More...
 
class  NodesIdTreeDrawingListener
 A TreeDrawingListener implementation that writes nodes id. More...
 
class  NodesIteratorClass
 
class  NodesIteratorClass< Graph::ALLGRAPHITER, is_const >
 
class  NodesIteratorClass< Graph::INCOMINGNEIGHBORITER, is_const >
 
class  NodesIteratorClass< Graph::OUTGOINGNEIGHBORITER, is_const >
 
class  NodeTemplate
 The NodeTemplate class. More...
 
class  NoGapSiteContainerIterator
 
class  NonHomogeneousSequenceSimulator
 Site and sequences simulation under non-homogeneous models. More...
 
class  NonHomogeneousTreeLikelihood
 Specialization of the TreeLikelihood interface for the branch non-homogeneous and non-stationary models. More...
 
class  NoTableColumnNamesException
 
class  NoTableRowNamesException
 
class  NotImplementedException
 
class  NucleicAcidsReplication
 
class  NucleicAlphabet
 
class  NucleicAlphabetState
 
class  NucleotideFrequenciesSet
 Parametrize a set of state frequencies for nucleotides. More...
 
class  NucleotideReversibleSubstitutionModel
 Specialisation interface for rversible nucleotide substitution model. More...
 
class  NucleotideSubstitutionModel
 Specialisation interface for nucleotide substitution model. More...
 
class  NullOutputStream
 
class  NullPointerException
 
class  Number
 
class  NumberFormatException
 
class  NumCalcApplicationTools
 
class  NumConstants
 
class  NumericAlphabet
 
class  NumTools
 
class  OAlignment
 
class  ODiscreteDistribution
 
class  ODistanceMatrix
 General interface for distance matrix writers. More...
 
class  OFrequenciesSet
 General interface for distance matrix writers. More...
 
class  OMultiTree
 General interface for tree writers. More...
 
class  OneChangeRegisterTransitionModel
 From a model, compute transition probabilities given there is at least a change of a category (ie a non null number in a register) in the branch. More...
 
class  OneChangeTransitionModel
 From a model, compute transition probabilities given there is at least a change in the branch. More...
 
class  OneDimensionOptimizationTools
 
class  OneJumpSubstitutionCount
 Computes the probability that at least one jump occured on a branch, given the initial and final state. More...
 
class  OParametrizable
 
class  Operator
 
class  OptimizationEvent
 
class  OptimizationListener
 
class  OptimizationStopCondition
 
class  OptimizationTools
 Optimization methods for phylogenetic inference. More...
 
class  Optimizer
 
class  OrderedSequenceContainer
 
class  OSequence
 
class  OSequenceStream
 
class  OSubstitutionModel
 General interface for distance matrix writers. More...
 
class  OTree
 General interface for tree writers. More...
 
class  OutOfRangeException
 
class  OutputStream
 
class  PairedSiteLikelihoods
 A container for paired-site likelihoods (likelihoods over the same sites for different models, especially topologies). An instance of this class is, roughly, a list of models, each of them having a name (stored in the modelNames attribute) and a set of site likelihoods (stored in the logLikelihoods attribute). More...
 
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  PatternTools
 Utilitary methods to compute site patterns. More...
 
class  PgfGraphicDevice
 
class  PGMA
 Compute WPGMA and UPGMA trees from a distance matrix. More...
 
struct  PGMAInfos
 Inner data structure for WPGMA and UPGMA distance methods. More...
 
class  PhredPhd
 
class  PhredPoly
 
class  Phylip
 
class  PhylipDistanceMatrixFormat
 Distance matrix I/O in Phylip format. More...
 
class  PhylogeneticsApplicationTools
 This class provides some common tools for applications. More...
 
class  PhylogramDrawBranchEvent
 
class  PhylogramPlot
 Phylogram representation of trees. More...
 
class  PhyloStatistics
 Compute several quantities on a tree simulateously, optimizing the recursions on the tree. More...
 
class  PlaceboTransformedParameter
 
class  Point2D
 
class  PowellMultiDimensions
 
class  PrincipalComponentAnalysis
 
class  ProbabilisticRewardMapping
 Data storage class for probabilistic rewards mappings. More...
 
class  ProbabilisticSubstitutionMapping
 Data storage class for probabilistic substitution mappings. More...
 
class  PropertyNotFoundException
 General exception thrown if a property could not be found. More...
 
class  ProteicAlphabet
 
class  ProteicAlphabetState
 
class  ProteinFrequenciesSet
 Parametrize a set of state frequencies for proteins. More...
 
class  ProteinReversibleSubstitutionModel
 Specialized interface for protein reversible substitution model. More...
 
class  ProteinSubstitutionModel
 Specialized interface for protein substitution model. More...
 
class  PseudoNewtonOptimizer
 This Optimizer implements Newton's algorithm for finding a minimum of a function. This is in fact a modified version of the algorithm, as suggested by Nicolas Galtier, for the purpose of optimizing phylogenetic likelihoods. More...
 
class  RandomFactory
 
class  RandomTools
 
class  Range
 
class  RangeCollection
 
class  rangeComp_
 
class  RangeSet
 
class  RASiteSimulationResult
 Data structure to store the result of a DetailedSiteSimulator. More...
 
class  RASTools
 Tools to deal with Rates Across Sites (RAS) models. More...
 
class  RColorSet
 
class  RE08
 The Rivas-Eddy substitution model with gap characters. More...
 
class  RE08Codon
 This is a wrapper class of RE08 for codon substitution models. More...
 
class  RE08Nucleotide
 This is a wrapper class of RE08 for nucleotide substitution models. More...
 
class  RE08Protein
 This is a wrapper class of RE08 for protein substitution models. More...
 
class  RegisterRatesSubstitutionModel
 From a model, substitution rates are set into categories following a given register. Each substitution of a category is then multiplied by a rate parameter specific to this category. More...
 
class  ReparametrizationDerivableFirstOrderWrapper
 
class  ReparametrizationDerivableSecondOrderWrapper
 
class  ReparametrizationFunctionWrapper
 
class  RescaledHmmLikelihood
 
class  ReverseTransliterator
 
class  ReversibleSubstitutionModel
 Interface for reversible substitution models. More...
 
class  Reward
 The Reward interface. More...
 
class  RewardMapping
 General interface for storing reward mapping data. More...
 
class  RewardMappingTools
 Provide methods to compute reward mappings. More...
 
class  RGBColor
 
class  RHomogeneousClockTreeLikelihood
 Likelihood computation with a global clock. More...
 
class  RHomogeneousMixedTreeLikelihood
 
class  RHomogeneousTreeLikelihood
 This class implement the 'traditional' way of computing likelihood for a tree. More...
 
class  RN95
 The model described by Rhetsky & Nei, where the only hypothesis is that the transversion rates are only dependent of the target nucleotide. This model is not reversible. More...
 
class  RN95s
 Intersection of models RN95 and L95. More...
 
class  RNA
 
class  RNonHomogeneousMixedTreeLikelihood
 
class  RNonHomogeneousTreeLikelihood
 This class implement the 'traditional' way of computing likelihood for a tree, allowing for non-homogeneous models of substitutions. More...
 
class  RNY
 
class  RowMatrix
 
class  RTransformedParameter
 
class  SelectedSubstitutionRegister
 Class inheriting from GeneralSubstitutionRegister, this one uses a special constructor which allows it to build a substitution matrix from string input specifying a desired substitutions. More...
 
class  SelfMutationProcess
 This class is mainly for testing purpose. It allow "self" mutation of the kind i->i;. More...
 
class  SENCA
 Class for non-synonymous and synonymous substitution models on codons with parameterized equilibrium frequencies and nucleotidic basic models. More...
 
class  Sequence
 
class  SequenceAnnotation
 
class  SequenceApplicationTools
 
class  SequenceContainer
 
class  SequenceContainerTools
 
class  SequenceException
 
class  SequenceFileIndex
 
class  SequenceIterator
 
class  SequenceMask
 
class  SequenceNotAlignedException
 
class  SequenceNotFoundException
 
class  SequencePositionIterator
 
class  SequenceQuality
 
class  SequenceSimulationTools
 Tools for sites and sequences simulation. More...
 
class  SequenceSimulator
 The SequenceSimulator interface. SequenceSimulator classes can simulate whole datasets. More...
 
class  SequenceTools
 
class  SequenceWalker
 
class  SequenceWithAnnotation
 
class  SequenceWithAnnotationTools
 
class  SequenceWithGapException
 
class  SequenceWithQuality
 
class  SequenceWithQualityIterator
 
class  SequenceWithQualityTools
 
class  SimData
 
class  SimpleDiscreteDistribution
 
class  SimpleIndexDistance
 
class  SimpleMultiDimensions
 
class  SimpleMutationProcess
 Generally used mutation process model. More...
 
class  SimpleNewtonMultiDimensions
 
class  SimpleScore
 
class  SimpleSequenceContainerIterator
 
class  SimpleSequencePositionIterator
 
class  SimpleSiteContainerIterator
 
class  Simplex
 
class  Site
 
class  SiteContainer
 
class  SiteContainerTools
 
class  SiteException
 
class  SiteIterator
 
class  SiteNotFoundException
 
class  SitePartitionHomogeneousTreeLikelihood
 Specialization of the TreeLikelihood interface for partition models, homogeneous case. More...
 
class  SitePatterns
 Data structure for site patterns. More...
 
class  SiteSimulationResult
 Data structure to store the result of a DetailedSiteSimulator. More...
 
class  SiteSimulator
 The SiteSimulator interface. SiteSimulator classes can simulate single sites. More...
 
class  SiteTools
 
class  SiteWithGapException
 
class  SSR
 The Strand Symmetric Reversible substitution model for nucleotides. More...
 
class  StandardGeneticCode
 
class  StateChangedEvent
 
class  StateListener
 
class  StateMap
 Map the states of a given alphabet which have a model state. More...
 
class  StatTest
 
class  StatTools
 
class  StdErr
 
class  StdOut
 
class  StdStr
 
class  StlOutputStream
 
class  StlOutputStreamWrapper
 
class  Stockholm
 
class  StopCodonException
 
class  StreamSequenceIterator
 
class  StreamSequenceWithQualityIterator
 
class  StringSequenceTools
 
class  StringTokenizer
 
class  SubstitutionCount
 The SubstitutionsCount interface. More...
 
class  SubstitutionMapping
 General interface for storing mapping data. More...
 
class  SubstitutionMappingTools
 Provide methods to compute substitution mappings. More...
 
class  SubstitutionModel
 Interface for all substitution models. More...
 
class  SubstitutionModelException
 Exception that may be thrown by susbstitution models. More...
 
class  SubstitutionModelSet
 Substitution models manager for non-homogeneous / non-reversible models of evolution. More...
 
class  SubstitutionModelSetTools
 Tools for automatically creating SubstitutionModelSet objects. More...
 
class  SubstitutionRegister
 The SubstitutionRegister interface. More...
 
class  SvgGraphicDevice
 
class  SWSubstitutionRegister
 Distinguishes substitutions given the link between the changed nucleotides : S for strong (GC) and W for weak (AT). More...
 
class  SymbolList
 
class  SymbolListDeletionEvent
 
class  SymbolListEditionEvent
 
class  SymbolListInsertionEvent
 
class  SymbolListListener
 
class  SymbolListSubstitutionEvent
 
class  SymbolListTools
 
class  T92
 The Tamura (1992) substitution model for nucleotides. More...
 
class  Table
 
class  TableColumnNameNotFoundException
 
class  TableColumnNamesException
 
class  TableNameNotFoundException
 
class  TableRowNameNotFoundException
 
class  TableRowNamesException
 
class  TestFunction
 
class  ThreePointsNumericalDerivative
 
class  TN93
 The Tamura and Nei (1993) substitution model for nucleotides. More...
 
class  TopologyChangeEvent
 Class for notifying new toplogy change events. More...
 
class  TopologyListener
 Implement this interface to be notified when the topology of a tree has changed during topology search. More...
 
class  TopologySearch
 Interface for topology search methods. More...
 
class  TotalSubstitutionRegister
 Count all substitutions. More...
 
class  TransformedParameter
 
class  TransitionModel
 
class  Transliterator
 
class  Tree
 Interface for phylogenetic tree objects. More...
 
class  TreeDrawing
 Basal interface for tree drawing classes. More...
 
class  TreeDrawingDisplayControler
 Easy tune of tree drawings display. More...
 
class  TreeDrawingListener
 Interface allowing to capture drawing events. More...
 
class  TreeDrawingListenerAdapter
 An empty implementation of the TreeDrawingListener interface. More...
 
class  TreeDrawingNodeInfo
 
class  TreeDrawingSettings
 A set of options to tune the display of a TreeDrawing object. More...
 
class  TreeException
 General exception thrown when something wrong happened in a tree. More...
 
class  TreeGraph
 
class  TreeGraphImpl
 
class  TreeLikelihood
 The TreeLikelihood interface. More...
 
class  TreeLikelihoodData
 TreeLikelihood data structure. More...
 
class  TreeLikelihoodNodeData
 TreeLikelihood partial data structure. More...
 
class  TreeLikelihoodTools
 Utilitary methods that work with TreeLikelihood objects. More...
 
class  TreeParsimonyData
 TreeParsimonyScore data structure. More...
 
class  TreeParsimonyNodeData
 TreeParsimonyScore node data structure. More...
 
class  TreeParsimonyScore
 Compute a parsimony score. More...
 
class  TreeTemplate
 The phylogenetic tree class. More...
 
class  TreeTemplateTools
 Utilitary methods working with TreeTemplate and Node objects. More...
 
class  TreeTools
 Generic utilitary methods dealing with trees. More...
 
class  TripletSubstitutionModel
 Class for neutral substitution models on triplets, which correspond to codons that do not have any significance (whether they are STOP or functional). More...
 
class  TruncatedExponentialDiscreteDistribution
 
class  TS98
 Tuffley and Steel's 1998 covarion model. More...
 
class  TsTvSubstitutionRegister
 Distinguishes transitions from transversions. More...
 
class  TwoPointsNumericalDerivative
 
class  TwoTreeLikelihood
 This class is a simplified version of DRHomogeneousTreeLikelihood for 2-Trees. More...
 
class  Uniform01K
 
class  Uniform01QD
 
class  Uniform01WH
 
class  UniformDiscreteDistribution
 
class  UniformizationSubstitutionCount
 Analytical (weighted) substitution count using the uniformization method. More...
 
class  UnrootedTreeException
 Exception thrown when a tree is expected to be rooted. More...
 
class  UnvalidFlagException
 
class  UserAlphabetIndex1
 
class  UserProteinSubstitutionModel
 Build an empirical protein substitution model from a file. More...
 
class  VectorException
 
class  VectorOfSubstitionRegisters
 Sets a Register based on a vector of Registers. The categories are intersection of categories of those Registers. More...
 
class  VectorSequenceContainer
 
class  VectorSiteContainer
 
class  VectorTools
 
class  VertebrateMitochondrialGeneticCode
 
class  WAG01
 The Whelan and Goldman substitution model for proteins. More...
 
class  WeightedSubstitutionCount
 Interface allowing for weighting of substitution counts according to state properties. More...
 
class  WordAlphabet
 
class  WordFrequenciesSet
 Frequencies in words computed from the frequencies on letters. The parameters are the parameters of the Frequencies on letters. The WordFrequenciesSet owns the FrequenciesSet* it is built on. Interface class. More...
 
class  WordFromIndependentFrequenciesSet
 the Frequencies in words are the product of Independent Frequencies in letters More...
 
class  WordFromUniqueFrequenciesSet
 
class  WordSubstitutionModel
 Basal class for words of substitution models. More...
 
class  WrappedModel
 Wrapping model class. More...
 
class  WrappedSubstitutionModel
 
class  XFigColorManager
 
class  XFigGraphicDevice
 
class  XFigLaTeXFontManager
 
class  XFigPostscriptFontManager
 
class  YeastMitochondrialGeneticCode
 
class  YN98
 The Yang and Nielsen (1998) substitution model for codons. More...
 
class  YNGP_M
 Abstract generic class for The Yang et al (2000) M substitution models for codons. al (2004). More...
 
class  YNGP_M1
 The Yang et al (2000) M1 substitution model for codons, with the more realistic modification in Wong & al (2004). More...
 
class  YNGP_M10
 The Yang et al (2000) M10 substitution model for codons. More...
 
class  YNGP_M2
 The Yang et al (2000) M2 substitution model for codons, with the more realistic modification in Wong & al (2004). More...
 
class  YNGP_M3
 The Yang et al (2000) M3 substitution model for codons. More...
 
class  YNGP_M7
 The Yang et al (2000) M7 substitution model for codons. More...
 
class  YNGP_M8
 The Yang et al (2000) M8 substitution model for codons. More...
 
class  YNGP_M9
 The Yang et al (2000) M9 substitution model for codons. More...
 
class  YpR
 YpR model. More...
 
class  YpR_Gen
 General YpR model. More...
 
class  YpR_Sym
 symetrical YpR model. More...
 
class  ZeroDivisionException
 

Typedefs

typedef AssociationDAGraphImplObserver< N, E, DAGlobalGraphAssociationDAGlobalGraphObserver
 
typedef AssociationGraphImplObserver< N, E, GlobalGraphAssociationGlobalGraphObserver
 
typedef AssociationTreeGraphImplObserver< N, E, TreeGlobalGraphAssociationTreeGlobalGraphObserver
 
typedef DAGraphImpl< GlobalGraphDAGlobalGraph
 
typedef TreeGraphImpl< GlobalGraphTreeGlobalGraph
 
typedef std::vector< std::complex< double > > Vcomplex
 
typedef std::vector< VcomplexVVcomplex
 
typedef std::vector< VVcomplexVVVcomplex
 
typedef std::vector< std::complex< long double > > Vlcomplex
 
typedef std::vector< VlcomplexVVlcomplex
 
typedef std::vector< VVlcomplexVVVlcomplex
 
typedef std::vector< double > Vdouble
 
typedef std::vector< VdoubleVVdouble
 
typedef std::vector< VVdoubleVVVdouble
 
typedef std::vector< VVVdoubleVVVVdouble
 
typedef std::vector< long double > Vldouble
 
typedef std::vector< VldoubleVVldouble
 
typedef std::vector< VVldoubleVVVldouble
 
typedef std::vector< VVVldoubleVVVVldouble
 
typedef std::vector< int > Vint
 
typedef std::vector< VintVVint
 
typedef std::vector< VVintVVVint
 
typedef std::vector< VVVintVVVVint
 
typedef std::vector< unsigned int > Vuint
 
typedef std::vector< VuintVVuint
 
typedef std::vector< VVuintVVVuint
 
typedef std::vector< VVVuintVVVVuint
 
typedef AssociationDAGraphImplObserver< N, E, DAGlobalGraphAssociationDAGlobalGraphObserver
 
typedef AssociationGraphImplObserver< N, E, GlobalGraphAssociationGlobalGraphObserver
 
typedef AssociationTreeGraphImplObserver< N, E, TreeGlobalGraphAssociationTreeGlobalGraphObserver
 
typedef DAGraphImpl< GlobalGraphDAGlobalGraph
 
typedef TreeGraphImpl< GlobalGraphTreeGlobalGraph
 
typedef std::vector< std::complex< double > > Vcomplex
 
typedef std::vector< VcomplexVVcomplex
 
typedef std::vector< VVcomplexVVVcomplex
 
typedef std::vector< std::complex< long double > > Vlcomplex
 
typedef std::vector< VlcomplexVVlcomplex
 
typedef std::vector< VVlcomplexVVVlcomplex
 
typedef std::vector< double > Vdouble
 
typedef std::vector< VdoubleVVdouble
 
typedef std::vector< VVdoubleVVVdouble
 
typedef std::vector< VVVdoubleVVVVdouble
 
typedef std::vector< long double > Vldouble
 
typedef std::vector< VldoubleVVldouble
 
typedef std::vector< VVldoubleVVVldouble
 
typedef std::vector< VVVldoubleVVVVldouble
 
typedef std::vector< int > Vint
 
typedef std::vector< VintVVint
 
typedef std::vector< VVintVVVint
 
typedef std::vector< VVVintVVVVint
 
typedef std::vector< unsigned int > Vuint
 
typedef std::vector< VuintVVuint
 
typedef std::vector< VVuintVVVuint
 
typedef std::vector< VVVuintVVVVuint
 
typedef std::vector< size_t > SequenceSelection
 
typedef std::vector< size_t > SiteSelection
 
typedef std::vector< std::string > Comments
 
typedef NodeTemplate< TreeDrawingNodeInfoINode
 
typedef std::bitset< 21 > Bitset
 
typedef NodeTemplate< SimDataSNode
 

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)
 

Typedef Documentation

typedef std::bitset<21> bpp::Bitset

Definition at line 55 of file DRTreeParsimonyData.h.

Definition at line 78 of file AbstractTreeDrawing.h.

Definition at line 88 of file NonHomogeneousSequenceSimulator.h.