- Gamma - Class in Maths
-
Provides methods associated with the gamma distribution.
- Gamma() - Constructor for class Maths.Gamma
-
- gammaRates(RateCategory, String, int) - Static method in class Models.Model
-
Creates a new model with multiple rate classes distributed by a gamma
distribution (see Yang 1993) based on a single rate class
- GeLL - Class in Executable
-
A general purpose driver around the library.
- GeneralException - Exception in Exceptions
-
Custom exception class that provides different levels of information in a call
to toString() based on a debug level.
- GeneralException(String, Throwable) - Constructor for exception Exceptions.GeneralException
-
Default constructor
- GeneralException.Debug - Enum in Exceptions
-
Enumeration of the different debug levels
- GenericAlignment - Class in Alignments
-
Static classes for reading/writing sequence alignment in a generic format.
- getAdapterL() - Method in class ModelTest.TestInstance
-
Get the likelihood of the adapter associated with this instance
- getAICs() - Method in class ModelTest.AIC
-
Returns the AIC for each instance
- getAlignment() - Method in class Ancestors.AncestralMarginal.Result
-
Gets the reconstructed alignment
- getAlignment(int) - Method in class Simulations.Simulate
-
Gets a simulated alignment, not returning the state of internal nodes
- getAlignment(int, boolean) - Method in class Simulations.Simulate
-
Gets a simulated alignment
- getAlignment(int, Map<String, String>) - Method in class Simulations.Simulate
-
Gets a simulated alignment, not returning the state of internal nodes.
- getAlignment(int, boolean, Map<String, String>) - Method in class Simulations.Simulate
-
Gets a simulated alignment.
- getAlignment(List<String>) - Method in class Simulations.Simulate
-
Gets a simulated alignment, not returning the state of the internal nodes.
- getAlignment(List<String>, boolean) - Method in class Simulations.Simulate
-
Gets a simulated alignment.
- getAlignment(List<String>, Map<String, String>) - Method in class Simulations.Simulate
-
Gets a simulated alignment, not returning the state of the internal nodes.
- getAlignment(List<String>, boolean, Map<String, String>) - Method in class Simulations.Simulate
-
Gets a simulated alignment.
- getAlignmentLength() - Method in class Likelihood.Calculator
-
Get the length of the alignment the calculator is using
- getAlignmentLength() - Method in class Likelihood.StandardCalculator
-
- getAllStates() - Method in class Likelihood.Probabilities
-
Gets the list of all possible states
- getAmbiguous() - Method in class Alignments.Site
-
Gets the information about ambiguous states for this site
- getArray() - Method in class Maths.SquareMatrix
-
Gets the matrix as an array of doubles
- getArrayMap() - Method in class Models.RateCategory
-
Gets the map that maps state to position in matrix
Called this as
RateCategory.getMap() is kept for comptability
- getAssignment(String) - Method in class Ancestors.Assignment
-
Gets the assignment for a node
- getBestAIC() - Method in class ModelTest.AIC
-
Returns the best AIC
- getBestBIC() - Method in class ModelTest.BIC
-
Returns the best BIC
- getBestInstance() - Method in class ModelTest.AIC
-
Returns the test instance with the best AIC
- getBestInstance() - Method in class ModelTest.BIC
-
Returns the test instance with the best BIC
- getBICs() - Method in class ModelTest.BIC
-
Returns the BIC for each instance
- getBranchByChild(String) - Method in class Trees.Tree
-
Gets the branch which has the given node as the child node
- getBranches() - Method in class Trees.Tree
-
Gets a list of branches.
- getBranchesByParent(String) - Method in class Trees.Tree
-
Gets the set of branches which have the passed node as a parent
- getBranchesReversed() - Method in class Trees.Tree
-
- getCalculator() - Method in class ModelTest.TestInstance
-
Get the calculator associated with this instance
- getCharacter(String) - Method in class Alignments.Site
-
Gets the possible characters for a given taxa.
- getChild() - Method in class Trees.Branch
-
Get the child node of the branch
- getCI(Parameter, double) - Method in class Likelihood.ConfidenceInterval
-
Calculates the confidence interval for a single parameter
- getClassSize(String) - Method in class Alignments.Alignment
-
Gets the size of a class, that is how many sites belong to the given class
- getColumn(double[][], int) - Static method in class Utils.Array2D
-
Returns a column of the array
- getCount() - Method in class Alignments.UniqueSite
-
Get the number of times the site occurs in the related alignment
- getD() - Method in class Maths.EigenvalueDecomposition
-
Return the block diagonal eigenvalue matrix
- getDoublePivot() - Method in class Maths.LUDecomposition
-
Return pivot permutation vector as a one-dimensional double array
- getEstimate() - Method in class Parameters.Parameter
-
Returns whether this parameter is a parameter that should be estimated
- getFreq(String) - Method in class Likelihood.FitzJohnRoot
-
- getFreq(String) - Method in interface Likelihood.Root
-
Get the frequency of the given state at the root
- getFreq(String) - Method in class Likelihood.StandardRoot
-
- getFreq(RateCategory) - Method in class Models.Model
-
Gets the frquency of a rate class
- getFreq() - Method in class Models.RateCategory
-
Gets the root frequencies
- getGroups() - Method in class Utils.SetSettings
-
Gets the set of all groups that have had a setting set within them
- getID() - Method in class Alignments.Site
-
Gets the ID of the site
- getImagEigenvalues() - Method in class Maths.EigenvalueDecomposition
-
Return the imaginary parts of the eigenvalues
- getInitialNodeLikelihoods(Tree, Map<String, Integer>) - Method in class Alignments.Site
-
Gets initial node likelihoods based on the site and tree.
- getInitialNodeLikelihoods(Tree, Site, Map<String, Integer>) - Method in class Ancestors.Assignment
-
Creates initial node likelihoods using this assignment.
- getInternal() - Method in class Trees.Tree
-
Gets a list of internal nodes.
- getInverseMembers() - Method in class Trees.Split
-
- getL() - Method in class Maths.LUDecomposition
-
Return lower triangular factor
- getLeaves() - Method in class Trees.Tree
-
Gets a list of leaves
- getLength() - Method in class Alignments.Alignment
-
Gets the length of the aligmnet
- getLength() - Method in class Trees.Branch
-
Get the length of the branch
- getLength() - Method in class Trees.Split
-
Gets the length of the branch associated with this split
- getLength() - Method in class Trees.Tree
-
Gets the length of the tree
- getLikelihood() - Method in class Likelihood.Likelihood
-
Gets the likelihood
- getLikelihood() - Method in class Likelihood.SiteLikelihood
-
Get the likelihood
- getLikelihood(String) - Method in class Likelihood.SiteLikelihood.NodeLikelihood
-
Returns the partial likelihood for a given state
- getLikelihood(int) - Method in class Likelihood.SiteLikelihood.NodeLikelihood
-
Returns the partial likelihood for the state at position i.
- getLikelihood() - Method in class Likelihood.SiteLikelihood.RateLikelihood
-
Returns the likelihood.
- getLikelihoods() - Method in class Likelihood.SiteLikelihood.NodeLikelihood
-
Returns the partial likelihood for each state as an array.
- getLikelihoods() - Method in class ModelTest.AIC
-
Returns the likelihood for each instance
- getLikelihoods() - Method in class ModelTest.BIC
-
Returns the likelihood for each instance
- getLowerBound() - Method in class Parameters.Parameter
-
Gets the lower bound of a parameter
- getMap() - Method in class Likelihood.Probabilities
-
Gets an Map linking states to position in an array
- getMap() - Method in class Models.Model
-
Gets a map from the rate name to its index in the rate matrix
- getMap() - Method in class Models.RateCategory
-
Gets the map that maps state to position in matrix
- getMembers() - Method in class Trees.Split
-
Returns the members of one "half" of the split.
- getMissingLikelihood(Site) - Method in class Likelihood.StandardLikelihood
-
Gets the likelihood result for a given missing site
- getModel() - Method in class Models.DNAModelFactory
-
Returns a new instance of the relevant model
- getMostProbableRateCategory() - Method in class Likelihood.SiteLikelihood
-
Gets the most probable rate category
- getName() - Method in class Models.RateCategory
-
Get the name of the rate category
- getName() - Method in class ModelTest.TestInstance
-
Get the name of this instance
- getName() - Method in class Parameters.Parameter
-
Gets the name of the parameter
- getNodeLikelihood(String) - Method in class Likelihood.SiteLikelihood.RateLikelihood
-
Returns the likelihood results for a given node on the tree
- getNum() - Method in class Alignments.Site
-
Get the number of taxa
- getNumber() - Method in class Alignments.Alignment
-
Gets the number of taxa in the alignment
- getNumberAdapterParams() - Method in class ModelTest.TestInstance
-
Get the number of parameters associated with the adapter for this instance
- getNumberBranches() - Method in class Trees.Tree
-
Gets the number of branches
- getNumberStates() - Method in class Models.Model
-
Get the number of states represented in the model
- getNumberStates() - Method in class Models.RateCategory
-
Gets the number of states in the rate class
- getP(RateCategory) - Method in class Likelihood.Probabilities
-
Gets a specific probability for a change from one state to another along
a specific branch under a specific RateClass
- getP(Branch) - Method in class Likelihood.Probabilities.RateProbabilities
-
Gets the probability matrix for a single branch
- getP(Branch, String, String) - Method in class Likelihood.Probabilities.RateProbabilities
-
Gets the probability of a single transition on a single branch
- getP(double) - Method in class Models.RateCategory
-
Gets the P-matrix for a given length
- getParam(String) - Method in class Parameters.Parameters
-
Gets the parameter with the given name
- getParameters() - Method in class Likelihood.Likelihood
-
Gets the parameters used to calculate the likelihood
- getParameters() - Method in class Models.DNAModelFactory
-
Gets the parameters for the relevant model
- getParameters() - Method in class ModelTest.TestInstance
-
Get the parameters associated with this instance
- getParameters() - Method in class Trees.Tree
-
Returns a Parameters object containing a parameter for each branch length.
- getParametersForEstimation() - Method in class Trees.Tree
-
Returns a Parameters object containing a parameter for each branch length.
- getParent() - Method in class Trees.Branch
-
Gets the parent node of the branch
- getParent(String) - Method in class Trees.Tree
-
Gets the parent node of the given node
- getPivot() - Method in class Maths.LUDecomposition
-
Return pivot permutation vector
- getPosition(int, int) - Method in class Maths.SquareMatrix
-
Returns the value in position (i,j) of the matrix
- getPossible(String) - Method in class Alignments.Ambiguous
-
Gets the characters an ambiguous character could represent
- getProbability(String, String) - Method in class Ancestors.AncestralMarginal.SiteResult
-
Gets thr probability of a given state at a given node
- getRateCategory() - Method in class Likelihood.Probabilities
-
Gets the set of RateClasses that we have calculated probabilities for
- getRateCategoryProbability(RateCategory) - Method in class Likelihood.SiteLikelihood
-
Gets the probability of being in a rate category
- getRateLikelihood(RateCategory) - Method in class Likelihood.SiteLikelihood
-
Get the likelihood for a single rate class
- getRateP(RateCategory) - Method in class Likelihood.Probabilities
-
Gets the probability of a rate class
- getRates() - Method in class Models.Model
-
Gets a set of rate classes in the model
- getRawCharacter(String) - Method in class Alignments.Site
-
Gets the raw charcater for a given taxa.
- getRawFreq(String) - Method in class Alignments.Alignment
-
Gets the frequency of a raw character
- getReal(RealFactory.RealType, double) - Static method in class Maths.RealFactory
-
Returns a new real of the given type and value
- getRealEigenvalues() - Method in class Maths.EigenvalueDecomposition
-
Return the real parts of the eigenvalues
- getResult() - Method in class Likelihood.Calculator.SiteCalculator
-
Gets the computed result
- getRoot(RateCategory) - Method in class Likelihood.Probabilities
-
Get a root object, for the given rate category, that can be used to
the total likelihood from the root node likelihoods or provide the
frequencies of the various states at the root
- getRoot() - Method in class Models.RateCategory
-
Get a root object that can be used to calculate the total likelihood
from the root node likelihoods or provide the frequencies of the various
states at the root
- getRoot() - Method in class Trees.Tree
-
Get the root node
- getScale() - Method in class Models.Model
-
Gets the scale - the value the rate matrices need to be multiplied by
to ensure an average rate of 1.
- getScaledMatrix() - Method in class Models.RateCategory
-
Gets the scaled rate matrix
- getSet() - Method in class Utils.SetSettings
-
Gets the set of root level settings that have been set
- getSet(String) - Method in class Utils.SetSettings
-
Gets the set of settings that have been set within a group
- getSetting(String) - Method in class Utils.SetSettings
-
Gets the value of a root level setting
- getSetting(String, String) - Method in class Utils.SetSettings
-
Gets the value of a setting within a group
- getSetting(String) - Method in class Utils.Settings
-
Gets the value of a root level setting
- getSetting(String, String) - Method in class Utils.Settings
-
Gets the value of a setting within a group
- getSingleElement(Set<T>) - Static method in class Utils.SetUtils
-
Gets the single element of a set if it has only one element.
- getSite(int) - Method in class Alignments.Alignment
-
Returns the site at a given position in the alignment
- getSite() - Method in class Ancestors.AncestralMarginal.SiteResult
-
Returns the reconstructed site
- getSite() - Method in class Simulations.Simulate
-
Gets a simulated site without returning the state of the internal nodes
- getSite(String) - Method in class Simulations.Simulate
-
Gets a simulated site without returning the state of the internal nodes
- getSite(Map<String, String>) - Method in class Simulations.Simulate
-
Gets a simulated site without returning the state of the internal nodes.
- getSite(Map<String, String>, String) - Method in class Simulations.Simulate
-
Gets a simulated site without returning the state of the internal nodes.
- getSite(boolean) - Method in class Simulations.Simulate
-
Gets a simulated site
- getSite(boolean, String) - Method in class Simulations.Simulate
-
Gets a simulated site
- getSite(boolean, Map<String, String>) - Method in class Simulations.Simulate
-
Gets a simulated site.
- getSite(boolean, Map<String, String>, String) - Method in class Simulations.Simulate
-
Gets a simulated site.
- getSiteClass() - Method in class Alignments.Site
-
Gets the class of this site
- getSiteClasses() - Method in class Alignments.Alignment
-
Returns a list of site classes in the same order as the sites in the
alignment.
- getSiteLikelihood(Site) - Method in class Likelihood.StandardLikelihood
-
Gets the likelihood result for a given site
- getSiteResult(Site) - Method in class Ancestors.AncestralMarginal.Result
-
Gets the site results for a given site
- getSize() - Method in class Trees.Tree
-
Gets the size of the tree, that is the number of taxa
- getSmallestReal(RealFactory.RealType) - Static method in class Maths.RealFactory
-
Returns the smallest possible real of the given type
- getSplits() - Method in class Trees.Tree
-
Gets the splits that represent the tree
- getStates() - Method in class Models.Model
-
Gets the set of all states in the model
- getTaxa() - Method in class Alignments.Alignment
-
Gets the names of the taxa in the aligment
- getTaxa() - Method in class Alignments.Site
-
Get the set of taxa
- getTotalRate() - Method in class Models.RateCategory
-
Gets the total rate of the rate class.
- getU() - Method in class Maths.LUDecomposition
-
Return upper triangular factor
- getUniqueSites() - Method in class Alignments.Alignment
-
Returns a list of unique sites in the aligment.
- getUpperBound() - Method in class Parameters.Parameter
-
Gets the upper bound of a parameter
- getV() - Method in class Maths.EigenvalueDecomposition
-
Return the eigenvector matrix
- getValue() - Method in class Parameters.Parameter
-
Gets the value of the parameter
- getValue(String) - Method in class Parameters.Parameters
-
Gets the value of a parameter
- getValues() - Method in class Parameters.Parameters
-
Gets a map from parameter name to the value of that parameter
- GoldenSection - Class in Optimizers
-
Implements a golden section search for parameter optimisation.
- GoldenSection() - Constructor for class Optimizers.GoldenSection
-
Constructor that uses default parameters for rigour and output level
- GoldenSection(GoldenSection.ProgressLevel) - Constructor for class Optimizers.GoldenSection
-
Constructor which allows a user define output level
- GoldenSection(double) - Constructor for class Optimizers.GoldenSection
-
Constructor which allows a user defined rigour
- GoldenSection(double, GoldenSection.ProgressLevel) - Constructor for class Optimizers.GoldenSection
-
Constructor which allows a user defined rigour and output level
- GoldenSection.ProgressLevel - Enum in Optimizers
-
Enumeration of the different levels of output
- greaterThan(Real) - Method in interface Maths.Real
-
Compares this real to another
- greaterThan(double) - Method in interface Maths.Real
-
Compares this real to a double
- greaterThan(Real) - Method in class Maths.SmallDouble
-
- greaterThan(double) - Method in class Maths.SmallDouble
-
- greaterThan(Real) - Method in class Maths.StandardDouble
-
- greaterThan(double) - Method in class Maths.StandardDouble
-
- GTR(Parameters) - Static method in class Models.DNAModelFactory
-
Creates an instance of a General Time Reversible model
- GTR() - Static method in class Models.DNAModelFactory
-
Creates an instance of a General Time Reversible model
- GTR_Gamma(Parameters, int) - Static method in class Models.DNAModelFactory
-
Creates an instance of a General Time Reversible model with gamma-distributed rate
across sites
- GTR_Gamma(int) - Static method in class Models.DNAModelFactory
-
Creates an instance of a General Time Reversible model with gamma-distributed rate
across sites