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G

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
getAlignment() - Method in class Ancestors.AncestralMarginal.Result
Gets the reconstructed alignment
getAlignment(int) - Method in class Simulations.Simulate
Gets a simulated alignment, not returing 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 returing the state of internal nodes.
getAlignment(int, boolean, Map<String, String>) - Method in class Simulations.Simulate
Gets a simulated alignment.
getAllStates() - Method in class Likelihood.Probabilities
Gets the set of all possible states
getArray() - Method in class Maths.SquareMatrix
Gets the matrix as an array of doubles
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
Gets the branches in the reverse order to that returned by Tree.getBranches().
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
getColumn(double[][], int) - Static method in class Utils.Array2D
Returns a column of the array
getConstraint(String) - Method in class Constraints.SiteConstraints
Gets the constraints for a node
getConstraints(Tree, Site) - Method in interface Constraints.Constrainer
Gets the consraints on an the external nodes of a site given the tree and the state of the leafs.
getConstraints(Tree, Site) - Method in class Constraints.NoConstraints
 
getCount(Site) - Method in class Alignments.Alignment
Gets a count of hoften a site occurs in the 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 paramater is a parameter that should be estimated
getFreq(RateCategory, String) - Method in class Likelihood.Probabilities
Gets the root frequency for a specified state under a specified RateClass
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
getImagEigenvalues() - Method in class Maths.EigenvalueDecomposition
Return the imaginary parts of the eigenvalues
getInternal() - Method in class Trees.Tree
Gets a list of internal nodes.
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.Tree
Gets the length of the tree
getLikelihood() - Method in class Likelihood.Likelihood
Gets the total likelihood
getLikelihood(String) - Method in class Likelihood.Likelihood.NodeLikelihood
Returns the partial likelihood for a given state
getLikelihood() - Method in class Likelihood.Likelihood.RateLikelihood
Returns the likelihood.
getLikelihood() - Method in class Likelihood.Likelihood.SiteLikelihood
Get the likelihood
getLowerBound() - Method in class Parameters.Parameter
Gets the lower bound of a parameter
getMap() - Method in class Models.Model
Gets a map from the rate name to its index in the rate matrix Should it really be a method of Model rather than Rate
getMap() - Method in class Models.RateCategory
Gets the map that maps state to position in matrix
getMaxKey() - Method in class Utils.ToDoubleHashMap
Returns the key which has the maximum value associated with it
getMissingLikelihood(Site) - Method in class Likelihood.Likelihood
Gets the likelihood result for a given missing site
getMostProbableRateCategory() - Method in class Likelihood.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 Parameters.Parameter
Gets the name of the parameter
getNodeLikelihood(String) - Method in class Likelihood.Likelihood.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
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, Branch, String, String) - 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(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 this likelihood
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 charcter 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 probailities for
getRateCategoryProbability(RateCategory) - Method in class Likelihood.Likelihood.SiteLikelihood
Gets the probability of being in a rate category
getRateLikelihood(RateCategory) - Method in class Likelihood.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.
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() - 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.
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(Map<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, Map<String, String>) - Method in class Simulations.Simulate
Gets a simulated site.
getSiteLikelihood(Site) - Method in class Likelihood.Likelihood
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
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 rigor and output level
GoldenSection(GoldenSection.ProgressLevel) - Constructor for class Optimizers.GoldenSection
Constrcutor which allows a user define output level
GoldenSection(double) - Constructor for class Optimizers.GoldenSection
Constructor which allows a user defined rigor
GoldenSection(double, GoldenSection.ProgressLevel) - Constructor for class Optimizers.GoldenSection
Constructor which allows a user defined rigor and output level
GoldenSection.ProgressLevel - Enum in Optimizers
Enumeration of the different levels of output
GTR(Parameters) - Static method in class Models.DNAModelFactory
Creates an instance of a General Time Reversable model
GTR_Gamma(Parameters, int) - Static method in class Models.DNAModelFactory
Creates an instance of a General Time Reversable model with gamma-distributed rate across sites
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