- Gamma - Class in Maths
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Provides methods associated with the gamma distribution.
- Gamma() - Constructor for class Maths.Gamma
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- gammaRates(RateCategory, String, int) - Static method in class Models.Model
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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
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A general purpose driver around the library.
- GeneralException - Exception in Exceptions
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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
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Default constructor
- GeneralException.Debug - Enum in Exceptions
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Enumeration of the different debug levels
- getAlignment() - Method in class Ancestors.AncestralMarginal.Result
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Gets the reconstructed alignment
- getAlignment(int) - Method in class Simulations.Simulate
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Gets a simulated alignment, not returing the state of internal nodes
- getAlignment(int, boolean) - Method in class Simulations.Simulate
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Gets a simulated alignment
- getAlignment(int, Map<String, String>) - Method in class Simulations.Simulate
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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
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Gets the matrix as an array of doubles
- getBranchByChild(String) - Method in class Trees.Tree
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Gets the branch which has the given node as the child node
- getBranches() - Method in class Trees.Tree
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Gets a list of branches.
- getBranchesByParent(String) - Method in class Trees.Tree
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Gets the set of branches which have the passed node as a parent
- getBranchesReversed() - Method in class Trees.Tree
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- 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
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Calculates the confidence interval for a single parameter
- getColumn(double[][], int) - Static method in class Utils.Array2D
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Returns a column of the array
- getConstraint(String) - Method in class Constraints.SiteConstraints
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Gets the constraints for a node
- getConstraints(Tree, Site) - Method in interface Constraints.Constrainer
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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
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- getCount(Site) - Method in class Alignments.Alignment
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Gets a count of hoften a site occurs in the alignment
- getD() - Method in class Maths.EigenvalueDecomposition
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Return the block diagonal eigenvalue matrix
- getDoublePivot() - Method in class Maths.LUDecomposition
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Return pivot permutation vector as a one-dimensional double array
- getEstimate() - Method in class Parameters.Parameter
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Returns whether this paramater is a parameter that should be estimated
- getFreq(RateCategory, String) - Method in class Likelihood.Probabilities
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Gets the root frequency for a specified state under a specified RateClass
- getFreq(RateCategory) - Method in class Models.Model
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Gets the frquency of a rate class
- getFreq() - Method in class Models.RateCategory
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Gets the root frequencies
- getGroups() - Method in class Utils.SetSettings
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Gets the set of all groups that have had a setting set within them
- getImagEigenvalues() - Method in class Maths.EigenvalueDecomposition
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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
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Return lower triangular factor
- getLeaves() - Method in class Trees.Tree
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Gets a list of leaves
- getLength() - Method in class Alignments.Alignment
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Gets the length of the aligmnet
- getLength() - Method in class Trees.Branch
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Get the length of the branch
- getLength() - Method in class Trees.Tree
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Gets the length of the tree
- getLikelihood() - Method in class Likelihood.Likelihood
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Gets the total likelihood
- getLikelihood(String) - Method in class Likelihood.Likelihood.NodeLikelihood
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Returns the partial likelihood for a given state
- getLikelihood() - Method in class Likelihood.Likelihood.RateLikelihood
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Returns the likelihood.
- getLikelihood() - Method in class Likelihood.Likelihood.SiteLikelihood
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Get the likelihood
- getLowerBound() - Method in class Parameters.Parameter
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Gets the lower bound of a parameter
- getMap() - Method in class Models.Model
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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
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Gets the map that maps state to position in matrix
- getMaxKey() - Method in class Utils.ToDoubleHashMap
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Returns the key which has the maximum value associated with it
- getMissingLikelihood(Site) - Method in class Likelihood.Likelihood
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Gets the likelihood result for a given missing site
- getMostProbableRateCategory() - Method in class Likelihood.Likelihood.SiteLikelihood
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Gets the most probable rate category
- getName() - Method in class Models.RateCategory
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Get the name of the rate category
- getName() - Method in class Parameters.Parameter
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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
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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
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Gets the number of branches
- getNumberStates() - Method in class Models.Model
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Get the number of states represented in the model
- getNumberStates() - Method in class Models.RateCategory
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Gets the number of states in the rate class
- getP(RateCategory, Branch, String, String) - Method in class Likelihood.Probabilities
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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
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Gets the P-matrix for a given length
- getParam(String) - Method in class Parameters.Parameters
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Gets the parameter with the given name
- getParameters() - Method in class Likelihood.Likelihood
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Gets the parameters used to calculate this likelihood
- getParameters() - Method in class Trees.Tree
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Returns a Parameters object containing a parameter for each branch length.
- getParametersForEstimation() - Method in class Trees.Tree
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Returns a Parameters object containing a parameter for each branch length.
- getParent() - Method in class Trees.Branch
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Gets the parent node of the branch
- getParent(String) - Method in class Trees.Tree
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Gets the parent node of the given node
- getPivot() - Method in class Maths.LUDecomposition
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Return pivot permutation vector
- getPosition(int, int) - Method in class Maths.SquareMatrix
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Returns the value in position (i,j) of the matrix
- getPossible(String) - Method in class Alignments.Ambiguous
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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
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Get the likelihood for a single rate class
- getRateP(RateCategory) - Method in class Likelihood.Probabilities
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Gets the probability of a rate class
- getRates() - Method in class Models.Model
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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
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Get the root node
- getScale() - Method in class Models.Model
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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
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Gets the set of root level settings that have been set
- getSet(String) - Method in class Utils.SetSettings
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Gets the set of settings that have been set within a group
- getSetting(String) - Method in class Utils.SetSettings
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Gets the value of a root level setting
- getSetting(String, String) - Method in class Utils.SetSettings
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Gets the value of a setting within a group
- getSetting(String) - Method in class Utils.Settings
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Gets the value of a root level setting
- getSetting(String, String) - Method in class Utils.Settings
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Gets the value of a setting within a group
- getSingleElement(Set<T>) - Static method in class Utils.SetUtils
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Gets the single element of a set if it has only one element.
- getSite(int) - Method in class Alignments.Alignment
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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
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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
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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
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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
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Gets the names of the taxa in the aligment
- getTaxa() - Method in class Alignments.Site
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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
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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
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Enumeration of the different levels of output
- GTR(Parameters) - Static method in class Models.DNAModelFactory
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Creates an instance of a General Time Reversable model
- GTR_Gamma(Parameters, int) - Static method in class Models.DNAModelFactory
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Creates an instance of a General Time Reversable model with gamma-distributed rate
across sites