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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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