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C

calculate(Parameters) - Method in class Ancestors.AncestralJoint
Calculates the reconstruction
calculate(Parameters) - Method in class Ancestors.AncestralJointBB
 
calculate(Parameters) - Method in class Ancestors.AncestralJointDP
 
calculate(Parameters) - Method in class Ancestors.AncestralMarginal
Calculates the reconstruction
calculate(Parameters) - Method in class Likelihood.Calculator
Calculates the likelihood for a given set of parameters
calculate() - Method in class Likelihood.Calculator.SiteCalculator
Calculates the likelihood
calculated() - Method in class Parameters.Parameters
Resets the testfor whether probability matrices need to be recalculalated.
Calculator - Class in Likelihood
Calculates the likelihood for different parameter values.
Calculator(Model, Alignment, Tree) - Constructor for class Likelihood.Calculator
Creates an object to calculate the likelihood for a given model, alignment, tree.
Calculator(Model, Alignment, Tree, Alignment) - Constructor for class Likelihood.Calculator
Creates a class to calculate the likelihood for a given model, alignment, tree, missing data and constraints
Calculator(Model, Alignment, Tree, Constrainer) - Constructor for class Likelihood.Calculator
Creates a class to calculate the likelihood for a given model, alignment, tree and constraints
Calculator(Model, Alignment, Tree, Alignment, Constrainer) - Constructor for class Likelihood.Calculator
Creates a class to calculate the likelihood for a given model, alignment, tree, unobserved data and constraints
Calculator(Map<String, Model>, Alignment, Tree) - Constructor for class Likelihood.Calculator
Creates a class to calculate the likelihood for a given set of models, an alignment, and a tree.
Calculator(Map<String, Model>, Alignment, Tree, Alignment) - Constructor for class Likelihood.Calculator
Creates a class to calculate the likelihood for a given set of models, an alignment, a tree, and unobserved data.
Calculator(Map<String, Model>, Alignment, Tree, Map<String, Constrainer>) - Constructor for class Likelihood.Calculator
Creates a class to calculate the likelihood for a given set of models, an alignment, a tree and a set of constraints.
Calculator(Map<String, Model>, Alignment, Tree, Alignment, Map<String, Constrainer>) - Constructor for class Likelihood.Calculator
Creates a class to calculate the likelihood for a given set of models, an alignment, a tree, unobserved data and a set of constraints.
Calculator.SiteCalculator - Class in Likelihood
Calculates the likelihood of a single site.
Calculator.SiteCalculator(Tree, Probabilities, ArrayMap<String, Likelihood.NodeLikelihood>) - Constructor for class Likelihood.Calculator.SiteCalculator
Standard constructor
Calculator.SiteCalculator(Site, Tree, SiteConstraints, Probabilities) - Constructor for class Likelihood.Calculator.SiteCalculator
Constructor mainly for backwards compitability although also still used by some of the ancestral calculations.
call() - Method in class Likelihood.Calculator.SiteCalculator
 
check(Map<String, ?>) - Method in class Alignments.Alignment
Checks whether the map contains an entry for every class in the alignment
chi2inv(double, double) - Static method in class Maths.Gamma
Returns the inverse chi-squared distribution.
clone() - Method in class Constraints.SiteConstraints
 
clone() - Method in class Likelihood.Likelihood.NodeLikelihood
 
clone() - Method in class Parameters.Parameter
 
clone() - Method in class Parameters.Parameters
 
close() - Method in class Utils.CommentedFileReader
Close the file reader
CommentedFileReader - Class in Utils
Reads from a commented file ignoring any comments
CommentedFileReader(File) - Constructor for class Utils.CommentedFileReader
Constructor
CompiledFunction - Interface in Maths
Represents a mahematical function, variable or constant
CompiledFunction.Add - Class in Maths
The addition function
CompiledFunction.Add(CompiledFunction, CompiledFunction) - Constructor for class Maths.CompiledFunction.Add
Default constructor
CompiledFunction.Constant - Class in Maths
Represents a constant
CompiledFunction.Constant(double) - Constructor for class Maths.CompiledFunction.Constant
Default constructor
CompiledFunction.Divide - Class in Maths
The divide function
CompiledFunction.Divide(CompiledFunction, CompiledFunction) - Constructor for class Maths.CompiledFunction.Divide
Default constructor
CompiledFunction.Function - Class in Maths
Represents an arbitary function defined in a FunctionParser
CompiledFunction.Function(FunctionParser, String, CompiledFunction[]) - Constructor for class Maths.CompiledFunction.Function
Default constructor
CompiledFunction.Multiply - Class in Maths
The multiply function
CompiledFunction.Multiply(CompiledFunction, CompiledFunction) - Constructor for class Maths.CompiledFunction.Multiply
Default constructor
CompiledFunction.Power - Class in Maths
The power function
CompiledFunction.Power(CompiledFunction, CompiledFunction) - Constructor for class Maths.CompiledFunction.Power
Default constructor
CompiledFunction.Subtract - Class in Maths
The subtract function
CompiledFunction.Subtract(CompiledFunction, CompiledFunction) - Constructor for class Maths.CompiledFunction.Subtract
Default constructor
CompiledFunction.Variable - Class in Maths
Represents a variable - simply returns the value of the variable
CompiledFunction.Variable(String) - Constructor for class Maths.CompiledFunction.Variable
Default constructor
compileFunction(String) - Method in class Maths.MathsParse
Parses an equation and returns a compiled function that can then be used to compute the value fo an equation.
compute(Map<String, Double>) - Method in class Maths.CompiledFunction.Add
 
compute(Map<String, Double>) - Method in interface Maths.CompiledFunction
Computes the result of the function
compute(Map<String, Double>) - Method in class Maths.CompiledFunction.Constant
 
compute(Map<String, Double>) - Method in class Maths.CompiledFunction.Divide
 
compute(Map<String, Double>) - Method in class Maths.CompiledFunction.Function
 
compute(Map<String, Double>) - Method in class Maths.CompiledFunction.Multiply
 
compute(Map<String, Double>) - Method in class Maths.CompiledFunction.Power
 
compute(Map<String, Double>) - Method in class Maths.CompiledFunction.Subtract
 
compute(Map<String, Double>) - Method in class Maths.CompiledFunction.Variable
 
ConfidenceInterval - Class in Likelihood
Used to calculate congfidence intervals for a parameter.
ConfidenceInterval(Calculator, Parameters) - Constructor for class Likelihood.ConfidenceInterval
Default constructor
Constrainer - Interface in Constraints
Interface for classes that constrain the values of internal nodes of a tree.
Constraints - package Constraints
Provides classes to constrain the state of internal nodes.
containsKey(K) - Method in class Utils.ArrayMap
Tests whether the map contains a key

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