- 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
-
Abstract method for actually calculating the likelihood
- calculate(SiteLikelihood.NodeLikelihood) - Method in class Likelihood.FitzJohnRoot
-
- calculate(SiteLikelihood.NodeLikelihood) - Method in interface Likelihood.Root
-
Calculate the total likelihood from the root node likelihood
- calculate(SiteLikelihood.NodeLikelihood) - Method in class Likelihood.StandardRoot
-
- calculate(Parameters) - Method in interface Optimizers.Optimizable
-
The optimisable likelihood function.
- calculateSite(Site, Tree, Parameters, Probabilities, Map<String, SiteLikelihood.NodeLikelihood>) - Method in class Likelihood.Calculator
-
Calculate the likelihood for a single site.
- calculateSite(Site, Tree, Parameters, Probabilities, Map<String, SiteLikelihood.NodeLikelihood>) - Method in class Likelihood.StandardCalculator
-
- Calculator<R extends Likelihood> - Class in Likelihood
-
Abstract class for calculating a likelihood.
- Calculator(Map<String, Model>, Map<String, Tree>, HashMap<Site, Map<String, SiteLikelihood.NodeLikelihood>>) - Constructor for class Likelihood.Calculator
-
Default constructor.
- Calculator.CalculatorException - Exception in Likelihood
-
Exception thrown when there is a problem with the calculation
- Calculator.CalculatorException(String) - Constructor for exception Likelihood.Calculator.CalculatorException
-
Constructor when there is no underlying Throwable that caused the problem.
- Calculator.CalculatorException(String, Exception) - Constructor for exception Likelihood.Calculator.CalculatorException
-
Constructor when there is an underlying Throwable that caused the problem.
- Calculator.SiteCalculator - Class in Likelihood
-
Calculates the likelihood of a single site.
- Calculator.SiteCalculator(Site, Tree, Parameters, Probabilities, Map<String, SiteLikelihood.NodeLikelihood>) - Constructor for class Likelihood.Calculator.SiteCalculator
-
Standard constructor
- 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 Ancestors.Assignment
-
- clone() - Method in class Likelihood.SiteLikelihood.NodeLikelihood
-
- clone() - Method in class Parameters.Parameter
-
- clone() - Method in class Parameters.Parameters
-
- close() - Method in class Utils.CommentedFileReader
-
Close the file reader
- combineSites(Map<Site, SiteLikelihood>, Parameters) - Method in class Likelihood.Calculator
-
Combines the likelihood from each site into a alignment likelihood
- combineSites(Map<Site, SiteLikelihood>, Parameters) - Method in class Likelihood.StandardCalculator
-
- 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 mathematical 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
-
- 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 confidence intervals for a parameter.
- ConfidenceInterval(StandardCalculator, Parameters) - Constructor for class Likelihood.ConfidenceInterval
-
Default constructor
- ConjugateGradient - Class in Optimizers
-
Implements the Conjugate Gradient method of parameter optimisation.
- ConjugateGradient() - Constructor for class Optimizers.ConjugateGradient
-
Constructor that uses default values for rigour (1e-7), update method
(BEALE_SORENSON_HESTENES_STIEFEL) and output (none)
- ConjugateGradient(double) - Constructor for class Optimizers.ConjugateGradient
-
Constructor that uses the given value for rigour and default values for update method
(BEALE_SORENSON_HESTENES_STIEFEL) and output (none)
- ConjugateGradient(ConjugateGradient.Update) - Constructor for class Optimizers.ConjugateGradient
-
Constructor that uses the givemn update method and default values for rigour (1e-7)
and output (none)
- ConjugateGradient(double, ConjugateGradient.Update) - Constructor for class Optimizers.ConjugateGradient
-
Constructor that uses the given tolerance and update method but
the default output (none)
- ConjugateGradient(ConjugateGradient.ProgressLevel) - Constructor for class Optimizers.ConjugateGradient
-
Constructor that uses the given output level but default values for rigour (1e-7)
and update method (BEALE_SORENSON_HESTENES_STIEFEL)
- ConjugateGradient(double, ConjugateGradient.ProgressLevel) - Constructor for class Optimizers.ConjugateGradient
-
Constructor that uses the given tolerance and output level but the default
update method (BEALE_SORENSON_HESTENES_STIEFEL)
- ConjugateGradient(ConjugateGradient.Update, ConjugateGradient.ProgressLevel) - Constructor for class Optimizers.ConjugateGradient
-
Constructor that uses the given update method
(BEALE_SORENSON_HESTENES_STIEFEL) and output (none) but
the default values for rigour (1e-7),
- ConjugateGradient(double, ConjugateGradient.Update, ConjugateGradient.ProgressLevel) - Constructor for class Optimizers.ConjugateGradient
-
Constructor that uses the given values for rigour, update method
and output
- ConjugateGradient.ProgressLevel - Enum in Optimizers
-
Enumeration of the different levels of output
- ConjugateGradient.Update - Enum in Optimizers
-
Enumeration of the different update methods