- scalarDivide(double) - Method in class Maths.SquareMatrix
-
Divides the matrix by a scalar and returns a new matrix as the result
- scalarMultiply(double) - Method in class Maths.SquareMatrix
-
Multiplies the matrix by a scalar and returns a new matrix as the result
- scaledTo(double) - Method in class Trees.Tree
-
Returns a new tree where the lengths are scales so the total length is
different
- SequenceAlignment - Class in Alignments
-
Represents a sequence alignment
- SequenceAlignment(File) - Constructor for class Alignments.SequenceAlignment
-
Creates a sequence alignment from a file.
- SequenceAlignment(File, Ambiguous) - Constructor for class Alignments.SequenceAlignment
-
Creates a sequence alignment from a file with ambiguouis data.
- setCheckPointFile(File) - Method in class Optimizers.GoldenSection
-
- setCheckPointFile(File) - Method in class Optimizers.NelderMead
-
- setCheckPointFile(File) - Method in interface Optimizers.Optimizer
-
Sets a checkpoint file.
- setCheckPointFrequency(int, TimeUnit) - Method in class Optimizers.GoldenSection
-
- setCheckPointFrequency(int, TimeUnit) - Method in class Optimizers.NelderMead
-
- setCheckPointFrequency(int, TimeUnit) - Method in interface Optimizers.Optimizer
-
Sets how often a checkpoint is saved (if a file has been set).
- setDebug(GeneralException.Debug) - Static method in exception Exceptions.GeneralException
-
Set debug level
- setExpMethod(SquareMatrix.Calculation) - Static method in class Maths.SquareMatrix
-
Sets the method to be used for Exponentiation
- setForce(int) - Static method in class Maths.SquareMatrix
-
Sets the minimum number of repeating squaring that will be performed
when using the Taylor method
- setMethod(Distributions.Calculation) - Static method in class Models.Distributions
-
Sets the calculation method to be used when calculating distributions
- setName(String) - Method in class Models.RateCategory
-
Sets the name of the rate category.
- setNoThreads(int) - Static method in class Likelihood.Calculator
-
Set the number of threads to be used during the calculations
- setNoThreads(int) - Static method in class Maths.SquareMatrix
-
Sets the number of threads to be used when doing matrix multiplication
- setParameters(Parameters) - Method in class Models.Model
-
Sets the parameters of a model to the values contained in the
Parameters
data structure.
- setParameters(Parameters) - Method in class Models.RateCategory
-
Updates the parameters in the RateCategory.
- setRescale(boolean) - Method in class Models.Model
-
Sets whether the matrix should be rescaled so the average rate of change
is one.
- SetSettings - Class in Utils
-
Represents the value of settings.
- SetSettings() - Constructor for class Utils.SetSettings
-
Default constructor
- SettingException - Exception in Utils
-
Exception thrown when there is a problem with the Settings machinery
- SettingException(String) - Constructor for exception Utils.SettingException
-
Deafult constructor
- Settings - Class in Utils
-
Represents the value of settings (including retutning default settings).
- Settings(PossibleSettings, SetSettings) - Constructor for class Utils.Settings
-
Creates an instance of this class
- SetUtils - Class in Utils
-
Utility class fo sets
- SetUtils.SetHasMultipleElementsException - Class in Utils
-
Exception thrown if an attempt is made to get the single element from
a set that has multiple elements.
- setValue(Parameter, double) - Method in class Parameters.Parameters
-
Sets the value of a parameter
- Simulate - Class in Simulations
-
Class for constructing simulated data
- Simulate(Model, Tree, Parameters) - Constructor for class Simulations.Simulate
-
Creates an object to simulate data for a given model, tree and parameters.
- Simulate(Model, Tree, Parameters, Alignment) - Constructor for class Simulations.Simulate
-
Creates an object to simulate data for a given model, tree, parameters
and unobserved states.
- Simulate(Model, Tree, Parameters, Alignment, Constrainer) - Constructor for class Simulations.Simulate
-
Creates an object to simulate data for a given model, tree, parameters,
unobserved states and constraints.
- Simulations - package Simulations
-
Provides a class to create simulate data.
- Site - Class in Alignments
-
Represents a "site" in an "alignment".
- Site(LinkedHashMap<String, String>) - Constructor for class Alignments.Site
-
Creates a site in a alignment with no ambiguous data
- Site(LinkedHashMap<String, String>, Ambiguous) - Constructor for class Alignments.Site
-
Creates a site in a alignment with ambiguous data
- SiteConstraints - Class in Constraints
-
Stores the constraints for a single site
- SiteConstraints(Set<String>) - Constructor for class Constraints.SiteConstraints
-
Standard constructor that creates an object with no constraints
- size() - Method in class Maths.SquareMatrix
-
Gets the size of the matrix.
- solve(SquareMatrix) - Method in class Maths.LUDecomposition
-
Solve A*X = B
- square() - Method in class Maths.SquareMatrix
-
Sqaures the matrix and returns a new Matrix that is the result
- SquareMatrix - Class in Maths
-
Represents a square matrix.
- SquareMatrix(double[][]) - Constructor for class Maths.SquareMatrix
-
Default constructor
- SquareMatrix.Calculation - Enum in Maths
-
Enumeration of the possible ways of calculating the matrix exponential
- SquareMatrix.SquareMatrixException - Exception in Maths
-
Exception thrown when there is a problem with a SquareMatrix operation
- SquareMatrix.SquareMatrixException(String) - Constructor for exception Maths.SquareMatrix.SquareMatrixException
-
Default constructor
- stationary(SquareMatrix) - Static method in class Models.Distributions
-
Calculates a stationary distribution from a given rate matrix.