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S

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
Deprecated. Replaced by PhylipAlignment to allow for easier use of multiple formats.
SequenceAlignment(File) - Constructor for class Alignments.SequenceAlignment
Deprecated. Creates a sequence alignment from a file.
SequenceAlignment(File, Ambiguous) - Constructor for class Alignments.SequenceAlignment
Deprecated. Creates a sequence alignment from a file with ambiguouis data.
setBranchColors(Map<Branch, String>) - Method in class Trees.TreeFigure
Sets the color of branches.
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
setLeafColor(Map<String, String>) - Method in class Trees.TreeFigure
Sets the color of the leaf text.
setLeavesText(Map<String, String>) - Method in class Trees.TreeFigure
Overwrites the default leaf text (the taxa names).
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.
setRootBranchColor(String) - Method in class Trees.TreeFigure
Sets the color of the root branch.
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
setVerticalSpacing(int) - Method in class Trees.TreeFigure
Sets the spacing (in co-ordinate terms) between the horizontal lines
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.
Simulate(Map<String, Model>, Tree, Parameters) - Constructor for class Simulations.Simulate
Creates an object to simulate data for a given set of models, a tree and parameters.
Simulate(Map<String, Model>, Tree, Parameters, Alignment) - Constructor for class Simulations.Simulate
Creates an object to simulate data for a given set of models, a tree, parameters and unobserved sattes.
Simulate(Map<String, Model>, Tree, Parameters, Alignment, Map<String, Constrainer>) - Constructor for class Simulations.Simulate
Creates an object to simulate data for a given set of models, a tree, parameters, unobserved states and constrainers.
Simulate.SimulationException - Exception in Simulations
Exception for when there is a problem with the simulation
Simulate.SimulationException(String) - Constructor for exception Simulations.Simulate.SimulationException
Constructor
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>, String) - Constructor for class Alignments.Site
Creates a site in a alignment with no ambiguous data and with the given class.
Site(LinkedHashMap<String, String>, Ambiguous) - Constructor for class Alignments.Site
Creates a site in a alignment with ambiguous data
Site(LinkedHashMap<String, String>, Ambiguous, String) - Constructor for class Alignments.Site
Creates a site in a alignment with ambiguous data and with the given class.
SiteConstraints - Class in Constraints
Stores the constraints for a single site
SiteConstraints(List<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.
size() - Method in class Utils.ArrayMap
Returns the size of the map.
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.

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