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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
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.
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