- 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
- setBranchColors(Map<Branch, String>) - Method in class Trees.TreeFigure
-
Sets the colour of branches.
- setCheckPointFile(File) - Method in class Optimizers.ConjugateGradient
-
- 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.ConjugateGradient
-
- 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 colour of the leaf text.
- setLeavesText(Map<String, String>) - Method in class Trees.TreeFigure
-
Overwrites the default leaf text (the taxa names).
- setMaximumRunTime(int, TimeUnit) - Method in class Optimizers.ConjugateGradient
-
- setMaximumRunTime(int, TimeUnit) - Method in class Optimizers.GoldenSection
-
- setMaximumRunTime(int, TimeUnit) - Method in class Optimizers.NelderMead
-
- setMaximumRunTime(int, TimeUnit) - Method in interface Optimizers.Optimizer
-
Set a maximum time the optimiser should run for
- 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 and recalculates matrices /
frequencies if necessary.
- 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 colour of the root branch.
- setSeed(long) - Method in class Simulations.Simulate
-
Seeds the random number generator with the give seed.
- SetSettings - Class in Utils
-
Represents the value of settings.
- SetSettings() - Constructor for class Utils.SetSettings
-
Default constructor
- setThread(boolean) - Method in class Likelihood.Calculator
-
Set whether threaded calculations should be performed
- SettingException - Exception in Utils
-
Exception thrown when there is a problem with the Settings machinery
- SettingException(String) - Constructor for exception Utils.SettingException
-
Default constructor
- Settings - Class in Utils
-
Represents the value of settings (including returning default settings).
- Settings(PossibleSettings, SetSettings) - Constructor for class Utils.Settings
-
Creates an instance of this class
- SetUtils - Class in Utils
-
Utility class for 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(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 states.
- Simulate(Model, Map<String, Tree>, Parameters) - Constructor for class Simulations.Simulate
-
Creates an object to simulate data for a given model, set of trees, parameters
and unobserved states.
- Simulate(Model, Map<String, Tree>, Parameters, Alignment) - Constructor for class Simulations.Simulate
-
Creates an object to simulate data for a given model, set of trees, parameters
and unobserved states.
- Simulate(Map<String, Model>, Map<String, Tree>, Parameters) - Constructor for class Simulations.Simulate
-
Creates an object to simulate data for a given set of models and trees,
parameters and unobserved states.
- Simulate(Map<String, Model>, Map<String, Tree>, Parameters, Alignment) - Constructor for class Simulations.Simulate
-
Creates an object to simulate data for a given set of models and trees,
parameters and unobserved states.
- 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 simulated 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.
- Site(String, LinkedHashMap<String, String>) - Constructor for class Alignments.Site
-
Creates a site in a alignment with no ambiguous data
- Site(String, 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(String, LinkedHashMap<String, String>, Ambiguous) - Constructor for class Alignments.Site
-
Creates a site in a alignment with ambiguous data
- Site(String, LinkedHashMap<String, String>, Ambiguous, String) - Constructor for class Alignments.Site
-
Creates a site in a alignment with ambiguous data and with the given
class.
- Site(Site) - Constructor for class Alignments.Site
-
Creates a copy of a site
- siteCalculate(Parameters) - Method in class Likelihood.Calculator
-
Calculates the likelihood for each site
- SiteLikelihood - Class in Likelihood
-
Stored the result of a likelihood calculation for a single site
- SiteLikelihood(Map<RateCategory, SiteLikelihood.RateLikelihood>, Probabilities) - Constructor for class Likelihood.SiteLikelihood
-
Default constructor
- SiteLikelihood.LikelihoodException - Exception in Likelihood
-
Exception related to a likelihood calculation
- SiteLikelihood.LikelihoodException(String) - Constructor for exception Likelihood.SiteLikelihood.LikelihoodException
-
Constructor
- SiteLikelihood.NodeLikelihood - Class in Likelihood
-
Stores the results of a likelihood calculation for a single node in a tree.
- SiteLikelihood.NodeLikelihood(Map<String, Integer>) - Constructor for class Likelihood.SiteLikelihood.NodeLikelihood
-
Constructor where all sates are allowed at a node
- SiteLikelihood.NodeLikelihood(Map<String, Integer>, Set<String>) - Constructor for class Likelihood.SiteLikelihood.NodeLikelihood
-
Constructor where only some states are allowed at a node
- SiteLikelihood.NodeLikelihood(Map<String, Integer>, String) - Constructor for class Likelihood.SiteLikelihood.NodeLikelihood
-
Constructor where only a single state is allowed at a node
- SiteLikelihood.RateLikelihood - Class in Likelihood
-
Stores the result of the likelihood calculations for a single site and
a single rate class.
- SiteLikelihood.RateLikelihood(Real, Map<String, SiteLikelihood.NodeLikelihood>) - Constructor for class Likelihood.SiteLikelihood.RateLikelihood
-
Default constructor
- size() - Method in class Maths.SquareMatrix
-
Gets the size of the matrix.
- SmallDouble - Class in Maths
-
Represents a real number.
- SmallDouble(double) - Constructor for class Maths.SmallDouble
-
Creates a SmallDouble representing the same number as a double
- SmallDouble(double, int) - Constructor for class Maths.SmallDouble
-
Creates a SmallDouble representing the same number as m*2^e
- SMALLEST - Static variable in class Maths.SmallDouble
-
A SmallDouble representing the smallest possible value SmallDouble can represent
- SMALLEST - Static variable in class Maths.StandardDouble
-
A StandardDouble representing the smallest possible value StandardDouble can represent
- snl - Variable in class Likelihood.Calculator
-
The site node likelihoods.
- solve(SquareMatrix) - Method in class Maths.LUDecomposition
-
Solve A*X = B
- Split - Class in Trees
-
Represents a split
- 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
- StandardCalculator - Class in Likelihood
-
Calculates the likelihood for different parameter values.
- StandardCalculator(Model, Alignment, Tree) - Constructor for class Likelihood.StandardCalculator
-
Creates an object to calculate the likelihood for a given model, alignment and
tree.
- StandardCalculator(Model, Alignment, Tree, Alignment) - Constructor for class Likelihood.StandardCalculator
-
Creates a class to calculate the likelihood for a given model, alignment,
tree and missing data
- StandardCalculator(Map<String, Model>, Alignment, Map<String, Tree>) - Constructor for class Likelihood.StandardCalculator
-
Creates a class to calculate the likelihood for a given set of models, an alignment,
and a tree.
- StandardCalculator(Map<String, Model>, Alignment, Tree) - Constructor for class Likelihood.StandardCalculator
-
Creates a class to calculate the likelihood for a given set of models, an alignment,
and a tree.
- StandardCalculator(Map<String, Model>, Alignment, Tree, Alignment) - Constructor for class Likelihood.StandardCalculator
-
Creates a class to calculate the likelihood for a given set of models, an alignment,
and a tree.
- StandardCalculator(Model, Alignment, Map<String, Tree>) - Constructor for class Likelihood.StandardCalculator
-
Creates a class to calculate the likelihood for a given set of models, an alignment,
and a tree.
- StandardCalculator(Model, Alignment, Map<String, Tree>, Alignment) - Constructor for class Likelihood.StandardCalculator
-
Creates a class to calculate the likelihood for a given set of models, an alignment,
and a tree.
- StandardCalculator(Map<String, Model>, Alignment, Map<String, Tree>, Alignment) - Constructor for class Likelihood.StandardCalculator
-
Creates a class to calculate the likelihood for a given set of models, an alignment,
a tree and unobserved data.
- StandardDouble - Class in Maths
-
Represents a real.
- StandardDouble(double) - Constructor for class Maths.StandardDouble
-
Creates a StandardDouble representing the same number as a double
- StandardLikelihood - Class in Likelihood
-
Stores the results of a likelihood calculation.
- StandardRoot - Class in Likelihood
-
Root class for the standard root methods - e.g.
- StandardRoot(double[], Map<String, Integer>) - Constructor for class Likelihood.StandardRoot
-
Default constructor
- stationary(SquareMatrix) - Static method in class Models.Distributions
-
Calculates a stationary distribution from a given rate matrix.
- subtract(Real) - Method in interface Maths.Real
-
Subtracts another Real from this one
- subtract(double) - Method in interface Maths.Real
-
Subtracts a double from this Real
- subtract(Real) - Method in class Maths.SmallDouble
-
- subtract(double) - Method in class Maths.SmallDouble
-
- subtract(Real) - Method in class Maths.StandardDouble
-
- subtract(double) - Method in class Maths.StandardDouble
-