Uses of Class
Parameters.Parameters

Packages that use Parameters
Ancestors Provides classed to calculate ancestral reconstruction. 
Likelihood Provides classes for calculating the likelihood of a tree given a model and an alignment. 
Models Provides classes for defing a phylogenetic model. 
Optimizers Provides classes for optimising a likelihood. 
Parameters Provides classes for defining parameters used in the various calculations. 
Simulations Provides a class to create simulate data. 
Trees Provides classes to define a tree and any constraints on that tree. 
 

Uses of Parameters in Ancestors
 

Methods in Ancestors with parameters of type Parameters
abstract  Alignment AncestralJoint.calculate(Parameters params)
          Calculates the reconstruction
 Alignment AncestralJointBB.calculate(Parameters p)
           
 Alignment AncestralJointDP.calculate(Parameters params)
           
 AncestralMarginal.Result AncestralMarginal.calculate(Parameters params)
          Calculates the reconstruction
 

Uses of Parameters in Likelihood
 

Methods in Likelihood that return Parameters
 Parameters Likelihood.getParameters()
          Gets the parameters used to calculate this likelihood
 

Methods in Likelihood with parameters of type Parameters
 Likelihood Calculator.calculate(Parameters p)
          Calculates the likelihood for a given set of parameters
 

Constructors in Likelihood with parameters of type Parameters
ConfidenceInterval(Calculator l, Parameters p)
          Default constructor
Probabilities(Model m, Tree t, Parameters p)
          Constructor
 

Uses of Parameters in Models
 

Methods in Models with parameters of type Parameters
static Model DuplicationModelFactory.BDI_Gamma(Parameters p, int num, int numCats)
          Creates a simple BDI model with gamma-distributed rate across sites
static Model DuplicationModelFactory.BDI(Parameters p, int num)
          Creates a simple BDI model
static Model DNAModelFactory.Felsenstein81_Gamma(Parameters p, int numCats)
          Creates an instance of a JFelsenstein 81 model with gamma-distributed rate across sites
static Model DNAModelFactory.Felsenstein81(Parameters p)
          Creates an instance of a Felsenstein 81 model
static Model DNAModelFactory.GTR_Gamma(Parameters p, int numCats)
          Creates an instance of a General Time Reversable model with gamma-distributed rate across sites
static Model DNAModelFactory.GTR(Parameters p)
          Creates an instance of a General Time Reversable model
static Model DNAModelFactory.HKY_Gamma(Parameters p, int numCats)
          Creates an instance of a HKY model with gamma-distributed rate across sites
static Model DNAModelFactory.HKY(Parameters p)
          Creates an instance of a HKY model
static Model DNAModelFactory.JukesCantor_Gamma(Parameters p, int numCats)
          Creates an instance of a Jukes-Cantor model with gamma-distributed rate across sites
static Model DNAModelFactory.JukesCantor(Parameters p)
          Creates an instance of a Jukes-Cantor model
static Model DNAModelFactory.Kimura_Gamma(Parameters p, int numCats)
          Creates an instance of a Kimura 2-parameter model with gamma-distributed rate across sites
static Model DNAModelFactory.Kimura(Parameters p)
          Creates an instance of a Kimura 2-paramter model
static Model DuplicationModelFactory.Parsimony_Gamma(Parameters p, int num, int numCats)
          Creates a simple parsimony-style model with gamma-distributed rate across sites
static Model DuplicationModelFactory.Parsimony(Parameters p, int num)
          Creates a simple parsimony-style model
 void Model.setParameters(Parameters p)
          Sets the parameters of a model to the values contained in the Parameters data structure.
 void RateCategory.setParameters(Parameters p)
          Updates the parameters in the RateCategory.
 

Uses of Parameters in Optimizers
 

Methods in Optimizers with parameters of type Parameters
 Likelihood GoldenSection.maximise(Calculator l, Parameters params)
           
 Likelihood NelderMead.maximise(Calculator l, Parameters params)
           
 Likelihood Optimizer.maximise(Calculator l, Parameters p)
          Maximises the likelihood, logging to screen.
 Likelihood GoldenSection.maximise(Calculator l, Parameters params, java.io.File log)
           
 Likelihood NelderMead.maximise(Calculator l, Parameters params, java.io.File log)
           
 Likelihood Optimizer.maximise(Calculator l, Parameters params, java.io.File log)
          Maximises the likelihood, logging to a file.
 

Uses of Parameters in Parameters
 

Methods in Parameters that return Parameters
 Parameters Parameters.clone()
           
static Parameters Parameters.fromFile(java.io.File f)
          Reads parameters from a file.
 

Methods in Parameters with parameters of type Parameters
 void Parameters.addParameters(Parameters pp)
          Adds the parameters from another set of parameters
 

Uses of Parameters in Simulations
 

Constructors in Simulations with parameters of type Parameters
Simulate(Model m, Tree t, Parameters p)
          Creates an object to simulate data for a given model, tree and parameters.
Simulate(Model m, Tree t, Parameters p, Alignment unobserved)
          Creates an object to simulate data for a given model, tree, parameters and unobserved states.
Simulate(Model m, Tree t, Parameters p, Alignment unobserved, Constrainer con)
          Creates an object to simulate data for a given model, tree, parameters, unobserved states and constraints.
 

Uses of Parameters in Trees
 

Methods in Trees that return Parameters
 Parameters Tree.getParameters()
          Returns a Parameters object containing a parameter for each branch length.
 Parameters Tree.getParametersForEstimation()
          Returns a Parameters object containing a parameter for each branch length.
 

Constructors in Trees with parameters of type Parameters
Tree(Tree old, Parameters p)
          Duplicates a tree topology while replacing branch lengths using the appropiate parameter