Uses of Class
Parameters.Parameters.ParameterException

Packages that use Parameters.ParameterException

Package	Description
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 defining a phylogenetic model.
Parameters	Provides classes for defining parameters used in the various calculations.
Simulations	Provides a class to create simulated data.
Trees	Provides classes to define a tree.

Uses of Parameters.ParameterException in Ancestors

Methods in Ancestors that throw Parameters.ParameterException

Modifier and Type	Method and Description
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.ParameterException in Likelihood

Methods in Likelihood that throw Parameters.ParameterException

Modifier and Type	Method and Description
R	Calculator.calculate(Parameters p) Abstract method for actually calculating the likelihood
abstract SiteLikelihood	Calculator.calculateSite(Site s, Tree t, Parameters p, Probabilities tp, java.util.Map<java.lang.String,SiteLikelihood.NodeLikelihood> nl) Calculate the likelihood for a single site.
SiteLikelihood	Calculator.SiteCalculator.call()
abstract R	Calculator.combineSites(java.util.Map<Site,SiteLikelihood> sites, Parameters p) Combines the likelihood from each site into a alignment likelihood
Range	ConfidenceInterval.getCI(Parameter param, double conf) Calculates the confidence interval for a single parameter
protected java.util.Map<Site,SiteLikelihood>	Calculator.siteCalculate(Parameters p) Calculates the likelihood for each site

Constructors in Likelihood that throw Parameters.ParameterException

Constructor and Description
Probabilities(Model m, Tree t, Parameters p) Constructor

Uses of Parameters.ParameterException in Models

Methods in Models that throw Parameters.ParameterException

Modifier and Type	Method and Description
static Model	DuplicationModelFactory.BD_NoZero_Gamma(Parameters p, int num, int numCats) Creates a Birth Death model with no zero state and gamma distributed rates-across sites.
static Model	DuplicationModelFactory.BD_NoZero_Gamma(Parameters p, int num, int numCats, boolean fixed) Creates a Birth Death model with no zero state and gamma distributed rates-across sites.
static Model	DuplicationModelFactory.BD_NoZero(Parameters p, int num) Creates a Birth Death model with no zero state.
static Model	DuplicationModelFactory.BD_NoZero(Parameters p, int num, boolean fixed) Creates a Birth Death model with no zero state.
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_Gamma(Parameters p, int num, int numCats, boolean fixed) 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	DuplicationModelFactory.BDI(Parameters p, int num, boolean fixed) Creates a simple BDI model
static Model	DuplicationModelFactory.BDIE_Gamma(Parameters p, int num, int numCats) Creates a simple BDI model with gamma-distributed rate across sites.
static Model	DuplicationModelFactory.BDIE_Gamma(Parameters p, int num, int numCats, boolean fixed) Creates a simple BDIE model with gamma-distributed rate across sites
static Model	DuplicationModelFactory.BDIE(Parameters p, int num, boolean fixed) Creates a simple BDIE 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 Reversible model with gamma-distributed rate across sites
static Model	DNAModelFactory.GTR(Parameters p) Creates an instance of a General Time Reversible 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.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_Gamma(Parameters p, int num, int numCats, boolean fixed) 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
static Model	DuplicationModelFactory.Parsimony(Parameters p, int num, boolean fixed) Creates a simple parsimony-style model
static Model	RYModelFactory.RY_Gamma(Parameters p, int numCats) Creates an instance of a RY model with gamma-distributed rate across sites
static Model	RYModelFactory.RY(Parameters p) Creates an instance of a RY 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 and recalculates matrices / frequencies if necessary.

Uses of Parameters.ParameterException in Parameters

Methods in Parameters that throw Parameters.ParameterException

Modifier and Type	Method and Description
void	Parameters.addParameter(Parameter p) Add a parameter
void	Parameters.addParameters(Parameters pp) Adds the parameters from another set of parameters
static Parameters	Parameters.fromFile(java.io.File f) Reads parameters from a file.
Parameter	Parameters.getParam(java.lang.String name) Gets the parameter with the given name
double	Parameters.getValue(java.lang.String name) Gets the value of a parameter
void	Parameters.setValue(Parameter p, double v) Sets the value of a parameter

Constructors in Parameters that throw Parameters.ParameterException

Constructor and Description
Parameters(java.util.List<Parameter> params) Creates a set of parameters containing the given parameters

Uses of Parameters.ParameterException in Simulations

Constructors in Simulations that throw Parameters.ParameterException

Constructor and Description
Simulate(java.util.Map<java.lang.String,Model> m, java.util.Map<java.lang.String,Tree> t, Parameters p) Creates an object to simulate data for a given set of models and trees, parameters and unobserved states.
Simulate(java.util.Map<java.lang.String,Model> m, java.util.Map<java.lang.String,Tree> t, Parameters p, Alignment unobserved) Creates an object to simulate data for a given set of models and trees, parameters and unobserved states.
Simulate(java.util.Map<java.lang.String,Model> m, Tree t, Parameters p) Creates an object to simulate data for a given set of models, a tree and parameters.
Simulate(java.util.Map<java.lang.String,Model> m, Tree t, Parameters p, Alignment unobserved) Creates an object to simulate data for a given set of models, a tree, parameters and unobserved states.
Simulate(Model m, java.util.Map<java.lang.String,Tree> t, Parameters p) Creates an object to simulate data for a given model, set of trees, parameters and unobserved states.
Simulate(Model m, java.util.Map<java.lang.String,Tree> t, Parameters p, Alignment unobserved) Creates an object to simulate data for a given model, set of trees, parameters and unobserved states.
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.

Uses of Parameters.ParameterException in Trees

Constructors in Trees that throw Parameters.ParameterException

Constructor and Description
Tree(Tree old, Parameters p) Duplicates a tree topology while replacing branch lengths using the appropriate parameter