Uses of Class
Models.Model.ModelException

Packages that use Model.ModelException

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.
Simulations	Provides a class to create simulated data.

Uses of Model.ModelException in Ancestors

Methods in Ancestors that throw Model.ModelException

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 Model.ModelException in Likelihood

Methods in Likelihood that throw Model.ModelException

Modifier and Type	Method and Description
R	Calculator.calculate(Parameters p) Abstract method for actually calculating the likelihood
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 Model.ModelException

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

Uses of Model.ModelException in Models

Methods in Models that throw Model.ModelException

Modifier and Type	Method and Description
static Model	Model.fromFile(java.io.File f) Creates a new model from a file.
void	Model.setParameters(Parameters p) Sets the parameters of a model to the values contained in the Parameters data structure.

Constructors in Models that throw Model.ModelException

Constructor and Description
DNAModelFactory(DNAModelFactory.DNAModel model, int numCats) Constructor so that calls to DNAModelFactory.getModel() and DNAModelFactory.getParameters() return the appropriate model or the appropriate parameters.
Model(java.util.Map<RateCategory,java.lang.String> freq) Creates a new model with multiple rate classes

Uses of Model.ModelException in Simulations

Constructors in Simulations that throw Model.ModelException

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.