Uses of Class
Models.Model.ModelException

Packages that use Model.ModelException
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. 
Simulations Provides a class to create simulate data. 
 

Uses of Model.ModelException in Ancestors
 

Methods in Ancestors that throw Model.ModelException
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
 Likelihood Calculator.calculate(Parameters p)
          Calculates the likelihood for a given set of parameters
 Range ConfidenceInterval.getCI(Parameter param, double conf)
          Calculates the confidence interval for a single parameter
 

Constructors in Likelihood that throw Model.ModelException
Probabilities(Model m, Tree t, Parameters p)
          Constructor
 

Uses of Model.ModelException in Models
 

Methods in Models that throw Model.ModelException
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
Model(java.util.Map<RateCategory,java.lang.String> freq)
          Creates a new model with multiple rate classes
 

Uses of Model.ModelException in Optimizers
 

Methods in Optimizers that throw Model.ModelException
 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.
 Likelihood GoldenSection.restart(Calculator l, java.io.File checkPoint)
           
 Likelihood NelderMead.restart(Calculator l, java.io.File checkPoint)
           
 Likelihood Optimizer.restart(Calculator l, java.io.File checkPoint)
          Maximises the likelihood starting from a checkpoint file (see Optimizer.setCheckPointFile(java.io.File), logging to the screen.
 Likelihood GoldenSection.restart(Calculator l, java.io.File checkPoint, java.io.File log)
           
 Likelihood NelderMead.restart(Calculator l, java.io.File checkPoint, java.io.File log)
           
 Likelihood Optimizer.restart(Calculator l, java.io.File checkPoint, java.io.File log)
          Maximises the likelihood starting from a checkpoint file (see Optimizer.setCheckPointFile(java.io.File), logging to a file.
 

Uses of Model.ModelException in Simulations
 

Methods in Simulations that throw Model.ModelException
 double HypothesisTest.test(Tree t, Alignment a, Alignment unobserved, Parameters nullParams, Parameters altParams)
          Does a hpyothesis test on the given data and gives a p-value
 double HypothesisTest.test(Tree t, Alignment a, Alignment unobserved, Parameters nullParams, Parameters altParams, java.util.Map<java.lang.String,java.lang.String> recode)
          Does a hpyothesis test on the given data and gives a p-value
 

Constructors in Simulations that throw Model.ModelException
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 sattes.
Simulate(java.util.Map<java.lang.String,Model> m, Tree t, Parameters p, Alignment unobserved, java.util.Map<java.lang.String,Constrainer> con)
          Creates an object to simulate data for a given set of models, a tree, parameters, unobserved states and constrainers.
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.