Uses of Class
Models.RateCategory.RateException

Packages that use RateCategory.RateException
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 RateCategory.RateException in Ancestors
 

Methods in Ancestors that throw RateCategory.RateException
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 RateCategory.RateException in Likelihood
 

Methods in Likelihood that throw RateCategory.RateException
 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 RateCategory.RateException
Probabilities(Model m, Tree t, Parameters p)
          Constructor
 

Uses of RateCategory.RateException in Models
 

Methods in Models that throw RateCategory.RateException
static Model Model.fromFile(java.io.File f)
          Creates a new model from a file.
static RateCategory RateCategory.fromFile(java.io.File mfile)
          Creates an instance from the information in a file.
 SquareMatrix RateCategory.getP(double length)
          Gets the P-matrix for a given length
 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.
 

Constructors in Models that throw RateCategory.RateException
RateCategory(java.lang.String[][] rates, RateCategory.FrequencyType freqType, java.util.HashMap<java.lang.String,java.lang.Integer> map)
          Constrcutor for when the root distribution is defined as the stationary or quasi-staionary distribution.
RateCategory(java.lang.String[][] rates, java.lang.String[] freq, java.util.HashMap<java.lang.String,java.lang.Integer> map)
          Constructor for when the root distribution is defined.
 

Uses of RateCategory.RateException in Optimizers
 

Methods in Optimizers that throw RateCategory.RateException
 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 RateCategory.RateException in Simulations
 

Constructors in Simulations that throw RateCategory.RateException
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.