Uses of Class
Models.RateCategory

Packages that use RateCategory
Likelihood Provides classes for calculating the likelihood of a tree given a model and an alignment. 
Models Provides classes for defing a phylogenetic model. 
 

Uses of RateCategory in Likelihood
 

Methods in Likelihood that return RateCategory
 RateCategory Likelihood.SiteLikelihood.getMostProbableRateCategory()
          Gets the most probable rate category
 

Methods in Likelihood that return types with arguments of type RateCategory
 java.util.Set<RateCategory> Probabilities.getRateCategory()
          Gets the set of RateClasses that we have calculated probailities for
 

Methods in Likelihood with parameters of type RateCategory
 double Probabilities.getFreq(RateCategory r, java.lang.String state)
          Gets the root frequency for a specified state under a specified RateClass
 Probabilities.RateProbabilities Probabilities.getP(RateCategory r)
          Gets a specific probability for a change from one state to another along a specific branch under a specific RateClass
 double Likelihood.SiteLikelihood.getRateCategoryProbability(RateCategory rc)
          Gets the probability of being in a rate category
 Likelihood.RateLikelihood Likelihood.SiteLikelihood.getRateLikelihood(RateCategory rate)
          Get the likelihood for a single rate class
 double Probabilities.getRateP(RateCategory r)
          Gets the probability of a rate class
 

Uses of RateCategory in Models
 

Methods in Models that return RateCategory
static RateCategory RateCategory.fromFile(java.io.File mfile)
          Creates an instance from the information in a file.
 

Methods in Models that return types with arguments of type RateCategory
 java.util.Set<RateCategory> Model.getRates()
          Gets a set of rate classes in the model
 java.util.Iterator<RateCategory> Model.iterator()
           
 

Methods in Models with parameters of type RateCategory
static Model Model.gammaRates(RateCategory r, java.lang.String gamma, int cats)
          Creates a new model with multiple rate classes distributed by a gamma distribution (see Yang 1993) based on a single rate class
 double Model.getFreq(RateCategory r)
          Gets the frquency of a rate class
 

Constructors in Models with parameters of type RateCategory
Model(RateCategory r)
          Creates a new model with a single rate class
 

Constructor parameters in Models with type arguments of type RateCategory
Model(java.util.Map<RateCategory,java.lang.String> freq)
          Creates a new model with multiple rate classes