Uses of Class
Models.RateCategory

Packages that use RateCategory

Package	Description
Likelihood	Provides classes for calculating the likelihood of a tree given a model and an alignment.
Models	Provides classes for defining a phylogenetic model.

Uses of RateCategory in Likelihood

Methods in Likelihood that return RateCategory

Modifier and Type	Method and Description
RateCategory	SiteLikelihood.getMostProbableRateCategory() Gets the most probable rate category

Methods in Likelihood that return types with arguments of type RateCategory

Modifier and Type	Method and Description
java.util.Set<RateCategory>	Probabilities.getRateCategory() Gets the set of RateClasses that we have calculated probabilities for

Methods in Likelihood with parameters of type RateCategory

Modifier and Type	Method and Description
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
Real	SiteLikelihood.getRateCategoryProbability(RateCategory rc) Gets the probability of being in a rate category
SiteLikelihood.RateLikelihood	SiteLikelihood.getRateLikelihood(RateCategory rate) Get the likelihood for a single rate class
double	Probabilities.getRateP(RateCategory r) Gets the probability of a rate class
Root	Probabilities.getRoot(RateCategory r) Get a root object, for the given rate category, that can be used to the total likelihood from the root node likelihoods or provide the frequencies of the various states at the root

Constructor parameters in Likelihood with type arguments of type RateCategory

Constructor and Description
SiteLikelihood(java.util.Map<RateCategory,SiteLikelihood.RateLikelihood> rateLikelihoods, Probabilities P) Default constructor

Uses of RateCategory in Models

Methods in Models that return RateCategory

Modifier and Type	Method and Description
static RateCategory	RateCategory.fromFile(java.io.File mfile) Creates an instance from the information in a file.
RateCategory	RateCategory.multiplyBy(java.lang.String mult) Returns a new RateCategory where every position in the rate matrix is multiplied by a given value

Methods in Models that return types with arguments of type RateCategory

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
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

Constructor and Description
Model(RateCategory r) Creates a new model with a single rate class

Constructor parameters in Models with type arguments of type RateCategory

Constructor and Description
Model(java.util.Map<RateCategory,java.lang.String> freq) Creates a new model with multiple rate classes