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H

hasClasses - Variable in class Alignments.Alignment
Whether the sites in this alignment contain site information
hasGroup(String) - Method in class Utils.Settings
Tests whether a group is present
hashCode() - Method in class Alignments.Site
 
hashCode() - Method in class Maths.SquareMatrix
 
hashCode() - Method in class Trees.Branch
 
hasLength() - Method in class Trees.Branch
Tests whether this branch has a length associated with it
hasParam(String) - Method in class Parameters.Parameters
Checks whether there is a parameter with the given name
hasPassed() - Method in class Utils.TimePassed
Check to see if the required amount of time has passed.
hasSingleRate() - Method in class Models.Model
Tests whether the model has a single rate class.
HKY(Parameters) - Static method in class Models.DNAModelFactory
Creates an instance of a HKY model
HKY_Gamma(Parameters, int) - Static method in class Models.DNAModelFactory
Creates an instance of a HKY model with gamma-distributed rate across sites
HypothesisTest - Class in Simulations
Class to do hypothesis testing using simulation to generate the null distribution.
HypothesisTest(Model, Model, Optimizer, int) - Constructor for class Simulations.HypothesisTest
Constructor for use when neither the null hypothesis and alternative hypothesis have constraints.
HypothesisTest(Model, Model, Constrainer, Constrainer, Optimizer, int) - Constructor for class Simulations.HypothesisTest
Constructor for use when one or both of the null hypothesis and alternative hypothesis have constraints.

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