- hasClasses() - Method in class Alignments.Alignment
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Checks whether the sites in this alignment have classes
- hasGroup(String) - Method in class Utils.Settings
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Tests whether a group is present
- hashCode() - Method in class Alignments.Alignment
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- hashCode() - Method in class Alignments.Site
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- hashCode() - Method in class Maths.SmallDouble
-
- hashCode() - Method in class Maths.SquareMatrix
-
- hashCode() - Method in class Maths.StandardDouble
-
- hashCode() - Method in class Trees.Branch
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- hashCode() - Method in class Trees.Split
-
- hashCode() - Method in class Trees.Tree
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- hasLength() - Method in class Trees.Branch
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Tests whether this branch has a length associated with it
- hasParam(String) - Method in class Parameters.Parameters
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Checks whether there is a parameter with the given name
- hasPassed() - Method in class Utils.TimePassed
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Check to see if the required amount of time has passed.
- hasSingleRate() - Method in class Models.Model
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Tests whether the model has a single rate class.
- HKY(Parameters) - Static method in class Models.DNAModelFactory
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Creates an instance of a HKY model
- HKY() - Static method in class Models.DNAModelFactory
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Creates an instance of a HKY model
- HKY_Gamma(Parameters, int) - Static method in class Models.DNAModelFactory
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Creates an instance of a HKY model with gamma-distributed rate
across sites
- HKY_Gamma(int) - Static method in class Models.DNAModelFactory
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Creates an instance of a HKY model with gamma-distributed rate
across sites
- HypothesisTest - Class in ModelTest
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Class to do hypothesis testing using simulation to generate the null distribution.
- HypothesisTest(Model, Model, Optimizer, int) - Constructor for class ModelTest.HypothesisTest
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Constructor
- HypothesisTest(Map<String, Model>, Map<String, Model>, Optimizer, int) - Constructor for class ModelTest.HypothesisTest
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Constructor