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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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