- Parameter - Class in Parameters
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Represents a parameter of a model
- Parameter.FormatException - Exception in Parameters
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Exception thrown when the format of a parameter string is incorrect
- Parameter.FormatException(String) - Constructor for exception Parameters.Parameter.FormatException
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Default constuctor
- Parameters - package Parameters
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Provides classes for defining parameters used in the various calculations.
- Parameters - Class in Parameters
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Represents a set of parameters
- Parameters() - Constructor for class Parameters.Parameters
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Creates an empty set of parameters
- Parameters(List<Parameter>) - Constructor for class Parameters.Parameters
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Creates a set of parameters containing the given parameters
- Parameters.ParameterException - Exception in Parameters
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Exception related to the parameters
- Parameters.ParameterException(String) - Constructor for exception Parameters.Parameters.ParameterException
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Constructor
- parseEquation(String, Map<String, Double>) - Method in class Maths.MathsParse
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Parses an equation and returns the result
- Parsimony(Parameters, int) - Static method in class Models.DuplicationModelFactory
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Creates a simple parsimony-style model
- Parsimony(Parameters, int, boolean) - Static method in class Models.DuplicationModelFactory
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Creates a simple parsimony-style model
- Parsimony_Gamma(Parameters, int, int) - Static method in class Models.DuplicationModelFactory
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Creates a simple parsimony-style model with gamma-distributed rate
across sites.
- Parsimony_Gamma(Parameters, int, int, boolean) - Static method in class Models.DuplicationModelFactory
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Creates a simple parsimony-style model with gamma-distributed rate
across sites
- PhylipAlignment - Class in Alignments
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Static classes for reading/writing sequence alignment in Phylip format
- PossibleSettings - Class in Utils
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Maintains a list of possible settings.
- PossibleSettings() - Constructor for class Utils.PossibleSettings
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Default constructor
- printSVG(File, boolean) - Method in class Trees.TreeFigure
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Prints the tree to the given file
- Probabilities - Class in Likelihood
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Stores the values of each transition, frequency etc for one set of parameters.
- Probabilities(Model, Tree, Parameters) - Constructor for class Likelihood.Probabilities
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Constructor
- Probabilities.RateProbabilities - Class in Likelihood
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Stores the values of each transition, frequency etc for one set of parameters
and for a single rate category.