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P

Parameter - Class in Parameters
Represents a parameter of a model
Parameter.FormatException - Exception in Parameters
Exception thrown when the format of a parameter string is incorrect
Parameter.FormatException(String) - Constructor for exception Parameters.Parameter.FormatException
Default constuctor
Parameters - package Parameters
Provides classes for defining parameters used in the various calculations.
Parameters - Class in Parameters
Represents a set of parameters
Parameters() - Constructor for class Parameters.Parameters
Creates an empty set of parameters
Parameters(ArrayList<Parameter>) - Constructor for class Parameters.Parameters
Creates a set of parameters containing the given parameters
Parameters.ParameterException - Exception in Parameters
Exception related to the parameters
Parameters.ParameterException(String) - Constructor for exception Parameters.Parameters.ParameterException
Constructor
parseEquation(String, Map<String, Double>) - Method in class Maths.MathsParse
Parses an equation and returns the result
Parsimony(Parameters, int) - Static method in class Models.DuplicationModelFactory
Creates a simple parsimony-style model
Parsimony_Gamma(Parameters, int, int) - Static method in class Models.DuplicationModelFactory
Creates a simple parsimony-style model with gamma-distributed rate across sites
PhylipAlignment - Class in Alignments
Represents a sequence alignment in Phylip format
PhylipAlignment(File) - Constructor for class Alignments.PhylipAlignment
Creates a sequence alignment from a file.
PhylipAlignment(File, Ambiguous) - Constructor for class Alignments.PhylipAlignment
Creates a sequence alignment from a file with ambiguouis data.
PossibleSettings - Class in Utils
Maintains a list of possible settings.
PossibleSettings() - Constructor for class Utils.PossibleSettings
Default constructor
printSVG(File, boolean) - Method in class Trees.TreeFigure
Prints the tree to the given file
Probabilities - Class in Likelihood
Stores the values of each transition, frequency etc for one set of parameters.
Probabilities(Model, Tree, Parameters) - Constructor for class Likelihood.Probabilities
Constructor
Probabilities.RateProbabilities - Class in Likelihood
Stores the values of each transition, frequency etc for one set of parameters and for a single rate category.
put(K, V) - Method in class Utils.ArrayMap
Puts a new key/value pair into the map Error checks are deliberately not done for effeciency reasons.
put(int, K, V) - Method in class Utils.ArrayMap
Puts a new key/value pair into the map at a given location Error checks are deliberately not done for effeciency reasons.

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