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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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