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main(String[])
- Static method in class Executable.
Example
Main function
main(String[])
- Static method in class Executable.
GeLL
Main function
MapUtils
- Class in
Utils
Utility class for maps
Maths
- package Maths
Provides maths classes.
MathsParse
- Class in
Maths
Class used to parse an equation represented by a string and return the result.
MathsParse(FunctionParser...)
- Constructor for class Maths.
MathsParse
Default constructor.
matrix()
- Method in class Parameters.
Parameter
Whether this parameter is in a rate matrix.
maximise(Calculator, Parameters)
- Method in class Optimizers.
GoldenSection
maximise(Calculator, Parameters, File)
- Method in class Optimizers.
GoldenSection
maximise(Calculator, Parameters)
- Method in class Optimizers.
NelderMead
maximise(Calculator, Parameters, File)
- Method in class Optimizers.
NelderMead
maximise(Calculator, Parameters)
- Method in interface Optimizers.
Optimizer
Maximises the likelihood, logging to screen.
maximise(Calculator, Parameters, File)
- Method in interface Optimizers.
Optimizer
Maximises the likelihood, logging to a file.
meetsConstrains(Site)
- Method in class Constraints.
SiteConstraints
Tests whether a given site (that should include data for internal nodes) meets the defined constraints
midPointRoot(String)
- Method in class Trees.
Tree
Mid point roots the tree and returns a new tree
Model
- Class in
Models
Represents an evolutionary model.
Model(RateCategory)
- Constructor for class Models.
Model
Creates a new model with a single rate class
Model(Map<RateCategory, String>)
- Constructor for class Models.
Model
Creates a new model with multiple rate classes
Model.ModelException
- Exception in
Models
Exception thrown when there is a problem with the model
Model.ModelException(String)
- Constructor for exception Models.
Model.ModelException
Constructor when there is no underlying Throwable that caused the problem.
Model.ModelException(String, Throwable)
- Constructor for exception Models.
Model.ModelException
Constructor when there is an underlying Throwable that caused the problem.
Models
- package Models
Provides classes for defing a phylogenetic model.
MRCA(List<String>)
- Method in class Trees.
Tree
Returns the most recent common ancestor of a set of leaves
multiply(SquareMatrix)
- Method in class Maths.
SquareMatrix
Multiplies this matrix by another (this × o) and returns a new matrix as a result
multiply(K, double)
- Method in class Utils.
ToDoubleHashMap
Multiply the value associated with a key
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