- 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