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M

m - Variable in class Likelihood.Calculator
The model to do the calculation on.
main(String[]) - Static method in class Executable.GeLL
Main function
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.
maximise(Optimizable<R>, Parameters) - Method in class Optimizers.ConjugateGradient
 
maximise(Optimizable<R>, Parameters, File) - Method in class Optimizers.ConjugateGradient
 
maximise(Optimizable<R>, Parameters) - Method in class Optimizers.GoldenSection
 
maximise(Optimizable<R>, Parameters, File) - Method in class Optimizers.GoldenSection
 
maximise(Optimizable<R>, Parameters) - Method in class Optimizers.NelderMead
 
maximise(Optimizable<R>, Parameters, File) - Method in class Optimizers.NelderMead
 
maximise(Optimizable<R>, Parameters) - Method in interface Optimizers.Optimizer
Maximises the likelihood, logging to screen.
maximise(Optimizable<R>, Parameters, File) - Method in interface Optimizers.Optimizer
Maximises the likelihood, logging to a file.
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 defining a phylogenetic model.
ModelTest - package ModelTest
 
MRCA(List<String>) - Method in class Trees.Tree
Returns the most recent common ancestor of a set of leaves.
multiply(String, Real) - Method in class Likelihood.SiteLikelihood.NodeLikelihood
This is a fudge to stop to allow this code to be reused in some of the ancestor classes.
multiply(String, double) - Method in class Likelihood.SiteLikelihood.NodeLikelihood
This is a fudge to stop to allow this code to be reused in some of the ancestor classes.
multiply(Real) - Method in interface Maths.Real
Multiplies this Real by another
multiply(double) - Method in interface Maths.Real
Multiplies this Real by a double
multiply(Real) - Method in class Maths.SmallDouble
 
multiply(double) - Method in class Maths.SmallDouble
 
multiply(SquareMatrix) - Method in class Maths.SquareMatrix
Multiplies this matrix by another (this × o) and returns a new matrix as a result
multiply(Real) - Method in class Maths.StandardDouble
 
multiply(double) - Method in class Maths.StandardDouble
 
multiplyBy(String) - Method in class Models.RateCategory
Returns a new RateCategory where every position in the rate matrix is multiplied by a given value
multiplyip(Real) - Method in interface Maths.Real
Multiplies this Real by another Real in place.
multiplyip(double) - Method in interface Maths.Real
Multiplies this Real by a double in place.
multiplyip(Real) - Method in class Maths.SmallDouble
 
multiplyip(double) - Method in class Maths.SmallDouble
 
multiplyip(Real) - Method in class Maths.StandardDouble
 
multiplyip(double) - Method in class Maths.StandardDouble
 
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