A B C D E F G H I J K L M N O P Q R S T U V W 

D

DaemonThreadFactory - Class in Utils
A thread factory that creates daemon threads
DaemonThreadFactory() - Constructor for class Utils.DaemonThreadFactory
 
det() - Method in class Maths.LUDecomposition
Determinant
Distributions - Class in Models
Class to calculate stationary and quasi-stationary distributions
Distributions() - Constructor for class Models.Distributions
 
Distributions.Calculation - Enum in Models
Enumeration of the different methods of calculating a distribution
Distributions.DistributionsException - Exception in Models
Exception for use there is a problem calculating a distribution
Distributions.DistributionsException(String) - Constructor for exception Models.Distributions.DistributionsException
Default constructor
divide(Real) - Method in interface Maths.Real
Divides this Real by another one
divide(double) - Method in interface Maths.Real
Divides this Real by a double
divide(Real) - Method in class Maths.SmallDouble
 
divide(double) - Method in class Maths.SmallDouble
 
divide(SquareMatrix) - Method in class Maths.SquareMatrix
Divides this matrix by another (this / B) and returns a new matrix as the result
divide(Real) - Method in class Maths.StandardDouble
 
divide(double) - Method in class Maths.StandardDouble
 
DNAModelFactory - Class in Models
A factory for easing the creation of many standard DNA models
DNAModelFactory(DNAModelFactory.DNAModel) - Constructor for class Models.DNAModelFactory
Constructor so that calls to DNAModelFactory.getModel() and DNAModelFactory.getParameters() return the appropiate model or the appropiate parameters.
DNAModelFactory(DNAModelFactory.DNAModel, int) - Constructor for class Models.DNAModelFactory
Constructor so that calls to DNAModelFactory.getModel() and DNAModelFactory.getParameters() return the appropriate model or the appropriate parameters.
DNAModelFactory.DNAModel - Enum in Models
Represents the various types of DNA models
DuplicationAlignment - Class in Alignments
Static classes for reading/writing duplication "alignments" - a set of gene families with their associated size in each species
DuplicationModelFactory - Class in Models
A factory for easing the creation of some simple gene-family models
A B C D E F G H I J K L M N O P Q R S T U V W