- DaemonThreadFactory - Class in Utils
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A thread factory that creates daemon threads
- DaemonThreadFactory() - Constructor for class Utils.DaemonThreadFactory
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- det() - Method in class Maths.LUDecomposition
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Determinant
- Distributions - Class in Models
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Class to calculate stationary and quasi-stationary distributions
- Distributions() - Constructor for class Models.Distributions
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- Distributions.Calculation - Enum in Models
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Enumeration of the different methods of calculating a distribution
- Distributions.DistributionsException - Exception in Models
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Exception for use there is a problem calculating a distribution
- Distributions.DistributionsException(String) - Constructor for exception Models.Distributions.DistributionsException
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Default constructor
- divide(Real) - Method in interface Maths.Real
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Divides this Real by another one
- divide(double) - Method in interface Maths.Real
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Divides this Real by a double
- divide(Real) - Method in class Maths.SmallDouble
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- divide(double) - Method in class Maths.SmallDouble
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- divide(SquareMatrix) - Method in class Maths.SquareMatrix
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Divides this matrix by another (this / B) and returns a new matrix as the
result
- divide(Real) - Method in class Maths.StandardDouble
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- divide(double) - Method in class Maths.StandardDouble
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- DNAModelFactory - Class in Models
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A factory for easing the creation of many standard DNA models
- DNAModelFactory(DNAModelFactory.DNAModel) - Constructor for class Models.DNAModelFactory
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- DNAModelFactory(DNAModelFactory.DNAModel, int) - Constructor for class Models.DNAModelFactory
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- DNAModelFactory.DNAModel - Enum in Models
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Represents the various types of DNA models
- DuplicationAlignment - Class in Alignments
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Static classes for reading/writing duplication "alignments" -
a set of gene families with their associated size in each species
- DuplicationModelFactory - Class in Models
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A factory for easing the creation of some simple gene-family models