- EigenvalueDecomposition - Class in Maths
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Eigenvalues and eigenvectors of a real matrix.
- EigenvalueDecomposition(SquareMatrix) - Constructor for class Maths.EigenvalueDecomposition
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Check for symmetry, then construct the eigenvalue decomposition
- EigenvalueDecomposition.ConvergenceException - Exception in Maths
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Exception for when the Eigendecomposition does not converge
- EigenvalueDecomposition.ConvergenceException() - Constructor for exception Maths.EigenvalueDecomposition.ConvergenceException
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Default constructor
- eigValues() - Method in class Maths.SquareMatrix
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Calculates the Eigenvalues.
- eigValuesDiag() - Method in class Maths.SquareMatrix
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Calculates the Eigenvalues.
- eigVectors() - Method in class Maths.SquareMatrix
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Calculates the Eigenvectors.
- EmpiricalAdapter - Class in ModelTest
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The empirical adapter.
- EmpiricalAdapter(Map<String, String>) - Constructor for class ModelTest.EmpiricalAdapter
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Creates an instance
- EmpiricalAdapter(Map<String, String>, Set<String>) - Constructor for class ModelTest.EmpiricalAdapter
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Creates an instance including a set of states to ignore in the calculation
(such as the gap state)
- EqualAdapter - Class in ModelTest
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The equal adapter.
- EqualAdapter(Map<String, String>) - Constructor for class ModelTest.EqualAdapter
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Creates an instance
- equalExceptLength(Split) - Method in class Trees.Split
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Tests whether two splits are equal except for length
- equals(Object) - Method in class Alignments.Alignment
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- equals(Object) - Method in class Alignments.Site
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- equals(Object) - Method in class Maths.SmallDouble
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- equals(Object) - Method in class Maths.SquareMatrix
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- equals(Object) - Method in class Maths.StandardDouble
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- equals(Object) - Method in class Trees.Branch
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- equals(Object) - Method in class Trees.Split
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- equals(Object) - Method in class Trees.Tree
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- evaluate(String, Double[]) - Method in interface Maths.FunctionParser
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A function that evaluates all the functions implemented
- Exceptions - package Exceptions
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Provides exceptions that are common across the package.
- Executable - package Executable
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Provides a general driver executable
- exp() - Method in class Maths.SquareMatrix
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Calculates e^A where A is the current matrix and returns a new matrix as
the result
- expMult(double) - Method in class Maths.SquareMatrix
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Calculates e^Ax where A is this matrix and returns a new matrix as the result.