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I

IdentityAdapter - Class in ModelTest
The identity adapter (i.e.
IdentityAdapter() - Constructor for class ModelTest.IdentityAdapter
Create an instance
implemented() - Method in interface Maths.FunctionParser
Returns a list of function names that this class can calculate
index(double[]) - Static method in class Utils.Array1D
Returns indexes from the input array in rank order.
InputException - Exception in Exceptions
General exception for an exception in or about an input file
InputException(String, String, String, Throwable) - Constructor for exception Exceptions.InputException
Default constructor
inverse() - Method in interface Maths.Real
Returns the inverse of this real (i.e.
inverse() - Method in class Maths.SmallDouble
 
inverse() - Method in class Maths.SquareMatrix
Calculates the inverse of this matrix and returns a new matrix as the result.
inverse() - Method in class Maths.StandardDouble
 
isExternal(Branch) - Method in class Trees.Tree
Tests whether the given branch is an external branch (i.e.
isNonsingular() - Method in class Maths.LUDecomposition
Is the matrix nonsingular?
isSet(String) - Method in class Utils.SetSettings
Tests whether a root level setting has been set
isSet(String, String) - Method in class Utils.SetSettings
Tests whether a setting within a groups has been set
iterator() - Method in class Alignments.Alignment
 
iterator() - Method in class Models.Model
 
iterator() - Method in class Parameters.Parameters
 
iterator() - Method in class Trees.Tree
 
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