- Adapter - Interface in ModelTest
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Interface for an adapter.
- add(Real) - Method in interface Maths.Real
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Adds this Real to another
- add(double) - Method in interface Maths.Real
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Adds this Real to a double
- add(Real) - Method in class Maths.SmallDouble
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- add(double) - Method in class Maths.SmallDouble
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- add(SquareMatrix) - Method in class Maths.SquareMatrix
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Adds a matrix to this one and returns a new matrix as the result
- add(Real) - Method in class Maths.StandardDouble
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- add(double) - Method in class Maths.StandardDouble
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- addAssignment(String, String) - Method in class Ancestors.Assignment
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Adds a assignment
- addGroup(String, boolean) - Method in class Utils.PossibleSettings
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Adds a new setting group
- addip(Real) - Method in interface Maths.Real
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Adds a Real to this Real in place.
- addip(Real) - Method in class Maths.SmallDouble
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- addip(Real) - Method in class Maths.StandardDouble
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- addNeededSetting(String) - Method in class Utils.PossibleSettings
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Add a required setting at the root level (i.e.
- addNeededSetting(String, String) - Method in class Utils.PossibleSettings
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Add a required setting within a group
- addOptionalSetting(String, String) - Method in class Utils.PossibleSettings
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Add an optional setting at the root level.
- addOptionalSetting(String, String, String) - Method in class Utils.PossibleSettings
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Add an optional setting to a group.
- addParameter(Parameter) - Method in class Parameters.Parameters
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Add a parameter
- addParameters(Parameters) - Method in class Parameters.Parameters
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Adds the parameters from another set of parameters
- addproductip(Real, double) - Method in interface Maths.Real
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Adds the product of a Real and a double to this Real in place.
- addproductip(Real, double) - Method in class Maths.SmallDouble
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- addproductip(Real, double) - Method in class Maths.StandardDouble
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- addSetting(String, String) - Method in class Utils.SetSettings
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Adds a new root level setting
- addSetting(String, String, String) - Method in class Utils.SetSettings
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Adds a new setting within a group
- AIC - Class in ModelTest
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Class for computing the AIC of several test instances (where an instance
is a calculator and a set of parameters.
- AIC(List<TestInstance>, Optimizer) - Constructor for class ModelTest.AIC
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Creates an object containing the AIC for several test instances
- Alignment - Class in Alignments
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Represents an "alignment", used very loosely.
- Alignment(List<Site>) - Constructor for class Alignments.Alignment
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Creates an alignment
- AlignmentException - Exception in Alignments
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Exception related to an alignment (currently only input errors)
- AlignmentException(String) - Constructor for exception Alignments.AlignmentException
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Constructor for when there is a problem unrelated to an input file
- AlignmentException(String, String, String, Throwable) - Constructor for exception Alignments.AlignmentException
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Constructor for when there is a problem in the input file
- Alignments - package Alignments
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Provides class for dealing with "alignments" and the sites in an alignment.
- Ambiguous - Class in Alignments
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Stores details of ambiguous characters
- Ambiguous() - Constructor for class Alignments.Ambiguous
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Default constructor for use when there are no ambiguous characters
- Ambiguous(Map<String, Set<String>>) - Constructor for class Alignments.Ambiguous
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Constructor for use when there are ambiguous characters
- Ancestors - package Ancestors
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Provides classed to calculate ancestral reconstruction.
- AncestralException - Exception in Ancestors
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Exception related to ancestral reconstruction
- AncestralException(String, Throwable) - Constructor for exception Ancestors.AncestralException
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Constructor
- AncestralJoint - Class in Ancestors
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Abstract class that the two different ways of doing ancestral reconstruction
extend.
- AncestralJoint() - Constructor for class Ancestors.AncestralJoint
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- AncestralJointBB - Class in Ancestors
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Class to perform joint ancestral reconstrion using the method of Pupko 2002
slightly modified
- AncestralJointDP - Class in Ancestors
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Class to perform joint ancestral reconstruction using the method of Pupko 2000
- AncestralMarginal - Class in Ancestors
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Class to perform marginal reconstruction of internal nodes.
- AncestralMarginal(Model, Alignment, Tree) - Constructor for class Ancestors.AncestralMarginal
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Creates an object to calculate an ancestral reconstruction for a given
model, alignment and tree
- AncestralMarginal(Model, Alignment, Map<String, Tree>) - Constructor for class Ancestors.AncestralMarginal
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Creates an object to calculate an ancestral reconstruction for a given
model, alignment and tree
- AncestralMarginal(Map<String, Model>, Alignment, Tree) - Constructor for class Ancestors.AncestralMarginal
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Creates an object to calculate an ancestral reconstruction for a given
set of models, an alignment and a tree.
- AncestralMarginal(Map<String, Model>, Alignment, Map<String, Tree>) - Constructor for class Ancestors.AncestralMarginal
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Creates an object to calculate an ancestral reconstruction for a given
set of models, an alignment and a tree.
- AncestralMarginal.Result - Class in Ancestors
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Class to store the results of a marginal ancestral reconstruction
- AncestralMarginal.SiteResult - Class in Ancestors
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Class to store the results of a marginal ancestral reconstruction for a single
site
- Array1D - Class in Utils
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Utility class for 1D arrays
- Array2D - Class in Utils
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Utility class for 2D arrays
- Assignment - Class in Ancestors
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Stores the ancestral reconstruction assignment for a single site
- Assignment() - Constructor for class Ancestors.Assignment
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Standard constructor that creates an object with no assignments
- averageLength(Set<String>) - Method in class Alignments.Alignment
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Returns the average length of the sequences