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A

add(SquareMatrix) - Method in class Maths.SquareMatrix
Adds a matrix to this one and returns a new matrix as the result
add(K, double) - Method in class Utils.ToDoubleHashMap
Add to the the value associated with a key
addConstraint(String, String) - Method in class Constraints.SiteConstraints
Adds a constraint where a node is constrained to a single state
addConstraint(String, Set<String>) - Method in class Constraints.SiteConstraints
Adds a constraint
addGroup(String, boolean) - Method in class Utils.PossibleSettings
Adds a new setting group
addNeededSetting(String) - Method in class Utils.PossibleSettings
Add a required setting at the root level (i.e.
addNeededSetting(String, String) - Method in class Utils.PossibleSettings
Add a required setting within a group
addOptionalSetting(String, String) - Method in class Utils.PossibleSettings
Add an optional setting at the root level.
addOptionalSetting(String, String, String) - Method in class Utils.PossibleSettings
Add an optional setting to a group.
addParameter(Parameter) - Method in class Parameters.Parameters
Add a parameter
addParameters(Parameters) - Method in class Parameters.Parameters
Adds the parameters from another set of parameters
addSetting(String, String) - Method in class Utils.SetSettings
Adds a new root level setting
addSetting(String, String, String) - Method in class Utils.SetSettings
Adds a new setting within a group
Alignment - Class in Alignments
Represents an "alignment", used very losely.
Alignment() - Constructor for class Alignments.Alignment
Default constructor.
Alignment(List<Site>) - Constructor for class Alignments.Alignment
Creates an alignment
AlignmentException - Exception in Alignments
Exception related to an alignment (currently only input errors)
AlignmentException(String) - Constructor for exception Alignments.AlignmentException
Constructor for when there is a problem unrelated to an input file
AlignmentException(String, String, String, Throwable) - Constructor for exception Alignments.AlignmentException
Constructor for when there is a problem in the input file
Alignments - package Alignments
Provides class for dealing with "alignments" and the sites in an alignment.
Ambiguous - Class in Alignments
Stores details of ambiguous characters
Ambiguous() - Constructor for class Alignments.Ambiguous
Default constructor for use when there are no ambiguous characters
Ambiguous(Map<String, Set<String>>) - Constructor for class Alignments.Ambiguous
Constructor for use when there are ambiguous characters
Ancestors - package Ancestors
Provides classed to calculate ancestral reconstruction.
AncestralException - Exception in Ancestors
Exception related to ancestral reconstruction
AncestralException(String, Throwable) - Constructor for exception Ancestors.AncestralException
Constructor
AncestralJoint - Class in Ancestors
Abstract class that the two different ways of doing ancestral reconstruction extend.
AncestralJoint() - Constructor for class Ancestors.AncestralJoint
 
AncestralJointBB - Class in Ancestors
Class to perform joint ancestral reconstrion using the method of Pupko 2002 slightly modified
AncestralJointDP - Class in Ancestors
Class to perform joint ancestral reconstrion using the method of Pupko 2000
AncestralMarginal - Class in Ancestors
Class to perform marginal reconstruction of internal nodes.
AncestralMarginal(Model, Alignment, Tree) - Constructor for class Ancestors.AncestralMarginal
Creates an object to calculate an ancestral reconstruction for a given model, alignment and tree
AncestralMarginal(Model, Alignment, Tree, Constrainer) - Constructor for class Ancestors.AncestralMarginal
Creates an object to calculate an ancestral reconstruction for a given model, alignment, tree and constraints
AncestralMarginal.Result - Class in Ancestors
Class to store the results of a marginal ancestral reconstruction
AncestralMarginal.SiteResult - Class in Ancestors
Class to store the results of a marginal ancestral reconstruction for a single site
Array1D - Class in Utils
Utility class for 1D arrays
Array2D - Class in Utils
Utility class for 2D arrays

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