- 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