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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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