Uses of Class
Alignments.AlignmentException

Packages that use AlignmentException

Package	Description
Alignments	Provides class for dealing with "alignments" and the sites in an alignment.
Ancestors	Provides classed to calculate ancestral reconstruction.
Likelihood	Provides classes for calculating the likelihood of a tree given a model and an alignment.
Simulations	Provides a class to create simulated data.

Uses of AlignmentException in Alignments

Methods in Alignments that throw AlignmentException

Modifier and Type	Method and Description
static Alignment	DuplicationAlignment.fromFile(java.io.File f) Creates a duplication alignment from a file.
static Alignment	FastaAlignment.fromFile(java.io.File f) Creates a sequence alignment from a file.
static Alignment	GenericAlignment.fromFile(java.io.File f) Creates a sequence alignment from a file.
static Alignment	PhylipAlignment.fromFile(java.io.File f) Creates a sequence alignment from a file.
static Alignment	DuplicationAlignment.fromFile(java.io.File f, Ambiguous ambig) Creates a duplication alignment which contains ambiguous data.
static Alignment	FastaAlignment.fromFile(java.io.File f, Ambiguous ambig) Creates a sequence alignment from a file with ambiguous data.
static Alignment	GenericAlignment.fromFile(java.io.File f, Ambiguous ambig) Creates a sequence alignment from a file with ambiguous data.
static Alignment	PhylipAlignment.fromFile(java.io.File f, Ambiguous ambig) Creates a sequence alignment from a file with ambiguous data.
java.lang.String	Site.getRawCharacter(java.lang.String taxa) Gets the raw charcater for a given taxa.

Constructors in Alignments that throw AlignmentException

Constructor and Description
Alignment(java.util.List<Site> data) Creates an alignment

Uses of AlignmentException in Ancestors

Methods in Ancestors that throw AlignmentException

Modifier and Type	Method and Description
abstract Alignment	AncestralJoint.calculate(Parameters params) Calculates the reconstruction
Alignment	AncestralJointBB.calculate(Parameters p)
Alignment	AncestralJointDP.calculate(Parameters params)
AncestralMarginal.Result	AncestralMarginal.calculate(Parameters params) Calculates the reconstruction
static AncestralJoint	AncestralJoint.newInstance(java.util.Map<java.lang.String,Model> m, Alignment a, java.util.Map<java.lang.String,Tree> t) Returns an object of this class that can be used for joint reconstruction.
static AncestralJoint	AncestralJoint.newInstance(java.util.Map<java.lang.String,Model> m, Alignment a, Tree t) Returns an object of this class that can be used for joint reconstruction.
static AncestralMarginal	AncestralMarginal.newInstance(java.util.Map<java.lang.String,Model> m, Alignment a, Tree t) Returns an object of this class that can be used for marginal reconstruction.
static AncestralJoint	AncestralJoint.newInstance(Model m, Alignment a, java.util.Map<java.lang.String,Tree> t) Returns an object of this class that can be used for joint reconstruction.

Constructors in Ancestors that throw AlignmentException

Constructor and Description
AncestralMarginal(java.util.Map<java.lang.String,Model> m, Alignment a, java.util.Map<java.lang.String,Tree> t) Creates an object to calculate an ancestral reconstruction for a given set of models, an alignment and a tree.
AncestralMarginal(java.util.Map<java.lang.String,Model> m, Alignment a, Tree t) Creates an object to calculate an ancestral reconstruction for a given set of models, an alignment and a tree.
AncestralMarginal(Model m, Alignment a, java.util.Map<java.lang.String,Tree> t) Creates an object to calculate an ancestral reconstruction for a given model, alignment and tree

Uses of AlignmentException in Likelihood

Constructors in Likelihood that throw AlignmentException

Constructor and Description
StandardCalculator(java.util.Map<java.lang.String,Model> m, Alignment a, java.util.Map<java.lang.String,Tree> t) Creates a class to calculate the likelihood for a given set of models, an alignment, and a tree.
StandardCalculator(java.util.Map<java.lang.String,Model> m, Alignment a, java.util.Map<java.lang.String,Tree> t, Alignment unobserved) Creates a class to calculate the likelihood for a given set of models, an alignment, a tree and unobserved data.
StandardCalculator(java.util.Map<java.lang.String,Model> m, Alignment a, Tree t) Creates a class to calculate the likelihood for a given set of models, an alignment, and a tree.
StandardCalculator(java.util.Map<java.lang.String,Model> m, Alignment a, Tree t, Alignment unobserved) Creates a class to calculate the likelihood for a given set of models, an alignment, and a tree.
StandardCalculator(Model m, Alignment a, java.util.Map<java.lang.String,Tree> t) Creates a class to calculate the likelihood for a given set of models, an alignment, and a tree.
StandardCalculator(Model m, Alignment a, java.util.Map<java.lang.String,Tree> t, Alignment unobserved) Creates a class to calculate the likelihood for a given set of models, an alignment, and a tree.
StandardCalculator(Model m, Alignment a, Tree t) Creates an object to calculate the likelihood for a given model, alignment and tree.
StandardCalculator(Model m, Alignment a, Tree t, Alignment unobserved) Creates a class to calculate the likelihood for a given model, alignment, tree and missing data

Uses of AlignmentException in Simulations

Methods in Simulations that throw AlignmentException

Modifier and Type	Method and Description
Alignment	Simulate.getAlignment(int length) Gets a simulated alignment, not returning the state of internal nodes
Alignment	Simulate.getAlignment(int length, boolean internal) Gets a simulated alignment
Alignment	Simulate.getAlignment(int length, boolean internal, java.util.Map<java.lang.String,java.lang.String> recode) Gets a simulated alignment.
Alignment	Simulate.getAlignment(int length, java.util.Map<java.lang.String,java.lang.String> recode) Gets a simulated alignment, not returning the state of internal nodes.
Alignment	Simulate.getAlignment(java.util.List<java.lang.String> siteClasses) Gets a simulated alignment, not returning the state of the internal nodes.
Alignment	Simulate.getAlignment(java.util.List<java.lang.String> siteClasses, boolean internal) Gets a simulated alignment.
Alignment	Simulate.getAlignment(java.util.List<java.lang.String> siteClasses, boolean internal, java.util.Map<java.lang.String,java.lang.String> recode) Gets a simulated alignment.
Alignment	Simulate.getAlignment(java.util.List<java.lang.String> siteClasses, java.util.Map<java.lang.String,java.lang.String> recode) Gets a simulated alignment, not returning the state of the internal nodes.