Uses of Class
Alignments.Alignment

Packages that use Alignment

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.
ModelTest
Simulations	Provides a class to create simulated data.

Uses of Alignment in Alignments

Methods in Alignments that return Alignment

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.
Alignment	Alignment.limitToTaxa(java.util.Collection<java.lang.String> limit) Returns a new Alignment which is the same as this one except it is limited to certain taxa
Alignment	Alignment.recode(java.util.Map<java.lang.String,java.lang.String> recode) Recodes the alignment and returns it
Alignment	Alignment.recode(java.util.Map<java.lang.String,java.lang.String> recode, Ambiguous ambig) Recodes the alignment and returns it and also allows the definition of new ambiguous states

Methods in Alignments with parameters of type Alignment

Modifier and Type	Method and Description
static void	DuplicationAlignment.writeFile(Alignment a, java.io.File f) Writes a alignment to a file in the duplication alignment format described above.
static void	FastaAlignment.writeFile(Alignment a, java.io.File f) Writes a alignment to a file in the format described in FastaAlignment.fromFile(java.io.File).
static void	GenericAlignment.writeFile(Alignment a, java.io.File f) Writes a alignment to a file in the format described in GenericAlignment.fromFile(java.io.File).
static void	PhylipAlignment.writeFile(Alignment a, java.io.File f) Writes a alignment to a file in the format described in PhylipAlignment.fromFile(java.io.File).
static void	PhylipAlignment.writeFilePAML(Alignment a, java.io.File f) Writes a alignment to a file in the format described in PhylipAlignment.fromFile(java.io.File).

Uses of Alignment in Ancestors

Methods in Ancestors that return Alignment

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)
Alignment	AncestralMarginal.Result.getAlignment() Gets the reconstructed alignment

Methods in Ancestors with parameters of type Alignment

Modifier and Type	Method and Description
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.
static AncestralJoint	AncestralJoint.newInstance(Model m, Alignment a, Tree t) Returns an object of this class that can be used for joint reconstruction.
static AncestralMarginal	AncestralMarginal.newInstance(Model m, Alignment a, Tree t) Returns an object of this class that can be used for marginal reconstruction.

Constructors in Ancestors with parameters of type Alignment

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
AncestralMarginal(Model m, Alignment a, Tree t) Creates an object to calculate an ancestral reconstruction for a given model, alignment and tree

Uses of Alignment in Likelihood

Constructors in Likelihood with parameters of type Alignment

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 Alignment in ModelTest

Methods in ModelTest with parameters of type Alignment

Modifier and Type	Method and Description
double	Adapter.likelihood(Alignment distinct) Return the likelihood of the adapter given the distinct alignment
double	EmpiricalAdapter.likelihood(Alignment distinct)
double	EqualAdapter.likelihood(Alignment distinct)
double	IdentityAdapter.likelihood(Alignment distinct)
double	HypothesisTest.test(java.util.Map<java.lang.String,Tree> t, Alignment a, Alignment unobserved, Parameters nullParams, Parameters altParams) Does a hypothesis test on the given data and gives a p-value
double	HypothesisTest.test(java.util.Map<java.lang.String,Tree> t, Alignment a, Alignment unobserved, Parameters nullParams, Parameters altParams, java.util.Map<java.lang.String,java.lang.String> recode) Does a hypothesis test on the given data and gives a p-value
double	HypothesisTest.test(Tree t, Alignment a, Alignment unobserved, Parameters nullParams, Parameters altParams) Does a hypothesis test on the given data and gives a p-value
double	HypothesisTest.test(Tree t, Alignment a, Alignment unobserved, Parameters nullParams, Parameters altParams, java.util.Map<java.lang.String,java.lang.String> recode) Does a hypothesis test on the given data and gives a p-value

Constructors in ModelTest with parameters of type Alignment

Constructor and Description
TestInstance(Calculator<Likelihood> c, Parameters p, Adapter adapter, Alignment distinct) Creates a named instance.
TestInstance(Calculator<Likelihood> c, Parameters p, java.lang.String name, Adapter adapter, Alignment distinct) Creates a named instance.

Uses of Alignment in Simulations

Methods in Simulations that return Alignment

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.

Constructors in Simulations with parameters of type Alignment

Constructor and Description
Simulate(java.util.Map<java.lang.String,Model> m, java.util.Map<java.lang.String,Tree> t, Parameters p, Alignment unobserved) Creates an object to simulate data for a given set of models and trees, parameters and unobserved states.
Simulate(java.util.Map<java.lang.String,Model> m, Tree t, Parameters p, Alignment unobserved) Creates an object to simulate data for a given set of models, a tree, parameters and unobserved states.
Simulate(Model m, java.util.Map<java.lang.String,Tree> t, Parameters p, Alignment unobserved) Creates an object to simulate data for a given model, set of trees, parameters and unobserved states.
Simulate(Model m, Tree t, Parameters p, Alignment unobserved) Creates an object to simulate data for a given model, tree, parameters and unobserved states.