Uses of Class
Alignments.Alignment

Packages that use Alignment
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 simulate data. 
 

Uses of Alignment in Alignments
 

Subclasses of Alignment in Alignments
 class DuplicationAlignment
          Represents a duplication "alignment" - a set of gene families with their associated size in each species
 class FastaAlignment
          Represents a sequence alignment in FASTA format
 class PhylipAlignment
          Represents a sequence alignment in Phylip format
 class SequenceAlignment
          Deprecated. Replaced by PhylipAlignment to allow for easier use of multiple formats.
 

Methods in Alignments that return Alignment
 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
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.FastaAlignment(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.PhylipAlignment(java.io.File).
static void SequenceAlignment.writeFile(Alignment a, java.io.File f)
          Deprecated. Writes a alignment to a file in the format described in SequenceAlignment.SequenceAlignment(java.io.File).
 

Uses of Alignment in Ancestors
 

Methods in Ancestors that return Alignment
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
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 AncestralJoint AncestralJoint.newInstance(Model m, Alignment a, Tree t)
          Returns an object of this class that can be used for joint reconstruction.
 

Constructors in Ancestors with parameters of type Alignment
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(java.util.Map<java.lang.String,Model> m, Alignment a, Tree t, java.util.Map<java.lang.String,Constrainer> con)
          Creates an object to calculate an ancestral reconstruction for a given set of models, an alignment, a tree and s et of constrainers.
AncestralMarginal(Model m, Alignment a, Tree t)
          Creates an object to calculate an ancestral reconstruction for a given model, alignment and tree
AncestralMarginal(Model m, Alignment a, Tree t, Constrainer con)
          Creates an object to calculate an ancestral reconstruction for a given model, alignment, tree and a constrainter
 

Uses of Alignment in Likelihood
 

Constructors in Likelihood with parameters of type Alignment
Calculator(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.
Calculator(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, a tree, and unobserved data.
Calculator(java.util.Map<java.lang.String,Model> m, Alignment a, Tree t, Alignment unobserved, java.util.Map<java.lang.String,Constrainer> con)
          Creates a class to calculate the likelihood for a given set of models, an alignment, a tree, unobserved data and a set of constraints.
Calculator(java.util.Map<java.lang.String,Model> m, Alignment a, Tree t, java.util.Map<java.lang.String,Constrainer> con)
          Creates a class to calculate the likelihood for a given set of models, an alignment, a tree and a set of constraints.
Calculator(Model m, Alignment a, Tree t)
          Creates an object to calculate the likelihood for a given model, alignment, tree.
Calculator(Model m, Alignment a, Tree t, Alignment unobserved)
          Creates a class to calculate the likelihood for a given model, alignment, tree, missing data and constraints
Calculator(Model m, Alignment a, Tree t, Alignment unobserved, Constrainer con)
          Creates a class to calculate the likelihood for a given model, alignment, tree, unobserved data and constraints
Calculator(Model m, Alignment a, Tree t, Constrainer con)
          Creates a class to calculate the likelihood for a given model, alignment, tree and constraints
 

Uses of Alignment in Simulations
 

Methods in Simulations that return Alignment
 Alignment Simulate.getAlignment(int length)
          Gets a simulated alignment, not returing 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 returing 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.
 

Methods in Simulations with parameters of type Alignment
 double HypothesisTest.test(Tree t, Alignment a, Alignment unobserved, Parameters nullParams, Parameters altParams)
          Does a hpyothesis 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 hpyothesis test on the given data and gives a p-value
 

Constructors in Simulations with parameters of type Alignment
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 sattes.
Simulate(java.util.Map<java.lang.String,Model> m, Tree t, Parameters p, Alignment unobserved, java.util.Map<java.lang.String,Constrainer> con)
          Creates an object to simulate data for a given set of models, a tree, parameters, unobserved states and constrainers.
Simulate(Model m, Tree t, Parameters p, Alignment unobserved)
          Creates an object to simulate data for a given model, tree, parameters and unobserved states.
Simulate(Model m, Tree t, Parameters p, Alignment unobserved, Constrainer con)
          Creates an object to simulate data for a given model, tree, parameters, unobserved states and constraints.