Uses of Class
Alignments.AlignmentException

Packages that use AlignmentException
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 AlignmentException in Alignments
 

Constructors in Alignments that throw AlignmentException
Alignment(java.util.List<Site> data)
          Creates an alignment
DuplicationAlignment(java.io.File f)
          Creates a duplication alignment from a file.
DuplicationAlignment(java.io.File f, Ambiguous ambig)
          Creates a duplication alignment which contains ambiguous data.
FastaAlignment(java.io.File f)
          Creates a sequence alignment from a file.
FastaAlignment(java.io.File f, Ambiguous ambig)
          Creates a sequence alignment from a file with ambiguouis data.
PhylipAlignment(java.io.File f)
          Creates a sequence alignment from a file.
PhylipAlignment(java.io.File f, Ambiguous ambig)
          Creates a sequence alignment from a file with ambiguouis data.
SequenceAlignment(java.io.File f)
          Deprecated. Creates a sequence alignment from a file.
SequenceAlignment(java.io.File f, Ambiguous ambig)
          Deprecated. Creates a sequence alignment from a file with ambiguouis data.
 

Uses of AlignmentException in Ancestors
 

Methods in Ancestors that throw AlignmentException
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, Tree t)
          Returns an object of this class that can be used for joint reconstruction.
 

Constructors in Ancestors that throw AlignmentException
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.
 

Uses of AlignmentException in Likelihood
 

Constructors in Likelihood that throw AlignmentException
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.
 

Uses of AlignmentException in Simulations
 

Methods in Simulations that throw AlignmentException
 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.
 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