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. 
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.
SequenceAlignment(java.io.File f)
          Creates a sequence alignment from a file.
SequenceAlignment(java.io.File f, Ambiguous ambig)
          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
 

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.