Uses of Class
Exceptions.InputException

Packages that use InputException
Alignments Provides class for dealing with "alignments" and the sites in an alignment. 
Models Provides classes for defing a phylogenetic model. 
Optimizers Provides classes for optimising a likelihood. 
Parameters Provides classes for defining parameters used in the various calculations. 
Trees Provides classes to define a tree and any constraints on that tree. 
 

Uses of InputException in Alignments
 

Methods in Alignments that throw InputException
static Ambiguous Ambiguous.fromFile(java.io.File f)
          Reads in amiguous data information from a file.
 

Constructors in Alignments that throw InputException
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 InputException in Models
 

Methods in Models that throw InputException
static Model Model.fromFile(java.io.File f)
          Creates a new model from a file.
static RateCategory RateCategory.fromFile(java.io.File mfile)
          Creates an instance from the information in a file.
 

Uses of InputException in Optimizers
 

Methods in Optimizers that throw InputException
 Likelihood GoldenSection.restart(Calculator l, java.io.File checkPoint)
           
 Likelihood NelderMead.restart(Calculator l, java.io.File checkPoint)
           
 Likelihood Optimizer.restart(Calculator l, java.io.File checkPoint)
          Maximises the likelihood starting from a checkpoint file (see Optimizer.setCheckPointFile(java.io.File), logging to the screen.
 Likelihood GoldenSection.restart(Calculator l, java.io.File checkPoint, java.io.File log)
           
 Likelihood NelderMead.restart(Calculator l, java.io.File checkPoint, java.io.File log)
           
 Likelihood Optimizer.restart(Calculator l, java.io.File checkPoint, java.io.File log)
          Maximises the likelihood starting from a checkpoint file (see Optimizer.setCheckPointFile(java.io.File), logging to a file.
 

Uses of InputException in Parameters
 

Methods in Parameters that throw InputException
static Parameters Parameters.fromFile(java.io.File f)
          Reads parameters from a file.
 

Uses of InputException in Trees
 

Methods in Trees that throw InputException
static Tree Tree.fromFile(java.io.File f)
          Creates a tree from a file containing a Newick string