Uses of Class
Exceptions.OutputException

Packages that use OutputException
Alignments Provides class for dealing with "alignments" and the sites in an alignment. 
Optimizers Provides classes for optimising a likelihood. 
Parameters Provides classes for defining parameters used in the various calculations. 
Simulations Provides a class to create simulate data. 
Trees Provides classes to define a tree and any constraints on that tree. 
 

Uses of OutputException in Alignments
 

Methods in Alignments that throw OutputException
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 OutputException in Optimizers
 

Methods in Optimizers that throw OutputException
 Likelihood GoldenSection.maximise(Calculator l, Parameters params)
           
 Likelihood NelderMead.maximise(Calculator l, Parameters params)
           
 Likelihood Optimizer.maximise(Calculator l, Parameters p)
          Maximises the likelihood, logging to screen.
 Likelihood GoldenSection.maximise(Calculator l, Parameters params, java.io.File log)
           
 Likelihood NelderMead.maximise(Calculator l, Parameters params, java.io.File log)
           
 Likelihood Optimizer.maximise(Calculator l, Parameters params, java.io.File log)
          Maximises the likelihood, logging to a file.
 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 OutputException in Parameters
 

Methods in Parameters that throw OutputException
 void Parameters.toFile(java.io.File f)
          Writes the parameter values to a file.
 void Parameters.toFile(java.io.File f, double like)
          Writes the parameter values to a file and writes a line labeled likelihood and which gives the likelihood given as input.
 

Uses of OutputException in Simulations
 

Methods in Simulations that throw OutputException
 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
 

Uses of OutputException in Trees
 

Methods in Trees that throw OutputException
 void Tree.toFile(java.io.File f)
          Writes the tree to a file in Newick format.
 void Tree.toFile(java.io.File f, boolean nameInternal)
          Write the tree to a file in Newick format.