Uses of Class
Exceptions.OutputException

Packages that use OutputException

Package	Description
Alignments	Provides class for dealing with "alignments" and the sites in an alignment.
Parameters	Provides classes for defining parameters used in the various calculations.
Trees	Provides classes to define a tree.

Uses of OutputException in Alignments

Methods in Alignments that throw OutputException

Modifier and Type	Method and Description
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.fromFile(java.io.File).
static void	GenericAlignment.writeFile(Alignment a, java.io.File f) Writes a alignment to a file in the format described in GenericAlignment.fromFile(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.fromFile(java.io.File).
static void	PhylipAlignment.writeFilePAML(Alignment a, java.io.File f) Writes a alignment to a file in the format described in PhylipAlignment.fromFile(java.io.File).

Uses of OutputException in Parameters

Methods in Parameters that throw OutputException

Modifier and Type	Method and Description
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 Trees

Methods in Trees that throw OutputException

Modifier and Type	Method and Description
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.
void	Tree.toFilePAML(java.io.File f) Writes the tree to a file with taxa names limited to 25 characters for use in PAML.