Uses of Class Exceptions.InputException (GeLL)

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

Methods in Alignments that throw InputException
Modifier and Type	Method and Description
`static Ambiguous`	Ambiguous.`fromFile(java.io.File f)` Reads in ambiguous data information from a file.
`static Alignment`	DuplicationAlignment.`fromFile(java.io.File f)` Creates a duplication alignment from a file.
`static Alignment`	FastaAlignment.`fromFile(java.io.File f)` Creates a sequence alignment from a file.
`static Alignment`	GenericAlignment.`fromFile(java.io.File f)` Creates a sequence alignment from a file.
`static Alignment`	PhylipAlignment.`fromFile(java.io.File f)` Creates a sequence alignment from a file.
`static Alignment`	DuplicationAlignment.`fromFile(java.io.File f, Ambiguous ambig)` Creates a duplication alignment which contains ambiguous data.
`static Alignment`	FastaAlignment.`fromFile(java.io.File f, Ambiguous ambig)` Creates a sequence alignment from a file with ambiguous data.
`static Alignment`	GenericAlignment.`fromFile(java.io.File f, Ambiguous ambig)` Creates a sequence alignment from a file with ambiguous data.
`static Alignment`	PhylipAlignment.`fromFile(java.io.File f, Ambiguous ambig)` Creates a sequence alignment from a file with ambiguous data.

Methods in Models that throw InputException
Modifier and Type	Method and Description
`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 ClassExceptions.InputException