Uses of Class
Alignments.Ambiguous

Packages that use Ambiguous

Package	Description
Alignments	Provides class for dealing with "alignments" and the sites in an alignment.

Uses of Ambiguous in Alignments

Methods in Alignments that return Ambiguous

Modifier and Type	Method and Description
static Ambiguous	Ambiguous.fromFile(java.io.File f) Reads in ambiguous data information from a file.
Ambiguous	Site.getAmbiguous() Gets the information about ambiguous states for this site

Methods in Alignments with parameters of type Ambiguous

Modifier and Type	Method and Description
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.
Alignment	Alignment.recode(java.util.Map<java.lang.String,java.lang.String> recode, Ambiguous ambig) Recodes the alignment and returns it and also allows the definition of new ambiguous states
Site	Site.recode(java.util.Map<java.lang.String,java.lang.String> recode, Ambiguous ambig) Recodes the alignment and returns it and also allows the definition of new ambiguous states

Constructors in Alignments with parameters of type Ambiguous

Constructor and Description
Site(java.util.LinkedHashMap<java.lang.String,java.lang.String> sites, Ambiguous ambig) Creates a site in a alignment with ambiguous data
Site(java.util.LinkedHashMap<java.lang.String,java.lang.String> sites, Ambiguous ambig, java.lang.String siteClass) Creates a site in a alignment with ambiguous data and with the given class.
Site(java.lang.String id, java.util.LinkedHashMap<java.lang.String,java.lang.String> sites, Ambiguous ambig) Creates a site in a alignment with ambiguous data
Site(java.lang.String id, java.util.LinkedHashMap<java.lang.String,java.lang.String> sites, Ambiguous ambig, java.lang.String siteClass) Creates a site in a alignment with ambiguous data and with the given class.