Uses of Class
Alignments.Ambiguous

Packages that use Ambiguous
Alignments Provides class for dealing with "alignments" and the sites in an alignment. 
 

Uses of Ambiguous in Alignments
 

Methods in Alignments that return Ambiguous
static Ambiguous Ambiguous.fromFile(java.io.File f)
          Reads in amiguous 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
 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
DuplicationAlignment(java.io.File f, Ambiguous ambig)
          Creates a duplication alignment which contains ambiguous data.
FastaAlignment(java.io.File f, Ambiguous ambig)
          Creates a sequence alignment from a file with ambiguouis data.
PhylipAlignment(java.io.File f, Ambiguous ambig)
          Creates a sequence alignment from a file with ambiguouis data.
SequenceAlignment(java.io.File f, Ambiguous ambig)
          Deprecated. Creates a sequence alignment from a file with ambiguouis data.
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.