Uses of Interface
pal.alignment.AnnotationAlignment

Packages that use AnnotationAlignment
pal.alignment Classes dealing with sequence alignments, including methods for reading and printing in several possible formats, as well as rearranging and concatenating. 
pal.popgen Classes for providing 'classical' population genetics analyses. 
 

Uses of AnnotationAlignment in pal.alignment
 

Classes in pal.alignment that implement AnnotationAlignment
 class ConcatenatedAnnotatedAlignment
          This is an annotation version of the ConcatenatedAlignment Unlike normal ConcatenatedAlignment, it permits for merges with different numbers of sequences.
 class IndelAnnotatedAlignment
          an extension of the IndelAlignment that includes annotation.
 class MultiLocusAnnotatedAlignment
          MultiLocusAnnotatedAlignment is an extension of the SimpleAlignment that includes Annotation, and is designed for multiple loci.
 class SimpleAnnotatedAlignment
          This is the basic implementation of the Annotation interface, which is designed to provide annotation for an alignment.
 class StrippedAnnotatedAlignment
          This is the stripped implementation of the Annotation interface, which is designed to provide stripped and annotated alignments.
 

Constructors in pal.alignment with parameters of type AnnotationAlignment
ConcatenatedAnnotatedAlignment(AnnotationAlignment[] list, boolean mergeByID, boolean union)
          concatenate alignments
IndelAnnotatedAlignment(AnnotationAlignment a, boolean anchored)
          Basic constructor.
MultiLocusAnnotatedAlignment(AnnotationAlignment a)
          Clone constructor for Annotated alignment
MultiLocusAnnotatedAlignment(AnnotationAlignment a, IdGroup newGroup)
          This constructor will subset the alignment based on the taxa in IdGroup
SimpleAnnotatedAlignment(AnnotationAlignment a)
          Clone constructor.
SimpleAnnotatedAlignment(AnnotationAlignment a, IdGroup newGroup)
          This constructor will subset the alignment based on the taxa in IdGroup
StrippedAnnotatedAlignment(AnnotationAlignment a)
          Simple constructor
 

Uses of AnnotationAlignment in pal.popgen
 

Fields in pal.popgen declared as AnnotationAlignment
protected  AnnotationAlignment LinkageDisequilibrium.theAnnotationAlignment
           
 

Methods in pal.popgen that return AnnotationAlignment
 AnnotationAlignment LinkageDisequilibrium.getAnnotatedAlignment()
          Returns an annotated aligment if one was used for this LD this could be used to access information of locus position