Uses of Interface pal.alignment.AnnotationAlignment

Packages that use AnnotationAlignment
Package	Description
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
Modifier and Type	Class	Description
`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
Constructor	Description
`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
Modifier and Type	Field	Description
`protected AnnotationAlignment`	LinkageDisequilibrium.`theAnnotationAlignment`

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