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 alignmentsIndelAnnotatedAlignment(AnnotationAlignment a, boolean anchored)
Basic constructor.MultiLocusAnnotatedAlignment(AnnotationAlignment a)
Clone constructor for Annotated alignmentMultiLocusAnnotatedAlignment(AnnotationAlignment a, IdGroup newGroup)
This constructor will subset the alignment based on the taxa in IdGroupSimpleAnnotatedAlignment(AnnotationAlignment a)
Clone constructor.SimpleAnnotatedAlignment(AnnotationAlignment a, IdGroup newGroup)
This constructor will subset the alignment based on the taxa in IdGroupStrippedAnnotatedAlignment(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
-