Uses of Interface
pal.alignment.AnnotationAlignment
Packages that use AnnotationAlignment
Package
Description
Classes dealing with sequence alignments, including methods for reading
and printing in several possible formats, as well as rearranging and
concatenating.
Classes for providing 'classical' population genetics analyses.
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Uses of AnnotationAlignment in pal.alignment
Classes in pal.alignment that implement AnnotationAlignmentModifier and TypeClassDescriptionclass
This is an annotation version of the ConcatenatedAlignment Unlike normal ConcatenatedAlignment, it permits for merges with different numbers of sequences.class
an extension of the IndelAlignment that includes annotation.class
MultiLocusAnnotatedAlignment is an extension of the SimpleAlignment that includes Annotation, and is designed for multiple loci.class
This is the basic implementation of the Annotation interface, which is designed to provide annotation for an alignment.class
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 AnnotationAlignmentModifierConstructorDescriptionConcatenatedAnnotatedAlignment
(AnnotationAlignment[] list, boolean mergeByID, boolean union) concatenate alignmentsIndelAnnotatedAlignment
(AnnotationAlignment a, boolean anchored) Basic constructor.Clone constructor for Annotated alignmentMultiLocusAnnotatedAlignment
(AnnotationAlignment a, IdGroup newGroup) This constructor will subset the alignment based on the taxa in IdGroupClone constructor.SimpleAnnotatedAlignment
(AnnotationAlignment a, IdGroup newGroup) This constructor will subset the alignment based on the taxa in IdGroupSimple constructor -
Uses of AnnotationAlignment in pal.popgen
Fields in pal.popgen declared as AnnotationAlignmentModifier and TypeFieldDescriptionprotected AnnotationAlignment
LinkageDisequilibrium.theAnnotationAlignment
Methods in pal.popgen that return AnnotationAlignmentModifier and TypeMethodDescriptionLinkageDisequilibrium.getAnnotatedAlignment()
Returns an annotated aligment if one was used for this LD this could be used to access information of locus position