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 TypeClassDescriptionclassThis is an annotation version of the ConcatenatedAlignment Unlike normal ConcatenatedAlignment, it permits for merges with different numbers of sequences.classan extension of the IndelAlignment that includes annotation.classMultiLocusAnnotatedAlignment is an extension of the SimpleAlignment that includes Annotation, and is designed for multiple loci.classThis is the basic implementation of the Annotation interface, which is designed to provide annotation for an alignment.classThis 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 AnnotationAlignmentLinkageDisequilibrium.theAnnotationAlignmentMethods 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