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Packages that use AnnotationAlignment | |
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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 |
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Classes in pal.alignment that implement AnnotationAlignment | |
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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 | |
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ConcatenatedAnnotatedAlignment(AnnotationAlignment[] list,
boolean mergeByID,
boolean union)
concatenate alignments |
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IndelAnnotatedAlignment(AnnotationAlignment a,
boolean anchored)
Basic constructor. |
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MultiLocusAnnotatedAlignment(AnnotationAlignment a)
Clone constructor for Annotated alignment |
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MultiLocusAnnotatedAlignment(AnnotationAlignment a,
IdGroup newGroup)
This constructor will subset the alignment based on the taxa in IdGroup |
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SimpleAnnotatedAlignment(AnnotationAlignment a)
Clone constructor. |
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SimpleAnnotatedAlignment(AnnotationAlignment a,
IdGroup newGroup)
This constructor will subset the alignment based on the taxa in IdGroup |
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StrippedAnnotatedAlignment(AnnotationAlignment a)
Simple constructor |
Uses of AnnotationAlignment in pal.popgen |
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Fields in pal.popgen declared as AnnotationAlignment | |
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protected AnnotationAlignment |
LinkageDisequilibrium.theAnnotationAlignment
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Methods in pal.popgen that return AnnotationAlignment | |
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AnnotationAlignment |
LinkageDisequilibrium.getAnnotatedAlignment()
Returns an annotated aligment if one was used for this LD this could be used to access information of locus position |
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