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.
|
Modifier and Type | Class and 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.
|
Constructor and Description |
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ConcatenatedAnnotatedAlignment(AnnotationAlignment[] list,
boolean mergeByID,
boolean union)
concatenate alignments
|
IndelAnnotatedAlignment(AnnotationAlignment a,
boolean anchored)
Basic constructor.
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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.
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SimpleAnnotatedAlignment(AnnotationAlignment a,
IdGroup newGroup)
This constructor will subset the alignment based on the taxa in IdGroup
|
StrippedAnnotatedAlignment(AnnotationAlignment a)
Simple constructor
|
Modifier and Type | Field and Description |
---|---|
protected AnnotationAlignment |
LinkageDisequilibrium.theAnnotationAlignment |
Modifier and Type | Method and 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
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