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 | 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 | Description |
---|---|
ConcatenatedAnnotatedAlignment(AnnotationAlignment[] list,
boolean mergeByID,
boolean union) |
concatenate alignments
|
IndelAnnotatedAlignment(AnnotationAlignment a,
boolean anchored) |
Basic constructor.
|
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.
|
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 | Description |
---|---|---|
protected AnnotationAlignment |
LinkageDisequilibrium.theAnnotationAlignment |
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
|