Class Summary |
Alignment |
Class Alignment. |
AlignmentAnnotation |
This is annotation over the coordinate frame defined by all the columns in
the alignment. |
AlignmentSequence |
Class AlignmentSequence. |
AlignmentSequenceAnnotation |
Class AlignmentSequenceAnnotation. |
AnnotationElement |
Class AnnotationElement. |
AppData |
Class AppData. |
ApplicationData |
Class ApplicationData. |
Attachment |
Class Attachment. |
Common |
Class Common. |
DataSet |
Class DataSet. |
DataSetAnnotations |
Class DataSetAnnotations. |
DbRef |
Store a list of database references for this sequence record - with optional
mapping from database sequence to the given sequence record |
Entry |
Class Entry. |
Glyph |
Discrete symbol - possibly graphically represented |
Input |
Class Input. |
Instance |
Class Instance. |
Link |
Class Link. |
Local |
|
LockFile |
Class LockFile. |
Map |
the local mapType maps from the parent sequence coordinate frame to the
reference frame defined by the dbRef element. |
MapList |
Class MapList. |
Mapped |
|
Mapping |
Class Mapping. |
MapRangeType |
Class MapRangeType. |
MapType |
Two sets of ranges defined between objects - usually sequences, indicating
which regions on each are mapped. |
Newick |
Class Newick. |
NodeType |
Class NodeType. |
Param |
Class Param. |
Pos |
a position within the associated object's coordinate system |
Property |
Class Property. |
Provenance |
Class Provenance. |
Range |
Class Range. |
RangeAnnotation |
Annotation for a rangeSpec - values can be attached for the whole
specification, and to each position within the spec. |
RangeType |
Specify an ordered set of positions and/or regions on the principle dimension
of some associated vamsas object Keeping to jaxb-1.0 specification for the
moment - this choice should become a substitution group when we use jaxb-2.0
capable bindings |
ReferenceType |
base type for citing arbitrary links between vamsas objects Optional human
readable description of the relationship |
Score |
Ordered set of optionally named float values for the whole annotation |
Seg |
a region from start to end, with flag for inclusivity of terminii |
Sequence |
Class Sequence. |
SequenceMapping |
Class SequenceMapping. |
SequenceType |
Class SequenceType. |
Tree |
Class Tree. |
Treenode |
node identity and mapping data between tree representations and vamsas
document objects |
User |
Class User. |
VAMSAS |
contains unassociated trees and a number of analysis sets |
VamsasDocument |
Class VamsasDocument. |
Vref |
Direct associations between this node and any vamsas objects |
Vxref |
explicitly named cross reference to other objects in the document. |