Package uk.ac.vamsas.objects.core

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.