Uses of Package
uk.ac.vamsas.objects.core

Packages that use uk.ac.vamsas.objects.core
uk.ac.vamsas.client   
uk.ac.vamsas.client.picking   
uk.ac.vamsas.client.simpleclient   
uk.ac.vamsas.objects   
uk.ac.vamsas.objects.core   
uk.ac.vamsas.objects.utils   
uk.ac.vamsas.objects.utils.trees   
uk.ac.vamsas.test.objects   
uk.ac.vamsas.test.simpleclient   
uk.ac.vamsas.test.simpleclient.simpleapp   
 

Classes in uk.ac.vamsas.objects.core used by uk.ac.vamsas.client
VAMSAS
          contains unassociated trees and a number of analysis sets
VamsasDocument
          Class VamsasDocument.
 

Classes in uk.ac.vamsas.objects.core used by uk.ac.vamsas.client.picking
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
 

Classes in uk.ac.vamsas.objects.core used by uk.ac.vamsas.client.simpleclient
AppData
          Class AppData.
ApplicationData
          Class ApplicationData.
Entry
          Class Entry.
User
          Class User.
VAMSAS
          contains unassociated trees and a number of analysis sets
VamsasDocument
          Class VamsasDocument.
 

Classes in uk.ac.vamsas.objects.core used by uk.ac.vamsas.objects
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.
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.
LockFile
          Class LockFile.
Map
          the local mapType maps from the parent sequence coordinate frame to the reference frame defined by the dbRef element.
Newick
          Class Newick.
Param
          Class Param.
Pos
          a position within the associated object's coordinate system
Property
          Class Property.
Provenance
          Class Provenance.
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
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.
User
          Class User.
VAMSAS
          contains unassociated trees and a number of analysis sets
VamsasDocument
          Class VamsasDocument.
 

Classes in uk.ac.vamsas.objects.core used by uk.ac.vamsas.objects.core
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
           
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.
 

Classes in uk.ac.vamsas.objects.core used by uk.ac.vamsas.objects.utils
Alignment
          Class Alignment.
AlignmentSequence
          Class AlignmentSequence.
ApplicationData
          Class ApplicationData.
Entry
          Class Entry.
MapType
          Two sets of ranges defined between objects - usually sequences, indicating which regions on each are mapped.
Property
          Class Property.
Provenance
          Class Provenance.
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
Seg
          a region from start to end, with flag for inclusivity of terminii
Sequence
          Class Sequence.
SequenceType
          Class SequenceType.
User
          Class User.
VAMSAS
          contains unassociated trees and a number of analysis sets
VamsasDocument
          Class VamsasDocument.
 

Classes in uk.ac.vamsas.objects.core used by uk.ac.vamsas.objects.utils.trees
Treenode
          node identity and mapping data between tree representations and vamsas document objects
 

Classes in uk.ac.vamsas.objects.core used by uk.ac.vamsas.test.objects
DataSet
          Class DataSet.
VAMSAS
          contains unassociated trees and a number of analysis sets
 

Classes in uk.ac.vamsas.objects.core used by uk.ac.vamsas.test.simpleclient
Alignment
          Class Alignment.
AppData
          Class AppData.
ApplicationData
          Class ApplicationData.
DataSet
          Class DataSet.
Entry
          Class Entry.
Instance
          Class Instance.
Provenance
          Class Provenance.
Tree
          Class Tree.
VAMSAS
          contains unassociated trees and a number of analysis sets
VamsasDocument
          Class VamsasDocument.
 

Classes in uk.ac.vamsas.objects.core used by uk.ac.vamsas.test.simpleclient.simpleapp
Entry
          Class Entry.