|
|||||||||||
| PREV NEXT | FRAMES NO FRAMES | ||||||||||
| 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. |
|
|
|||||||||||
| PREV NEXT | FRAMES NO FRAMES | ||||||||||