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Classes in uk.ac.vamsas.objects.core used by uk.ac.vamsas.client | |
VAMSAS
contains unassociated trees and a number of analysis sets |
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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. |
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ApplicationData
Class ApplicationData. |
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Entry
Class Entry. |
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User
Class User. |
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VAMSAS
contains unassociated trees and a number of analysis sets |
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VamsasDocument
Class VamsasDocument. |
Classes in uk.ac.vamsas.objects.core used by uk.ac.vamsas.objects | |
Alignment
Class Alignment. |
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AlignmentAnnotation
This is annotation over the coordinate frame defined by all the columns in the alignment. |
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AlignmentSequence
Class AlignmentSequence. |
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AlignmentSequenceAnnotation
Class AlignmentSequenceAnnotation. |
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AnnotationElement
Class AnnotationElement. |
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AppData
Class AppData. |
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ApplicationData
Class ApplicationData. |
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Common
Class Common. |
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DataSet
Class DataSet. |
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DataSetAnnotations
Class DataSetAnnotations. |
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DbRef
Store a list of database references for this sequence record - with optional mapping from database sequence to the given sequence record |
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Entry
Class Entry. |
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Glyph
Discrete symbol - possibly graphically represented |
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Input
Class Input. |
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Instance
Class Instance. |
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Link
Class Link. |
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LockFile
Class LockFile. |
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Map
the local mapType maps from the parent sequence coordinate frame to the reference frame defined by the dbRef element. |
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Newick
Class Newick. |
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Param
Class Param. |
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Pos
a position within the associated object's coordinate system |
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Property
Class Property. |
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Provenance
Class Provenance. |
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RangeAnnotation
Annotation for a rangeSpec - values can be attached for the whole specification, and to each position within the spec. |
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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 |
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Score
Ordered set of optionally named float values for the whole annotation |
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Seg
a region from start to end, with flag for inclusivity of terminii |
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Sequence
Class Sequence. |
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SequenceMapping
Class SequenceMapping. |
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SequenceType
Class SequenceType. |
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Tree
Class Tree. |
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User
Class User. |
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VAMSAS
contains unassociated trees and a number of analysis sets |
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VamsasDocument
Class VamsasDocument. |
Classes in uk.ac.vamsas.objects.core used by uk.ac.vamsas.objects.core | |
Alignment
Class Alignment. |
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AlignmentAnnotation
This is annotation over the coordinate frame defined by all the columns in the alignment. |
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AlignmentSequence
Class AlignmentSequence. |
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AlignmentSequenceAnnotation
Class AlignmentSequenceAnnotation. |
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AnnotationElement
Class AnnotationElement. |
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AppData
Class AppData. |
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ApplicationData
Class ApplicationData. |
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Attachment
Class Attachment. |
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Common
Class Common. |
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DataSet
Class DataSet. |
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DataSetAnnotations
Class DataSetAnnotations. |
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DbRef
Store a list of database references for this sequence record - with optional mapping from database sequence to the given sequence record |
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Entry
Class Entry. |
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Glyph
Discrete symbol - possibly graphically represented |
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Input
Class Input. |
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Instance
Class Instance. |
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Link
Class Link. |
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Local
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LockFile
Class LockFile. |
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Map
the local mapType maps from the parent sequence coordinate frame to the reference frame defined by the dbRef element. |
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MapList
Class MapList. |
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Mapped
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MapRangeType
Class MapRangeType. |
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MapType
Two sets of ranges defined between objects - usually sequences, indicating which regions on each are mapped. |
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Newick
Class Newick. |
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NodeType
Class NodeType. |
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Param
Class Param. |
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Pos
a position within the associated object's coordinate system |
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Property
Class Property. |
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Provenance
Class Provenance. |
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Range
Class Range. |
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RangeAnnotation
Annotation for a rangeSpec - values can be attached for the whole specification, and to each position within the spec. |
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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 |
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ReferenceType
base type for citing arbitrary links between vamsas objects Optional human readable description of the relationship |
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Score
Ordered set of optionally named float values for the whole annotation |
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Seg
a region from start to end, with flag for inclusivity of terminii |
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Sequence
Class Sequence. |
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SequenceMapping
Class SequenceMapping. |
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SequenceType
Class SequenceType. |
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Tree
Class Tree. |
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Treenode
node identity and mapping data between tree representations and vamsas document objects |
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User
Class User. |
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VAMSAS
contains unassociated trees and a number of analysis sets |
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VamsasDocument
Class VamsasDocument. |
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Vref
Direct associations between this node and any vamsas objects |
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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. |
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AlignmentSequence
Class AlignmentSequence. |
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ApplicationData
Class ApplicationData. |
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Entry
Class Entry. |
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MapType
Two sets of ranges defined between objects - usually sequences, indicating which regions on each are mapped. |
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Property
Class Property. |
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Provenance
Class Provenance. |
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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 |
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Seg
a region from start to end, with flag for inclusivity of terminii |
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Sequence
Class Sequence. |
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SequenceType
Class SequenceType. |
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User
Class User. |
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VAMSAS
contains unassociated trees and a number of analysis sets |
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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. |
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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. |
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AppData
Class AppData. |
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ApplicationData
Class ApplicationData. |
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DataSet
Class DataSet. |
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Entry
Class Entry. |
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Instance
Class Instance. |
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Provenance
Class Provenance. |
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Tree
Class Tree. |
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VAMSAS
contains unassociated trees and a number of analysis sets |
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VamsasDocument
Class VamsasDocument. |
Classes in uk.ac.vamsas.objects.core used by uk.ac.vamsas.test.simpleclient.simpleapp | |
Entry
Class Entry. |
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