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Uses of Vobject in uk.ac.vamsas.client |
Fields in uk.ac.vamsas.client declared as Vobject | |
protected Vobject |
Vobject.V_parent
reference to containing object for this Vobject. |
Methods in uk.ac.vamsas.client that return Vobject | |
Vobject |
IClientDocument.getObject(VorbaId id)
Get a single Vobject. |
Vobject[] |
IClientDocument.getObjects(VorbaId[] ids)
Get a list of objects. |
Vobject |
Vobject.getV_parent()
|
Methods in uk.ac.vamsas.client with parameters of type Vobject | |
protected VorbaId |
ClientDocument._registerObject(Vobject unregistered)
|
VorbaId |
IClientDocument.registerObject(Vobject unregistered)
Returns an Vobject with a valid VorbaId, and provenance element. |
VorbaId[] |
IClientDocument.registerObjects(Vobject[] unregistered)
Returns an array of objects, each with a valid VorbaId (and completed provenance entry). |
void |
IObjectUpdate.update(Vobject updated,
IClientDocument cdoc)
Method called by Vamsas Client Library for all updated objects that the handler is registered for. |
VorbaId |
IVorbaIdFactory.makeVorbaId(Vobject vobject)
construct a new id appropriate for this client in the vamsas session. |
void |
IVorbaIdFactory.updateHashValue(Vobject vobject)
called when an object is touched by the vamsas library prior to writing to record last hash for the object's VorbaId |
protected boolean |
Vobject.merge(Vobject laterCopy)
TODO: combine two versions of the same collection Vobject to resolve asynchronous updates to the same vamsas Vobject Merges two vamsas objects, one of which is a later version of the earlier (ie they have the same vorbaId but one is a later version recently read from the vamsasDocument collection. |
protected void |
Vobject.setV_parent(Vobject V_parent)
|
boolean |
Vobjhash.isUpdated(Vobject unmarshalled)
compares the old hash value with the unmarshalled object's most recently computed hash value and updates internal record. |
protected static VorbaId |
VorbaId.newId(IVorbaIdFactory vorbaObject,
Vobject vobject)
|
abstract VorbaId |
VorbaIdFactory.makeVorbaId(Vobject vobject)
construct a new id appropriate for this client in the vamsas session. |
void |
VorbaIdFactory.updateHashValue(Vobject vobject)
|
static java.lang.Object[] |
VorbaXmlBinder.getVamsasObjects(java.io.Reader instream,
VorbaIdFactory factory,
Vobject root)
Unmarshals a vamsasDocument Vobject from a stream, registers unregistered objects, records existing VorbaIds, and completes the uk.ac.vamsas.client.Vobject housekeeping fields. |
Constructors in uk.ac.vamsas.client with parameters of type Vobject | |
Vobjhash(Vobject tobemarshalled)
creates a record of the hash value for a vamsas document object |
Uses of Vobject in uk.ac.vamsas.client.simpleclient |
Methods in uk.ac.vamsas.client.simpleclient that return Vobject | |
Vobject |
ClientDocument.getObject(VorbaId id)
|
Vobject[] |
ClientDocument.getObjects(VorbaId[] ids)
|
static Vobject[] |
VamsasArchive.getOriginalRoots(VamsasArchive ths)
Access original document if it exists, and get VAMSAS root objects. |
Vobject[] |
VamsasArchive.getOriginalRoots()
returns original document's root vamsas elements. |
Methods in uk.ac.vamsas.client.simpleclient with parameters of type Vobject | |
VorbaId[] |
ClientDocument.registerObjects(Vobject[] unregistered)
|
VorbaId |
ClientDocument.registerObject(Vobject unregistered)
|
VorbaId |
IdFactory.makeVorbaId(Vobject vobject)
|
Uses of Vobject in uk.ac.vamsas.objects |
Methods in uk.ac.vamsas.objects that return Vobject | |
Vobject |
IVorbaBinding.getVamsasObjectFor(java.lang.Object appObject)
get the Vamsas session object bound to an internal object. |
Methods in uk.ac.vamsas.objects with parameters of type Vobject | |
java.lang.Object |
IVorbaBinding.getAppsObjectFor(Vobject vObject)
Get the Application's own object bound to an existing Vamsas session object |
void |
IVorbaBinding.bindAppsObjectToVamsasObject(java.lang.Object appObject,
Vobject vObject)
Record a mapping between a vamsas document object and an application's internal object. |
Uses of Vobject in uk.ac.vamsas.objects.core |
Subclasses of Vobject in uk.ac.vamsas.objects.core | |
class |
Alignment
Class Alignment. |
class |
AlignmentAnnotation
This is annotation over the coordinate frame defined by all the columns in the alignment. |
class |
AlignmentSequence
Class AlignmentSequence. |
class |
AlignmentSequenceAnnotation
Class AlignmentSequenceAnnotation. |
class |
AnnotationElement
Class AnnotationElement. |
class |
AppData
Class AppData. |
class |
ApplicationData
Class ApplicationData. |
class |
Attachment
Class Attachment. |
class |
Common
Class Common. |
class |
DataSet
Class DataSet. |
class |
DataSetAnnotations
Class DataSetAnnotations. |
class |
DbRef
Store a list of database references for this sequence record - with optional mapping from database sequence to the given sequence record |
class |
Entry
Class Entry. |
class |
Glyph
Discrete symbol - possibly graphically represented |
class |
Input
Class Input. |
class |
Instance
Class Instance. |
class |
Link
Class Link. |
class |
Local
|
class |
LockFile
Class LockFile. |
class |
Map
the local mapType maps from the parent sequence coordinate frame to the reference frame defined by the dbRef element. |
class |
MapList
Class MapList. |
class |
Mapped
|
class |
Mapping
Class Mapping. |
class |
MapRangeType
Class MapRangeType. |
class |
MapType
Two sets of ranges defined between objects - usually sequences, indicating which regions on each are mapped. |
class |
Newick
Class Newick. |
class |
NodeType
Class NodeType. |
class |
Param
Class Param. |
class |
Pos
a position within the associated object's coordinate system |
class |
Property
Class Property. |
class |
Provenance
Class Provenance. |
class |
Range
Class Range. |
class |
RangeAnnotation
Annotation for a rangeSpec - values can be attached for the whole specification, and to each position within the spec. |
class |
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 |
class |
ReferenceType
base type for citing arbitrary links between vamsas objects Optional human readable description of the relationship |
class |
Score
Ordered set of optionally named float values for the whole annotation |
class |
Seg
a region from start to end, with flag for inclusivity of terminii |
class |
Sequence
Class Sequence. |
class |
SequenceMapping
Class SequenceMapping. |
class |
SequenceType
Class SequenceType. |
class |
Tree
Class Tree. |
class |
Treenode
node identity and mapping data between tree representations and vamsas document objects |
class |
User
Class User. |
class |
VAMSAS
contains unassociated trees and a number of analysis sets |
class |
VamsasDocument
Class VamsasDocument. |
class |
Vref
Direct associations between this node and any vamsas objects |
class |
Vxref
explicitly named cross reference to other objects in the document. |
Uses of Vobject in uk.ac.vamsas.objects.utils |
Subclasses of Vobject in uk.ac.vamsas.objects.utils | |
class |
SeqAln
|
Uses of Vobject in uk.ac.vamsas.objects.utils.trees |
Methods in uk.ac.vamsas.objects.utils.trees that return Vobject | |
Vobject |
BinaryNode.element()
DOCUMENT ME! |
Vobject |
BinaryNode.setElement(Vobject v)
DOCUMENT ME! |
Methods in uk.ac.vamsas.objects.utils.trees with parameters of type Vobject | |
Vobject |
BinaryNode.setElement(Vobject v)
DOCUMENT ME! |
Treenode[] |
NewickFile.matchTreeNodeNames(java.lang.String[] names,
Vobject[] boundObjects)
|
Constructors in uk.ac.vamsas.objects.utils.trees with parameters of type Vobject | |
BinaryNode(Vobject val,
BinaryNode parent,
java.lang.String name)
Creates a new BinaryNode object. |
|
SequenceNode(Vobject val,
SequenceNode parent,
float dist,
java.lang.String name)
Creates a new SequenceNode object. |
|
SequenceNode(Vobject val,
SequenceNode parent,
java.lang.String name,
float dist,
int bootstrap,
boolean dummy)
Creates a new SequenceNode object. |
Uses of Vobject in uk.ac.vamsas.test.simpleclient |
Methods in uk.ac.vamsas.test.simpleclient that return Vobject | |
Vobject |
ArchiveClient.getObject(VorbaId id)
|
Vobject |
ClientDoc.getObject(VorbaId id)
|
Vobject[] |
ClientDoc.getObjects(VorbaId[] ids)
|
Methods in uk.ac.vamsas.test.simpleclient with parameters of type Vobject | |
static void |
ArchiveReports.outputVobjectState(Vobject v,
java.io.PrintStream outstr)
|
VorbaId[] |
ClientDoc.registerObjects(Vobject[] unregistered)
|
VorbaId |
ClientDoc.registerObject(Vobject unregistered)
|
Uses of Vobject in uk.ac.vamsas.test.simpleclient.simpleapp |
Methods in uk.ac.vamsas.test.simpleclient.simpleapp that return Vobject | |
protected Vobject |
VamsasDatastore.getjv2vObj(java.lang.Object jvobj)
|
Methods in uk.ac.vamsas.test.simpleclient.simpleapp with parameters of type Vobject | |
protected java.lang.Object |
VamsasDatastore.getvObj2jv(Vobject vobj)
|
protected void |
VamsasDatastore.bindjvvobj(java.lang.Object jvobj,
Vobject vobj)
|
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