Uses of Class
uk.ac.vamsas.client.Vobject

Packages that use Vobject
uk.ac.vamsas.client   
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.simpleclient   
uk.ac.vamsas.test.simpleclient.simpleapp   
 

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)