A B C D E F G H I J L M N O P R S T U V W Z _

A

ALPHA_VERSION - Static variable in class uk.ac.vamsas.objects.utils.document.VersionEntries
 
Alignment - class uk.ac.vamsas.objects.core.Alignment.
Class Alignment.
Alignment() - Constructor for class uk.ac.vamsas.objects.core.Alignment
 
AlignmentAnnotation - class uk.ac.vamsas.objects.core.AlignmentAnnotation.
This is annotation over the coordinate frame defined by all the columns in the alignment.
AlignmentAnnotation() - Constructor for class uk.ac.vamsas.objects.core.AlignmentAnnotation
 
AlignmentAnnotationDescriptor - class uk.ac.vamsas.objects.core.descriptors.AlignmentAnnotationDescriptor.
Class AlignmentAnnotationDescriptor.
AlignmentAnnotationDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.AlignmentAnnotationDescriptor
 
AlignmentDescriptor - class uk.ac.vamsas.objects.core.descriptors.AlignmentDescriptor.
Class AlignmentDescriptor.
AlignmentDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.AlignmentDescriptor
 
AlignmentSequence - class uk.ac.vamsas.objects.core.AlignmentSequence.
Class AlignmentSequence.
AlignmentSequence() - Constructor for class uk.ac.vamsas.objects.core.AlignmentSequence
 
AlignmentSequenceAnnotation - class uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation.
Class AlignmentSequenceAnnotation.
AlignmentSequenceAnnotation() - Constructor for class uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation
 
AlignmentSequenceAnnotationDescriptor - class uk.ac.vamsas.objects.core.descriptors.AlignmentSequenceAnnotationDescriptor.
Class AlignmentSequenceAnnotationDescriptor.
AlignmentSequenceAnnotationDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.AlignmentSequenceAnnotationDescriptor
 
AlignmentSequenceDescriptor - class uk.ac.vamsas.objects.core.descriptors.AlignmentSequenceDescriptor.
Class AlignmentSequenceDescriptor.
AlignmentSequenceDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.AlignmentSequenceDescriptor
 
AnnotationElement - class uk.ac.vamsas.objects.core.AnnotationElement.
Class AnnotationElement.
AnnotationElement() - Constructor for class uk.ac.vamsas.objects.core.AnnotationElement
 
AnnotationElementDescriptor - class uk.ac.vamsas.objects.core.descriptors.AnnotationElementDescriptor.
Class AnnotationElementDescriptor.
AnnotationElementDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.AnnotationElementDescriptor
 
AppData - class uk.ac.vamsas.objects.core.AppData.
Class AppData.
AppData() - Constructor for class uk.ac.vamsas.objects.core.AppData
 
AppDataDescriptor - class uk.ac.vamsas.objects.core.descriptors.AppDataDescriptor.
Class AppDataDescriptor.
AppDataDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.AppDataDescriptor
 
AppDataInputStream - class uk.ac.vamsas.client.AppDataInputStream.
 
AppDataInputStream(InputStream) - Constructor for class uk.ac.vamsas.client.AppDataInputStream
Wrapper for writing to/from AppData Entries in a Vamsas Document.
AppDataOutputStream - class uk.ac.vamsas.client.AppDataOutputStream.
 
AppDataOutputStream(OutputStream) - Constructor for class uk.ac.vamsas.client.AppDataOutputStream
 
AppDataReference - class uk.ac.vamsas.objects.utils.AppDataReference.
Form, accessors and validation for ApplicationData references in vamsas document.
AppDataReference() - Constructor for class uk.ac.vamsas.objects.utils.AppDataReference
 
ApplicationData - class uk.ac.vamsas.objects.core.ApplicationData.
Class ApplicationData.
ApplicationData() - Constructor for class uk.ac.vamsas.objects.core.ApplicationData
 
ApplicationDataDescriptor - class uk.ac.vamsas.objects.core.descriptors.ApplicationDataDescriptor.
Class ApplicationDataDescriptor.
ApplicationDataDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.ApplicationDataDescriptor
 
ArchiveClient - class uk.ac.vamsas.test.simpleclient.ArchiveClient.
 
ArchiveClient(UserHandle, VamsasFile) - Constructor for class uk.ac.vamsas.test.simpleclient.ArchiveClient
 
ArchiveClient(String, String, File) - Constructor for class uk.ac.vamsas.test.simpleclient.ArchiveClient
 
ArchiveClient(String, String, String, String, File) - Constructor for class uk.ac.vamsas.test.simpleclient.ArchiveClient
 
ArchiveReader - class uk.ac.vamsas.test.simpleclient.ArchiveReader.
 
ArchiveReader() - Constructor for class uk.ac.vamsas.test.simpleclient.ArchiveReader
 
ArchiveReports - class uk.ac.vamsas.test.simpleclient.ArchiveReports.
this class contains static methods for writing info to stdout about a vamsas document Methods have a 'cascade' switch to indicate if sub-objects should have info printed on them.
ArchiveReports() - Constructor for class uk.ac.vamsas.test.simpleclient.ArchiveReports
 
ArchiveStreamReader - class uk.ac.vamsas.test.simpleclient.ArchiveStreamReader.
 
ArchiveStreamReader() - Constructor for class uk.ac.vamsas.test.simpleclient.ArchiveStreamReader
 
ArchiveUrn - class uk.ac.vamsas.client.simpleclient.ArchiveUrn.
Vamsas Document URN for files understood by ArchiveReader and written by VamsasArchive.
ArchiveUrn(File) - Constructor for class uk.ac.vamsas.client.simpleclient.ArchiveUrn
 
ArchiveWatcher - class uk.ac.vamsas.test.simpleclient.ArchiveWatcher.
demo of archive watching process - should mimic the clientsfileTest watcher/monitor process.
ArchiveWatcher() - Constructor for class uk.ac.vamsas.test.simpleclient.ArchiveWatcher
 
ArchiveWriter - class uk.ac.vamsas.test.simpleclient.ArchiveWriter.
 
ArchiveWriter() - Constructor for class uk.ac.vamsas.test.simpleclient.ArchiveWriter
 
AscendTree() - Method in class uk.ac.vamsas.objects.utils.trees.SequenceNode
ascends the tree but doesn't stop until a non-dummy node is discovered.
AsiExtraField - class org.apache.tools.zip.AsiExtraField.
Adds Unix file permission and UID/GID fields as well as symbolic link handling.
AsiExtraField() - Constructor for class org.apache.tools.zip.AsiExtraField
Constructor for AsiExtraField.
Attachment - class uk.ac.vamsas.objects.core.Attachment.
Class Attachment.
Attachment() - Constructor for class uk.ac.vamsas.objects.core.Attachment
 
AttachmentDescriptor - class uk.ac.vamsas.objects.core.descriptors.AttachmentDescriptor.
Class AttachmentDescriptor.
AttachmentDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.AttachmentDescriptor
 
accessedDocument - Variable in class uk.ac.vamsas.client.simpleclient.SimpleClientAppdata
has the session's document been accessed to get the AppData entrys?
addAlignment(Alignment) - Method in class uk.ac.vamsas.objects.core.DataSet
 
addAlignment(int, Alignment) - Method in class uk.ac.vamsas.objects.core.DataSet
 
addAlignmentAnnotation(AlignmentAnnotation) - Method in class uk.ac.vamsas.objects.core.Alignment
 
addAlignmentAnnotation(int, AlignmentAnnotation) - Method in class uk.ac.vamsas.objects.core.Alignment
 
addAlignmentSequence(AlignmentSequence) - Method in class uk.ac.vamsas.objects.core.Alignment
 
addAlignmentSequence(int, AlignmentSequence) - Method in class uk.ac.vamsas.objects.core.Alignment
 
addAlignmentSequenceAnnotation(AlignmentSequenceAnnotation) - Method in class uk.ac.vamsas.objects.core.AlignmentSequence
 
addAlignmentSequenceAnnotation(int, AlignmentSequenceAnnotation) - Method in class uk.ac.vamsas.objects.core.AlignmentSequence
 
addAnnotationElement(AnnotationElement) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
 
addAnnotationElement(int, AnnotationElement) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
 
addAppDataEntry(VamsasArchive, VamsasDocument, VamsasArchiveReader, ApplicationData) - Static method in class uk.ac.vamsas.test.simpleclient.ArchiveWriter
safely copies an appData from one archive to another.
addApplicationData(ApplicationData) - Method in class uk.ac.vamsas.objects.core.VamsasDocument
 
addApplicationData(int, ApplicationData) - Method in class uk.ac.vamsas.objects.core.VamsasDocument
 
addAttachment(Attachment) - Method in class uk.ac.vamsas.objects.core.VamsasDocument
 
addAttachment(int, Attachment) - Method in class uk.ac.vamsas.objects.core.VamsasDocument
 
addClient(ClientHandle, Lock) - Method in class uk.ac.vamsas.client.simpleclient.ClientsFile
adds clientHandle me to the clientList under an existing lock extantLock.
addClient(ClientHandle, boolean, Lock) - Method in class uk.ac.vamsas.client.simpleclient.ClientsFile
adds clientHandle me to the clientList under an existing lock.
addClient(ClientHandle) - Method in class uk.ac.vamsas.client.simpleclient.ClientsFile
adds the ClientHandle to the list - if it is not unique, then the ClientHandle object is modified to make it unique in the list.
addClient(ClientHandle, boolean) - Method in class uk.ac.vamsas.client.simpleclient.ClientsFile
Adds a ClientHandle to the ClientList file - optionally disambiguating the ClientHandle (modifes the URN).
addClient(SimpleClient) - Method in class uk.ac.vamsas.client.simpleclient.VamsasSession
add a IClient to the session add the client to the client list file
addCommand(String, int, String) - Method in class uk.ac.vamsas.test.simpleclient.CommandProcessor
 
addDataSet(DataSet) - Method in class uk.ac.vamsas.objects.core.VAMSAS
 
addDataSet(int, DataSet) - Method in class uk.ac.vamsas.objects.core.VAMSAS
 
addDataSetAnnotations(DataSetAnnotations) - Method in class uk.ac.vamsas.objects.core.DataSet
 
addDataSetAnnotations(int, DataSetAnnotations) - Method in class uk.ac.vamsas.objects.core.DataSet
 
addDbRef(DbRef) - Method in class uk.ac.vamsas.objects.core.Sequence
 
addDbRef(int, DbRef) - Method in class uk.ac.vamsas.objects.core.Sequence
 
addDocumentUpdateHandler(PropertyChangeListener) - Method in interface uk.ac.vamsas.client.IClient
register handler for updates for the current session
addDocumentUpdateHandler(PropertyChangeListener) - Method in class uk.ac.vamsas.client.simpleclient.SimpleClient
 
addElement(WatcherElement) - Method in class uk.ac.vamsas.client.simpleclient.VamsasFileWatcherThread
 
addEntry(Entry) - Method in class uk.ac.vamsas.objects.core.Provenance
 
addEntry(int, Entry) - Method in class uk.ac.vamsas.objects.core.Provenance
 
addExtraField(ZipExtraField) - Method in class org.apache.tools.zip.ZipEntry
Adds an extra fields - replacing an already present extra field of the same type.
addGlyph(Glyph) - Method in class uk.ac.vamsas.objects.core.AnnotationElement
 
addGlyph(int, Glyph) - Method in class uk.ac.vamsas.objects.core.AnnotationElement
 
addInput(Input) - Method in class uk.ac.vamsas.objects.core.Entry
 
addInput(int, Input) - Method in class uk.ac.vamsas.objects.core.Entry
 
addInstance(Instance) - Method in class uk.ac.vamsas.objects.core.ApplicationData
 
addInstance(int, Instance) - Method in class uk.ac.vamsas.objects.core.ApplicationData
 
addLink(Link) - Method in class uk.ac.vamsas.objects.core.DbRef
 
addLink(int, Link) - Method in class uk.ac.vamsas.objects.core.DbRef
 
addLink(Link) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
 
addLink(int, Link) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
 
addMap(Map) - Method in class uk.ac.vamsas.objects.core.DbRef
 
addMap(int, Map) - Method in class uk.ac.vamsas.objects.core.DbRef
 
addNewick(Newick) - Method in class uk.ac.vamsas.objects.core.Tree
 
addNewick(int, Newick) - Method in class uk.ac.vamsas.objects.core.Tree
 
addObjRef(Object) - Method in class uk.ac.vamsas.objects.core.Input
 
addObjRef(int, Object) - Method in class uk.ac.vamsas.objects.core.Input
 
addOrReplace(Vector, Property) - Static method in class uk.ac.vamsas.objects.utils.Properties
add newprop to properties, or update the value of an existing property with the same exact name and type.
addParam(Param) - Method in class uk.ac.vamsas.objects.core.Entry
 
addParam(int, Param) - Method in class uk.ac.vamsas.objects.core.Entry
 
addPos(Pos) - Method in class uk.ac.vamsas.objects.core.RangeType
 
addPos(int, Pos) - Method in class uk.ac.vamsas.objects.core.RangeType
 
addProperty(Property) - Method in class uk.ac.vamsas.objects.core.Alignment
 
addProperty(int, Property) - Method in class uk.ac.vamsas.objects.core.Alignment
 
addProperty(Property) - Method in class uk.ac.vamsas.objects.core.DbRef
 
addProperty(int, Property) - Method in class uk.ac.vamsas.objects.core.DbRef
 
addProperty(Property) - Method in class uk.ac.vamsas.objects.core.Entry
 
addProperty(int, Property) - Method in class uk.ac.vamsas.objects.core.Entry
 
addProperty(Property) - Method in class uk.ac.vamsas.objects.core.NodeType
 
addProperty(int, Property) - Method in class uk.ac.vamsas.objects.core.NodeType
 
addProperty(Property) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
 
addProperty(int, Property) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
 
addProperty(Property) - Method in class uk.ac.vamsas.objects.core.SequenceType
 
addProperty(int, Property) - Method in class uk.ac.vamsas.objects.core.SequenceType
 
addProperty(Property) - Method in class uk.ac.vamsas.objects.core.Tree
 
addProperty(int, Property) - Method in class uk.ac.vamsas.objects.core.Tree
 
addRefs(Object) - Method in class uk.ac.vamsas.objects.core.ReferenceType
 
addRefs(int, Object) - Method in class uk.ac.vamsas.objects.core.ReferenceType
 
addScore(Score) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
 
addScore(int, Score) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
 
addSeg(Seg) - Method in class uk.ac.vamsas.objects.core.RangeType
 
addSeg(int, Seg) - Method in class uk.ac.vamsas.objects.core.RangeType
 
addSeqRef(Object) - Method in class uk.ac.vamsas.objects.core.DataSetAnnotations
 
addSeqRef(int, Object) - Method in class uk.ac.vamsas.objects.core.DataSetAnnotations
 
addSeqrefs(Object) - Method in class uk.ac.vamsas.objects.core.AlignmentAnnotation
 
addSeqrefs(int, Object) - Method in class uk.ac.vamsas.objects.core.AlignmentAnnotation
 
addSequence(Sequence) - Method in class uk.ac.vamsas.objects.core.DataSet
 
addSequence(int, Sequence) - Method in class uk.ac.vamsas.objects.core.DataSet
 
addSequenceMapping(SequenceMapping) - Method in class uk.ac.vamsas.objects.core.DataSet
 
addSequenceMapping(int, SequenceMapping) - Method in class uk.ac.vamsas.objects.core.DataSet
 
addSession(SessionHandle, Lock) - Method in class uk.ac.vamsas.client.simpleclient.SessionsFile
adds SessionHandle me to the sessionList under an existing lock extantLock.
addSession(SessionHandle, boolean, Lock) - Method in class uk.ac.vamsas.client.simpleclient.SessionsFile
adds SessionsHandle me to the sessionsList under an existing lock.
addSession(SessionHandle, boolean) - Method in class uk.ac.vamsas.client.simpleclient.SessionsFile
Adds a SessionHandle to the SessionList file - optionally disambiguating the SessionHandle (modifes the URN).
addSession(SessionHandle) - Method in class uk.ac.vamsas.client.simpleclient.SimpleSessionManager
adds SessionHandle me to the sessionList
addStoreDocumentRequest(ClientHandle, UserHandle) - Method in class uk.ac.vamsas.client.simpleclient.VamsasSession
write to the StoreWatcher file to indicate that a storeDocumentRequest has been made.
addTree(Tree) - Method in class uk.ac.vamsas.objects.core.Alignment
 
addTree(int, Tree) - Method in class uk.ac.vamsas.objects.core.Alignment
 
addTree(Tree) - Method in class uk.ac.vamsas.objects.core.DataSet
 
addTree(int, Tree) - Method in class uk.ac.vamsas.objects.core.DataSet
 
addTree(Tree) - Method in class uk.ac.vamsas.objects.core.VAMSAS
 
addTree(int, Tree) - Method in class uk.ac.vamsas.objects.core.VAMSAS
 
addTreeId(Object) - Method in class uk.ac.vamsas.objects.core.Treenode
 
addTreeId(int, Object) - Method in class uk.ac.vamsas.objects.core.Treenode
 
addTreenode(Treenode) - Method in class uk.ac.vamsas.objects.core.Tree
 
addTreenode(int, Treenode) - Method in class uk.ac.vamsas.objects.core.Tree
 
addUser(User) - Method in class uk.ac.vamsas.objects.core.ApplicationData
 
addUser(int, User) - Method in class uk.ac.vamsas.objects.core.ApplicationData
 
addVAMSAS(VAMSAS) - Method in class uk.ac.vamsas.objects.core.VamsasDocument
 
addVAMSAS(int, VAMSAS) - Method in class uk.ac.vamsas.objects.core.VamsasDocument
 
addValue(float) - Method in class uk.ac.vamsas.objects.core.AnnotationElement
 
addValue(int, float) - Method in class uk.ac.vamsas.objects.core.AnnotationElement
 
addVamsasRoot(VAMSAS) - Method in interface uk.ac.vamsas.client.IClientDocument
Adds a new VAMSAS root entry TODO: decide on same InvalidVamsasObject exceptions.
addVamsasRoot(VAMSAS) - Method in class uk.ac.vamsas.client.simpleclient.ClientDocument
 
addVamsasRoot(VAMSAS) - Method in class uk.ac.vamsas.test.simpleclient.ClientDoc
 
addVorbaEventHandler(String, PropertyChangeListener) - Method in interface uk.ac.vamsas.client.IClient
Add a listener to a particular event chain.
addVorbaEventHandler(String, PropertyChangeListener) - Method in class uk.ac.vamsas.client.simpleclient.SimpleClient
 
addVref(Vref) - Method in class uk.ac.vamsas.objects.core.NodeType
 
addVref(int, Vref) - Method in class uk.ac.vamsas.objects.core.NodeType
 
addVxref(Vxref) - Method in class uk.ac.vamsas.objects.core.Sequence
 
addVxref(int, Vxref) - Method in class uk.ac.vamsas.objects.core.Sequence
 
adjustToLong(int) - Static method in class org.apache.tools.zip.ZipOutputStream
Assumes a negative integer really is a positive integer that has wrapped around and re-creates the original value.
alignmentReport(Alignment[], boolean, PrintStream) - Static method in class uk.ac.vamsas.test.simpleclient.ArchiveReports
 
appDataEntryReport(AppData, VamsasArchiveReader, boolean, PrintStream) - Static method in class uk.ac.vamsas.test.simpleclient.ArchiveReports
 
appDataReport(ApplicationData, VamsasArchiveReader, boolean, PrintStream) - Static method in class uk.ac.vamsas.test.simpleclient.ArchiveReports
 
appsGlobal - Variable in class uk.ac.vamsas.client.simpleclient.SimpleClientAppdata
set by extractAppData
asFile() - Method in class uk.ac.vamsas.client.simpleclient.ArchiveUrn
TODO: LATER: think about this again.
asFile() - Method in class uk.ac.vamsas.client.simpleclient.SessionUrn
TODO: LATER: think about this again.
ascendLeft() - Method in class uk.ac.vamsas.objects.utils.trees.BinaryNode
Traverses up through the tree until a node with a free leftchild is discovered.
ascendRight() - Method in class uk.ac.vamsas.objects.utils.trees.BinaryNode
Traverses up through the tree until a node with a free rightchild is discovered.
atof(String) - Static method in class uk.ac.vamsas.objects.utils.Format
Converts a string of digits to an double
atoi(String) - Static method in class uk.ac.vamsas.objects.utils.Format
Converts a string of digits (decimal, octal or hex) to an integer
atol(String) - Static method in class uk.ac.vamsas.objects.utils.Format
Converts a string of digits (decimal, octal or hex) to a long integer
attachTreeMap(Treenode[]) - Method in class uk.ac.vamsas.objects.utils.trees.NewickFile
re-decorate the newick node representation with the VorbaId of an object mapped by its corresponding TreeNode.
attributesProcessed(Object) - Method in class uk.ac.vamsas.client.VorbaXmlBinder
 
available() - Method in class uk.ac.vamsas.client.AppDataInputStream
Will return zero if stream has been closed.

B

BETA_VERSION - Static variable in class uk.ac.vamsas.objects.utils.document.VersionEntries
 
BOOLEANTYPE - Static variable in class uk.ac.vamsas.objects.utils.Properties
 
BinaryNode - class uk.ac.vamsas.objects.utils.trees.BinaryNode.
 
BinaryNode() - Constructor for class uk.ac.vamsas.objects.utils.trees.BinaryNode
Creates a new BinaryNode object.
BinaryNode(Vobject, BinaryNode, String) - Constructor for class uk.ac.vamsas.objects.utils.trees.BinaryNode
Creates a new BinaryNode object.
backupFile() - Method in class uk.ac.vamsas.client.simpleclient.VamsasArchive
called by app to get name of backup if it was made.
backupSessionFile() - Method in class uk.ac.vamsas.client.simpleclient.SessionFile
Makes a backup of the sessionFile.
backupSessionFile(Lock, String, String, File) - Method in class uk.ac.vamsas.client.simpleclient.SessionFile
 
bindAppsObjectToVamsasObject(Object, Vobject) - Method in interface uk.ac.vamsas.objects.IVorbaBinding
Record a mapping between a vamsas document object and an application's internal object.
bindjvvobj(Object, Vobject) - Method in class uk.ac.vamsas.test.simpleclient.simpleapp.VamsasDatastore
 
bootstrap - Variable in class uk.ac.vamsas.objects.utils.trees.BinaryNode
bootstrap is non-negative integer
buf - Variable in class org.apache.tools.zip.ZipOutputStream
This buffer servers as a Deflater.

C

CFH_SIG - Static variable in class org.apache.tools.zip.ZipOutputStream
central file header signature
CLIENT_CREATION - Static variable in class uk.ac.vamsas.client.Events
Generated when a new vamsas client is attached to a session (Handle is passed) Note: the newly created client does not receive the event.
CLIENT_FINALIZATION - Static variable in class uk.ac.vamsas.client.Events
Generated when a vamsas client leaves a session (Handle is passed to all others).
CLIENT_LIST - Static variable in class uk.ac.vamsas.client.simpleclient.VamsasSession
 
CLOSEANDSAVE_FILE - Static variable in class uk.ac.vamsas.client.simpleclient.VamsasSession
indicator file for informing other processes that they should finalise their vamsas datasets for storing into a vamsas archive.
ClientDoc - class uk.ac.vamsas.test.simpleclient.ClientDoc.
 
ClientDoc(VamsasDocument, VamsasArchive, VamsasArchiveReader, String, String, Hashtable) - Constructor for class uk.ac.vamsas.test.simpleclient.ClientDoc
 
ClientDocument - class uk.ac.vamsas.client.ClientDocument.
skeleton abstract class to allow client implementations access to vamsas.client.Vobject registry mechanism.
ClientDocument(Hashtable, IVorbaIdFactory) - Constructor for class uk.ac.vamsas.client.ClientDocument
 
ClientDocument - class uk.ac.vamsas.client.simpleclient.ClientDocument.
Maintains a collection of vamsas objects, appdatas and states, and provides api for a SimpleClient's client.
ClientDocument(VamsasDocument, VamsasArchive, IdFactory, SimpleClient) - Constructor for class uk.ac.vamsas.client.simpleclient.ClientDocument
prepare Application-side dataset from the vamsas Document iohandler
ClientHandle - class uk.ac.vamsas.client.ClientHandle.
Uniquely describes a vamsas client application.
ClientHandle(String, String) - Constructor for class uk.ac.vamsas.client.ClientHandle
 
ClientSessionFileWatcherElement - class uk.ac.vamsas.client.simpleclient.ClientSessionFileWatcherElement.
 
ClientSessionFileWatcherElement(SessionFile, WatcherCallBack) - Constructor for class uk.ac.vamsas.client.simpleclient.ClientSessionFileWatcherElement
 
ClientSessionFileWatcherElement(SessionFile, WatcherCallBack, boolean) - Constructor for class uk.ac.vamsas.client.simpleclient.ClientSessionFileWatcherElement
 
ClientsFile - class uk.ac.vamsas.client.simpleclient.ClientsFile.
Handler for the clientsFile within a vamsas session thread.
ClientsFile(File) - Constructor for class uk.ac.vamsas.client.simpleclient.ClientsFile
 
ClientsFileTest - class uk.ac.vamsas.test.simpleclient.ClientsFileTest.
 
ClientsFileTest() - Constructor for class uk.ac.vamsas.test.simpleclient.ClientsFileTest
 
CommandProcessor - class uk.ac.vamsas.test.simpleclient.CommandProcessor.
 
CommandProcessor() - Constructor for class uk.ac.vamsas.test.simpleclient.CommandProcessor
 
Common - class uk.ac.vamsas.objects.core.Common.
Class Common.
Common() - Constructor for class uk.ac.vamsas.objects.core.Common
 
CommonDescriptor - class uk.ac.vamsas.objects.core.descriptors.CommonDescriptor.
Class CommonDescriptor.
CommonDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.CommonDescriptor
 
Core - class uk.ac.vamsas.test.objects.Core.
 
Core() - Constructor for class uk.ac.vamsas.test.objects.Core
 
CustomMessage - class uk.ac.vamsas.client.picking.CustomMessage.
Defines a custom message that applications can use to send message types that haven't been predefined in the API.
CustomMessage(String) - Constructor for class uk.ac.vamsas.client.picking.CustomMessage
Constructs a new custom message.
callHandler(Lock) - Method in class uk.ac.vamsas.client.simpleclient.WatcherElement
Calls the current eventhandler
callHandlers(IClientDocument) - Method in class uk.ac.vamsas.objects.DocumentUpdaterEngine
call the necessary update handlers at each point on the VamsasDocument OM TODO: later: Make this more elegant (use reflection and factor to single update(Object) method) ? - we take the plodding, explicit approach rather than a funky generalised one here
cancelArchive() - Method in class uk.ac.vamsas.client.simpleclient.VamsasArchive
Stops any current write to archive, and reverts to the backup if it exists.
cdocument - Variable in class uk.ac.vamsas.client.simpleclient.SimpleClient
 
checkFlag() - Method in class uk.ac.vamsas.client.simpleclient.SessionFlagFile
 
clearElements() - Method in class uk.ac.vamsas.client.simpleclient.VamsasFileWatcherThread
 
clearFlag() - Method in class uk.ac.vamsas.client.simpleclient.SessionFlagFile
 
clearList() - Method in class uk.ac.vamsas.client.simpleclient.ClientsFile
 
clearList() - Method in class uk.ac.vamsas.client.simpleclient.SessionsFile
 
clearUnsavedFlag() - Method in class uk.ac.vamsas.client.simpleclient.VamsasSession
called to clear update flag after a successful offline storage event
client - Variable in class uk.ac.vamsas.client.simpleclient.SimpleClient
 
clientFileDirectory - Variable in class uk.ac.vamsas.client.simpleclient.VamsasSession
 
clientfile - Variable in class uk.ac.vamsas.client.simpleclient.EventGeneratorThread
Watcher element for list of all the clientHandles for the session
clone() - Method in class org.apache.tools.zip.ZipEntry
Overwrite clone.
close() - Method in class org.apache.tools.zip.ZipFile
Closes the archive.
close() - Method in class org.apache.tools.zip.ZipOutputStream
Closes this output stream and releases any system resources associated with the stream.
close() - Method in class uk.ac.vamsas.client.AppDataInputStream
 
close() - Method in class uk.ac.vamsas.client.AppDataOutputStream
Sets an internal flag preventing further write operations to the AppData output stream and flushes any pending writes.
close() - Method in class uk.ac.vamsas.client.simpleclient.LockedFileOutputStream
closes - actually just flushes the stream instead.
close() - Method in class uk.ac.vamsas.client.simpleclient.VamsasArchiveReader
silently close the jar file.
closeArchive() - Method in class uk.ac.vamsas.client.simpleclient.VamsasArchive
Tidies up and closes archive, removing any backups that were created.
closeDoc() - Method in class uk.ac.vamsas.test.simpleclient.ClientDoc
tell vamsas client to close the document and reset the object.
closeEntry() - Method in class org.apache.tools.zip.ZipOutputStream
Writes all necessary data for this entry.
closeForWriting() - Method in class uk.ac.vamsas.client.simpleclient.SimpleClientAppdata
flush and close outstanding output streams.
closeQuietly(ZipFile) - Static method in class org.apache.tools.zip.ZipFile
close a zipfile quietly; throw no io fault, do nothing on a null parameter
compare(String, String) - Static method in class uk.ac.vamsas.objects.utils.document.VersionEntries
returns 0 if levels are equivalent, 1 if higher is valid and higher, 2 if lower is valid and higher -1 if both levels are invalid
complainArgs(int, int, Vector) - Method in class uk.ac.vamsas.test.simpleclient.CommandProcessor
Integer argl, Integer argpos, String cmd, Integer argneed, String msg in vector
complete(DataSet) - Static method in class uk.ac.vamsas.test.objects.Core
 
countHandlersFor(String) - Method in class uk.ac.vamsas.client.simpleclient.EventGeneratorThread
count handlers for a particular vamsas event
createActiveClientFile() - Method in class uk.ac.vamsas.client.simpleclient.SimpleClient
 
createExtraField(ZipShort) - Static method in class org.apache.tools.zip.ExtraFieldUtils
Create an instance of the approriate ExtraField, falls back to UnrecognizedExtraField.
cycleCountSinceModif - Variable in class uk.ac.vamsas.client.simpleclient.ClientSessionFileWatcherElement
count of cycles since last modification on the file

D

DD_SIG - Static variable in class org.apache.tools.zip.ZipOutputStream
data descriptor signature
DEFAULT - Static variable in class uk.ac.vamsas.objects.utils.GlyphDictionary
default glyph type attribute indicates a UTF8 character
DEFAULT_COMPRESSION - Static variable in class org.apache.tools.zip.ZipOutputStream
Default compression level for deflated entries.
DEFAULT_DIR_PERM - Static variable in interface org.apache.tools.zip.UnixStat
Default permissions for directories.
DEFAULT_FILE_PERM - Static variable in interface org.apache.tools.zip.UnixStat
Default permissions for plain files.
DEFAULT_LINK_PERM - Static variable in interface org.apache.tools.zip.UnixStat
Default permissions for symbolic links.
DEFLATED - Static variable in class org.apache.tools.zip.ZipOutputStream
Compression method for deflated entries.
DIR_FLAG - Static variable in interface org.apache.tools.zip.UnixStat
Indicates directories.
DOCUMENT_CREATE - Static variable in class uk.ac.vamsas.client.Events
Generated when a new vamsas document is created (perhaps from some existing Vamsas data) so an application may do its own data space initialization.
DOCUMENT_FINALIZEAPPDATA - Static variable in class uk.ac.vamsas.client.Events
Generated for all clients when any client calls IClient.storeDocument() to allow them to store any updates before an offline copy of the session is created.
DOCUMENT_REQUESTTOCLOSE - Static variable in class uk.ac.vamsas.client.Events
Generated by Vorba stub for the sole remaining client instance in a session, when it makes a call to finalizeClient().
DOCUMENT_UPDATE - Static variable in class uk.ac.vamsas.client.Events
Generated when a client has finished updating the document.
DOCUMENT_VERSION - Static variable in class uk.ac.vamsas.client.simpleclient.VamsasArchiveReader
the vamsas document version(s) handled by this Reader
DataSet - class uk.ac.vamsas.objects.core.DataSet.
Class DataSet.
DataSet() - Constructor for class uk.ac.vamsas.objects.core.DataSet
 
DataSetAnnotations - class uk.ac.vamsas.objects.core.DataSetAnnotations.
Class DataSetAnnotations.
DataSetAnnotations() - Constructor for class uk.ac.vamsas.objects.core.DataSetAnnotations
 
DataSetAnnotationsDescriptor - class uk.ac.vamsas.objects.core.descriptors.DataSetAnnotationsDescriptor.
Class DataSetAnnotationsDescriptor.
DataSetAnnotationsDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.DataSetAnnotationsDescriptor
 
DataSetDescriptor - class uk.ac.vamsas.objects.core.descriptors.DataSetDescriptor.
Class DataSetDescriptor.
DataSetDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.DataSetDescriptor
 
DbRef - class uk.ac.vamsas.objects.core.DbRef.
Store a list of database references for this sequence record - with optional mapping from database sequence to the given sequence record
DbRef() - Constructor for class uk.ac.vamsas.objects.core.DbRef
 
DbRefDescriptor - class uk.ac.vamsas.objects.core.descriptors.DbRefDescriptor.
Class DbRefDescriptor.
DbRefDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.DbRefDescriptor
 
DocumentStuff - class uk.ac.vamsas.objects.utils.DocumentStuff.
various vamsas-client independent helpers for creating and manipulating the vamsasDocument Vobject
DocumentStuff() - Constructor for class uk.ac.vamsas.objects.utils.DocumentStuff
 
DocumentUpdaterEngine - class uk.ac.vamsas.objects.DocumentUpdaterEngine.
Implements a depth first traversal over the document tree calling update handlers based on the Vobject.isUpdated() and Vobject.isNewInDocument() state at each backtrack.
DocumentUpdaterEngine(IDocumentUpdater) - Constructor for class uk.ac.vamsas.objects.DocumentUpdaterEngine
initialise the engine with an implementation of the interface.
datasetReport(DataSet, boolean, PrintStream) - Static method in class uk.ac.vamsas.test.simpleclient.ArchiveReports
 
def - Variable in class org.apache.tools.zip.ZipOutputStream
This Deflater object is used for output.
deflate() - Method in class org.apache.tools.zip.ZipOutputStream
Writes next block of compressed data to the output stream.
deleteAfter() - Method in class uk.ac.vamsas.objects.core.AnnotationElement
 
deleteAligned() - Method in class uk.ac.vamsas.objects.core.Alignment
 
deleteCompressed() - Method in class uk.ac.vamsas.objects.core.Attachment
 
deleteContent() - Method in class uk.ac.vamsas.objects.core.Score
 
deleteEnd() - Method in class uk.ac.vamsas.objects.core.MapList
 
deleteEnd() - Method in class uk.ac.vamsas.objects.core.Seg
 
deleteEnd() - Method in class uk.ac.vamsas.objects.core.SequenceType
 
deleteFrom() - Method in class uk.ac.vamsas.objects.core.MapList
 
deleteGraph() - Method in class uk.ac.vamsas.objects.core.AlignmentAnnotation
 
deleteGraph() - Method in class uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation
 
deleteI() - Method in class uk.ac.vamsas.objects.core.Pos
 
deleteInclusive() - Method in class uk.ac.vamsas.objects.core.Seg
 
deletePosition() - Method in class uk.ac.vamsas.objects.core.AnnotationElement
 
deleteSeqAEnd() - Method in class uk.ac.vamsas.objects.core.Range
 
deleteSeqAStart() - Method in class uk.ac.vamsas.objects.core.Range
 
deleteSeqBEnd() - Method in class uk.ac.vamsas.objects.core.Range
 
deleteSeqBStart() - Method in class uk.ac.vamsas.objects.core.Range
 
deleteStart() - Method in class uk.ac.vamsas.objects.core.MapList
 
deleteStart() - Method in class uk.ac.vamsas.objects.core.Seg
 
deleteStart() - Method in class uk.ac.vamsas.objects.core.SequenceType
 
deleteTo() - Method in class uk.ac.vamsas.objects.core.MapList
 
deleteUnit() - Method in class uk.ac.vamsas.objects.core.MapRangeType
 
detach() - Method in class uk.ac.vamsas.objects.utils.trees.BinaryNode
Detaches the node from the binary tree, along with all its child nodes.
deuniquify(Hashtable, SequenceType[]) - Static method in class uk.ac.vamsas.objects.utils.SeqSet
 
diffState(long[], long[]) - Method in class uk.ac.vamsas.client.simpleclient.FileWatcher
safely compare an externally recorded state with the current state for significant modifications.
disableCycleTimeOut() - Method in class uk.ac.vamsas.client.simpleclient.ClientSessionFileWatcherElement
Disables the checking on the count of cycles
disableDocumentWatch() - Method in class uk.ac.vamsas.client.simpleclient.EventGeneratorThread
 
disableGui(boolean) - Method in class uk.ac.vamsas.test.simpleclient.simpleapp.VamsasClient
disable (if b is true) or enable (if b is true) the VamsasClient's vamsas session gui bits whilst a document change is being updated to the app.
dist - Variable in class uk.ac.vamsas.objects.utils.trees.SequenceNode
DOCUMENT ME!!
doHash() - Method in class uk.ac.vamsas.client.Vobject
calculate a hash for the Vobject with all housekeeping fields at standard values.
doUpdate(ClientDoc) - Method in class uk.ac.vamsas.test.simpleclient.ArchiveClient
trust client to not do anything stupid to the document roots which will now be written to the archive.
doWatch() - Method in class uk.ac.vamsas.client.simpleclient.ClientSessionFileWatcherElement
 
doWatch() - Method in class uk.ac.vamsas.client.simpleclient.WatcherElement
Originally from the uk.ac.vamsas.test.simpleclient.ArchiveClient method
doc - Variable in class uk.ac.vamsas.test.simpleclient.ClientDoc
 
documentChanged(Lock) - Method in class uk.ac.vamsas.client.simpleclient.EventGeneratorThread
 
dummy - Variable in class uk.ac.vamsas.objects.utils.trees.SequenceNode
DOCUMENT ME!!

E

EOCD_SIG - Static variable in class org.apache.tools.zip.ZipOutputStream
end of central dir signature
EmptyDocumentUpdater - class uk.ac.vamsas.objects.EmptyDocumentUpdater.
 
EmptyDocumentUpdater() - Constructor for class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
Entry - class uk.ac.vamsas.objects.core.Entry.
Class Entry.
Entry() - Constructor for class uk.ac.vamsas.objects.core.Entry
 
EntryDescriptor - class uk.ac.vamsas.objects.core.descriptors.EntryDescriptor.
Class EntryDescriptor.
EntryDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.EntryDescriptor
 
EventGeneratorThread - class uk.ac.vamsas.client.simpleclient.EventGeneratorThread.
monitors watcher objects and generates events.
EventList - Static variable in class uk.ac.vamsas.client.Events
 
Events - class uk.ac.vamsas.client.Events.
Enumerates the event types generated during the lifecycle of a Vamsas session.
Events() - Constructor for class uk.ac.vamsas.client.Events
 
ExampleApplication - class uk.ac.vamsas.test.ExampleApplication.
Toy vamsas command line client application demonstrating the API.
ExampleApplication() - Constructor for class uk.ac.vamsas.test.ExampleApplication
 
ExtraFieldUtils - class org.apache.tools.zip.ExtraFieldUtils.
ZipExtraField related methods
ExtraFieldUtils() - Constructor for class org.apache.tools.zip.ExtraFieldUtils
 
element() - Method in class uk.ac.vamsas.objects.utils.trees.BinaryNode
DOCUMENT ME!
enableDocumentWatch() - Method in class uk.ac.vamsas.client.simpleclient.EventGeneratorThread
 
enableWatch() - Method in class uk.ac.vamsas.client.simpleclient.WatcherElement
must be called by implementations of enablewatch
endWatch() - Method in class uk.ac.vamsas.client.simpleclient.SessionFileWatcherElement
 
endWatch() - Method in class uk.ac.vamsas.client.simpleclient.SessionFlagWatcherElement
 
endWatch() - Method in class uk.ac.vamsas.client.simpleclient.VamsasFileWatcherElement
 
endWatch() - Method in class uk.ac.vamsas.client.simpleclient.WatcherElement
called by haltWatch before clearing the FileWatcher reference.
end_session() - Method in class uk.ac.vamsas.test.simpleclient.simpleapp.VamsasClient
 
enumerateAlignment() - Method in class uk.ac.vamsas.objects.core.DataSet
Method enumerateAlignment.
enumerateAlignmentAnnotation() - Method in class uk.ac.vamsas.objects.core.Alignment
Method enumerateAlignmentAnnotation.
enumerateAlignmentSequence() - Method in class uk.ac.vamsas.objects.core.Alignment
Method enumerateAlignmentSequence.
enumerateAlignmentSequenceAnnotation() - Method in class uk.ac.vamsas.objects.core.AlignmentSequence
Method enumerateAlignmentSequenceAnnotation.
enumerateAnnotationElement() - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Method enumerateAnnotationElement.
enumerateApplicationData() - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Method enumerateApplicationData.
enumerateAttachment() - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Method enumerateAttachment.
enumerateDataSet() - Method in class uk.ac.vamsas.objects.core.VAMSAS
Method enumerateDataSet.
enumerateDataSetAnnotations() - Method in class uk.ac.vamsas.objects.core.DataSet
Method enumerateDataSetAnnotations.
enumerateDbRef() - Method in class uk.ac.vamsas.objects.core.Sequence
Method enumerateDbRef.
enumerateEntry() - Method in class uk.ac.vamsas.objects.core.Provenance
Method enumerateEntry.
enumerateGlyph() - Method in class uk.ac.vamsas.objects.core.AnnotationElement
Method enumerateGlyph.
enumerateInput() - Method in class uk.ac.vamsas.objects.core.Entry
Method enumerateInput.
enumerateInstance() - Method in class uk.ac.vamsas.objects.core.ApplicationData
Method enumerateInstance.
enumerateLink() - Method in class uk.ac.vamsas.objects.core.DbRef
Method enumerateLink.
enumerateLink() - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Method enumerateLink.
enumerateMap() - Method in class uk.ac.vamsas.objects.core.DbRef
Method enumerateMap.
enumerateNewick() - Method in class uk.ac.vamsas.objects.core.Tree
Method enumerateNewick.
enumerateObjRef() - Method in class uk.ac.vamsas.objects.core.Input
Method enumerateObjRef.
enumerateParam() - Method in class uk.ac.vamsas.objects.core.Entry
Method enumerateParam.
enumeratePos() - Method in class uk.ac.vamsas.objects.core.RangeType
Method enumeratePos.
enumerateProperty() - Method in class uk.ac.vamsas.objects.core.Alignment
Method enumerateProperty.
enumerateProperty() - Method in class uk.ac.vamsas.objects.core.DbRef
Method enumerateProperty.
enumerateProperty() - Method in class uk.ac.vamsas.objects.core.Entry
Method enumerateProperty.
enumerateProperty() - Method in class uk.ac.vamsas.objects.core.NodeType
Method enumerateProperty.
enumerateProperty() - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Method enumerateProperty.
enumerateProperty() - Method in class uk.ac.vamsas.objects.core.SequenceType
Method enumerateProperty.
enumerateProperty() - Method in class uk.ac.vamsas.objects.core.Tree
Method enumerateProperty.
enumerateRefs() - Method in class uk.ac.vamsas.objects.core.ReferenceType
Method enumerateRefs.
enumerateScore() - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Method enumerateScore.
enumerateSeg() - Method in class uk.ac.vamsas.objects.core.RangeType
Method enumerateSeg.
enumerateSeqRef() - Method in class uk.ac.vamsas.objects.core.DataSetAnnotations
Method enumerateSeqRef.
enumerateSeqrefs() - Method in class uk.ac.vamsas.objects.core.AlignmentAnnotation
Method enumerateSeqrefs.
enumerateSequence() - Method in class uk.ac.vamsas.objects.core.DataSet
Method enumerateSequence.
enumerateSequenceMapping() - Method in class uk.ac.vamsas.objects.core.DataSet
Method enumerateSequenceMapping.
enumerateTree() - Method in class uk.ac.vamsas.objects.core.Alignment
Method enumerateTree.
enumerateTree() - Method in class uk.ac.vamsas.objects.core.DataSet
Method enumerateTree.
enumerateTree() - Method in class uk.ac.vamsas.objects.core.VAMSAS
Method enumerateTree.
enumerateTreeId() - Method in class uk.ac.vamsas.objects.core.Treenode
Method enumerateTreeId.
enumerateTreenode() - Method in class uk.ac.vamsas.objects.core.Tree
Method enumerateTreenode.
enumerateUser() - Method in class uk.ac.vamsas.objects.core.ApplicationData
Method enumerateUser.
enumerateVAMSAS() - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Method enumerateVAMSAS.
enumerateValue() - Method in class uk.ac.vamsas.objects.core.AnnotationElement
Method enumerateValue.
enumerateVref() - Method in class uk.ac.vamsas.objects.core.NodeType
Method enumerateVref.
enumerateVxref() - Method in class uk.ac.vamsas.objects.core.Sequence
Method enumerateVxref.
equals(Object) - Method in class org.apache.tools.zip.ZipEntry
The equality method.
equals(Object) - Method in class org.apache.tools.zip.ZipLong
Override to make two instances with same value equal.
equals(Object) - Method in class org.apache.tools.zip.ZipShort
Override to make two instances with same value equal.
equals(Object) - Method in class uk.ac.vamsas.client.ClientHandle
 
equals(ClientHandle) - Method in class uk.ac.vamsas.client.ClientHandle
 
equals(Object) - Method in class uk.ac.vamsas.client.SessionHandle
 
equals(SessionHandle) - Method in class uk.ac.vamsas.client.SessionHandle
 
equals(Object) - Method in class uk.ac.vamsas.client.VorbaId
 
equals(Message) - Method in class uk.ac.vamsas.client.picking.Message
compare the on-wire message content of the given message to this.
equals(Object) - Method in class uk.ac.vamsas.objects.core.Alignment
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.AlignmentAnnotation
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.AlignmentSequence
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.AnnotationElement
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.AppData
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.ApplicationData
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.Attachment
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.Common
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.DataSet
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.DataSetAnnotations
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.DbRef
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.Entry
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.Glyph
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.Input
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.Instance
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.Link
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.Local
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.LockFile
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.Map
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.MapList
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.MapRangeType
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.MapType
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.Mapped
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.Mapping
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.Newick
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.NodeType
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.Param
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.Pos
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.Property
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.Provenance
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.Range
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.RangeType
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.ReferenceType
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.Score
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.Seg
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.Sequence
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.SequenceMapping
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.SequenceType
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.Tree
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.Treenode
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.User
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.VAMSAS
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.Vref
Overrides the java.lang.Object.equals method.
equals(Object) - Method in class uk.ac.vamsas.objects.core.Vxref
Overrides the java.lang.Object.equals method.
equals(User, UserHandle) - Static method in class uk.ac.vamsas.objects.utils.AppDataReference
 
equals(ApplicationData, ClientHandle) - Static method in class uk.ac.vamsas.objects.utils.AppDataReference
returns true if Name matches in c and p, and Urn's match (or c.getUrn()==null) and Version's match (or c.getVersion()==null)
equals(MapList) - Method in class uk.ac.vamsas.objects.utils.MapList
 
equals(Mapping) - Method in class uk.ac.vamsas.objects.utils.Mapping
Equals that compares both the to references and MapList mappings.
eraseExistence() - Method in class uk.ac.vamsas.client.simpleclient.SessionFile
remove all trace of the sessionFile file
evgen - Variable in class uk.ac.vamsas.client.simpleclient.SimpleClient
 
extanthashv - Variable in class uk.ac.vamsas.client.VorbaIdFactory
hash of VorbaIds to persisted hash values
extantids - Variable in class uk.ac.vamsas.client.VorbaIdFactory
hash of VorbaIds to Vobject.
extantobjects - Variable in class uk.ac.vamsas.client.simpleclient.SimpleClient
object hash table that persists in each client holding vorbaIds and hash values after a document write

F

FILE_FLAG - Static variable in interface org.apache.tools.zip.UnixStat
Indicates plain files.
FLOATTYPE - Static variable in class uk.ac.vamsas.objects.utils.Properties
 
FileLock - class uk.ac.vamsas.client.simpleclient.FileLock.
File based Locking mechanism to get around some bizarre limitations of JarEntry seeking.
FileLock(File, boolean) - Constructor for class uk.ac.vamsas.client.simpleclient.FileLock
 
FileWatcher - class uk.ac.vamsas.client.simpleclient.FileWatcher.
Watches a particular file for its creation, deletion, or modification.
FileWatcher(File) - Constructor for class uk.ac.vamsas.client.simpleclient.FileWatcher
Make a watcher for a particular file.
Format - class uk.ac.vamsas.objects.utils.Format.
 
Format(String) - Constructor for class uk.ac.vamsas.objects.utils.Format
Formats the number following printf conventions.
fieldAdded(String, Object, Object) - Method in class uk.ac.vamsas.client.VorbaXmlBinder
 
fileLock - Variable in class uk.ac.vamsas.client.simpleclient.SessionFile
 
finalize() - Method in class uk.ac.vamsas.client.Vobject
 
finalize() - Method in class uk.ac.vamsas.client.simpleclient.ClientDocument
 
finalize() - Method in class uk.ac.vamsas.client.simpleclient.FileLock
 
finalize() - Method in class uk.ac.vamsas.client.simpleclient.Lock
 
finalize() - Method in class uk.ac.vamsas.client.simpleclient.NativeLock
 
finalize() - Method in class uk.ac.vamsas.client.simpleclient.SimpleClientAppdata
 
finalize() - Method in class uk.ac.vamsas.test.simpleclient.ClientDoc
 
finalizeClient() - Method in interface uk.ac.vamsas.client.IClient
Method called by client application on exit.
finalizeClient() - Method in class uk.ac.vamsas.client.simpleclient.SimpleClient
 
findLeaves(SequenceNode, Vector) - Method in class uk.ac.vamsas.objects.utils.trees.NewickFile
Search for leaf nodes.
finish() - Method in class org.apache.tools.zip.ZipOutputStream
Finishs writing the contents and closes this as well as the underlying stream.
flagFile - Variable in class uk.ac.vamsas.client.simpleclient.SessionFlagFile
 
flush() - Method in class org.apache.tools.zip.ZipOutputStream
Flushes this output stream and forces any buffered output bytes to be written out to the stream.
flush() - Method in class uk.ac.vamsas.client.AppDataOutputStream
 
flush() - Method in class uk.ac.vamsas.client.simpleclient.LockedFileOutputStream
 
form(double) - Method in class uk.ac.vamsas.objects.utils.Format
Formats a double into a string (like sprintf in C)
form(long) - Method in class uk.ac.vamsas.objects.utils.Format
Formats a long integer into a string (like sprintf in C)
form(char) - Method in class uk.ac.vamsas.objects.utils.Format
Formats a character into a string (like sprintf in C)
form(String) - Method in class uk.ac.vamsas.objects.utils.Format
Formats a string into a larger string (like sprintf in C)
fromDosTime(ZipLong) - Static method in class org.apache.tools.zip.ZipFile
Convert a DOS date/time field to a Date object.
fromShifts - Variable in class uk.ac.vamsas.objects.utils.MapList
 

G

Glyph - class uk.ac.vamsas.objects.core.Glyph.
Discrete symbol - possibly graphically represented
Glyph() - Constructor for class uk.ac.vamsas.objects.core.Glyph
 
GlyphDescriptor - class uk.ac.vamsas.objects.core.descriptors.GlyphDescriptor.
Class GlyphDescriptor.
GlyphDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.GlyphDescriptor
 
GlyphDictionary - class uk.ac.vamsas.objects.utils.GlyphDictionary.
dict attribute values for glyph symbol sets found in uk.ac.vamsas.objects.core.AnnotationElement TODO: add validators and multilength symbols.
GlyphDictionary() - Constructor for class uk.ac.vamsas.objects.utils.GlyphDictionary
 
getAbout() - Method in interface uk.ac.vamsas.client.IClient
Self-documenting/describing info for the application to present to the user.
getAbout() - Method in class uk.ac.vamsas.client.simpleclient.SimpleClient
construct new SimpleClientsession by importing objects from an existing vamsas document
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.AlignmentAnnotationDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.AlignmentDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.AlignmentSequenceAnnotationDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.AlignmentSequenceDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.AnnotationElementDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.AppDataDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.ApplicationDataDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.AttachmentDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.CommonDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.DataSetAnnotationsDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.DataSetDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.DbRefDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.EntryDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.GlyphDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.InputDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.InstanceDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.LinkDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.LocalDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.LockFileDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.MapDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.MapListDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.MapRangeTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.MapTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.MappedDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.MappingDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.NewickDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.NodeTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.ParamDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.PosDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.PropertyDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.ProvenanceDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.RangeAnnotationDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.RangeDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.RangeTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.ReferenceTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.ScoreDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.SegDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.SequenceDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.SequenceMappingDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.SequenceTypeDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.TreeDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.TreenodeDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.UserDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.VAMSASDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.VamsasDocumentDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.VrefDescriptor
Method getAccessMode.
getAccessMode() - Method in class uk.ac.vamsas.objects.core.descriptors.VxrefDescriptor
Method getAccessMode.
getAccessionId() - Method in class uk.ac.vamsas.objects.core.DbRef
Returns the value of field 'accessionId'.
getAction() - Method in class uk.ac.vamsas.objects.core.Entry
Returns the value of field 'action'.
getAfter() - Method in class uk.ac.vamsas.objects.core.AnnotationElement
Returns the value of field 'after'.
getAligned() - Method in class uk.ac.vamsas.objects.core.Alignment
Returns the value of field 'aligned'.
getAlignment(int) - Method in class uk.ac.vamsas.objects.core.DataSet
Method getAlignment.
getAlignment() - Method in class uk.ac.vamsas.objects.core.DataSet
Method getAlignment.Returns the contents of the collection in an Array.
getAlignmentAnnotation(int) - Method in class uk.ac.vamsas.objects.core.Alignment
Method getAlignmentAnnotation.
getAlignmentAnnotation() - Method in class uk.ac.vamsas.objects.core.Alignment
Method getAlignmentAnnotation.Returns the contents of the collection in an Array.
getAlignmentAnnotationAsReference() - Method in class uk.ac.vamsas.objects.core.Alignment
Method getAlignmentAnnotationAsReference.Returns a reference to '_alignmentAnnotationList'.
getAlignmentAnnotationCount() - Method in class uk.ac.vamsas.objects.core.Alignment
Method getAlignmentAnnotationCount.
getAlignmentAsReference() - Method in class uk.ac.vamsas.objects.core.DataSet
Method getAlignmentAsReference.Returns a reference to '_alignmentList'.
getAlignmentCount() - Method in class uk.ac.vamsas.objects.core.DataSet
Method getAlignmentCount.
getAlignmentSequence(int) - Method in class uk.ac.vamsas.objects.core.Alignment
Method getAlignmentSequence.
getAlignmentSequence() - Method in class uk.ac.vamsas.objects.core.Alignment
Method getAlignmentSequence.Returns the contents of the collection in an Array.
getAlignmentSequenceAnnotation(int) - Method in class uk.ac.vamsas.objects.core.AlignmentSequence
Method getAlignmentSequenceAnnotation.
getAlignmentSequenceAnnotation() - Method in class uk.ac.vamsas.objects.core.AlignmentSequence
Method getAlignmentSequenceAnnotation.Returns the contents of the collection in an Array.
getAlignmentSequenceAnnotationAsReference() - Method in class uk.ac.vamsas.objects.core.AlignmentSequence
Method getAlignmentSequenceAnnotationAsReference.Returns a reference to '_alignmentSequenceAnnotationList'.
getAlignmentSequenceAnnotationCount() - Method in class uk.ac.vamsas.objects.core.AlignmentSequence
Method getAlignmentSequenceAnnotationCount.
getAlignmentSequenceAsReference() - Method in class uk.ac.vamsas.objects.core.Alignment
Method getAlignmentSequenceAsReference.Returns a reference to '_alignmentSequenceList'.
getAlignmentSequenceCount() - Method in class uk.ac.vamsas.objects.core.Alignment
Method getAlignmentSequenceCount.
getAnnotationElement(int) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Method getAnnotationElement.
getAnnotationElement() - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Method getAnnotationElement.Returns the contents of the collection in an Array.
getAnnotationElementAsReference() - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Method getAnnotationElementAsReference.Returns a reference to '_annotationElementList'.
getAnnotationElementCount() - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Method getAnnotationElementCount.
getApp() - Method in class uk.ac.vamsas.objects.core.Entry
Returns the value of field 'app'.
getAppDataReferences(VamsasDocument) - Static method in class uk.ac.vamsas.objects.utils.AppDataReference
collect all appData reference strings in a vamsas document
getAppDataStream(String) - Method in class uk.ac.vamsas.client.simpleclient.VamsasArchive
Opens and returns the applicationData output stream for the appdataReference string.
getAppdataEntry(String) - Method in class uk.ac.vamsas.client.simpleclient.VamsasArchiveReader
 
getAppdataStream(String) - Method in class uk.ac.vamsas.client.simpleclient.VamsasArchiveReader
 
getApplicationData(int) - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Method getApplicationData.
getApplicationData() - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Method getApplicationData.Returns the contents of the collection in an Array.
getApplicationDataAsReference() - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Method getApplicationDataAsReference.Returns a reference to '_applicationDataList'.
getApplicationDataCount() - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Method getApplicationDataCount.
getAppsObjectFor(Vobject) - Method in interface uk.ac.vamsas.objects.IVorbaBinding
Get the Application's own object bound to an existing Vamsas session object
getAttachment(int) - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Method getAttachment.
getAttachment() - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Method getAttachment.Returns the contents of the collection in an Array.
getAttachmentAsReference() - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Method getAttachmentAsReference.Returns a reference to '_attachmentList'.
getAttachmentCount() - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Method getAttachmentCount.
getBootstrap() - Method in class uk.ac.vamsas.objects.utils.trees.BinaryNode
DOCUMENT ME!
getBounds(RangeType) - Static method in class uk.ac.vamsas.objects.utils.Range
get real bounds of a RangeType's specification.
getBufferedInputStream(boolean) - Method in class uk.ac.vamsas.client.simpleclient.Lock
return buffered input stream for locked file.
getBufferedInputStream(boolean) - Method in class uk.ac.vamsas.client.simpleclient.SessionFile
 
getBufferedOutputStream(boolean) - Method in class uk.ac.vamsas.client.simpleclient.FileLock
 
getBufferedOutputStream(boolean) - Method in class uk.ac.vamsas.client.simpleclient.Lock
return buffered output stream to locked file.
getBufferedOutputStream(boolean) - Method in class uk.ac.vamsas.client.simpleclient.NativeLock
return buffered output stream to locked file.
getBufferedOutputStream(boolean) - Method in class uk.ac.vamsas.client.simpleclient.SessionFile
 
getBytes() - Method in class org.apache.tools.zip.ZipLong
Get value as four bytes in big endian byte order.
getBytes(long) - Static method in class org.apache.tools.zip.ZipLong
Get value as four bytes in big endian byte order.
getBytes(String) - Method in class org.apache.tools.zip.ZipOutputStream
Retrieve the bytes for the given String in the encoding set for this Stream.
getBytes() - Method in class org.apache.tools.zip.ZipShort
Get value as two bytes in big endian byte order.
getBytes(int) - Static method in class org.apache.tools.zip.ZipShort
Get value as two bytes in big endian byte order.
getCentralDirectoryData() - Method in class org.apache.tools.zip.AsiExtraField
Delegate to local file data.
getCentralDirectoryData() - Method in class org.apache.tools.zip.JarMarker
The actual data to put central directory - without Header-ID or length specifier.
getCentralDirectoryData() - Method in class org.apache.tools.zip.UnrecognizedExtraField
Get the central data.
getCentralDirectoryData() - Method in interface org.apache.tools.zip.ZipExtraField
The actual data to put central directory - without Header-ID or length specifier.
getCentralDirectoryExtra() - Method in class org.apache.tools.zip.ZipEntry
Retrieves the extra data for the central directory.
getCentralDirectoryLength() - Method in class org.apache.tools.zip.AsiExtraField
Delegate to local file data.
getCentralDirectoryLength() - Method in class org.apache.tools.zip.JarMarker
Length of the extra field in the central directory - without Header-ID or length specifier.
getCentralDirectoryLength() - Method in class org.apache.tools.zip.UnrecognizedExtraField
Get the central data length.
getCentralDirectoryLength() - Method in interface org.apache.tools.zip.ZipExtraField
Length of the extra field in the central directory - without Header-ID or length specifier.
getChangedState() - Method in class uk.ac.vamsas.client.simpleclient.FileWatcher
passes lock back to caller if hasChanged returned true.
getChannel() - Method in class uk.ac.vamsas.client.simpleclient.LockedFileOutputStream
 
getChoiceValue() - Method in class uk.ac.vamsas.objects.core.AppData
Returns the value of field 'choiceValue'.
getChoiceValue() - Method in class uk.ac.vamsas.objects.core.RangeType
Returns the value of field 'choiceValue'.
getClientAppdata() - Method in interface uk.ac.vamsas.client.IClientAppdata
 
getClientAppdata() - Method in interface uk.ac.vamsas.client.IClientDocument
Get instance of Client and User specific vamsas document data access interface.
getClientAppdata() - Method in class uk.ac.vamsas.client.simpleclient.ClientDocument
 
getClientAppdata() - Method in class uk.ac.vamsas.client.simpleclient.SimpleClientAppdata
 
getClientAppdata() - Method in class uk.ac.vamsas.test.simpleclient.ClientDoc
 
getClientDocument() - Method in interface uk.ac.vamsas.client.IClient
get vamsas document with user and app specific data IClientDocuments are not thread-safe.
getClientDocument() - Method in class uk.ac.vamsas.client.simpleclient.SimpleClient
 
getClientHandle() - Method in interface uk.ac.vamsas.client.IClient
Included for applications with several ClientHandle identities.
getClientHandle() - Method in interface uk.ac.vamsas.client.IVorbaIdFactory
 
getClientHandle() - Method in class uk.ac.vamsas.client.VorbaIdFactory
 
getClientHandle() - Method in class uk.ac.vamsas.client.simpleclient.IdFactory
 
getClientHandle() - Method in class uk.ac.vamsas.client.simpleclient.SimpleClient
 
getClientInputStream() - Method in interface uk.ac.vamsas.client.IClientAppdata
 
getClientInputStream() - Method in class uk.ac.vamsas.client.simpleclient.SimpleClientAppdata
 
getClientLock() - Method in class uk.ac.vamsas.client.simpleclient.SimpleClient
 
getClientNCname() - Method in class uk.ac.vamsas.client.ClientHandle
 
getClientName() - Method in class uk.ac.vamsas.client.ClientHandle
 
getClientOutputStream() - Method in interface uk.ac.vamsas.client.IClientAppdata
 
getClientOutputStream() - Method in class uk.ac.vamsas.client.simpleclient.SimpleClientAppdata
 
getClientUrn() - Method in class uk.ac.vamsas.client.ClientHandle
 
getClientWatcher() - Method in class uk.ac.vamsas.client.simpleclient.VamsasSession
make a new watcher object for the clientFile
getClientWatcherElement() - Method in class uk.ac.vamsas.client.simpleclient.VamsasSession
get or create a watcher on clist.
getClientlockFile() - Method in class uk.ac.vamsas.client.simpleclient.SimpleClient
 
getCommand(String[], int) - Method in class uk.ac.vamsas.test.simpleclient.CommandProcessor
find and verify a command
getCommon() - Method in class uk.ac.vamsas.objects.core.ApplicationData
Returns the value of field 'common'.
getCompressed() - Method in class uk.ac.vamsas.objects.core.Attachment
Returns the value of field 'compressed'.
getContent() - Method in class uk.ac.vamsas.objects.core.Glyph
Returns the value of field 'content'.
getContent() - Method in class uk.ac.vamsas.objects.core.Link
Returns the value of field 'content'.
getContent() - Method in class uk.ac.vamsas.objects.core.LockFile
Returns the value of field 'content'.
getContent() - Method in class uk.ac.vamsas.objects.core.Newick
Returns the value of field 'content'.
getContent() - Method in class uk.ac.vamsas.objects.core.Param
Returns the value of field 'content'.
getContent() - Method in class uk.ac.vamsas.objects.core.Property
Returns the value of field 'content'.
getContent() - Method in class uk.ac.vamsas.objects.core.ReferenceType
Returns the value of field 'content'.
getContent() - Method in class uk.ac.vamsas.objects.core.Score
Returns the value of field 'content'.
getCurrentSessions() - Method in interface uk.ac.vamsas.client.IClientFactory
enumerate the active sessions this IClientFactory instance knows about.
getCurrentSessions() - Method in class uk.ac.vamsas.client.simpleclient.SimpleClientFactory
 
getCurrentSessions() - Method in class uk.ac.vamsas.client.simpleclient.SimpleSessionManager
 
getCurrentState() - Method in class uk.ac.vamsas.client.simpleclient.FileWatcher
safely? getting current state of the watched file
getData() - Method in class uk.ac.vamsas.objects.core.AppData
Returns the value of field 'data'.
getDataReference() - Method in class uk.ac.vamsas.objects.core.AppData
Returns the value of field 'dataReference'.
getDataSet(int) - Method in class uk.ac.vamsas.objects.core.VAMSAS
Method getDataSet.
getDataSet() - Method in class uk.ac.vamsas.objects.core.VAMSAS
Method getDataSet.Returns the contents of the collection in an Array.
getDataSetAnnotations(int) - Method in class uk.ac.vamsas.objects.core.DataSet
Method getDataSetAnnotations.
getDataSetAnnotations() - Method in class uk.ac.vamsas.objects.core.DataSet
Method getDataSetAnnotations.Returns the contents of the collection in an Array.
getDataSetAnnotationsAsReference() - Method in class uk.ac.vamsas.objects.core.DataSet
Method getDataSetAnnotationsAsReference.Returns a reference to '_dataSetAnnotationsList'.
getDataSetAnnotationsCount() - Method in class uk.ac.vamsas.objects.core.DataSet
Method getDataSetAnnotationsCount.
getDataSetAsReference() - Method in class uk.ac.vamsas.objects.core.VAMSAS
Method getDataSetAsReference.Returns a reference to '_dataSetList'.
getDataSetCount() - Method in class uk.ac.vamsas.objects.core.VAMSAS
Method getDataSetCount.
getDate() - Method in class uk.ac.vamsas.objects.core.Entry
Returns the value of field 'date'.
getDbRef(int) - Method in class uk.ac.vamsas.objects.core.Sequence
Method getDbRef.
getDbRef() - Method in class uk.ac.vamsas.objects.core.Sequence
Method getDbRef.Returns the contents of the collection in an Array.
getDbRefAsReference() - Method in class uk.ac.vamsas.objects.core.Sequence
Method getDbRefAsReference.Returns a reference to '_dbRefList'.
getDbRefCount() - Method in class uk.ac.vamsas.objects.core.Sequence
Method getDbRefCount.
getDemoVamsas() - Static method in class uk.ac.vamsas.test.objects.Core
 
getDescription() - Method in class uk.ac.vamsas.objects.core.AnnotationElement
Returns the value of field 'description'.
getDescription() - Method in class uk.ac.vamsas.objects.core.NodeType
Returns the value of field 'description'.
getDescription() - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Returns the value of field 'description'.
getDescription() - Method in class uk.ac.vamsas.objects.core.SequenceType
Returns the value of field 'description'.
getDict() - Method in class uk.ac.vamsas.objects.core.Glyph
Returns the value of field 'dict'.
getDictionary() - Method in class uk.ac.vamsas.objects.core.Sequence
Returns the value of field 'dictionary'.
getDocWatcher() - Method in class uk.ac.vamsas.client.simpleclient.VamsasSession
make a new watcher object for the vamsas Document
getDocumentJarEntry() - Method in class uk.ac.vamsas.client.simpleclient.VamsasArchive
 
getDocumentOutputStream() - Method in class uk.ac.vamsas.client.simpleclient.VamsasArchive
Safely initializes the VAMSAS XML document Jar Entry.
getDummyFactory(String) - Static method in class uk.ac.vamsas.client.simpleclient.IdFactory
Convenience method used for default behaviour in testing and any anonymous internal vamsasDocument unmarshalling
getEncoding() - Method in class org.apache.tools.zip.ZipFile
The encoding to use for filenames and the file comment.
getEncoding() - Method in class org.apache.tools.zip.ZipOutputStream
The encoding to use for filenames and the file comment.
getEnd() - Method in class uk.ac.vamsas.objects.core.MapList
Returns the value of field 'end'.
getEnd() - Method in class uk.ac.vamsas.objects.core.Seg
Returns the value of field 'end'.
getEnd() - Method in class uk.ac.vamsas.objects.core.SequenceType
Returns the value of field 'end'.
getEntries() - Method in class org.apache.tools.zip.ZipFile
Returns all entries.
getEntry(String) - Method in class org.apache.tools.zip.ZipFile
Returns a named entry - or null if no entry by that name exists.
getEntry(int) - Method in class uk.ac.vamsas.objects.core.Provenance
Method getEntry.
getEntry() - Method in class uk.ac.vamsas.objects.core.Provenance
Method getEntry.Returns the contents of the collection in an Array.
getEntryAsReference() - Method in class uk.ac.vamsas.objects.core.Provenance
Method getEntryAsReference.Returns a reference to '_entryList'.
getEntryCount() - Method in class uk.ac.vamsas.objects.core.Provenance
Method getEntryCount.
getExternalAttributes() - Method in class org.apache.tools.zip.ZipEntry
Retrieves the external file attributes.
getExtraEntries() - Method in class uk.ac.vamsas.client.simpleclient.VamsasArchiveReader
returns all entries not matching the filespec of a vamsas xml entry
getExtraFields() - Method in class org.apache.tools.zip.ZipEntry
Retrieves extra fields.
getFileInputStream(boolean) - Method in class uk.ac.vamsas.client.simpleclient.FileLock
 
getFileInputStream(boolean) - Method in class uk.ac.vamsas.client.simpleclient.Lock
gets Locked Stream for reading from
getFileInputStream(boolean) - Method in class uk.ac.vamsas.client.simpleclient.NativeLock
gets Locked Stream for reading from
getFileInputStream(boolean) - Method in class uk.ac.vamsas.client.simpleclient.SessionFile
 
getFileOutputStream(boolean) - Method in class uk.ac.vamsas.client.simpleclient.FileLock
 
getFileOutputStream(boolean) - Method in class uk.ac.vamsas.client.simpleclient.Lock
gets Locked stream to write to FileInput always starts at the *end* of the file (after any truncation)
getFileOutputStream(boolean) - Method in class uk.ac.vamsas.client.simpleclient.NativeLock
gets Locked stream to write to FileInput always starts at the *end* of the file (after any truncation)
getFileOutputStream(boolean) - Method in class uk.ac.vamsas.client.simpleclient.SessionFile
 
getFrom() - Method in class uk.ac.vamsas.objects.core.MapList
Returns the value of field 'from'.
getFromHighest() - Method in class uk.ac.vamsas.objects.utils.MapList
 
getFromLowest() - Method in class uk.ac.vamsas.objects.utils.MapList
 
getFromRanges() - Method in class uk.ac.vamsas.objects.utils.MapList
 
getFromRatio() - Method in class uk.ac.vamsas.objects.utils.MapList
 
getFullName() - Method in class uk.ac.vamsas.client.UserHandle
 
getFullname() - Method in class uk.ac.vamsas.objects.core.User
Returns the value of field 'fullname'.
getGapChar() - Method in class uk.ac.vamsas.objects.core.Alignment
Returns the value of field 'gapChar'.
getGlyph(int) - Method in class uk.ac.vamsas.objects.core.AnnotationElement
Method getGlyph.
getGlyph() - Method in class uk.ac.vamsas.objects.core.AnnotationElement
Method getGlyph.Returns the contents of the collection in an Array.
getGlyphAsReference() - Method in class uk.ac.vamsas.objects.core.AnnotationElement
Method getGlyphAsReference.Returns a reference to '_glyphList'.
getGlyphCount() - Method in class uk.ac.vamsas.objects.core.AnnotationElement
Method getGlyphCount.
getGraph() - Method in class uk.ac.vamsas.objects.core.AlignmentAnnotation
Returns the value of field 'graph'.
getGraph() - Method in class uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation
Returns the value of field 'graph'.
getGroup() - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Returns the value of field 'group'.
getGroupId() - Method in class org.apache.tools.zip.AsiExtraField
Get the group id.
getHandler() - Method in class uk.ac.vamsas.client.simpleclient.WatcherElement
 
getHeaderId() - Method in class org.apache.tools.zip.AsiExtraField
The Header-ID.
getHeaderId() - Method in class org.apache.tools.zip.JarMarker
The Header-ID.
getHeaderId() - Method in class org.apache.tools.zip.UnrecognizedExtraField
Get the header id.
getHeaderId() - Method in interface org.apache.tools.zip.ZipExtraField
The Header-ID.
getHref() - Method in class uk.ac.vamsas.objects.core.Link
Returns the value of field 'href'.
getI() - Method in class uk.ac.vamsas.objects.core.Pos
Returns the value of field 'i'.
getIClient(ClientHandle) - Method in interface uk.ac.vamsas.client.IClientFactory
Create a new Vorba Session
getIClient(ClientHandle, String) - Method in interface uk.ac.vamsas.client.IClientFactory
returns new Vorba for a given session.
getIClient(ClientHandle, UserHandle, String) - Method in interface uk.ac.vamsas.client.IClientFactory
returns new vorba for a given session acting as a particular identity
getIClient(ClientHandle, UserHandle) - Method in interface uk.ac.vamsas.client.IClientFactory
New session for application and specific user
getIClient(ClientHandle) - Method in class uk.ac.vamsas.client.simpleclient.SimpleClientFactory
 
getIClient(ClientHandle, String) - Method in class uk.ac.vamsas.client.simpleclient.SimpleClientFactory
the URN should be something like simpleclient:FILEPATH URL encoded
getIClient(ClientHandle, UserHandle, String) - Method in class uk.ac.vamsas.client.simpleclient.SimpleClientFactory
 
getIClient(ClientHandle, UserHandle) - Method in class uk.ac.vamsas.client.simpleclient.SimpleClientFactory
 
getId() - Method in class uk.ac.vamsas.client.VorbaId
 
getId() - Method in class uk.ac.vamsas.objects.core.Alignment
Returns the value of field 'id'.
getId() - Method in class uk.ac.vamsas.objects.core.AlignmentSequence
Returns the value of field 'id'.
getId() - Method in class uk.ac.vamsas.objects.core.AnnotationElement
Returns the value of field 'id'.
getId() - Method in class uk.ac.vamsas.objects.core.Attachment
Returns the value of field 'id'.
getId() - Method in class uk.ac.vamsas.objects.core.DataSet
Returns the value of field 'id'.
getId() - Method in class uk.ac.vamsas.objects.core.DbRef
Returns the value of field 'id'.
getId() - Method in class uk.ac.vamsas.objects.core.Entry
Returns the value of field 'id'.
getId() - Method in class uk.ac.vamsas.objects.core.Map
Returns the value of field 'id'.
getId() - Method in class uk.ac.vamsas.objects.core.Newick
Returns the value of field 'id'.
getId() - Method in class uk.ac.vamsas.objects.core.NodeType
Returns the value of field 'id'.
getId() - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Returns the value of field 'id'.
getId() - Method in class uk.ac.vamsas.objects.core.ReferenceType
Returns the value of field 'id'.
getId() - Method in class uk.ac.vamsas.objects.core.Sequence
Returns the value of field 'id'.
getId() - Method in class uk.ac.vamsas.objects.core.SequenceMapping
Returns the value of field 'id'.
getId() - Method in class uk.ac.vamsas.objects.core.Tree
Returns the value of field 'id'.
getId() - Method in class uk.ac.vamsas.objects.core.VAMSAS
Returns the value of field 'id'.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.AlignmentAnnotationDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.AlignmentDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.AlignmentSequenceAnnotationDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.AlignmentSequenceDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.AnnotationElementDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.AppDataDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.ApplicationDataDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.AttachmentDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.CommonDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.DataSetAnnotationsDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.DataSetDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.DbRefDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.EntryDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.GlyphDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.InputDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.InstanceDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.LinkDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.LocalDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.LockFileDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.MapDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.MapListDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.MapRangeTypeDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.MapTypeDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.MappedDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.MappingDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.NewickDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.NodeTypeDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.ParamDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.PosDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.PropertyDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.ProvenanceDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.RangeAnnotationDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.RangeDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.RangeTypeDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.ReferenceTypeDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.ScoreDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.SegDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.SequenceDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.SequenceMappingDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.SequenceTypeDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.TreeDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.TreenodeDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.UserDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.VAMSASDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.VamsasDocumentDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.VrefDescriptor
Method getIdentity.
getIdentity() - Method in class uk.ac.vamsas.objects.core.descriptors.VxrefDescriptor
Method getIdentity.
getInclusive() - Method in class uk.ac.vamsas.objects.core.Seg
Returns the value of field 'inclusive'.
getInput(int) - Method in class uk.ac.vamsas.objects.core.Entry
Method getInput.
getInput() - Method in class uk.ac.vamsas.objects.core.Entry
Method getInput.Returns the contents of the collection in an Array.
getInputAsReference() - Method in class uk.ac.vamsas.objects.core.Entry
Method getInputAsReference.Returns a reference to '_inputList'.
getInputCount() - Method in class uk.ac.vamsas.objects.core.Entry
Method getInputCount.
getInputStream(ZipEntry) - Method in class org.apache.tools.zip.ZipFile
Returns an InputStream for reading the contents of the given entry.
getInstance() - Static method in class org.apache.tools.zip.JarMarker
Since JarMarker is stateless we can always use the same instance.
getInstance(int) - Method in class uk.ac.vamsas.objects.core.ApplicationData
Method getInstance.
getInstance() - Method in class uk.ac.vamsas.objects.core.ApplicationData
Method getInstance.Returns the contents of the collection in an Array.
getInstanceAsReference() - Method in class uk.ac.vamsas.objects.core.ApplicationData
Method getInstanceAsReference.Returns a reference to '_instanceList'.
getInstanceCount() - Method in class uk.ac.vamsas.objects.core.ApplicationData
Method getInstanceCount.
getInternalAttributes() - Method in class org.apache.tools.zip.ZipEntry
Retrieves the internal file attributes.
getIntervals(RangeType) - Static method in class uk.ac.vamsas.objects.utils.Range
 
getInverse() - Method in class uk.ac.vamsas.objects.utils.MapList
 
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.AlignmentAnnotationDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.AlignmentDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.AlignmentSequenceAnnotationDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.AlignmentSequenceDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.AnnotationElementDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.AppDataDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.ApplicationDataDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.AttachmentDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.CommonDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.DataSetAnnotationsDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.DataSetDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.DbRefDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.EntryDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.GlyphDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.InputDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.InstanceDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.LinkDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.LocalDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.LockFileDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.MapDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.MapListDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.MapRangeTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.MapTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.MappedDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.MappingDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.NewickDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.NodeTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.ParamDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.PosDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.PropertyDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.ProvenanceDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.RangeAnnotationDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.RangeDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.RangeTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.ReferenceTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.ScoreDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.SegDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.SequenceDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.SequenceMappingDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.SequenceTypeDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.TreeDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.TreenodeDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.UserDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.VAMSASDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.VamsasDocumentDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.VrefDescriptor
Method getJavaClass.
getJavaClass() - Method in class uk.ac.vamsas.objects.core.descriptors.VxrefDescriptor
Method getJavaClass.
getLabel() - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Returns the value of field 'label'.
getLink(int) - Method in class uk.ac.vamsas.objects.core.DbRef
Method getLink.
getLink() - Method in class uk.ac.vamsas.objects.core.DbRef
Method getLink.Returns the contents of the collection in an Array.
getLink(int) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Method getLink.
getLink() - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Method getLink.Returns the contents of the collection in an Array.
getLinkAsReference() - Method in class uk.ac.vamsas.objects.core.DbRef
Method getLinkAsReference.Returns a reference to '_linkList'.
getLinkAsReference() - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Method getLinkAsReference.Returns a reference to '_linkList'.
getLinkCount() - Method in class uk.ac.vamsas.objects.core.DbRef
Method getLinkCount.
getLinkCount() - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Method getLinkCount.
getLinkedFile() - Method in class org.apache.tools.zip.AsiExtraField
Name of linked file
getLoc() - Method in class uk.ac.vamsas.objects.core.SequenceMapping
Returns the value of field 'loc'.
getLocal() - Method in class uk.ac.vamsas.objects.core.MapType
Returns the value of field 'local'.
getLocalFileDataData() - Method in class org.apache.tools.zip.AsiExtraField
The actual data to put into local file data - without Header-ID or length specifier.
getLocalFileDataData() - Method in class org.apache.tools.zip.JarMarker
The actual data to put into local file data - without Header-ID or length specifier.
getLocalFileDataData() - Method in class org.apache.tools.zip.UnrecognizedExtraField
Get the local data.
getLocalFileDataData() - Method in interface org.apache.tools.zip.ZipExtraField
The actual data to put into local file data - without Header-ID or length specifier.
getLocalFileDataExtra() - Method in class org.apache.tools.zip.ZipEntry
Retrieves the extra data for the local file data.
getLocalFileDataLength() - Method in class org.apache.tools.zip.AsiExtraField
Length of the extra field in the local file data - without Header-ID or length specifier.
getLocalFileDataLength() - Method in class org.apache.tools.zip.JarMarker
Length of the extra field in the local file data - without Header-ID or length specifier.
getLocalFileDataLength() - Method in class org.apache.tools.zip.UnrecognizedExtraField
Get the length of the local data.
getLocalFileDataLength() - Method in interface org.apache.tools.zip.ZipExtraField
Length of the extra field in the local file data - without Header-ID or length specifier.
getLock(File) - Static method in class uk.ac.vamsas.client.simpleclient.LockFactory
lock target (blocks until lock is obtained)
getLock(File, boolean) - Static method in class uk.ac.vamsas.client.simpleclient.LockFactory
 
getLock() - Method in class uk.ac.vamsas.client.simpleclient.VamsasFile
public interface for getting a lock.
getLock(Lock) - Method in class uk.ac.vamsas.client.simpleclient.VamsasFile
 
getLockFile() - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Returns the value of field 'lockFile'.
getMap(int) - Method in class uk.ac.vamsas.objects.core.DbRef
Method getMap.
getMap() - Method in class uk.ac.vamsas.objects.core.DbRef
Method getMap.Returns the contents of the collection in an Array.
getMap() - Method in class uk.ac.vamsas.objects.core.SequenceMapping
Returns the value of field 'map'.
getMap() - Method in class uk.ac.vamsas.objects.utils.Mapping
 
getMapAsReference() - Method in class uk.ac.vamsas.objects.core.DbRef
Method getMapAsReference.Returns a reference to '_mapList'.
getMapCount() - Method in class uk.ac.vamsas.objects.core.DbRef
Method getMapCount.
getMapped() - Method in class uk.ac.vamsas.objects.core.MapType
Returns the value of field 'mapped'.
getMappedPosition(int) - Method in class uk.ac.vamsas.objects.utils.MapList
get From position in the associated reference frame for position pos in the associated sequence.
getMappedPosition(int) - Method in class uk.ac.vamsas.objects.utils.Mapping
get mapped position in the associated reference frame for position pos in the associated sequence.
getMappedWidth() - Method in class uk.ac.vamsas.objects.utils.Mapping
width of unit in mapped reference frame
getMappedWord(int) - Method in class uk.ac.vamsas.objects.utils.MapList
 
getMappedWord(int) - Method in class uk.ac.vamsas.objects.utils.Mapping
 
getMapping(RangeType) - Static method in class uk.ac.vamsas.objects.utils.Range
map from a rangeType's internal frame to the referenced object's coordinate frame.
getMode() - Method in class org.apache.tools.zip.AsiExtraField
File mode of this file.
getMode(int) - Method in class org.apache.tools.zip.AsiExtraField
Get the file mode for given permissions with the correct file type.
getModifiable() - Method in class uk.ac.vamsas.objects.core.Alignment
Returns the value of field 'modifiable'.
getModifiable() - Method in class uk.ac.vamsas.objects.core.Newick
Returns the value of field 'modifiable'.
getModifiable() - Method in class uk.ac.vamsas.objects.core.NodeType
Returns the value of field 'modifiable'.
getModifiable() - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Returns the value of field 'modifiable'.
getModifiable() - Method in class uk.ac.vamsas.objects.core.Tree
Returns the value of field 'modifiable'.
getModifiable() - Method in class uk.ac.vamsas.objects.core.VAMSAS
Returns the value of field 'modifiable'.
getName() - Method in class org.apache.tools.zip.ZipEntry
Get the name of the entry.
getName() - Method in class uk.ac.vamsas.objects.core.ApplicationData
Returns the value of field 'name'.
getName() - Method in class uk.ac.vamsas.objects.core.Input
Returns the value of field 'name'.
getName() - Method in class uk.ac.vamsas.objects.core.NodeType
Returns the value of field 'name'.
getName() - Method in class uk.ac.vamsas.objects.core.Param
Returns the value of field 'name'.
getName() - Method in class uk.ac.vamsas.objects.core.Property
Returns the value of field 'name'.
getName() - Method in class uk.ac.vamsas.objects.core.Score
Returns the value of field 'name'.
getName() - Method in class uk.ac.vamsas.objects.core.SequenceType
Returns the value of field 'name'.
getName() - Method in class uk.ac.vamsas.objects.utils.trees.BinaryNode
DOCUMENT ME!
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.AlignmentAnnotationDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.AlignmentDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.AlignmentSequenceAnnotationDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.AlignmentSequenceDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.AnnotationElementDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.AppDataDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.ApplicationDataDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.AttachmentDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.CommonDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.DataSetAnnotationsDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.DataSetDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.DbRefDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.EntryDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.GlyphDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.InputDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.InstanceDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.LinkDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.LocalDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.LockFileDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.MapDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.MapListDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.MapRangeTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.MapTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.MappedDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.MappingDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.NewickDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.NodeTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.ParamDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.PosDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.PropertyDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.ProvenanceDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.RangeAnnotationDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.RangeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.RangeTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.ReferenceTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.ScoreDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.SegDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.SequenceDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.SequenceMappingDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.SequenceTypeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.TreeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.TreenodeDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.UserDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.VAMSASDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.VamsasDocumentDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.VrefDescriptor
Method getNameSpacePrefix.
getNameSpacePrefix() - Method in class uk.ac.vamsas.objects.core.descriptors.VxrefDescriptor
Method getNameSpacePrefix.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.AlignmentAnnotationDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.AlignmentDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.AlignmentSequenceAnnotationDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.AlignmentSequenceDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.AnnotationElementDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.AppDataDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.ApplicationDataDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.AttachmentDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.CommonDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.DataSetAnnotationsDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.DataSetDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.DbRefDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.EntryDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.GlyphDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.InputDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.InstanceDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.LinkDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.LocalDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.LockFileDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.MapDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.MapListDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.MapRangeTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.MapTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.MappedDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.MappingDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.NewickDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.NodeTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.ParamDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.PosDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.PropertyDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.ProvenanceDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.RangeAnnotationDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.RangeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.RangeTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.ReferenceTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.ScoreDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.SegDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.SequenceDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.SequenceMappingDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.SequenceTypeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.TreeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.TreenodeDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.UserDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.VAMSASDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.VamsasDocumentDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.VrefDescriptor
Method getNameSpaceURI.
getNameSpaceURI() - Method in class uk.ac.vamsas.objects.core.descriptors.VxrefDescriptor
Method getNameSpaceURI.
getNewSessionIClient(ClientHandle) - Method in interface uk.ac.vamsas.client.IClientFactory
Create a new sesssion for the application with the current user
getNewSessionIClient(ClientHandle, UserHandle) - Method in interface uk.ac.vamsas.client.IClientFactory
Create a new session for the application using a particular user identity
getNewSessionIClient(ClientHandle) - Method in class uk.ac.vamsas.client.simpleclient.SimpleClientFactory
 
getNewSessionIClient(ClientHandle, UserHandle) - Method in class uk.ac.vamsas.client.simpleclient.SimpleClientFactory
 
getNewick(int) - Method in class uk.ac.vamsas.objects.core.Tree
Method getNewick.
getNewick() - Method in class uk.ac.vamsas.objects.core.Tree
Method getNewick.Returns the contents of the collection in an Array.
getNewickAsReference() - Method in class uk.ac.vamsas.objects.core.Tree
Method getNewickAsReference.Returns a reference to '_newickList'.
getNewickCount() - Method in class uk.ac.vamsas.objects.core.Tree
Method getNewickCount.
getNodespec() - Method in class uk.ac.vamsas.objects.core.Treenode
Returns the value of field 'nodespec'.
getObjRef(int) - Method in class uk.ac.vamsas.objects.core.Input
Method getObjRef.
getObjRef() - Method in class uk.ac.vamsas.objects.core.Input
Method getObjRef.Returns the contents of the collection in an Array.
getObjRefAsReference() - Method in class uk.ac.vamsas.objects.core.Input
Method getObjRefAsReference.Returns a reference to '_objRef'.
getObjRefCount() - Method in class uk.ac.vamsas.objects.core.Input
Method getObjRefCount.
getObject(VorbaId) - Method in interface uk.ac.vamsas.client.IClientDocument
Get a single Vobject.
getObject(VorbaId) - Method in class uk.ac.vamsas.client.simpleclient.ClientDocument
 
getObject(VorbaId) - Method in class uk.ac.vamsas.test.simpleclient.ArchiveClient
 
getObject(VorbaId) - Method in class uk.ac.vamsas.test.simpleclient.ClientDoc
 
getObjectref() - Method in class uk.ac.vamsas.objects.core.Attachment
Returns the value of field 'objectref'.
getObjects(VorbaId[]) - Method in interface uk.ac.vamsas.client.IClientDocument
Get a list of objects.
getObjects(VorbaId[]) - Method in class uk.ac.vamsas.client.simpleclient.ClientDocument
 
getObjects(VorbaId[]) - Method in class uk.ac.vamsas.test.simpleclient.ClientDoc
 
getOnto() - Method in class uk.ac.vamsas.objects.core.Mapping
Returns the value of field 'onto'.
getOrganization() - Method in class uk.ac.vamsas.client.UserHandle
 
getOrganization() - Method in class uk.ac.vamsas.objects.core.User
Returns the value of field 'organization'.
getOriginalArchiveReader() - Method in class uk.ac.vamsas.client.simpleclient.VamsasArchive
Access original archive if it exists, pass the reader to the client Note: this is NOT thread safe and a call to closeArchive() will by necessity close and invalidate the VamsasArchiveReader object.
getOriginalRoots(VamsasArchive) - Static method in class uk.ac.vamsas.client.simpleclient.VamsasArchive
Access original document if it exists, and get VAMSAS root objects.
getOriginalRoots() - Method in class uk.ac.vamsas.client.simpleclient.VamsasArchive
returns original document's root vamsas elements.
getOriginalVamsasDocument(VamsasArchive) - Static method in class uk.ac.vamsas.client.simpleclient.VamsasArchive
Access the original vamsas document for a VamsasArchive class, and return it.
getOriginalVamsasDocument(VamsasArchive, VorbaIdFactory) - Static method in class uk.ac.vamsas.client.simpleclient.VamsasArchive
Uses VorbaXmlBinder to retrieve the VamsasDocument from the original archive referred to by ths
getParam(int) - Method in class uk.ac.vamsas.objects.core.Entry
Method getParam.
getParam() - Method in class uk.ac.vamsas.objects.core.Entry
Method getParam.Returns the contents of the collection in an Array.
getParamAsReference() - Method in class uk.ac.vamsas.objects.core.Entry
Method getParamAsReference.Returns a reference to '_paramList'.
getParamCount() - Method in class uk.ac.vamsas.objects.core.Entry
Method getParamCount.
getPickManager() - Method in interface uk.ac.vamsas.client.IClient
get the Vamsas Pick Manager for registering pick handlers and sending messages for the current session.
getPickManager() - Method in class uk.ac.vamsas.client.simpleclient.SimpleClient
 
getPlatform() - Method in class org.apache.tools.zip.ZipEntry
Platform specification to put into the "version made by" part of the central file header.
getPos(int) - Method in class uk.ac.vamsas.objects.core.RangeType
Method getPos.
getPos() - Method in class uk.ac.vamsas.objects.core.RangeType
Method getPos.Returns the contents of the collection in an Array.
getPosAsReference() - Method in class uk.ac.vamsas.objects.core.RangeType
Method getPosAsReference.Returns a reference to '_posList'.
getPosCount() - Method in class uk.ac.vamsas.objects.core.RangeType
Method getPosCount.
getPosition() - Method in class uk.ac.vamsas.client.picking.MouseOverMessage
Returns the position value associated with this message.
getPosition() - Method in class uk.ac.vamsas.objects.core.AnnotationElement
Returns the value of field 'position'.
getPosition(int) - Method in class uk.ac.vamsas.objects.utils.Mapping
get the 'initial' position in the associated sequence for a position in the mapped reference frame
getProperty(int) - Method in class uk.ac.vamsas.objects.core.Alignment
Method getProperty.
getProperty() - Method in class uk.ac.vamsas.objects.core.Alignment
Method getProperty.Returns the contents of the collection in an Array.
getProperty(int) - Method in class uk.ac.vamsas.objects.core.DbRef
Method getProperty.
getProperty() - Method in class uk.ac.vamsas.objects.core.DbRef
Method getProperty.Returns the contents of the collection in an Array.
getProperty(int) - Method in class uk.ac.vamsas.objects.core.Entry
Method getProperty.
getProperty() - Method in class uk.ac.vamsas.objects.core.Entry
Method getProperty.Returns the contents of the collection in an Array.
getProperty(int) - Method in class uk.ac.vamsas.objects.core.NodeType
Method getProperty.
getProperty() - Method in class uk.ac.vamsas.objects.core.NodeType
Method getProperty.Returns the contents of the collection in an Array.
getProperty(int) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Method getProperty.
getProperty() - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Method getProperty.Returns the contents of the collection in an Array.
getProperty(int) - Method in class uk.ac.vamsas.objects.core.SequenceType
Method getProperty.
getProperty() - Method in class uk.ac.vamsas.objects.core.SequenceType
Method getProperty.Returns the contents of the collection in an Array.
getProperty(int) - Method in class uk.ac.vamsas.objects.core.Tree
Method getProperty.
getProperty() - Method in class uk.ac.vamsas.objects.core.Tree
Method getProperty.Returns the contents of the collection in an Array.
getPropertyAsReference() - Method in class uk.ac.vamsas.objects.core.Alignment
Method getPropertyAsReference.Returns a reference to '_propertyList'.
getPropertyAsReference() - Method in class uk.ac.vamsas.objects.core.DbRef
Method getPropertyAsReference.Returns a reference to '_propertyList'.
getPropertyAsReference() - Method in class uk.ac.vamsas.objects.core.Entry
Method getPropertyAsReference.Returns a reference to '_propertyList'.
getPropertyAsReference() - Method in class uk.ac.vamsas.objects.core.NodeType
Method getPropertyAsReference.Returns a reference to '_propertyList'.
getPropertyAsReference() - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Method getPropertyAsReference.Returns a reference to '_propertyList'.
getPropertyAsReference() - Method in class uk.ac.vamsas.objects.core.SequenceType
Method getPropertyAsReference.Returns a reference to '_propertyList'.
getPropertyAsReference() - Method in class uk.ac.vamsas.objects.core.Tree
Method getPropertyAsReference.Returns a reference to '_propertyList'.
getPropertyCount() - Method in class uk.ac.vamsas.objects.core.Alignment
Method getPropertyCount.
getPropertyCount() - Method in class uk.ac.vamsas.objects.core.DbRef
Method getPropertyCount.
getPropertyCount() - Method in class uk.ac.vamsas.objects.core.Entry
Method getPropertyCount.
getPropertyCount() - Method in class uk.ac.vamsas.objects.core.NodeType
Method getPropertyCount.
getPropertyCount() - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Method getPropertyCount.
getPropertyCount() - Method in class uk.ac.vamsas.objects.core.SequenceType
Method getPropertyCount.
getPropertyCount() - Method in class uk.ac.vamsas.objects.core.Tree
Method getPropertyCount.
getProvenance() - Method in class uk.ac.vamsas.objects.core.Alignment
Returns the value of field 'provenance'.
getProvenance() - Method in class uk.ac.vamsas.objects.core.AlignmentAnnotation
Returns the value of field 'provenance'.
getProvenance() - Method in class uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation
Returns the value of field 'provenance'.
getProvenance() - Method in class uk.ac.vamsas.objects.core.DataSet
Returns the value of field 'provenance'.
getProvenance() - Method in class uk.ac.vamsas.objects.core.DataSetAnnotations
Returns the value of field 'provenance'.
getProvenance() - Method in class uk.ac.vamsas.objects.core.SequenceMapping
Returns the value of field 'provenance'.
getProvenance() - Method in class uk.ac.vamsas.objects.core.Tree
Returns the value of field 'provenance'.
getProvenance() - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Returns the value of field 'provenance'.
getProvenanceEntry(String) - Method in class uk.ac.vamsas.client.simpleclient.SimpleClient
construct a provenance entry for this client with the specified action string.
getProvenanceEntry(String) - Method in class uk.ac.vamsas.test.simpleclient.ClientDoc
 
getProvenanceUser() - Method in class uk.ac.vamsas.client.simpleclient.SimpleClient
 
getProvenanceUser() - Method in class uk.ac.vamsas.test.simpleclient.ArchiveClient
from SimpleClient
getRaChannel() - Method in class uk.ac.vamsas.client.simpleclient.FileLock
 
getRaChannel() - Method in class uk.ac.vamsas.client.simpleclient.Lock
 
getRaChannel() - Method in class uk.ac.vamsas.client.simpleclient.NativeLock
 
getRaFile() - Method in class uk.ac.vamsas.client.simpleclient.FileLock
 
getRaFile() - Method in class uk.ac.vamsas.client.simpleclient.Lock
 
getRaFile() - Method in class uk.ac.vamsas.client.simpleclient.NativeLock
 
getRanges() - Method in class uk.ac.vamsas.client.picking.SelectionMessage
 
getRawMessage() - Method in class uk.ac.vamsas.client.picking.Message
Returns the raw message content as a string.
getReader() - Method in class uk.ac.vamsas.test.simpleclient.ClientDoc
 
getReferencedEntries(VamsasDocument, VamsasArchiveReader) - Method in class uk.ac.vamsas.client.simpleclient.SimpleDocBinding
Extract all jarEntries in an archive referenced by the vamsas document LATER: a family of methods for finding extraneous jarEntries , and invalid appDataReferences
getRefid() - Method in class uk.ac.vamsas.objects.core.AlignmentSequence
Returns the value of field 'refid'.
getRefs(int) - Method in class uk.ac.vamsas.objects.core.ReferenceType
Method getRefs.
getRefs() - Method in class uk.ac.vamsas.objects.core.ReferenceType
Method getRefs.Returns the contents of the collection in an Array.
getRefsAsReference() - Method in class uk.ac.vamsas.objects.core.ReferenceType
Method getRefsAsReference.Returns a reference to '_refs'.
getRefsCount() - Method in class uk.ac.vamsas.objects.core.ReferenceType
Method getRefsCount.
getRootVobject() - Method in interface uk.ac.vamsas.client.IObjectUpdate
Called by the library to find out which vamsas document object this update handler is interested in
getScore(int) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Method getScore.
getScore() - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Method getScore.Returns the contents of the collection in an Array.
getScoreAsReference() - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Method getScoreAsReference.Returns a reference to '_scoreList'.
getScoreCount() - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Method getScoreCount.
getSeg(int) - Method in class uk.ac.vamsas.objects.core.RangeType
Method getSeg.
getSeg() - Method in class uk.ac.vamsas.objects.core.RangeType
Method getSeg.Returns the contents of the collection in an Array.
getSegAsReference() - Method in class uk.ac.vamsas.objects.core.RangeType
Method getSegAsReference.Returns a reference to '_segList'.
getSegCount() - Method in class uk.ac.vamsas.objects.core.RangeType
Method getSegCount.
getSegRange(Seg, boolean) - Static method in class uk.ac.vamsas.objects.utils.Range
get startgetSelectionID() - Method in class uk.ac.vamsas.client.picking.SelectionMessage
 
getSeqAEnd() - Method in class uk.ac.vamsas.objects.core.Range
Returns the value of field 'seqAEnd'.
getSeqAStart() - Method in class uk.ac.vamsas.objects.core.Range
Returns the value of field 'seqAStart'.
getSeqBEnd() - Method in class uk.ac.vamsas.objects.core.Range
Returns the value of field 'seqBEnd'.
getSeqBStart() - Method in class uk.ac.vamsas.objects.core.Range
Returns the value of field 'seqBStart'.
getSeqRef(int) - Method in class uk.ac.vamsas.objects.core.DataSetAnnotations
Method getSeqRef.
getSeqRef() - Method in class uk.ac.vamsas.objects.core.DataSetAnnotations
Method getSeqRef.Returns the contents of the collection in an Array.
getSeqRefAsReference() - Method in class uk.ac.vamsas.objects.core.DataSetAnnotations
Method getSeqRefAsReference.Returns a reference to '_seqRef'.
getSeqRefCount() - Method in class uk.ac.vamsas.objects.core.DataSetAnnotations
Method getSeqRefCount.
getSeqrefs(int) - Method in class uk.ac.vamsas.objects.core.AlignmentAnnotation
Method getSeqrefs.
getSeqrefs() - Method in class uk.ac.vamsas.objects.core.AlignmentAnnotation
Method getSeqrefs.Returns the contents of the collection in an Array.
getSeqrefsAsReference() - Method in class uk.ac.vamsas.objects.core.AlignmentAnnotation
Method getSeqrefsAsReference.Returns a reference to '_seqrefs'.
getSeqrefsCount() - Method in class uk.ac.vamsas.objects.core.AlignmentAnnotation
Method getSeqrefsCount.
getSequence(int) - Method in class uk.ac.vamsas.objects.core.DataSet
Method getSequence.
getSequence() - Method in class uk.ac.vamsas.objects.core.DataSet
Method getSequence.Returns the contents of the collection in an Array.
getSequence() - Method in class uk.ac.vamsas.objects.core.SequenceType
Returns the value of field 'sequence'.
getSequenceAsReference() - Method in class uk.ac.vamsas.objects.core.DataSet
Method getSequenceAsReference.Returns a reference to '_sequenceList'.
getSequenceCount() - Method in class uk.ac.vamsas.objects.core.DataSet
Method getSequenceCount.
getSequenceMapping(int) - Method in class uk.ac.vamsas.objects.core.DataSet
Method getSequenceMapping.
getSequenceMapping() - Method in class uk.ac.vamsas.objects.core.DataSet
Method getSequenceMapping.Returns the contents of the collection in an Array.
getSequenceMappingAsReference() - Method in class uk.ac.vamsas.objects.core.DataSet
Method getSequenceMappingAsReference.Returns a reference to '_sequenceMappingList'.
getSequenceMappingCount() - Method in class uk.ac.vamsas.objects.core.DataSet
Method getSequenceMappingCount.
getSessionHandle() - Method in interface uk.ac.vamsas.client.IClient
Returns a valid URN for other applications to connect to the vamsas session.
getSessionHandle() - Method in interface uk.ac.vamsas.client.IVorbaIdFactory
 
getSessionHandle() - Method in class uk.ac.vamsas.client.VorbaIdFactory
 
getSessionHandle() - Method in class uk.ac.vamsas.client.simpleclient.IdFactory
 
getSessionHandle() - Method in class uk.ac.vamsas.client.simpleclient.SimpleClient
 
getSessionManager() - Method in class uk.ac.vamsas.client.simpleclient.VamsasSession
 
getSessionUrn() - Method in interface uk.ac.vamsas.client.IClient
convenience method to get the SessionUrn as a string (for passing directly to a text box...).
getSessionUrn() - Method in class uk.ac.vamsas.client.SessionHandle
 
getSessionUrn() - Method in class uk.ac.vamsas.client.SessionUrn
 
getSessionUrn() - Method in class uk.ac.vamsas.client.simpleclient.SimpleClient
 
getSessionsWatcher() - Method in class uk.ac.vamsas.client.simpleclient.SimpleSessionManager
make a new watcher object for the sessionsFile
getSimpleClientConfig() - Method in class uk.ac.vamsas.client.simpleclient.SimpleClient
 
getSource() - Method in class uk.ac.vamsas.objects.core.DbRef
Returns the value of field 'source'.
getStart() - Method in class uk.ac.vamsas.objects.core.MapList
Returns the value of field 'start'.
getStart() - Method in class uk.ac.vamsas.objects.core.Seg
Returns the value of field 'start'.
getStart() - Method in class uk.ac.vamsas.objects.core.SequenceType
Returns the value of field 'start'.
getStatus() - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Returns the value of field 'status'.
getStoreDocFile() - Method in class uk.ac.vamsas.client.simpleclient.VamsasSession
 
getStoreWatcher() - Method in class uk.ac.vamsas.client.simpleclient.VamsasSession
make a new watcher object for the messages file
getString(byte[]) - Method in class org.apache.tools.zip.ZipFile
Retrieve a String from the given bytes using the encoding set for this ZipFile.
getSubject() - Method in class uk.ac.vamsas.client.simpleclient.FileWatcher
 
getSubject() - Method in class uk.ac.vamsas.client.simpleclient.SessionFileWatcherElement
 
getSubject() - Method in class uk.ac.vamsas.client.simpleclient.SessionFlagWatcherElement
 
getSubject() - Method in class uk.ac.vamsas.client.simpleclient.VamsasFileWatcherElement
 
getSubject() - Method in class uk.ac.vamsas.client.simpleclient.WatcherElement
implemented for debug information purposes.
getTempSessionFile(String, String) - Method in class uk.ac.vamsas.client.simpleclient.VamsasSession
create a uniquely named uk.ac.vamsas.client.simpleclient.ClientsFile.addClient(ClientHandle)ile in the session Directory
getTitle() - Method in class uk.ac.vamsas.objects.core.Newick
Returns the value of field 'title'.
getTitle() - Method in class uk.ac.vamsas.objects.core.Tree
Returns the value of field 'title'.
getTo() - Method in class uk.ac.vamsas.objects.core.MapList
Returns the value of field 'to'.
getToHighest() - Method in class uk.ac.vamsas.objects.utils.MapList
 
getToLowest() - Method in class uk.ac.vamsas.objects.utils.MapList
 
getToPosition(int) - Method in class uk.ac.vamsas.objects.utils.MapList
get the 'initial' position of mpos in To
getToRanges() - Method in class uk.ac.vamsas.objects.utils.MapList
 
getToRatio() - Method in class uk.ac.vamsas.objects.utils.MapList
 
getToWord(int) - Method in class uk.ac.vamsas.objects.utils.MapList
get range of positions in To frame for the mpos word in From
getTree(int) - Method in class uk.ac.vamsas.objects.core.Alignment
Method getTree.
getTree() - Method in class uk.ac.vamsas.objects.core.Alignment
Method getTree.Returns the contents of the collection in an Array.
getTree(int) - Method in class uk.ac.vamsas.objects.core.DataSet
Method getTree.
getTree() - Method in class uk.ac.vamsas.objects.core.DataSet
Method getTree.Returns the contents of the collection in an Array.
getTree(int) - Method in class uk.ac.vamsas.objects.core.VAMSAS
Method getTree.
getTree() - Method in class uk.ac.vamsas.objects.core.VAMSAS
Method getTree.Returns the contents of the collection in an Array.
getTree() - Method in class uk.ac.vamsas.objects.utils.trees.NewickFile
DOCUMENT ME!
getTreeAsReference() - Method in class uk.ac.vamsas.objects.core.Alignment
Method getTreeAsReference.Returns a reference to '_treeList'.
getTreeAsReference() - Method in class uk.ac.vamsas.objects.core.DataSet
Method getTreeAsReference.Returns a reference to '_treeList'.
getTreeAsReference() - Method in class uk.ac.vamsas.objects.core.VAMSAS
Method getTreeAsReference.Returns a reference to '_treeList'.
getTreeCount() - Method in class uk.ac.vamsas.objects.core.Alignment
Method getTreeCount.
getTreeCount() - Method in class uk.ac.vamsas.objects.core.DataSet
Method getTreeCount.
getTreeCount() - Method in class uk.ac.vamsas.objects.core.VAMSAS
Method getTreeCount.
getTreeId(int) - Method in class uk.ac.vamsas.objects.core.Treenode
Method getTreeId.
getTreeId() - Method in class uk.ac.vamsas.objects.core.Treenode
Method getTreeId.Returns the contents of the collection in an Array.
getTreeIdAsReference() - Method in class uk.ac.vamsas.objects.core.Treenode
Method getTreeIdAsReference.Returns a reference to '_treeId'.
getTreeIdCount() - Method in class uk.ac.vamsas.objects.core.Treenode
Method getTreeIdCount.
getTreenode(int) - Method in class uk.ac.vamsas.objects.core.Tree
Method getTreenode.
getTreenode() - Method in class uk.ac.vamsas.objects.core.Tree
Method getTreenode.Returns the contents of the collection in an Array.
getTreenodeAsReference() - Method in class uk.ac.vamsas.objects.core.Tree
Method getTreenodeAsReference.Returns a reference to '_treenodeList'.
getTreenodeCount() - Method in class uk.ac.vamsas.objects.core.Tree
Method getTreenodeCount.
getType() - Method in class uk.ac.vamsas.objects.core.Attachment
Returns the value of field 'type'.
getType() - Method in class uk.ac.vamsas.objects.core.Param
Returns the value of field 'type'.
getType() - Method in class uk.ac.vamsas.objects.core.Property
Returns the value of field 'type'.
getType() - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Returns the value of field 'type'.
getUnit() - Method in class uk.ac.vamsas.objects.core.MapRangeType
Returns the value of field 'unit'.
getUnixMode() - Method in class org.apache.tools.zip.ZipEntry
Unix permission.
getUnsavedFlag() - Method in class uk.ac.vamsas.client.simpleclient.VamsasSession
 
getUpdateHandler(Class) - Method in interface uk.ac.vamsas.client.IClient
 
getUpdateHandler(Class) - Method in class uk.ac.vamsas.client.simpleclient.SimpleClient
 
getUpdateHandlers() - Method in interface uk.ac.vamsas.client.IClient
 
getUpdateHandlers() - Method in class uk.ac.vamsas.client.simpleclient.SimpleClient
 
getUpdateable() - Method in class uk.ac.vamsas.test.simpleclient.ArchiveClient
 
getUpdateable(Lock) - Method in class uk.ac.vamsas.test.simpleclient.ArchiveClient
 
getUpdatedObjects() - Method in class uk.ac.vamsas.client.simpleclient.ClientDocument
 
getUrn() - Method in class uk.ac.vamsas.objects.core.Instance
Returns the value of field 'urn'.
getUser(int) - Method in class uk.ac.vamsas.objects.core.ApplicationData
Method getUser.
getUser() - Method in class uk.ac.vamsas.objects.core.ApplicationData
Method getUser.Returns the contents of the collection in an Array.
getUser() - Method in class uk.ac.vamsas.objects.core.Entry
Returns the value of field 'user'.
getUserAppdata() - Method in interface uk.ac.vamsas.client.IClientAppdata
 
getUserAppdata() - Method in class uk.ac.vamsas.client.simpleclient.SimpleClientAppdata
 
getUserAsReference() - Method in class uk.ac.vamsas.objects.core.ApplicationData
Method getUserAsReference.Returns a reference to '_userList'.
getUserCount() - Method in class uk.ac.vamsas.objects.core.ApplicationData
Method getUserCount.
getUserHandle() - Method in interface uk.ac.vamsas.client.IClient
 
getUserHandle() - Method in interface uk.ac.vamsas.client.IVorbaIdFactory
 
getUserHandle() - Method in class uk.ac.vamsas.client.VorbaIdFactory
 
getUserHandle() - Method in class uk.ac.vamsas.client.simpleclient.IdFactory
 
getUserHandle() - Method in class uk.ac.vamsas.client.simpleclient.SimpleClient
 
getUserId() - Method in class org.apache.tools.zip.AsiExtraField
Get the user id.
getUserInputStream() - Method in interface uk.ac.vamsas.client.IClientAppdata
 
getUserInputStream() - Method in class uk.ac.vamsas.client.simpleclient.SimpleClientAppdata
 
getUserOutputStream() - Method in interface uk.ac.vamsas.client.IClientAppdata
 
getUserOutputStream() - Method in class uk.ac.vamsas.client.simpleclient.SimpleClientAppdata
 
getUserandApplicationsData(VamsasDocument, UserHandle, ClientHandle) - Static method in class uk.ac.vamsas.objects.utils.AppDataReference
Searches document appData structure for particular combinations of client and user data
getVAMSAS(int) - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Method getVAMSAS.
getVAMSAS() - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Method getVAMSAS.Returns the contents of the collection in an Array.
getVAMSASAsReference() - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Method getVAMSASAsReference.Returns a reference to '_VAMSASList'.
getVAMSASCount() - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Method getVAMSASCount.
getV_parent() - Method in class uk.ac.vamsas.client.Vobject
 
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.AlignmentAnnotationDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.AlignmentDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.AlignmentSequenceAnnotationDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.AlignmentSequenceDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.AnnotationElementDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.AppDataDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.ApplicationDataDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.AttachmentDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.CommonDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.DataSetAnnotationsDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.DataSetDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.DbRefDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.EntryDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.GlyphDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.InputDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.InstanceDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.LinkDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.LocalDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.LockFileDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.MapDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.MapListDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.MapRangeTypeDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.MapTypeDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.MappedDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.MappingDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.NewickDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.NodeTypeDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.ParamDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.PosDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.PropertyDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.ProvenanceDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.RangeAnnotationDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.RangeDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.RangeTypeDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.ReferenceTypeDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.ScoreDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.SegDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.SequenceDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.SequenceMappingDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.SequenceTypeDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.TreeDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.TreenodeDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.UserDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.VAMSASDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.VamsasDocumentDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.VrefDescriptor
Method getValidator.
getValidator() - Method in class uk.ac.vamsas.objects.core.descriptors.VxrefDescriptor
Method getValidator.
getValue() - Method in class org.apache.tools.zip.ZipLong
Get value as Java long.
getValue(byte[], int) - Static method in class org.apache.tools.zip.ZipLong
Helper method to get the value as a Java long from four bytes starting at given array offset
getValue(byte[]) - Static method in class org.apache.tools.zip.ZipLong
Helper method to get the value as a Java long from a four-byte array
getValue() - Method in class org.apache.tools.zip.ZipShort
Get value as Java int.
getValue(byte[], int) - Static method in class org.apache.tools.zip.ZipShort
Helper method to get the value as a java int from two bytes starting at given array offset
getValue(byte[]) - Static method in class org.apache.tools.zip.ZipShort
Helper method to get the value as a java int from a two-byte array
getValue(int) - Method in class uk.ac.vamsas.objects.core.AnnotationElement
Method getValue.
getValue() - Method in class uk.ac.vamsas.objects.core.AnnotationElement
Method getValue.Returns the contents of the collection in an Array.
getValueAsReference() - Method in class uk.ac.vamsas.objects.core.AnnotationElement
Method getValueAsReference.Returns a reference to '_valueList'.
getValueCount() - Method in class uk.ac.vamsas.objects.core.AnnotationElement
Method getValueCount.
getVamsasArchiveReader() - Method in class uk.ac.vamsas.client.simpleclient.ClientDocument
returns the read-only IO interface for the vamsas document Jar file
getVamsasDocument() - Method in class uk.ac.vamsas.client.simpleclient.ClientDocument
access the vamsas document
getVamsasDocument(VamsasArchiveReader) - Method in class uk.ac.vamsas.client.simpleclient.SimpleDocBinding
Uses VorbaXmlBinder to retrieve the VamsasDocument from the given stream
getVamsasDocument() - Method in class uk.ac.vamsas.client.simpleclient.VamsasArchive
 
getVamsasDocument(String, String, String) - Method in class uk.ac.vamsas.client.simpleclient.VamsasArchive
Return the original document or a new empty document with initial provenance entry.
getVamsasDocument() - Method in class uk.ac.vamsas.client.simpleclient.VamsasSession
Creates a VamsasArchive Vobject for accessing and updating document Note: this will lock the Vamsas Document for exclusive access to the client.
getVamsasDocumentEntry() - Method in class uk.ac.vamsas.client.simpleclient.VamsasArchiveReader
 
getVamsasDocumentStream() - Method in class uk.ac.vamsas.client.simpleclient.VamsasArchiveReader
get the VamsasDocument input stream, if it exists.
getVamsasFile() - Method in class uk.ac.vamsas.client.simpleclient.VamsasFile
 
getVamsasObjectFor(Object) - Method in interface uk.ac.vamsas.objects.IVorbaBinding
get the Vamsas session object bound to an internal object.
getVamsasObjects(Reader, VorbaIdFactory, Vobject) - Static method in class uk.ac.vamsas.client.VorbaXmlBinder
Unmarshals a vamsasDocument Vobject from a stream, registers unregistered objects, records existing VorbaIds, and completes the uk.ac.vamsas.client.Vobject housekeeping fields.
getVamsasRoots() - Method in interface uk.ac.vamsas.client.IClientDocument
Returns all root objects in document.
getVamsasRoots() - Method in class uk.ac.vamsas.client.simpleclient.ClientDocument
 
getVamsasRoots() - Method in class uk.ac.vamsas.test.simpleclient.ClientDoc
 
getVamsasXmlEntry() - Method in class uk.ac.vamsas.client.simpleclient.VamsasArchiveReader
 
getVamsasXmlStream() - Method in class uk.ac.vamsas.client.simpleclient.VamsasArchiveReader
get the VamsasXML input stream, if it exists.
getVersion() - Method in class uk.ac.vamsas.client.ClientHandle
 
getVersion() - Method in class uk.ac.vamsas.objects.core.ApplicationData
Returns the value of field 'version'.
getVersion() - Method in class uk.ac.vamsas.objects.core.DbRef
Returns the value of field 'version'.
getVersion() - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Returns the value of field 'version'.
getVobjhashVals() - Method in class uk.ac.vamsas.client.simpleclient.IdFactory
values for keys in this hash are Vobjhash objects created for each Vobj with a VorbaId after this factory has been used to write a vamsas archive.
getVorba() - Method in class uk.ac.vamsas.client.simpleclient.SimpleDocBinding
 
getVorba() - Method in class uk.ac.vamsas.client.simpleclient.VamsasArchive
 
getVorbaID() - Method in class uk.ac.vamsas.client.picking.MouseOverMessage
Returns the VAMSAS object ID associated with this message.
getVorbaIDs() - Method in class uk.ac.vamsas.client.picking.SelectionMessage
 
getVorbaId() - Method in class uk.ac.vamsas.client.Vobject
Method to get fixed reference for the Vobject in the vamsas document.
getVorbaIdHash() - Method in class uk.ac.vamsas.client.simpleclient.IdFactory
values for keys in this hash can be used to reference the uk.ac.vamsas.client.Vobject instance for the VorbaId string.
getVref(int) - Method in class uk.ac.vamsas.objects.core.NodeType
Method getVref.
getVref() - Method in class uk.ac.vamsas.objects.core.NodeType
Method getVref.Returns the contents of the collection in an Array.
getVrefAsReference() - Method in class uk.ac.vamsas.objects.core.NodeType
Method getVrefAsReference.Returns a reference to '_vrefList'.
getVrefCount() - Method in class uk.ac.vamsas.objects.core.NodeType
Method getVrefCount.
getVxref(int) - Method in class uk.ac.vamsas.objects.core.Sequence
Method getVxref.
getVxref() - Method in class uk.ac.vamsas.objects.core.Sequence
Method getVxref.Returns the contents of the collection in an Array.
getVxrefAsReference() - Method in class uk.ac.vamsas.objects.core.Sequence
Method getVxrefAsReference.Returns a reference to '_vxrefList'.
getVxrefCount() - Method in class uk.ac.vamsas.objects.core.Sequence
Method getVxrefCount.
getWatched() - Method in class uk.ac.vamsas.client.simpleclient.SessionFileWatcherElement
 
getWatched() - Method in class uk.ac.vamsas.client.simpleclient.SessionFlagWatcherElement
 
getWatched() - Method in class uk.ac.vamsas.client.simpleclient.VamsasFileWatcherElement
 
getWatcher() - Method in class uk.ac.vamsas.client.simpleclient.WatcherElement
 
getWidth() - Method in class uk.ac.vamsas.objects.utils.Mapping
width of mapped unit in associated sequence
getWord(int) - Method in class uk.ac.vamsas.objects.utils.Mapping
gets boundary in direction of mapping
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.AlignmentAnnotationDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.AlignmentDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.AlignmentSequenceAnnotationDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.AlignmentSequenceDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.AnnotationElementDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.AppDataDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.ApplicationDataDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.AttachmentDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.CommonDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.DataSetAnnotationsDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.DataSetDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.DbRefDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.EntryDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.GlyphDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.InputDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.InstanceDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.LinkDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.LocalDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.LockFileDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.MapDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.MapListDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.MapRangeTypeDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.MapTypeDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.MappedDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.MappingDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.NewickDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.NodeTypeDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.ParamDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.PosDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.PropertyDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.ProvenanceDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.RangeAnnotationDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.RangeDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.RangeTypeDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.ReferenceTypeDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.ScoreDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.SegDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.SequenceDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.SequenceMappingDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.SequenceTypeDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.TreeDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.TreenodeDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.UserDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.VAMSASDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.VamsasDocumentDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.VrefDescriptor
Method getXMLName.
getXMLName() - Method in class uk.ac.vamsas.objects.core.descriptors.VxrefDescriptor
Method getXMLName.
get__last_hash() - Method in class uk.ac.vamsas.client.Vobject
__last_hash is the hash value computed when the Vobject was last checked against a IClientDocument generated by the Vobject's parent IClient instance.
get_session() - Method in class uk.ac.vamsas.client.simpleclient.SimpleClient
retrieves the current VamsasSession to which belong the client
getjv2vObj(Object) - Method in class uk.ac.vamsas.test.simpleclient.simpleapp.VamsasDatastore
 
getvObj2jv(Vobject) - Method in class uk.ac.vamsas.test.simpleclient.simpleapp.VamsasDatastore
 

H

HasBootstrap() - Method in class uk.ac.vamsas.objects.utils.trees.NewickFile
 
HasDistances() - Method in class uk.ac.vamsas.objects.utils.trees.NewickFile
 
HasRootDistance() - Method in class uk.ac.vamsas.objects.utils.trees.NewickFile
 
haltWatch() - Method in class uk.ac.vamsas.client.simpleclient.WatcherElement
will instruct watcher to stop and wait around for one WATCH_SLEEP before returning.
haltWatchers() - Method in class uk.ac.vamsas.client.simpleclient.VamsasFileWatcherThread
 
handleMessage(Message) - Method in interface uk.ac.vamsas.client.picking.IMessageHandler
Responds to a message received event.
handleMessage(Message) - Method in class uk.ac.vamsas.client.picking.TestApp
 
handleMessage(Message) - Method in class uk.ac.vamsas.client.simpleclient.SimplePickManager
pass message onto the Apps handler, or wait until passThru is true before passing message on.
handleWatchEvent(WatcherElement, Lock) - Method in interface uk.ac.vamsas.client.simpleclient.WatcherCallBack
 
handler - Variable in class uk.ac.vamsas.client.simpleclient.WatcherElement
 
handlerCalled - Variable in class uk.ac.vamsas.client.simpleclient.WatcherElement
true when the handler is being called for this watcher
handlesSubtreeUpdates() - Method in interface uk.ac.vamsas.client.IObjectUpdate
Called to test if this handler is to be called for updates to any Vobjects below the Root Vobject in the vamsas document.
hasAfter() - Method in class uk.ac.vamsas.objects.core.AnnotationElement
Method hasAfter.
hasAligned() - Method in class uk.ac.vamsas.objects.core.Alignment
Method hasAligned.
hasChanged() - Method in class uk.ac.vamsas.client.simpleclient.FileWatcher
Test for change in file state.
hasClientAppdata() - Method in interface uk.ac.vamsas.client.IClientAppdata
 
hasClientAppdata() - Method in class uk.ac.vamsas.client.simpleclient.SimpleClientAppdata
 
hasCompressed() - Method in class uk.ac.vamsas.objects.core.Attachment
Method hasCompressed.
hasContent() - Method in class uk.ac.vamsas.objects.core.Score
Method hasContent.
hasEnd() - Method in class uk.ac.vamsas.objects.core.MapList
Method hasEnd.
hasEnd() - Method in class uk.ac.vamsas.objects.core.Seg
Method hasEnd.
hasEnd() - Method in class uk.ac.vamsas.objects.core.SequenceType
Method hasEnd.
hasFrom() - Method in class uk.ac.vamsas.objects.core.MapList
Method hasFrom.
hasGraph() - Method in class uk.ac.vamsas.objects.core.AlignmentAnnotation
Method hasGraph.
hasGraph() - Method in class uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation
Method hasGraph.
hasI() - Method in class uk.ac.vamsas.objects.core.Pos
Method hasI.
hasInclusive() - Method in class uk.ac.vamsas.objects.core.Seg
Method hasInclusive.
hasPosition() - Method in class uk.ac.vamsas.objects.core.AnnotationElement
Method hasPosition.
hasSeqAEnd() - Method in class uk.ac.vamsas.objects.core.Range
Method hasSeqAEnd.
hasSeqAStart() - Method in class uk.ac.vamsas.objects.core.Range
Method hasSeqAStart.
hasSeqBEnd() - Method in class uk.ac.vamsas.objects.core.Range
Method hasSeqBEnd.
hasSeqBStart() - Method in class uk.ac.vamsas.objects.core.Range
Method hasSeqBStart.
hasStart() - Method in class uk.ac.vamsas.objects.core.MapList
Method hasStart.
hasStart() - Method in class uk.ac.vamsas.objects.core.Seg
Method hasStart.
hasStart() - Method in class uk.ac.vamsas.objects.core.SequenceType
Method hasStart.
hasTo() - Method in class uk.ac.vamsas.objects.core.MapList
Method hasTo.
hasUnit() - Method in class uk.ac.vamsas.objects.core.MapRangeType
Method hasUnit.
hasUserAppdata() - Method in interface uk.ac.vamsas.client.IClientAppdata
 
hasUserAppdata() - Method in class uk.ac.vamsas.client.simpleclient.SimpleClientAppdata
 
hashCode() - Method in class org.apache.tools.zip.ZipEntry
Get the hashCode of the entry.
hashCode() - Method in class org.apache.tools.zip.ZipLong
Override to make two instances with same value equal.
hashCode() - Method in class org.apache.tools.zip.ZipShort
Override to make two instances with same value equal.
hashCode() - Method in class uk.ac.vamsas.client.Vobject
Override Object.hashCode with base value for castor generated object hashcodes.
hashCode() - Method in class uk.ac.vamsas.client.VorbaId
 
hashCode() - Method in class uk.ac.vamsas.objects.core.Alignment
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.AlignmentAnnotation
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.AlignmentSequence
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.AnnotationElement
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.AppData
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.ApplicationData
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.Attachment
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.Common
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.DataSet
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.DataSetAnnotations
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.DbRef
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.Entry
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.Glyph
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.Input
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.Instance
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.Link
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.Local
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.LockFile
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.Map
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.MapList
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.MapRangeType
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.MapType
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.Mapped
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.Mapping
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.Newick
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.NodeType
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.Param
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.Pos
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.Property
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.Provenance
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.Range
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.RangeType
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.ReferenceType
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.Score
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.Seg
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.Sequence
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.SequenceMapping
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.SequenceType
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.Tree
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.Treenode
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.User
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.VAMSAS
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.Vref
Overrides the java.lang.Object.hashCode method.
hashCode() - Method in class uk.ac.vamsas.objects.core.Vxref
Overrides the java.lang.Object.hashCode method.
hashOfAppDatas(Hashtable, Instance[]) - Static method in class uk.ac.vamsas.test.simpleclient.ArchiveWriter
 

I

IClient - interface uk.ac.vamsas.client.IClient.
Defines the methods availabable to a vamsas application for interacting with its Vorba agent created by an IClientFactory instance for a particular session, user, and application handle.
IClientAppdata - interface uk.ac.vamsas.client.IClientAppdata.
Object for accessing Client and User specific data in an IClientDocument instance.
IClientDocument - interface uk.ac.vamsas.client.IClientDocument.
Defines the API for the Vamsas XML Document as accessed by a Vamsas SimpleClient Application.
IClientFactory - interface uk.ac.vamsas.client.IClientFactory.
Defines methods for instantiating Vorba client application agents
IDocumentUpdater - interface uk.ac.vamsas.objects.IDocumentUpdater.
 
IMessageHandler - interface uk.ac.vamsas.client.picking.IMessageHandler.
Interface that defines the methods required for a message handler.
INTEGERTYPE - Static variable in class uk.ac.vamsas.objects.utils.Properties
 
INVALID_DOC - Static variable in class uk.ac.vamsas.client.InvalidSessionDocumentException
basic error for this exception
IObjectUpdate - interface uk.ac.vamsas.client.IObjectUpdate.
Methods implemented by a Vamsas Application's Object Update handler
IPickManager - interface uk.ac.vamsas.client.picking.IPickManager.
Interface that defines the methods required for a pick manager.
IVorbaBinding - interface uk.ac.vamsas.objects.IVorbaBinding.
Provides methods to map between VorbaIds and arbitrary object references for use by a vamsas Application when moving between its own datamodel and the Vamsas session objects.
IVorbaIdFactory - interface uk.ac.vamsas.client.IVorbaIdFactory.
 
Iapp - interface uk.ac.vamsas.client.Iapp.
 
IdFactory - class uk.ac.vamsas.client.simpleclient.IdFactory.
Simplest VorbaId constructor
IdFactory() - Constructor for class uk.ac.vamsas.client.simpleclient.IdFactory
 
IdFactory(SessionHandle, ClientHandle, UserHandle) - Constructor for class uk.ac.vamsas.client.simpleclient.IdFactory
 
IdFactory(SessionHandle, ClientHandle, UserHandle, Hashtable) - Constructor for class uk.ac.vamsas.client.simpleclient.IdFactory
Create IdFactory with existing object hashes and id set
Input - class uk.ac.vamsas.objects.core.Input.
Class Input.
Input() - Constructor for class uk.ac.vamsas.objects.core.Input
 
InputDescriptor - class uk.ac.vamsas.objects.core.descriptors.InputDescriptor.
Class InputDescriptor.
InputDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.InputDescriptor
 
Instance - class uk.ac.vamsas.objects.core.Instance.
Class Instance.
Instance() - Constructor for class uk.ac.vamsas.objects.core.Instance
 
InstanceDescriptor - class uk.ac.vamsas.objects.core.descriptors.InstanceDescriptor.
Class InstanceDescriptor.
InstanceDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.InstanceDescriptor
 
InvalidSessionDocumentException - exception uk.ac.vamsas.client.InvalidSessionDocumentException.
 
InvalidSessionDocumentException() - Constructor for class uk.ac.vamsas.client.InvalidSessionDocumentException
 
InvalidSessionDocumentException(String) - Constructor for class uk.ac.vamsas.client.InvalidSessionDocumentException
 
InvalidSessionDocumentException(Throwable) - Constructor for class uk.ac.vamsas.client.InvalidSessionDocumentException
 
InvalidSessionDocumentException(String, Throwable) - Constructor for class uk.ac.vamsas.client.InvalidSessionDocumentException
 
InvalidSessionUrnException - exception uk.ac.vamsas.client.InvalidSessionUrnException.
 
InvalidSessionUrnException() - Constructor for class uk.ac.vamsas.client.InvalidSessionUrnException
 
InvalidSessionUrnException(String, Throwable) - Constructor for class uk.ac.vamsas.client.InvalidSessionUrnException
 
InvalidSessionUrnException(String) - Constructor for class uk.ac.vamsas.client.InvalidSessionUrnException
 
InvalidSessionUrnException(Throwable) - Constructor for class uk.ac.vamsas.client.InvalidSessionUrnException
 
id - Variable in class uk.ac.vamsas.client.VorbaId
 
importDocument(File) - Method in interface uk.ac.vamsas.client.IClient
Any application may call importDocument to merge a stored vamsasDocument into the current session.
importDocument(File) - Method in class uk.ac.vamsas.client.simpleclient.SimpleClient
 
increaseCycleCount() - Method in class uk.ac.vamsas.client.simpleclient.ClientSessionFileWatcherElement
Increases the count of cycles
initMapType(MapType, MapList, boolean) - Static method in class uk.ac.vamsas.objects.utils.Range
initialise a MapType object from a MapList object.
initMapType(MapType, MapList, boolean, boolean) - Static method in class uk.ac.vamsas.objects.utils.Range
 
initRangeType(RangeType, int[]) - Static method in class uk.ac.vamsas.objects.utils.Range
initialise a range type object from a set of start/end inclusive intervals
initWatch() - Method in class uk.ac.vamsas.client.simpleclient.SessionFileWatcherElement
 
initWatch() - Method in class uk.ac.vamsas.client.simpleclient.SessionFlagWatcherElement
 
initWatch() - Method in class uk.ac.vamsas.client.simpleclient.VamsasFileWatcherElement
 
initWatch() - Method in class uk.ac.vamsas.client.simpleclient.WatcherElement
called to generate the watcher object by enableWatch and in doWatch
initial_update() - Method in class uk.ac.vamsas.test.simpleclient.simpleapp.VamsasClient
Called by gui to read anything from the vamsas session into the apps datamodel after it has started up.
initialized(Object) - Method in class uk.ac.vamsas.client.VorbaXmlBinder
 
interrupt() - Method in class uk.ac.vamsas.client.simpleclient.VamsasFileWatcherThread
 
interruptWatching() - Method in class uk.ac.vamsas.client.simpleclient.EventGeneratorThread
 
intersectVisContigs(int[]) - Method in class uk.ac.vamsas.objects.utils.Mapping
return a new mapping object with a maplist modifed to only map the visible regions defined by viscontigs.
iohandler - Variable in class uk.ac.vamsas.client.simpleclient.ClientDocument
 
iohandler - Variable in class uk.ac.vamsas.test.simpleclient.ClientDoc
 
isAfter() - Method in class uk.ac.vamsas.objects.core.AnnotationElement
Returns the value of field 'after'.
isAligned() - Method in class uk.ac.vamsas.objects.core.Alignment
Returns the value of field 'aligned'.
isBoolean(Property) - Static method in class uk.ac.vamsas.objects.utils.Properties
Boolean content test
isCompressed() - Method in class uk.ac.vamsas.objects.core.Attachment
Returns the value of field 'compressed'.
isDirectory() - Method in class org.apache.tools.zip.AsiExtraField
Is this entry a directory?
isDirectory() - Method in class org.apache.tools.zip.ZipEntry
Is this entry a directory?
isDocumentWatchEnabled() - Method in class uk.ac.vamsas.client.simpleclient.EventGeneratorThread
 
isDocumentWritten() - Method in class uk.ac.vamsas.client.simpleclient.VamsasArchive
 
isDummy() - Method in class uk.ac.vamsas.objects.utils.trees.SequenceNode
 
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.AlignmentAnnotationDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.AlignmentDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.AlignmentSequenceAnnotationDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.AlignmentSequenceDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.AnnotationElementDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.AppDataDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.ApplicationDataDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.AttachmentDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.CommonDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.DataSetAnnotationsDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.DataSetDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.DbRefDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.EntryDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.GlyphDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.InputDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.InstanceDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.LinkDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.LocalDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.LockFileDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.MapDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.MapListDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.MapRangeTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.MapTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.MappedDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.MappingDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.NewickDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.NodeTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.ParamDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.PosDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.PropertyDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.ProvenanceDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.RangeAnnotationDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.RangeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.RangeTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.ReferenceTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.ScoreDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.SegDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.SequenceDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.SequenceMappingDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.SequenceTypeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.TreeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.TreenodeDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.UserDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.VAMSASDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.VamsasDocumentDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.VrefDescriptor
Method isElementDefinition.
isElementDefinition() - Method in class uk.ac.vamsas.objects.core.descriptors.VxrefDescriptor
Method isElementDefinition.
isFloat(Property) - Static method in class uk.ac.vamsas.objects.utils.Properties
Float content test
isGraph() - Method in class uk.ac.vamsas.objects.core.AlignmentAnnotation
Returns the value of field 'graph'.
isGraph() - Method in class uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation
Returns the value of field 'graph'.
isHandlerCalled() - Method in class uk.ac.vamsas.client.simpleclient.WatcherElement
 
isInclusive() - Method in class uk.ac.vamsas.objects.core.Seg
Returns the value of field 'inclusive'.
isInteger(Property) - Static method in class uk.ac.vamsas.objects.utils.Properties
Integer content test
isInvalidModification() - Method in class uk.ac.vamsas.client.simpleclient.ClientDocument
if this is set the document will never be written back to the session unless the corruption is fixed.
isLeaf() - Method in class uk.ac.vamsas.objects.utils.trees.BinaryNode
DOCUMENT ME!
isLink() - Method in class org.apache.tools.zip.AsiExtraField
Is this entry a symbolic link?
isLocked() - Method in class uk.ac.vamsas.client.simpleclient.FileLock
 
isLocked() - Method in class uk.ac.vamsas.client.simpleclient.Lock
 
isLocked() - Method in class uk.ac.vamsas.client.simpleclient.NativeLock
 
isModified() - Method in class uk.ac.vamsas.client.simpleclient.ClientDocument
Public method for internal use by SimpleClient.
isModified() - Method in class uk.ac.vamsas.client.simpleclient.SimpleClientAppdata
 
isModified - Variable in class uk.ac.vamsas.test.simpleclient.ClientDoc
 
isNewInDocument() - Method in class uk.ac.vamsas.client.Vobject
 
isNone() - Method in class uk.ac.vamsas.client.picking.SelectionMessage
 
isOpen() - Method in class uk.ac.vamsas.client.AppDataOutputStream
 
isPassThru() - Method in class uk.ac.vamsas.client.simpleclient.SimplePickManager
 
isPlaceholder() - Method in class uk.ac.vamsas.objects.utils.trees.SequenceNode
 
isRegisterable() - Method in class uk.ac.vamsas.client.Vobject
 
isRegistered() - Method in class uk.ac.vamsas.client.Vobject
 
isSeekable() - Method in class org.apache.tools.zip.ZipOutputStream
This method indicates whether this archive is writing to a seekable stream (i.e., to a random access file).
isString(Property) - Static method in class uk.ac.vamsas.objects.utils.Properties
String content test
isTargetLockFile(File) - Method in class uk.ac.vamsas.client.simpleclient.FileLock
 
isTargetLockFile(File) - Method in class uk.ac.vamsas.client.simpleclient.Lock
test whether the given file is a target or related to the lock on the target file.
isTargetLockFile(File) - Method in class uk.ac.vamsas.client.simpleclient.NativeLock
 
isType(Property, String) - Static method in class uk.ac.vamsas.objects.utils.Properties
 
isUpdated() - Method in class uk.ac.vamsas.client.Vobject
 
isUpdated(Vobject) - Method in class uk.ac.vamsas.client.Vobjhash
compares the old hash value with the unmarshalled object's most recently computed hash value and updates internal record.
isValid() - Method in class uk.ac.vamsas.client.simpleclient.VamsasArchiveReader
Test for valid vamsas document archive
isValid() - Method in class uk.ac.vamsas.objects.core.Alignment
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.AlignmentAnnotation
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.AlignmentSequence
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.AnnotationElement
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.AppData
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.ApplicationData
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.Attachment
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.Common
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.DataSet
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.DataSetAnnotations
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.DbRef
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.Entry
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.Glyph
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.Input
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.Instance
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.Link
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.Local
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.LockFile
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.Map
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.MapList
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.MapRangeType
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.MapType
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.Mapped
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.Mapping
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.Newick
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.NodeType
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.Param
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.Pos
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.Property
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.Provenance
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.Range
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.RangeType
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.ReferenceType
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.Score
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.Seg
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.Sequence
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.SequenceMapping
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.SequenceType
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.Tree
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.Treenode
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.User
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.VAMSAS
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.Vref
Method isValid.
isValid() - Method in class uk.ac.vamsas.objects.core.Vxref
Method isValid.
isValid(Property) - Static method in class uk.ac.vamsas.objects.utils.Properties
validate property p against the known type strings and try to parse the content string accordingly
isVersion(String) - Static method in class uk.ac.vamsas.objects.utils.document.VersionEntries
 
isWatchEnabled() - Method in class uk.ac.vamsas.client.simpleclient.WatcherElement
 
isWatcherAlive() - Method in class uk.ac.vamsas.client.simpleclient.EventGeneratorThread
 
is__stored_in_document() - Method in class uk.ac.vamsas.client.Vobject
 
is_valid_aa_seq(SequenceType) - Static method in class uk.ac.vamsas.objects.utils.Seq
 

J

JarMarker - class org.apache.tools.zip.JarMarker.
If this extra field is added as the very first extra field of the archive, Solaris will consider it an executable jar file.
JarMarker() - Constructor for class org.apache.tools.zip.JarMarker
No-arg constructor
joinSession() - Method in interface uk.ac.vamsas.client.IClient
Client application calls this after any pre-session initialization (registering of Handlers, etc) Exceptions are raised for any failures.
joinSession() - Method in class uk.ac.vamsas.client.simpleclient.SimpleClient
 

L

LFH_SIG - Static variable in class org.apache.tools.zip.ZipOutputStream
local file header signature
LINK_FLAG - Static variable in interface org.apache.tools.zip.UnixStat
Indicates symbolic links.
Link - class uk.ac.vamsas.objects.core.Link.
Class Link.
Link() - Constructor for class uk.ac.vamsas.objects.core.Link
 
LinkDescriptor - class uk.ac.vamsas.objects.core.descriptors.LinkDescriptor.
Class LinkDescriptor.
LinkDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.LinkDescriptor
 
ListFile - class uk.ac.vamsas.client.simpleclient.ListFile.
base class for generic list storage and retrieval operations from a locked IO file TODO: LATER: generalize for all list storage and retrieval operations (pull-up from ClientsFile object)
ListFile(File) - Constructor for class uk.ac.vamsas.client.simpleclient.ListFile
 
Local - class uk.ac.vamsas.objects.core.Local.
 
Local() - Constructor for class uk.ac.vamsas.objects.core.Local
 
LocalDescriptor - class uk.ac.vamsas.objects.core.descriptors.LocalDescriptor.
Class LocalDescriptor.
LocalDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.LocalDescriptor
 
Lock - class uk.ac.vamsas.client.simpleclient.Lock.
transient object representing a file lock This lock should hold for all processes interacting in a session.
Lock(File) - Constructor for class uk.ac.vamsas.client.simpleclient.Lock
creates a valid Lock (test with isLocked) if a lock could be obtained for lockfile
LockFactory - class uk.ac.vamsas.client.simpleclient.LockFactory.
 
LockFactory() - Constructor for class uk.ac.vamsas.client.simpleclient.LockFactory
 
LockFile - class uk.ac.vamsas.objects.core.LockFile.
Class LockFile.
LockFile() - Constructor for class uk.ac.vamsas.objects.core.LockFile
 
LockFileDescriptor - class uk.ac.vamsas.objects.core.descriptors.LockFileDescriptor.
Class LockFileDescriptor.
LockFileDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.LockFileDescriptor
 
LockTimeoutException - exception uk.ac.vamsas.client.simpleclient.LockTimeoutException.
 
LockTimeoutException() - Constructor for class uk.ac.vamsas.client.simpleclient.LockTimeoutException
 
LockTimeoutException(String, Throwable) - Constructor for class uk.ac.vamsas.client.simpleclient.LockTimeoutException
 
LockTimeoutException(String) - Constructor for class uk.ac.vamsas.client.simpleclient.LockTimeoutException
 
LockTimeoutException(Throwable) - Constructor for class uk.ac.vamsas.client.simpleclient.LockTimeoutException
 
LockedFileOutputStream - class uk.ac.vamsas.client.simpleclient.LockedFileOutputStream.
 
LockedFileOutputStream(File) - Constructor for class uk.ac.vamsas.client.simpleclient.LockedFileOutputStream
 
LockedFileOutputStream(File, boolean) - Constructor for class uk.ac.vamsas.client.simpleclient.LockedFileOutputStream
 
LockedFileOutputStream(FileDescriptor) - Constructor for class uk.ac.vamsas.client.simpleclient.LockedFileOutputStream
 
LockedFileOutputStream(String) - Constructor for class uk.ac.vamsas.client.simpleclient.LockedFileOutputStream
 
LockedFileOutputStream(String, boolean) - Constructor for class uk.ac.vamsas.client.simpleclient.LockedFileOutputStream
 
latestVersion() - Static method in class uk.ac.vamsas.objects.utils.document.VersionEntries
 
left() - Method in class uk.ac.vamsas.objects.utils.trees.BinaryNode
DOCUMENT ME!
length() - Method in class uk.ac.vamsas.client.simpleclient.FileLock
 
length() - Method in class uk.ac.vamsas.client.simpleclient.Lock
safe lock target length() function.
length() - Method in class uk.ac.vamsas.client.simpleclient.NativeLock
 
locateFeature(int, int) - Method in class uk.ac.vamsas.objects.utils.Mapping
locates the region of feature f in the associated (local) sequence's reference frame
locateInFrom(int, int) - Method in class uk.ac.vamsas.objects.utils.MapList
find series of intervals mapping from start-end in the From map.
locateInTo(int, int) - Method in class uk.ac.vamsas.objects.utils.MapList
find series of intervals mapping from start-end in the to map.
locateMappedRange(int, int) - Method in class uk.ac.vamsas.objects.utils.Mapping
return a series of mapped contigs mapped from a range on the associated sequence
locateRange(int, int) - Method in class uk.ac.vamsas.objects.utils.Mapping
return a series of contigs on the associated sequence corresponding to the from,to interval on the mapped reference frame
lock - Variable in class uk.ac.vamsas.client.simpleclient.NativeLock
 
lockFile(Lock) - Method in class uk.ac.vamsas.client.simpleclient.SessionFile
 
lockFile() - Method in class uk.ac.vamsas.client.simpleclient.SessionFile
Get a lock for the SessionFile
locktype - Static variable in class uk.ac.vamsas.client.simpleclient.LockFactory
 
locktypes - Static variable in class uk.ac.vamsas.client.simpleclient.LockFactory
 
log - Variable in class uk.ac.vamsas.client.simpleclient.Lock
 
log - Static variable in class uk.ac.vamsas.client.simpleclient.LockFactory
 
log - Static variable in class uk.ac.vamsas.client.simpleclient.SimpleDocBinding
 

M

MODIFIEDDOC_FILE - Static variable in class uk.ac.vamsas.client.simpleclient.VamsasSession
session file storing the last_stored_stat data
Map - class uk.ac.vamsas.objects.core.Map.
the local mapType maps from the parent sequence coordinate frame to the reference frame defined by the dbRef element.
Map() - Constructor for class uk.ac.vamsas.objects.core.Map
 
MapDescriptor - class uk.ac.vamsas.objects.core.descriptors.MapDescriptor.
Class MapDescriptor.
MapDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.MapDescriptor
 
MapList - class uk.ac.vamsas.objects.core.MapList.
Class MapList.
MapList() - Constructor for class uk.ac.vamsas.objects.core.MapList
 
MapList - class uk.ac.vamsas.objects.utils.MapList.
MapList Simple way of bijectively mapping a non-contiguous linear range to another non-contiguous linear range Use at your own risk! TODO: efficient implementation of private posMap method TODO: test/ensure that sense of from and to ratio start position is conserved (codon start position recovery) TODO: optimize to use int[][] arrays rather than vectors.
MapList(int[], int[], int, int) - Constructor for class uk.ac.vamsas.objects.utils.MapList
 
MapList(MapList) - Constructor for class uk.ac.vamsas.objects.utils.MapList
 
MapListDescriptor - class uk.ac.vamsas.objects.core.descriptors.MapListDescriptor.
Class MapListDescriptor.
MapListDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.MapListDescriptor
 
MapRangeType - class uk.ac.vamsas.objects.core.MapRangeType.
Class MapRangeType.
MapRangeType() - Constructor for class uk.ac.vamsas.objects.core.MapRangeType
 
MapRangeTypeDescriptor - class uk.ac.vamsas.objects.core.descriptors.MapRangeTypeDescriptor.
Class MapRangeTypeDescriptor.
MapRangeTypeDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.MapRangeTypeDescriptor
 
MapType - class uk.ac.vamsas.objects.core.MapType.
Two sets of ranges defined between objects - usually sequences, indicating which regions on each are mapped.
MapType() - Constructor for class uk.ac.vamsas.objects.core.MapType
 
MapTypeDescriptor - class uk.ac.vamsas.objects.core.descriptors.MapTypeDescriptor.
Class MapTypeDescriptor.
MapTypeDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.MapTypeDescriptor
 
Mapped - class uk.ac.vamsas.objects.core.Mapped.
 
Mapped() - Constructor for class uk.ac.vamsas.objects.core.Mapped
 
MappedDescriptor - class uk.ac.vamsas.objects.core.descriptors.MappedDescriptor.
Class MappedDescriptor.
MappedDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.MappedDescriptor
 
Mapping - class uk.ac.vamsas.objects.core.Mapping.
Class Mapping.
Mapping() - Constructor for class uk.ac.vamsas.objects.core.Mapping
 
Mapping - class uk.ac.vamsas.objects.utils.Mapping.
 
Mapping(MapList) - Constructor for class uk.ac.vamsas.objects.utils.Mapping
The seuqence that map maps the associated seuqence to (if any).
Mapping(int[], int[], int, int) - Constructor for class uk.ac.vamsas.objects.utils.Mapping
create a new mapping from (in Jalview) param to was the destination sequence being mapped
Mapping(Mapping) - Constructor for class uk.ac.vamsas.objects.utils.Mapping
create a duplicate (and independent) mapping object with the same reference to any SequenceI being mapped to.
MappingDescriptor - class uk.ac.vamsas.objects.core.descriptors.MappingDescriptor.
Class MappingDescriptor.
MappingDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.MappingDescriptor
 
Message - class uk.ac.vamsas.client.picking.Message.
Abstract base class for all message types supported by the picking API.
Message() - Constructor for class uk.ac.vamsas.client.picking.Message
Constructs a new message.
MouseOverMessage - class uk.ac.vamsas.client.picking.MouseOverMessage.
Message class that can be used to send mouse over events.
MouseOverMessage(String, int) - Constructor for class uk.ac.vamsas.client.picking.MouseOverMessage
Constructs a new mouse over message.
main(String[]) - Static method in class uk.ac.vamsas.client.picking.TestApp
 
main(String[]) - Static method in class uk.ac.vamsas.objects.utils.Format
a test stub for the format class
main(String[]) - Static method in class uk.ac.vamsas.objects.utils.MapList
 
main(String[]) - Static method in class uk.ac.vamsas.objects.utils.Mapping
 
main(String[]) - Static method in class uk.ac.vamsas.objects.utils.trees.NewickFile
 
main(String[]) - Static method in class uk.ac.vamsas.test.ExampleApplication
 
main(String[]) - Static method in class uk.ac.vamsas.test.objects.Core
 
main(String[]) - Static method in class uk.ac.vamsas.test.simpleclient.ArchiveClient
 
main(String[]) - Static method in class uk.ac.vamsas.test.simpleclient.ArchiveReader
tests VamsasArchiveReader archive reader on a vamsas jar file
main(String[]) - Static method in class uk.ac.vamsas.test.simpleclient.ArchiveStreamReader
tests VamsasArchiveReader archive reader on a vamsas jar file opened as a stream
main(String[]) - Static method in class uk.ac.vamsas.test.simpleclient.ArchiveWatcher
 
main(String[]) - Static method in class uk.ac.vamsas.test.simpleclient.ArchiveWriter
 
main(String[]) - Static method in class uk.ac.vamsas.test.simpleclient.ClientsFileTest
 
main(String[]) - Static method in class uk.ac.vamsas.test.simpleclient.TestSessionURN
 
main(String[]) - Static method in class uk.ac.vamsas.test.simpleclient.VamsasArchive
 
main(String[]) - Static method in class uk.ac.vamsas.test.simpleclient.ZipTest
 
main(String[]) - Static method in class uk.ac.vamsas.test.simpleclient.simpleapp.VamsasClient
 
makeDemoAppdata(VamsasArchive, String, String, String) - Static method in class uk.ac.vamsas.test.simpleclient.VamsasArchive
 
makeFromMap() - Method in class uk.ac.vamsas.objects.utils.MapList
get all mapped positions from 'from' to 'to'
makeToMap() - Method in class uk.ac.vamsas.objects.utils.MapList
get all mapped positions from 'to' to 'from'
makeTreeNodes() - Method in class uk.ac.vamsas.objects.utils.trees.NewickFile
make tree node vector from a newick tree structure with associated vamsas objects
makeTreeNodes(boolean) - Method in class uk.ac.vamsas.objects.utils.trees.NewickFile
make treenode vector for a parsed tree with/out leaf node associations
makeVorbaId(Vobject) - Method in interface uk.ac.vamsas.client.IVorbaIdFactory
construct a new id appropriate for this client in the vamsas session.
makeVorbaId(Vobject) - Method in class uk.ac.vamsas.client.VorbaIdFactory
construct a new id appropriate for this client in the vamsas session.
makeVorbaId(Vobject) - Method in class uk.ac.vamsas.client.simpleclient.IdFactory
 
make_Alignment(Entry, Sequence[]) - Static method in class uk.ac.vamsas.objects.utils.SeqAln
manufacture an alignment/dataset from an array of sequences
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.Alignment
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.Alignment
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.AlignmentAnnotation
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.AlignmentAnnotation
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.AlignmentSequence
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.AlignmentSequence
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.AnnotationElement
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.AnnotationElement
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.AppData
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.AppData
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.ApplicationData
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.ApplicationData
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.Attachment
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.Attachment
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.Common
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.Common
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.DataSet
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.DataSet
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.DataSetAnnotations
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.DataSetAnnotations
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.DbRef
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.DbRef
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.Entry
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.Entry
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.Glyph
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.Glyph
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.Input
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.Input
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.Instance
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.Instance
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.Link
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.Link
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.Local
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.Local
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.LockFile
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.LockFile
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.Map
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.Map
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.MapList
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.MapList
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.MapRangeType
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.MapRangeType
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.MapType
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.MapType
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.Mapped
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.Mapped
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.Mapping
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.Mapping
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.Newick
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.Newick
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.NodeType
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.NodeType
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.Param
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.Param
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.Pos
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.Pos
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.Property
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.Property
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.Provenance
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.Provenance
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.Range
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.Range
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.ReferenceType
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.ReferenceType
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.Score
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.Score
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.Seg
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.Seg
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.Sequence
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.Sequence
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.SequenceMapping
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.SequenceMapping
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.SequenceType
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.SequenceType
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.Tree
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.Tree
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.Treenode
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.Treenode
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.User
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.User
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.VAMSAS
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.VAMSAS
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.VamsasDocument
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.VamsasDocument
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.Vref
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.Vref
 
marshal(Writer) - Method in class uk.ac.vamsas.objects.core.Vxref
 
marshal(ContentHandler) - Method in class uk.ac.vamsas.objects.core.Vxref
 
matchTreeNodeNames(String[], Vobject[]) - Method in class uk.ac.vamsas.objects.utils.trees.NewickFile
 
merge(Vobject) - Method in class uk.ac.vamsas.client.Vobject
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.
mergeCentralDirectoryData(ZipExtraField[]) - Static method in class org.apache.tools.zip.ExtraFieldUtils
Merges the central directory fields of the given ZipExtraFields.
mergeDocs(VamsasArchive, VamsasDocument, VamsasArchiveReader, VamsasDocument) - Static method in class uk.ac.vamsas.test.simpleclient.ArchiveWriter
Copy new datasets and appdatas from one vamsas document to another.
mergeLocalFileDataData(ZipExtraField[]) - Static method in class org.apache.tools.zip.ExtraFieldUtils
Merges the local file data fields of the given ZipExtraFields.
message - Variable in class uk.ac.vamsas.client.picking.Message
 

N

NativeLock - class uk.ac.vamsas.client.simpleclient.NativeLock.
 
NativeLock(File, boolean) - Constructor for class uk.ac.vamsas.client.simpleclient.NativeLock
 
Newick - class uk.ac.vamsas.objects.core.Newick.
Class Newick.
Newick() - Constructor for class uk.ac.vamsas.objects.core.Newick
 
NewickDescriptor - class uk.ac.vamsas.objects.core.descriptors.NewickDescriptor.
Class NewickDescriptor.
NewickDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.NewickDescriptor
 
NewickFile - class uk.ac.vamsas.objects.utils.trees.NewickFile.
DOCUMENT ME!
NewickFile(String) - Constructor for class uk.ac.vamsas.objects.utils.trees.NewickFile
Creates a new NewickFile object
NewickFile(File) - Constructor for class uk.ac.vamsas.objects.utils.trees.NewickFile
 
NewickFile(SequenceNode) - Constructor for class uk.ac.vamsas.objects.utils.trees.NewickFile
Creates a new NewickFile object.
NewickFile(SequenceNode, boolean) - Constructor for class uk.ac.vamsas.objects.utils.trees.NewickFile
Creates a new NewickFile object.
NewickFile(SequenceNode, boolean, boolean) - Constructor for class uk.ac.vamsas.objects.utils.trees.NewickFile
Creates a new NewickFile object.
NewickFile(SequenceNode, boolean, boolean, boolean) - Constructor for class uk.ac.vamsas.objects.utils.trees.NewickFile
Creates a new NewickFile object.
NoDefaultSessionException - exception uk.ac.vamsas.client.NoDefaultSessionException.
 
NoDefaultSessionException() - Constructor for class uk.ac.vamsas.client.NoDefaultSessionException
 
NoDefaultSessionException(String) - Constructor for class uk.ac.vamsas.client.NoDefaultSessionException
 
NoDefaultSessionException(Throwable) - Constructor for class uk.ac.vamsas.client.NoDefaultSessionException
 
NoDefaultSessionException(String, Throwable) - Constructor for class uk.ac.vamsas.client.NoDefaultSessionException
 
NodeType - class uk.ac.vamsas.objects.core.NodeType.
Class NodeType.
NodeType() - Constructor for class uk.ac.vamsas.objects.core.NodeType
 
NodeTypeDescriptor - class uk.ac.vamsas.objects.core.descriptors.NodeTypeDescriptor.
Class NodeTypeDescriptor.
NodeTypeDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.NodeTypeDescriptor
 
newAlignmentSequence(String, String, Sequence, long, long) - Static method in class uk.ac.vamsas.objects.utils.Seq
 
newId(IVorbaIdFactory, Vobject) - Static method in class uk.ac.vamsas.client.VorbaId
 
newId(String) - Static method in class uk.ac.vamsas.client.VorbaId
protected VorbaId constructor used when turning XML ID strings into vorba IDs
newId(String) - Method in class uk.ac.vamsas.client.VorbaIdFactory
internal method to access the protected VorbaId object constructor This shennanigan is to prevent casual generation of VorbaIds (which may destroy the integrity of a Vamsas Document!)
newProperty(String, String, String) - Static method in class uk.ac.vamsas.objects.utils.Properties
 
newProvenance(Entry) - Static method in class uk.ac.vamsas.objects.utils.ProvenanceStuff
 
newProvenance(String, String) - Static method in class uk.ac.vamsas.objects.utils.ProvenanceStuff
 
newProvenance(String, String, String) - Static method in class uk.ac.vamsas.objects.utils.ProvenanceStuff
 
newProvenanceEntry(String, String, String) - Static method in class uk.ac.vamsas.objects.utils.ProvenanceStuff
 
newSequence(String, String, String, int, int) - Static method in class uk.ac.vamsas.objects.utils.Seq
 
newVamsasDocument(VAMSAS[], String) - Static method in class uk.ac.vamsas.objects.utils.DocumentStuff
 
newVamsasDocument(VAMSAS[]) - Static method in class uk.ac.vamsas.objects.utils.DocumentStuff
 
newVamsasDocument(VAMSAS[], Provenance, String) - Static method in class uk.ac.vamsas.objects.utils.DocumentStuff
 
newobj - Variable in class uk.ac.vamsas.client.VorbaIdFactory
list of Vobjects added since last Document read.
nextLine() - Method in class uk.ac.vamsas.objects.utils.trees.NewickFile
 

O

openAsNewSessionIClient(ClientHandle, File) - Method in interface uk.ac.vamsas.client.IClientFactory
Create a new session and import an existing vamsas document into it.
openAsNewSessionIClient(ClientHandle, UserHandle, File) - Method in interface uk.ac.vamsas.client.IClientFactory
Create a new session as a particular user and import an existing vamsas document into it.
openAsNewSessionIClient(ClientHandle, File) - Method in class uk.ac.vamsas.client.simpleclient.SimpleClientFactory
 
openAsNewSessionIClient(ClientHandle, UserHandle, File) - Method in class uk.ac.vamsas.client.simpleclient.SimpleClientFactory
 
org.apache.tools.zip - package org.apache.tools.zip
 
outputVobjectState(Vobject, PrintStream) - Static method in class uk.ac.vamsas.test.simpleclient.ArchiveReports
 

P

PERM_MASK - Static variable in interface org.apache.tools.zip.UnixStat
Bits used for permissions (and sticky bit)
PROTEIN_HD_HYDRO - Static variable in class uk.ac.vamsas.objects.utils.GlyphDictionary
kyte and doolittle hydrophobicity TODO: specify this glyph set.
PROTEIN_SS_3STATE - Static variable in class uk.ac.vamsas.objects.utils.GlyphDictionary
standard H, E, or C three state secondary structure assignment.
Param - class uk.ac.vamsas.objects.core.Param.
Class Param.
Param() - Constructor for class uk.ac.vamsas.objects.core.Param
 
ParamDescriptor - class uk.ac.vamsas.objects.core.descriptors.ParamDescriptor.
Class ParamDescriptor.
ParamDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.ParamDescriptor
 
Pos - class uk.ac.vamsas.objects.core.Pos.
a position within the associated object's coordinate system
Pos() - Constructor for class uk.ac.vamsas.objects.core.Pos
 
PosDescriptor - class uk.ac.vamsas.objects.core.descriptors.PosDescriptor.
Class PosDescriptor.
PosDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.PosDescriptor
 
Properties - class uk.ac.vamsas.objects.utils.Properties.
 
Properties() - Constructor for class uk.ac.vamsas.objects.utils.Properties
 
Property - class uk.ac.vamsas.objects.core.Property.
Class Property.
Property() - Constructor for class uk.ac.vamsas.objects.core.Property
 
PropertyDescriptor - class uk.ac.vamsas.objects.core.descriptors.PropertyDescriptor.
Class PropertyDescriptor.
PropertyDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.PropertyDescriptor
 
Provenance - class uk.ac.vamsas.objects.core.Provenance.
Class Provenance.
Provenance() - Constructor for class uk.ac.vamsas.objects.core.Provenance
 
ProvenanceDescriptor - class uk.ac.vamsas.objects.core.descriptors.ProvenanceDescriptor.
Class ProvenanceDescriptor.
ProvenanceDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.ProvenanceDescriptor
 
ProvenanceStuff - class uk.ac.vamsas.objects.utils.ProvenanceStuff.
 
ProvenanceStuff() - Constructor for class uk.ac.vamsas.objects.utils.ProvenanceStuff
 
parent() - Method in class uk.ac.vamsas.objects.utils.trees.BinaryNode
DOCUMENT ME!
parse(byte[]) - Static method in class org.apache.tools.zip.ExtraFieldUtils
Split the array into ExtraFields and populate them with the give data.
parse() - Method in class uk.ac.vamsas.objects.utils.trees.NewickFile
call this to convert the newick string into a binary node linked tree Note: this is automatically called by the constructors, so you normally wouldn't need to use this.
parseFromLocalFileData(byte[], int, int) - Method in class org.apache.tools.zip.AsiExtraField
Populate data from this array as if it was in local file data.
parseFromLocalFileData(byte[], int, int) - Method in class org.apache.tools.zip.JarMarker
Populate data from this array as if it was in local file data.
parseFromLocalFileData(byte[], int, int) - Method in class org.apache.tools.zip.UnrecognizedExtraField
 
parseFromLocalFileData(byte[], int, int) - Method in interface org.apache.tools.zip.ZipExtraField
Populate data from this array as if it was in local file data.
parsemapType(MapType, int, int) - Static method in class uk.ac.vamsas.objects.utils.Range
 
parsemapType(MapType) - Static method in class uk.ac.vamsas.objects.utils.Range
Parse map with default units of 1,1
pollUpdate() - Method in interface uk.ac.vamsas.client.IClient
client application calls this to force the Vorba client to check for updates immediately.
pollUpdate() - Method in class uk.ac.vamsas.client.simpleclient.SimpleClient
 
print(PrintStream, String, double) - Static method in class uk.ac.vamsas.objects.utils.Format
prints a formatted number following printf conventions
print(PrintStream, String, long) - Static method in class uk.ac.vamsas.objects.utils.Format
prints a formatted number following printf conventions
print(PrintStream, String, char) - Static method in class uk.ac.vamsas.objects.utils.Format
prints a formatted number following printf conventions
print(PrintStream, String, String) - Static method in class uk.ac.vamsas.objects.utils.Format
prints a formatted number following printf conventions
print() - Method in class uk.ac.vamsas.objects.utils.trees.NewickFile
Generate a newick format tree according to internal flags for bootstraps, distances and root distances.
print(boolean) - Method in class uk.ac.vamsas.objects.utils.trees.NewickFile
Generate a newick format tree according to internal flags for distances and root distances and user specificied writing of bootstraps.
print(boolean, boolean) - Method in class uk.ac.vamsas.objects.utils.trees.NewickFile
Generate newick format tree according to internal flags for writing root node distances.
print(boolean, boolean, boolean) - Method in class uk.ac.vamsas.objects.utils.trees.NewickFile
Generate newick format tree according to user specified flags
print(StringBuffer, SequenceNode) - Method in class uk.ac.vamsas.objects.utils.trees.NewickFile
 
push_update() - Method in class uk.ac.vamsas.test.simpleclient.simpleapp.VamsasClient
Called by app when internal datamodel should exported (syncrhonised outwards) to vamsas document
putClientList(ClientHandle[]) - Method in class uk.ac.vamsas.client.simpleclient.ClientsFile
safely writes clients array to the file referred to by sessionFile.
putNextEntry(ZipEntry) - Method in class org.apache.tools.zip.ZipOutputStream
Begin writing next entry.
putSessionsList(SessionHandle[]) - Method in class uk.ac.vamsas.client.simpleclient.SessionsFile
safely writes sessions array to the file referred to by sessionFile.
putVamsasDocument(PrintWriter, VorbaIdFactory, VamsasDocument) - Static method in class uk.ac.vamsas.client.VorbaXmlBinder
writes the VamsasDocument to the given stream.
putVamsasDocument(VamsasDocument) - Method in class uk.ac.vamsas.client.simpleclient.VamsasArchive
 
putVamsasDocument(VamsasDocument, VorbaIdFactory) - Method in class uk.ac.vamsas.client.simpleclient.VamsasArchive
 

R

Range - class uk.ac.vamsas.objects.core.Range.
Class Range.
Range() - Constructor for class uk.ac.vamsas.objects.core.Range
 
Range - class uk.ac.vamsas.objects.utils.Range.
Utilities for working with RangeType and MapType objects.
Range() - Constructor for class uk.ac.vamsas.objects.utils.Range
 
RangeAnnotation - class uk.ac.vamsas.objects.core.RangeAnnotation.
Annotation for a rangeSpec - values can be attached for the whole specification, and to each position within the spec.
RangeAnnotation() - Constructor for class uk.ac.vamsas.objects.core.RangeAnnotation
 
RangeAnnotationDescriptor - class uk.ac.vamsas.objects.core.descriptors.RangeAnnotationDescriptor.
Class RangeAnnotationDescriptor.
RangeAnnotationDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.RangeAnnotationDescriptor
 
RangeDescriptor - class uk.ac.vamsas.objects.core.descriptors.RangeDescriptor.
Class RangeDescriptor.
RangeDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.RangeDescriptor
 
RangeType - class uk.ac.vamsas.objects.core.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
RangeType() - Constructor for class uk.ac.vamsas.objects.core.RangeType
 
RangeTypeDescriptor - class uk.ac.vamsas.objects.core.descriptors.RangeTypeDescriptor.
Class RangeTypeDescriptor.
RangeTypeDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.RangeTypeDescriptor
 
ReadClustalFile(InputStream) - Static method in class uk.ac.vamsas.objects.utils.SeqAln
 
ReferenceType - class uk.ac.vamsas.objects.core.ReferenceType.
base type for citing arbitrary links between vamsas objects Optional human readable description of the relationship
ReferenceType() - Constructor for class uk.ac.vamsas.objects.core.ReferenceType
 
ReferenceTypeDescriptor - class uk.ac.vamsas.objects.core.descriptors.ReferenceTypeDescriptor.
Class ReferenceTypeDescriptor.
ReferenceTypeDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.ReferenceTypeDescriptor
 
rafile - Variable in class uk.ac.vamsas.client.simpleclient.Lock
 
read_ClustalAlignment(InputStream, Entry) - Static method in class uk.ac.vamsas.objects.utils.SeqAln
 
read_FastaAlignment(InputStream, Entry) - Static method in class uk.ac.vamsas.objects.utils.SeqAln
 
read_SeqFasta(InputStream) - Static method in class uk.ac.vamsas.objects.utils.SeqSet
TODO: introduce a dictionary parameter for qualified sequence symbols Reads a sequence set from a stream - will only read prescribed amino acid symbols.
reader - Variable in class uk.ac.vamsas.test.simpleclient.ClientDoc
 
register(Class) - Static method in class org.apache.tools.zip.ExtraFieldUtils
Register a ZipExtraField implementation.
registerMessageHandler(IMessageHandler) - Method in interface uk.ac.vamsas.client.picking.IPickManager
Registers a message handler with the manager that allows the manager to perform a method callback on that object whenever a message is received.
registerMessageHandler(IMessageHandler) - Method in class uk.ac.vamsas.client.picking.SocketManager
Registers a message handler with the manager that allows the manager to perform a method callback on that object whenever a message is received.
registerMessageHandler(IMessageHandler) - Method in class uk.ac.vamsas.client.simpleclient.SimplePickManager
 
registerObject(Vobject) - Method in interface uk.ac.vamsas.client.IClientDocument
Returns an Vobject with a valid VorbaId, and provenance element.
registerObject(Vobject) - Method in class uk.ac.vamsas.client.simpleclient.ClientDocument
 
registerObject(Vobject) - Method in class uk.ac.vamsas.test.simpleclient.ClientDoc
 
registerObjects(Vobject[]) - Method in interface uk.ac.vamsas.client.IClientDocument
Returns an array of objects, each with a valid VorbaId (and completed provenance entry).
registerObjects(Vobject[]) - Method in class uk.ac.vamsas.client.simpleclient.ClientDocument
 
registerObjects(Vobject[]) - Method in class uk.ac.vamsas.test.simpleclient.ClientDoc
 
registerable - Variable in class uk.ac.vamsas.client.Vobject
set by testInstanceForIdField() if Vobject should have a VorbaId
release() - Method in class uk.ac.vamsas.client.simpleclient.FileLock
 
release(boolean) - Method in class uk.ac.vamsas.client.simpleclient.FileLock
 
release() - Method in class uk.ac.vamsas.client.simpleclient.Lock
release lock and close all managed channels to file
release(boolean) - Method in class uk.ac.vamsas.client.simpleclient.Lock
optionally close the open random access channel on the file when releasing lock
release() - Method in class uk.ac.vamsas.client.simpleclient.NativeLock
 
release(boolean) - Method in class uk.ac.vamsas.client.simpleclient.NativeLock
 
releaseActiveClientFile() - Method in class uk.ac.vamsas.client.simpleclient.SimpleClient
 
removeAlignment(Alignment) - Method in class uk.ac.vamsas.objects.core.DataSet
Method removeAlignment.
removeAlignmentAnnotation(AlignmentAnnotation) - Method in class uk.ac.vamsas.objects.core.Alignment
Method removeAlignmentAnnotation.
removeAlignmentAnnotationAt(int) - Method in class uk.ac.vamsas.objects.core.Alignment
Method removeAlignmentAnnotationAt.
removeAlignmentAt(int) - Method in class uk.ac.vamsas.objects.core.DataSet
Method removeAlignmentAt.
removeAlignmentSequence(AlignmentSequence) - Method in class uk.ac.vamsas.objects.core.Alignment
Method removeAlignmentSequence.
removeAlignmentSequenceAnnotation(AlignmentSequenceAnnotation) - Method in class uk.ac.vamsas.objects.core.AlignmentSequence
Method removeAlignmentSequenceAnnotation.
removeAlignmentSequenceAnnotationAt(int) - Method in class uk.ac.vamsas.objects.core.AlignmentSequence
Method removeAlignmentSequenceAnnotationAt.
removeAlignmentSequenceAt(int) - Method in class uk.ac.vamsas.objects.core.Alignment
Method removeAlignmentSequenceAt.
removeAllAlignment() - Method in class uk.ac.vamsas.objects.core.DataSet
 
removeAllAlignmentAnnotation() - Method in class uk.ac.vamsas.objects.core.Alignment
 
removeAllAlignmentSequence() - Method in class uk.ac.vamsas.objects.core.Alignment
 
removeAllAlignmentSequenceAnnotation() - Method in class uk.ac.vamsas.objects.core.AlignmentSequence
 
removeAllAnnotationElement() - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
 
removeAllApplicationData() - Method in class uk.ac.vamsas.objects.core.VamsasDocument
 
removeAllAttachment() - Method in class uk.ac.vamsas.objects.core.VamsasDocument
 
removeAllDataSet() - Method in class uk.ac.vamsas.objects.core.VAMSAS
 
removeAllDataSetAnnotations() - Method in class uk.ac.vamsas.objects.core.DataSet
 
removeAllDbRef() - Method in class uk.ac.vamsas.objects.core.Sequence
 
removeAllEntry() - Method in class uk.ac.vamsas.objects.core.Provenance
 
removeAllGlyph() - Method in class uk.ac.vamsas.objects.core.AnnotationElement
 
removeAllInput() - Method in class uk.ac.vamsas.objects.core.Entry
 
removeAllInstance() - Method in class uk.ac.vamsas.objects.core.ApplicationData
 
removeAllLink() - Method in class uk.ac.vamsas.objects.core.DbRef
 
removeAllLink() - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
 
removeAllMap() - Method in class uk.ac.vamsas.objects.core.DbRef
 
removeAllNewick() - Method in class uk.ac.vamsas.objects.core.Tree
 
removeAllObjRef() - Method in class uk.ac.vamsas.objects.core.Input
 
removeAllParam() - Method in class uk.ac.vamsas.objects.core.Entry
 
removeAllPos() - Method in class uk.ac.vamsas.objects.core.RangeType
 
removeAllProperty() - Method in class uk.ac.vamsas.objects.core.Alignment
 
removeAllProperty() - Method in class uk.ac.vamsas.objects.core.DbRef
 
removeAllProperty() - Method in class uk.ac.vamsas.objects.core.Entry
 
removeAllProperty() - Method in class uk.ac.vamsas.objects.core.NodeType
 
removeAllProperty() - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
 
removeAllProperty() - Method in class uk.ac.vamsas.objects.core.SequenceType
 
removeAllProperty() - Method in class uk.ac.vamsas.objects.core.Tree
 
removeAllRefs() - Method in class uk.ac.vamsas.objects.core.ReferenceType
 
removeAllScore() - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
 
removeAllSeg() - Method in class uk.ac.vamsas.objects.core.RangeType
 
removeAllSeqRef() - Method in class uk.ac.vamsas.objects.core.DataSetAnnotations
 
removeAllSeqrefs() - Method in class uk.ac.vamsas.objects.core.AlignmentAnnotation
 
removeAllSequence() - Method in class uk.ac.vamsas.objects.core.DataSet
 
removeAllSequenceMapping() - Method in class uk.ac.vamsas.objects.core.DataSet
 
removeAllTree() - Method in class uk.ac.vamsas.objects.core.Alignment
 
removeAllTree() - Method in class uk.ac.vamsas.objects.core.DataSet
 
removeAllTree() - Method in class uk.ac.vamsas.objects.core.VAMSAS
 
removeAllTreeId() - Method in class uk.ac.vamsas.objects.core.Treenode
 
removeAllTreenode() - Method in class uk.ac.vamsas.objects.core.Tree
 
removeAllUser() - Method in class uk.ac.vamsas.objects.core.ApplicationData
 
removeAllVAMSAS() - Method in class uk.ac.vamsas.objects.core.VamsasDocument
 
removeAllValue() - Method in class uk.ac.vamsas.objects.core.AnnotationElement
 
removeAllVref() - Method in class uk.ac.vamsas.objects.core.NodeType
 
removeAllVxref() - Method in class uk.ac.vamsas.objects.core.Sequence
 
removeAnnotationElement(AnnotationElement) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Method removeAnnotationElement.
removeAnnotationElementAt(int) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Method removeAnnotationElementAt.
removeApplicationData(ApplicationData) - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Method removeApplicationData.
removeApplicationDataAt(int) - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Method removeApplicationDataAt.
removeAttachment(Attachment) - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Method removeAttachment.
removeAttachmentAt(int) - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Method removeAttachmentAt.
removeClient(ClientHandle, Lock) - Method in class uk.ac.vamsas.client.simpleclient.ClientsFile
removes 'me' from the session ClientList without complaint if 'me' isn't in the clientList already.
removeClient(SimpleClient) - Method in class uk.ac.vamsas.client.simpleclient.VamsasSession
removes a client from the current session removes the client from the session client list if the client is the last one from the session (ClientList), the current session is removed from active session list.
removeDataSet(DataSet) - Method in class uk.ac.vamsas.objects.core.VAMSAS
Method removeDataSet.
removeDataSetAnnotations(DataSetAnnotations) - Method in class uk.ac.vamsas.objects.core.DataSet
Method removeDataSetAnnotations.
removeDataSetAnnotationsAt(int) - Method in class uk.ac.vamsas.objects.core.DataSet
Method removeDataSetAnnotationsAt.
removeDataSetAt(int) - Method in class uk.ac.vamsas.objects.core.VAMSAS
Method removeDataSetAt.
removeDbRef(DbRef) - Method in class uk.ac.vamsas.objects.core.Sequence
Method removeDbRef.
removeDbRefAt(int) - Method in class uk.ac.vamsas.objects.core.Sequence
Method removeDbRefAt.
removeElemenet(WatcherElement) - Method in class uk.ac.vamsas.client.simpleclient.VamsasFileWatcherThread
 
removeEntry(Entry) - Method in class uk.ac.vamsas.objects.core.Provenance
Method removeEntry.
removeEntryAt(int) - Method in class uk.ac.vamsas.objects.core.Provenance
Method removeEntryAt.
removeExtraField(ZipShort) - Method in class org.apache.tools.zip.ZipEntry
Remove an extra fields.
removeGlyph(Glyph) - Method in class uk.ac.vamsas.objects.core.AnnotationElement
Method removeGlyph.
removeGlyphAt(int) - Method in class uk.ac.vamsas.objects.core.AnnotationElement
Method removeGlyphAt.
removeInput(Input) - Method in class uk.ac.vamsas.objects.core.Entry
Method removeInput.
removeInputAt(int) - Method in class uk.ac.vamsas.objects.core.Entry
Method removeInputAt.
removeInstance(Instance) - Method in class uk.ac.vamsas.objects.core.ApplicationData
Method removeInstance.
removeInstanceAt(int) - Method in class uk.ac.vamsas.objects.core.ApplicationData
Method removeInstanceAt.
removeLink(Link) - Method in class uk.ac.vamsas.objects.core.DbRef
Method removeLink.
removeLink(Link) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Method removeLink.
removeLinkAt(int) - Method in class uk.ac.vamsas.objects.core.DbRef
Method removeLinkAt.
removeLinkAt(int) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Method removeLinkAt.
removeMap(Map) - Method in class uk.ac.vamsas.objects.core.DbRef
Method removeMap.
removeMapAt(int) - Method in class uk.ac.vamsas.objects.core.DbRef
Method removeMapAt.
removeNewick(Newick) - Method in class uk.ac.vamsas.objects.core.Tree
Method removeNewick.
removeNewickAt(int) - Method in class uk.ac.vamsas.objects.core.Tree
Method removeNewickAt.
removeObjRef(Object) - Method in class uk.ac.vamsas.objects.core.Input
Method removeObjRef.
removeObjRefAt(int) - Method in class uk.ac.vamsas.objects.core.Input
Method removeObjRefAt.
removeParam(Param) - Method in class uk.ac.vamsas.objects.core.Entry
Method removeParam.
removeParamAt(int) - Method in class uk.ac.vamsas.objects.core.Entry
Method removeParamAt.
removePos(Pos) - Method in class uk.ac.vamsas.objects.core.RangeType
Method removePos.
removePosAt(int) - Method in class uk.ac.vamsas.objects.core.RangeType
Method removePosAt.
removeProperty(Property) - Method in class uk.ac.vamsas.objects.core.Alignment
Method removeProperty.
removeProperty(Property) - Method in class uk.ac.vamsas.objects.core.DbRef
Method removeProperty.
removeProperty(Property) - Method in class uk.ac.vamsas.objects.core.Entry
Method removeProperty.
removeProperty(Property) - Method in class uk.ac.vamsas.objects.core.NodeType
Method removeProperty.
removeProperty(Property) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Method removeProperty.
removeProperty(Property) - Method in class uk.ac.vamsas.objects.core.SequenceType
Method removeProperty.
removeProperty(Property) - Method in class uk.ac.vamsas.objects.core.Tree
Method removeProperty.
removePropertyAt(int) - Method in class uk.ac.vamsas.objects.core.Alignment
Method removePropertyAt.
removePropertyAt(int) - Method in class uk.ac.vamsas.objects.core.DbRef
Method removePropertyAt.
removePropertyAt(int) - Method in class uk.ac.vamsas.objects.core.Entry
Method removePropertyAt.
removePropertyAt(int) - Method in class uk.ac.vamsas.objects.core.NodeType
Method removePropertyAt.
removePropertyAt(int) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Method removePropertyAt.
removePropertyAt(int) - Method in class uk.ac.vamsas.objects.core.SequenceType
Method removePropertyAt.
removePropertyAt(int) - Method in class uk.ac.vamsas.objects.core.Tree
Method removePropertyAt.
removeRefs(Object) - Method in class uk.ac.vamsas.objects.core.ReferenceType
Method removeRefs.
removeRefsAt(int) - Method in class uk.ac.vamsas.objects.core.ReferenceType
Method removeRefsAt.
removeScore(Score) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Method removeScore.
removeScoreAt(int) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Method removeScoreAt.
removeSeg(Seg) - Method in class uk.ac.vamsas.objects.core.RangeType
Method removeSeg.
removeSegAt(int) - Method in class uk.ac.vamsas.objects.core.RangeType
Method removeSegAt.
removeSeqRef(Object) - Method in class uk.ac.vamsas.objects.core.DataSetAnnotations
Method removeSeqRef.
removeSeqRefAt(int) - Method in class uk.ac.vamsas.objects.core.DataSetAnnotations
Method removeSeqRefAt.
removeSeqrefs(Object) - Method in class uk.ac.vamsas.objects.core.AlignmentAnnotation
Method removeSeqrefs.
removeSeqrefsAt(int) - Method in class uk.ac.vamsas.objects.core.AlignmentAnnotation
Method removeSeqrefsAt.
removeSequence(Sequence) - Method in class uk.ac.vamsas.objects.core.DataSet
Method removeSequence.
removeSequenceAt(int) - Method in class uk.ac.vamsas.objects.core.DataSet
Method removeSequenceAt.
removeSequenceMapping(SequenceMapping) - Method in class uk.ac.vamsas.objects.core.DataSet
Method removeSequenceMapping.
removeSequenceMappingAt(int) - Method in class uk.ac.vamsas.objects.core.DataSet
Method removeSequenceMappingAt.
removeSession(SessionHandle, Lock) - Method in class uk.ac.vamsas.client.simpleclient.SessionsFile
removes the current session from the SessionsList without complaint if the session isn't in the sessionsList already.
removeSession(SessionHandle) - Method in class uk.ac.vamsas.client.simpleclient.SimpleSessionManager
Removes a session from the list of currently active session
removeTree(Tree) - Method in class uk.ac.vamsas.objects.core.Alignment
Method removeTree.
removeTree(Tree) - Method in class uk.ac.vamsas.objects.core.DataSet
Method removeTree.
removeTree(Tree) - Method in class uk.ac.vamsas.objects.core.VAMSAS
Method removeTree.
removeTreeAt(int) - Method in class uk.ac.vamsas.objects.core.Alignment
Method removeTreeAt.
removeTreeAt(int) - Method in class uk.ac.vamsas.objects.core.DataSet
Method removeTreeAt.
removeTreeAt(int) - Method in class uk.ac.vamsas.objects.core.VAMSAS
Method removeTreeAt.
removeTreeId(Object) - Method in class uk.ac.vamsas.objects.core.Treenode
Method removeTreeId.
removeTreeIdAt(int) - Method in class uk.ac.vamsas.objects.core.Treenode
Method removeTreeIdAt.
removeTreenode(Treenode) - Method in class uk.ac.vamsas.objects.core.Tree
Method removeTreenode.
removeTreenodeAt(int) - Method in class uk.ac.vamsas.objects.core.Tree
Method removeTreenodeAt.
removeUpdateHandler(Class) - Method in interface uk.ac.vamsas.client.IClient
 
removeUpdateHandler(Class) - Method in class uk.ac.vamsas.client.simpleclient.SimpleClient
 
removeUser(User) - Method in class uk.ac.vamsas.objects.core.ApplicationData
Method removeUser.
removeUserAt(int) - Method in class uk.ac.vamsas.objects.core.ApplicationData
Method removeUserAt.
removeVAMSAS(VAMSAS) - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Method removeVAMSAS.
removeVAMSASAt(int) - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Method removeVAMSASAt.
removeValue(float) - Method in class uk.ac.vamsas.objects.core.AnnotationElement
Method removeValue.
removeValueAt(int) - Method in class uk.ac.vamsas.objects.core.AnnotationElement
Method removeValueAt.
removeVref(Vref) - Method in class uk.ac.vamsas.objects.core.NodeType
Method removeVref.
removeVrefAt(int) - Method in class uk.ac.vamsas.objects.core.NodeType
Method removeVrefAt.
removeVxref(Vxref) - Method in class uk.ac.vamsas.objects.core.Sequence
Method removeVxref.
removeVxrefAt(int) - Method in class uk.ac.vamsas.objects.core.Sequence
Method removeVxrefAt.
reportDocument(VamsasDocument, VamsasArchiveReader, boolean, PrintStream) - Static method in class uk.ac.vamsas.test.simpleclient.ArchiveReports
 
reportProvenance(Provenance, PrintStream) - Static method in class uk.ac.vamsas.test.simpleclient.ArchiveReports
print an informative summary on a VamsasDocument
resetCycleCount() - Method in class uk.ac.vamsas.client.simpleclient.ClientSessionFileWatcherElement
resets count of watch cycles (default value : 0)
retrieveClientList() - Method in class uk.ac.vamsas.client.simpleclient.ClientsFile
get the clientList from the file.
retrieveClientList(Lock) - Method in class uk.ac.vamsas.client.simpleclient.ClientsFile
get list from the locked ClientList.
retrieveSessionsList() - Method in class uk.ac.vamsas.client.simpleclient.SessionsFile
get the SessionsList from the file.
retrieveSessionsList(Lock) - Method in class uk.ac.vamsas.client.simpleclient.SessionsFile
get list from the locked SessionsList.
right() - Method in class uk.ac.vamsas.objects.utils.trees.BinaryNode
DOCUMENT ME!
rootReport(VAMSAS[], boolean, PrintStream) - Static method in class uk.ac.vamsas.test.simpleclient.ArchiveReports
summarises all the datasets in a vamsas document.
run() - Method in class uk.ac.vamsas.client.simpleclient.VamsasFileWatcherThread
check each watcher in sequence, monitoring any events generated.
run() - Method in class uk.ac.vamsas.test.simpleclient.simpleapp.VamsasClient.VamsasClientWatcher
 
runMe(String[]) - Method in class uk.ac.vamsas.test.ExampleApplication
 

S

SESSION_LOG - Static variable in class uk.ac.vamsas.client.simpleclient.VamsasSession
log file location
SESSION_SHUTDOWN - Static variable in class uk.ac.vamsas.client.Events
Generated prior to session Shutdown, after the last participating vamsas client has finalized.
SIMPLECLIENT - Static variable in class uk.ac.vamsas.client.simpleclient.SessionUrn
a simple client session urn prefix
STANDARD_AA - Static variable in class uk.ac.vamsas.objects.utils.SymbolDictionary
defines standard names and properties for vamsas sequence dictionaries
STANDARD_NA - Static variable in class uk.ac.vamsas.objects.utils.SymbolDictionary
 
STORED - Static variable in class org.apache.tools.zip.ZipOutputStream
Compression method for stored entries.
STRINGTYPE - Static variable in class uk.ac.vamsas.objects.utils.Properties
 
Score - class uk.ac.vamsas.objects.core.Score.
Ordered set of optionally named float values for the whole annotation
Score() - Constructor for class uk.ac.vamsas.objects.core.Score
 
ScoreDescriptor - class uk.ac.vamsas.objects.core.descriptors.ScoreDescriptor.
Class ScoreDescriptor.
ScoreDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.ScoreDescriptor
 
Seg - class uk.ac.vamsas.objects.core.Seg.
a region from start to end, with flag for inclusivity of terminii
Seg() - Constructor for class uk.ac.vamsas.objects.core.Seg
 
SegDescriptor - class uk.ac.vamsas.objects.core.descriptors.SegDescriptor.
Class SegDescriptor.
SegDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.SegDescriptor
 
SelectionMessage - class uk.ac.vamsas.client.picking.SelectionMessage.
Send and receive details about vamsas object selections and selection ranges defined on one or more objects.
SelectionMessage(String) - Constructor for class uk.ac.vamsas.client.picking.SelectionMessage
parse a message payload as a selection message
SelectionMessage(String, String[], RangeType) - Constructor for class uk.ac.vamsas.client.picking.SelectionMessage
create a new selection message
SelectionMessage(String, String[], RangeType, boolean) - Constructor for class uk.ac.vamsas.client.picking.SelectionMessage
 
Seq - class uk.ac.vamsas.objects.utils.Seq.
 
Seq() - Constructor for class uk.ac.vamsas.objects.utils.Seq
 
SeqAln - class uk.ac.vamsas.objects.utils.SeqAln.
 
SeqAln() - Constructor for class uk.ac.vamsas.objects.utils.SeqAln
 
SeqSet - class uk.ac.vamsas.objects.utils.SeqSet.
 
SeqSet() - Constructor for class uk.ac.vamsas.objects.utils.SeqSet
 
Sequence - class uk.ac.vamsas.objects.core.Sequence.
Class Sequence.
Sequence() - Constructor for class uk.ac.vamsas.objects.core.Sequence
 
SequenceDescriptor - class uk.ac.vamsas.objects.core.descriptors.SequenceDescriptor.
Class SequenceDescriptor.
SequenceDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.SequenceDescriptor
 
SequenceMapping - class uk.ac.vamsas.objects.core.SequenceMapping.
Class SequenceMapping.
SequenceMapping() - Constructor for class uk.ac.vamsas.objects.core.SequenceMapping
 
SequenceMappingDescriptor - class uk.ac.vamsas.objects.core.descriptors.SequenceMappingDescriptor.
Class SequenceMappingDescriptor.
SequenceMappingDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.SequenceMappingDescriptor
 
SequenceNode - class uk.ac.vamsas.objects.utils.trees.SequenceNode.
 
SequenceNode() - Constructor for class uk.ac.vamsas.objects.utils.trees.SequenceNode
Creates a new SequenceNode object.
SequenceNode(Vobject, SequenceNode, float, String) - Constructor for class uk.ac.vamsas.objects.utils.trees.SequenceNode
Creates a new SequenceNode object.
SequenceNode(Vobject, SequenceNode, String, float, int, boolean) - Constructor for class uk.ac.vamsas.objects.utils.trees.SequenceNode
Creates a new SequenceNode object.
SequenceType - class uk.ac.vamsas.objects.core.SequenceType.
Class SequenceType.
SequenceType() - Constructor for class uk.ac.vamsas.objects.core.SequenceType
 
SequenceTypeDescriptor - class uk.ac.vamsas.objects.core.descriptors.SequenceTypeDescriptor.
Class SequenceTypeDescriptor.
SequenceTypeDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.SequenceTypeDescriptor
 
SessionFile - class uk.ac.vamsas.client.simpleclient.SessionFile.
Basic methods for classes handling locked IO on files monitored by all (simpleclient) clients in a vamsas session.
SessionFile(File) - Constructor for class uk.ac.vamsas.client.simpleclient.SessionFile
 
SessionFileWatcherElement - class uk.ac.vamsas.client.simpleclient.SessionFileWatcherElement.
Element of the VamsasFileWatcherThread event generator chain.
SessionFileWatcherElement(SessionFile, WatcherCallBack) - Constructor for class uk.ac.vamsas.client.simpleclient.SessionFileWatcherElement
create a new, enabled watch element
SessionFileWatcherElement(SessionFile, WatcherCallBack, boolean) - Constructor for class uk.ac.vamsas.client.simpleclient.SessionFileWatcherElement
new watcher with flag to initially skip watching this sessionfile
SessionFlagFile - class uk.ac.vamsas.client.simpleclient.SessionFlagFile.
methods for setting and checking binary flags in a vamsas session directory.
SessionFlagFile(File) - Constructor for class uk.ac.vamsas.client.simpleclient.SessionFlagFile
 
SessionFlagWatcherElement - class uk.ac.vamsas.client.simpleclient.SessionFlagWatcherElement.
Element of the VamsasFileWatcherThread event generator chain.
SessionFlagWatcherElement(SessionFlagFile, WatcherCallBack) - Constructor for class uk.ac.vamsas.client.simpleclient.SessionFlagWatcherElement
create a new, enabled watch element
SessionFlagWatcherElement(SessionFlagFile, WatcherCallBack, boolean) - Constructor for class uk.ac.vamsas.client.simpleclient.SessionFlagWatcherElement
new watcher with flag to initially skip watching this sessionfile
SessionHandle - class uk.ac.vamsas.client.SessionHandle.
Uniquely locates a particular VAMSAS session.
SessionHandle(String) - Constructor for class uk.ac.vamsas.client.SessionHandle
 
SessionUrn - class uk.ac.vamsas.client.SessionUrn.
 
SessionUrn() - Constructor for class uk.ac.vamsas.client.SessionUrn
 
SessionUrn(String, URL) - Constructor for class uk.ac.vamsas.client.SessionUrn
construct urn for a locally stored session file
SessionUrn(String, URI) - Constructor for class uk.ac.vamsas.client.SessionUrn
 
SessionUrn - class uk.ac.vamsas.client.simpleclient.SessionUrn.
SessionUrn for simpleclient sessions: simpleclient://{Absolute path to session directory} For simpleclient urn, it consideres as on the same machine, using the path to the session directory to generate the session URN
SessionUrn(String) - Constructor for class uk.ac.vamsas.client.simpleclient.SessionUrn
Creates a SessionUrn object from a String.
SessionUrn(File) - Constructor for class uk.ac.vamsas.client.simpleclient.SessionUrn
Generates a sessionURN bases on a session directory location
SessionUrn(VamsasSession) - Constructor for class uk.ac.vamsas.client.simpleclient.SessionUrn
Generates a sessionURN bases on a vamsas session
SessionsFile - class uk.ac.vamsas.client.simpleclient.SessionsFile.
 
SessionsFile(File) - Constructor for class uk.ac.vamsas.client.simpleclient.SessionsFile
 
SetChildren(BinaryNode, BinaryNode) - Method in class uk.ac.vamsas.objects.utils.trees.BinaryNode
attaches FIRST and SECOND node arguments as the LEFT and RIGHT children of this node (removing any old references) a null parameter DOES NOT mean that the pointer to the corresponding child node is set to NULL - you should use setChild(null), or detach() for this.
SimpleClient - class uk.ac.vamsas.client.simpleclient.SimpleClient.
 
SimpleClient(UserHandle, ClientHandle, VamsasSession) - Constructor for class uk.ac.vamsas.client.simpleclient.SimpleClient
construct SimpleClient for user, client and VamsasSession directory use the SimpleClientFactory rather than this constructor directly.
SimpleClientAppdata - class uk.ac.vamsas.client.simpleclient.SimpleClientAppdata.
 
SimpleClientAppdata(ClientDocument) - Constructor for class uk.ac.vamsas.client.simpleclient.SimpleClientAppdata
state flags - accessed ClientAppdata - accessed UserAppdata => inputStream from embedded xml or jar entry of backup has been created - set ClientAppdata - set UserAppdata => an output stream has been created and written to - or a data chunk has been written.
SimpleClientConfig - class uk.ac.vamsas.client.simpleclient.SimpleClientConfig.
Config for SimpleClient - a basic Vamsas Client Interface implementation.
SimpleClientConfig() - Constructor for class uk.ac.vamsas.client.simpleclient.SimpleClientConfig
 
SimpleClientFactory - class uk.ac.vamsas.client.simpleclient.SimpleClientFactory.
creates a session arena in the user home directory under .vamsas.
SimpleClientFactory() - Constructor for class uk.ac.vamsas.client.simpleclient.SimpleClientFactory
default constructor - called by CreateClientFactory only.
SimpleClientFactory(String) - Constructor for class uk.ac.vamsas.client.simpleclient.SimpleClientFactory
Create a client factory that works with sessions at the given path.
SimpleDocBinding - class uk.ac.vamsas.client.simpleclient.SimpleDocBinding.
Base class for SimpleClient Vamsas Document Object Manipulation holds static vamsasDocument from XML routines and state objects for a particular unmarshalled Document instance.
SimpleDocBinding() - Constructor for class uk.ac.vamsas.client.simpleclient.SimpleDocBinding
 
SimpleDocument - class uk.ac.vamsas.client.simpleclient.SimpleDocument.
 
SimpleDocument(String) - Constructor for class uk.ac.vamsas.client.simpleclient.SimpleDocument
 
SimpleDocument(VorbaIdFactory) - Constructor for class uk.ac.vamsas.client.simpleclient.SimpleDocument
 
SimplePickManager - class uk.ac.vamsas.client.simpleclient.SimplePickManager.
Blocking message handler
SimpleSessionManager - class uk.ac.vamsas.client.simpleclient.SimpleSessionManager.
Class to deal with sessions retrieves list of available sessions adds an active session removes a close session (the last client has been closed)
SimpleSessionManager(File) - Constructor for class uk.ac.vamsas.client.simpleclient.SimpleSessionManager
 
SocketManager - class uk.ac.vamsas.client.picking.SocketManager.
Concrete implementation of the IPickManager interface that uses sockets for message communication.
SocketManager() - Constructor for class uk.ac.vamsas.client.picking.SocketManager
Constructs a new PickManager.
SymbolDictionary - class uk.ac.vamsas.objects.utils.SymbolDictionary.
 
SymbolDictionary() - Constructor for class uk.ac.vamsas.objects.utils.SymbolDictionary
 
sclient - Variable in class uk.ac.vamsas.client.simpleclient.ClientDocument
 
searchAppDatas(VamsasDocument, AppDataReference.IAppDSearch, boolean) - Static method in class uk.ac.vamsas.objects.utils.AppDataReference
General search through the set of AppData objects for a particular profile of Client and User handle.
sendMessage(Message) - Method in interface uk.ac.vamsas.client.picking.IPickManager
Sends a message.
sendMessage(Message) - Method in class uk.ac.vamsas.client.picking.SocketManager
Sends a message to other clients.
sendMessage(Message) - Method in class uk.ac.vamsas.client.simpleclient.SimplePickManager
 
session - Variable in class uk.ac.vamsas.client.simpleclient.SimpleClient
 
sessionDir - Variable in class uk.ac.vamsas.client.simpleclient.VamsasSession
the sessionDir is given as the session location for new clients.
sessionFile - Variable in class uk.ac.vamsas.client.simpleclient.SessionFile
 
setAccessionId(String) - Method in class uk.ac.vamsas.objects.core.DbRef
Sets the value of field 'accessionId'.
setAction(String) - Method in class uk.ac.vamsas.objects.core.Entry
Sets the value of field 'action'.
setAfter(boolean) - Method in class uk.ac.vamsas.objects.core.AnnotationElement
Sets the value of field 'after'.
setAligned(boolean) - Method in class uk.ac.vamsas.objects.core.Alignment
Sets the value of field 'aligned'.
setAlignment(int, Alignment) - Method in class uk.ac.vamsas.objects.core.DataSet
 
setAlignment(Alignment[]) - Method in class uk.ac.vamsas.objects.core.DataSet
 
setAlignment(Vector) - Method in class uk.ac.vamsas.objects.core.DataSet
Sets the value of '_alignmentList' by copying the given Vector.
setAlignmentAnnotation(int, AlignmentAnnotation) - Method in class uk.ac.vamsas.objects.core.Alignment
 
setAlignmentAnnotation(AlignmentAnnotation[]) - Method in class uk.ac.vamsas.objects.core.Alignment
 
setAlignmentAnnotation(Vector) - Method in class uk.ac.vamsas.objects.core.Alignment
Sets the value of '_alignmentAnnotationList' by copying the given Vector.
setAlignmentAnnotationAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.Alignment
Deprecated.  
setAlignmentAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.DataSet
Deprecated.  
setAlignmentSequence(int, AlignmentSequence) - Method in class uk.ac.vamsas.objects.core.Alignment
 
setAlignmentSequence(AlignmentSequence[]) - Method in class uk.ac.vamsas.objects.core.Alignment
 
setAlignmentSequence(Vector) - Method in class uk.ac.vamsas.objects.core.Alignment
Sets the value of '_alignmentSequenceList' by copying the given Vector.
setAlignmentSequenceAnnotation(int, AlignmentSequenceAnnotation) - Method in class uk.ac.vamsas.objects.core.AlignmentSequence
 
setAlignmentSequenceAnnotation(AlignmentSequenceAnnotation[]) - Method in class uk.ac.vamsas.objects.core.AlignmentSequence
 
setAlignmentSequenceAnnotation(Vector) - Method in class uk.ac.vamsas.objects.core.AlignmentSequence
Sets the value of '_alignmentSequenceAnnotationList' by copying the given Vector.
setAlignmentSequenceAnnotationAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.AlignmentSequence
Deprecated.  
setAlignmentSequenceAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.Alignment
Deprecated.  
setAnnotationElement(int, AnnotationElement) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
 
setAnnotationElement(AnnotationElement[]) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
 
setAnnotationElement(Vector) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Sets the value of '_annotationElementList' by copying the given Vector.
setAnnotationElementAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Deprecated.  
setApp(String) - Method in class uk.ac.vamsas.objects.core.Entry
Sets the value of field 'app'.
setApplicationData(int, ApplicationData) - Method in class uk.ac.vamsas.objects.core.VamsasDocument
 
setApplicationData(ApplicationData[]) - Method in class uk.ac.vamsas.objects.core.VamsasDocument
 
setApplicationData(Vector) - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Sets the value of '_applicationDataList' by copying the given Vector.
setApplicationDataAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Deprecated.  
setAttachment(int, Attachment) - Method in class uk.ac.vamsas.objects.core.VamsasDocument
 
setAttachment(Attachment[]) - Method in class uk.ac.vamsas.objects.core.VamsasDocument
 
setAttachment(Vector) - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Sets the value of '_attachmentList' by copying the given Vector.
setAttachmentAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Deprecated.  
setBootstrap(int) - Method in class uk.ac.vamsas.objects.utils.trees.BinaryNode
DOCUMENT ME!
setCentralDirectoryData(byte[]) - Method in class org.apache.tools.zip.UnrecognizedExtraField
Set the extra field data in central directory.
setClient(ClientHandle) - Method in class uk.ac.vamsas.client.VorbaIdFactory
 
setClient(ClientHandle) - Method in class uk.ac.vamsas.client.simpleclient.IdFactory
 
setClientAppdata(byte[]) - Method in interface uk.ac.vamsas.client.IClientAppdata
set the non-User-specific application data
setClientAppdata(byte[]) - Method in class uk.ac.vamsas.client.simpleclient.SimpleClientAppdata
 
setClientName(String) - Method in class uk.ac.vamsas.client.ClientHandle
 
setClientUrn(String) - Method in class uk.ac.vamsas.client.ClientHandle
May become protected - should only be set by a Vorba object.
setComment(String) - Method in class org.apache.tools.zip.ZipOutputStream
Set the file comment.
setCommon(Common) - Method in class uk.ac.vamsas.objects.core.ApplicationData
Sets the value of field 'common'.
setComprSize(long) - Method in class org.apache.tools.zip.ZipEntry
Deprecated. since 1.7. Use setCompressedSize directly.
setCompressed(boolean) - Method in class uk.ac.vamsas.objects.core.Attachment
Sets the value of field 'compressed'.
setContent(String) - Method in class uk.ac.vamsas.objects.core.Glyph
Sets the value of field 'content'.
setContent(String) - Method in class uk.ac.vamsas.objects.core.Link
Sets the value of field 'content'.
setContent(String) - Method in class uk.ac.vamsas.objects.core.LockFile
Sets the value of field 'content'.
setContent(String) - Method in class uk.ac.vamsas.objects.core.Newick
Sets the value of field 'content'.
setContent(String) - Method in class uk.ac.vamsas.objects.core.Param
Sets the value of field 'content'.
setContent(String) - Method in class uk.ac.vamsas.objects.core.Property
Sets the value of field 'content'.
setContent(String) - Method in class uk.ac.vamsas.objects.core.ReferenceType
Sets the value of field 'content'.
setContent(float) - Method in class uk.ac.vamsas.objects.core.Score
Sets the value of field 'content'.
setData(byte[]) - Method in class uk.ac.vamsas.objects.core.AppData
Sets the value of field 'data'.
setDataReference(String) - Method in class uk.ac.vamsas.objects.core.AppData
Sets the value of field 'dataReference'.
setDataSet(int, DataSet) - Method in class uk.ac.vamsas.objects.core.VAMSAS
 
setDataSet(DataSet[]) - Method in class uk.ac.vamsas.objects.core.VAMSAS
 
setDataSet(Vector) - Method in class uk.ac.vamsas.objects.core.VAMSAS
Sets the value of '_dataSetList' by copying the given Vector.
setDataSetAnnotations(int, DataSetAnnotations) - Method in class uk.ac.vamsas.objects.core.DataSet
 
setDataSetAnnotations(DataSetAnnotations[]) - Method in class uk.ac.vamsas.objects.core.DataSet
 
setDataSetAnnotations(Vector) - Method in class uk.ac.vamsas.objects.core.DataSet
Sets the value of '_dataSetAnnotationsList' by copying the given Vector.
setDataSetAnnotationsAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.DataSet
Deprecated.  
setDataSetAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.VAMSAS
Deprecated.  
setDate(Date) - Method in class uk.ac.vamsas.objects.core.Entry
Sets the value of field 'date'.
setDbRef(int, DbRef) - Method in class uk.ac.vamsas.objects.core.Sequence
 
setDbRef(DbRef[]) - Method in class uk.ac.vamsas.objects.core.Sequence
 
setDbRef(Vector) - Method in class uk.ac.vamsas.objects.core.Sequence
Sets the value of '_dbRefList' by copying the given Vector.
setDbRefAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.Sequence
Deprecated.  
setDescription(String) - Method in class uk.ac.vamsas.objects.core.AnnotationElement
Sets the value of field 'description'.
setDescription(String) - Method in class uk.ac.vamsas.objects.core.NodeType
Sets the value of field 'description'.
setDescription(String) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Sets the value of field 'description'.
setDescription(String) - Method in class uk.ac.vamsas.objects.core.SequenceType
Sets the value of field 'description'.
setDict(String) - Method in class uk.ac.vamsas.objects.core.Glyph
Sets the value of field 'dict'.
setDictionary(String) - Method in class uk.ac.vamsas.objects.core.Sequence
Sets the value of field 'dictionary'.
setDirectory(boolean) - Method in class org.apache.tools.zip.AsiExtraField
Indicate whether this entry is a directory.
setDummy(boolean) - Method in class uk.ac.vamsas.objects.utils.trees.SequenceNode
DOCUMENT ME!
setElement(Vobject) - Method in class uk.ac.vamsas.objects.utils.trees.BinaryNode
DOCUMENT ME!
setEncoding(String) - Method in class org.apache.tools.zip.ZipOutputStream
The encoding to use for filenames and the file comment.
setEnd(long) - Method in class uk.ac.vamsas.objects.core.MapList
Sets the value of field 'end'.
setEnd(int) - Method in class uk.ac.vamsas.objects.core.Seg
Sets the value of field 'end'.
setEnd(long) - Method in class uk.ac.vamsas.objects.core.SequenceType
Sets the value of field 'end'.
setEntry(int, Entry) - Method in class uk.ac.vamsas.objects.core.Provenance
 
setEntry(Entry[]) - Method in class uk.ac.vamsas.objects.core.Provenance
 
setEntry(Vector) - Method in class uk.ac.vamsas.objects.core.Provenance
Sets the value of '_entryList' by copying the given Vector.
setEntryAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.Provenance
Deprecated.  
setExternalAttributes(long) - Method in class org.apache.tools.zip.ZipEntry
Sets the external file attributes.
setExtra(byte[]) - Method in class org.apache.tools.zip.ZipEntry
Throws an Exception if extra data cannot be parsed into extra fields.
setExtra() - Method in class org.apache.tools.zip.ZipEntry
Unfortunately java.util.zip.ZipOutputStream seems to access the extra data directly, so overriding getExtra doesn't help - we need to modify super's data directly.
setExtraFields(ZipExtraField[]) - Method in class org.apache.tools.zip.ZipEntry
Replaces all currently attached extra fields with the new array.
setFlag() - Method in class uk.ac.vamsas.client.simpleclient.SessionFlagFile
will log a warning if exceptions occur during flag creation.
setFrom(long) - Method in class uk.ac.vamsas.objects.core.MapList
Sets the value of field 'from'.
setFullName(String) - Method in class uk.ac.vamsas.client.UserHandle
 
setFullname(String) - Method in class uk.ac.vamsas.objects.core.User
Sets the value of field 'fullname'.
setGapChar(String) - Method in class uk.ac.vamsas.objects.core.Alignment
Sets the value of field 'gapChar'.
setGlyph(int, Glyph) - Method in class uk.ac.vamsas.objects.core.AnnotationElement
 
setGlyph(Glyph[]) - Method in class uk.ac.vamsas.objects.core.AnnotationElement
 
setGlyph(Vector) - Method in class uk.ac.vamsas.objects.core.AnnotationElement
Sets the value of '_glyphList' by copying the given Vector.
setGlyphAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.AnnotationElement
Deprecated.  
setGraph(boolean) - Method in class uk.ac.vamsas.objects.core.AlignmentAnnotation
Sets the value of field 'graph'.
setGraph(boolean) - Method in class uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation
Sets the value of field 'graph'.
setGroup(String) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Sets the value of field 'group'.
setGroupId(int) - Method in class org.apache.tools.zip.AsiExtraField
Set the group id.
setHandler(WatcherCallBack) - Method in class uk.ac.vamsas.client.simpleclient.WatcherElement
 
setHeaderId(ZipShort) - Method in class org.apache.tools.zip.UnrecognizedExtraField
Set the header id.
setHref(String) - Method in class uk.ac.vamsas.objects.core.Link
Sets the value of field 'href'.
setI(int) - Method in class uk.ac.vamsas.objects.core.Pos
Sets the value of field 'i'.
setId(String) - Method in class uk.ac.vamsas.objects.core.Alignment
Sets the value of field 'id'.
setId(String) - Method in class uk.ac.vamsas.objects.core.AlignmentSequence
Sets the value of field 'id'.
setId(String) - Method in class uk.ac.vamsas.objects.core.AnnotationElement
Sets the value of field 'id'.
setId(String) - Method in class uk.ac.vamsas.objects.core.Attachment
Sets the value of field 'id'.
setId(String) - Method in class uk.ac.vamsas.objects.core.DataSet
Sets the value of field 'id'.
setId(String) - Method in class uk.ac.vamsas.objects.core.DbRef
Sets the value of field 'id'.
setId(String) - Method in class uk.ac.vamsas.objects.core.Entry
Sets the value of field 'id'.
setId(String) - Method in class uk.ac.vamsas.objects.core.Map
Sets the value of field 'id'.
setId(String) - Method in class uk.ac.vamsas.objects.core.Newick
Sets the value of field 'id'.
setId(String) - Method in class uk.ac.vamsas.objects.core.NodeType
Sets the value of field 'id'.
setId(String) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Sets the value of field 'id'.
setId(String) - Method in class uk.ac.vamsas.objects.core.ReferenceType
Sets the value of field 'id'.
setId(String) - Method in class uk.ac.vamsas.objects.core.Sequence
Sets the value of field 'id'.
setId(String) - Method in class uk.ac.vamsas.objects.core.SequenceMapping
Sets the value of field 'id'.
setId(String) - Method in class uk.ac.vamsas.objects.core.Tree
Sets the value of field 'id'.
setId(String) - Method in class uk.ac.vamsas.objects.core.VAMSAS
Sets the value of field 'id'.
setInclusive(boolean) - Method in class uk.ac.vamsas.objects.core.Seg
Sets the value of field 'inclusive'.
setInput(int, Input) - Method in class uk.ac.vamsas.objects.core.Entry
 
setInput(Input[]) - Method in class uk.ac.vamsas.objects.core.Entry
 
setInput(Vector) - Method in class uk.ac.vamsas.objects.core.Entry
Sets the value of '_inputList' by copying the given Vector.
setInputAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.Entry
Deprecated.  
setInstance(int, Instance) - Method in class uk.ac.vamsas.objects.core.ApplicationData
 
setInstance(Instance[]) - Method in class uk.ac.vamsas.objects.core.ApplicationData
 
setInstance(Vector) - Method in class uk.ac.vamsas.objects.core.ApplicationData
Sets the value of '_instanceList' by copying the given Vector.
setInstanceAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.ApplicationData
Deprecated.  
setInstanceIdField() - Method in class uk.ac.vamsas.client.Vobject
update the Vobject instance's _id field, based on the contents of the VorbaId.
setInternalAttributes(int) - Method in class org.apache.tools.zip.ZipEntry
Sets the internal file attributes.
setInvalidModification(boolean) - Method in class uk.ac.vamsas.client.simpleclient.ClientDocument
set if the client has corrupted the Vamsas Document structure somehow.
setLabel(String) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Sets the value of field 'label'.
setLeft(BinaryNode) - Method in class uk.ac.vamsas.objects.utils.trees.BinaryNode
DOCUMENT ME!
setLevel(int) - Method in class org.apache.tools.zip.ZipOutputStream
Sets the compression level for subsequent entries.
setLink(int, Link) - Method in class uk.ac.vamsas.objects.core.DbRef
 
setLink(Link[]) - Method in class uk.ac.vamsas.objects.core.DbRef
 
setLink(Vector) - Method in class uk.ac.vamsas.objects.core.DbRef
Sets the value of '_linkList' by copying the given Vector.
setLink(int, Link) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
 
setLink(Link[]) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
 
setLink(Vector) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Sets the value of '_linkList' by copying the given Vector.
setLinkAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.DbRef
Deprecated.  
setLinkAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Deprecated.  
setLinkedFile(String) - Method in class org.apache.tools.zip.AsiExtraField
Indicate that this entry is a symbolic link to the given filename.
setLoc(Object) - Method in class uk.ac.vamsas.objects.core.SequenceMapping
Sets the value of field 'loc'.
setLocal(Local) - Method in class uk.ac.vamsas.objects.core.MapType
Sets the value of field 'local'.
setLocalFileDataData(byte[]) - Method in class org.apache.tools.zip.UnrecognizedExtraField
Set the extra field data in the local file data - without Header-ID or length specifier.
setLockFile(LockFile) - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Sets the value of field 'lockFile'.
setMap(int, Map) - Method in class uk.ac.vamsas.objects.core.DbRef
 
setMap(Map[]) - Method in class uk.ac.vamsas.objects.core.DbRef
 
setMap(Vector) - Method in class uk.ac.vamsas.objects.core.DbRef
Sets the value of '_mapList' by copying the given Vector.
setMap(Object) - Method in class uk.ac.vamsas.objects.core.SequenceMapping
Sets the value of field 'map'.
setMap(MapList) - Method in class uk.ac.vamsas.objects.utils.Mapping
 
setMapAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.DbRef
Deprecated.  
setMapped(Mapped) - Method in class uk.ac.vamsas.objects.core.MapType
Sets the value of field 'mapped'.
setMethod(int) - Method in class org.apache.tools.zip.ZipOutputStream
Sets the default compression method for subsequent entries.
setMode(int) - Method in class org.apache.tools.zip.AsiExtraField
File mode of this file.
setModifiable(String) - Method in class uk.ac.vamsas.objects.core.Alignment
Sets the value of field 'modifiable'.
setModifiable(String) - Method in class uk.ac.vamsas.objects.core.Newick
Sets the value of field 'modifiable'.
setModifiable(String) - Method in class uk.ac.vamsas.objects.core.NodeType
Sets the value of field 'modifiable'.
setModifiable(String) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Sets the value of field 'modifiable'.
setModifiable(String) - Method in class uk.ac.vamsas.objects.core.Tree
Sets the value of field 'modifiable'.
setModifiable(String) - Method in class uk.ac.vamsas.objects.core.VAMSAS
Sets the value of field 'modifiable'.
setName(String) - Method in class org.apache.tools.zip.ZipEntry
Set the name of the entry.
setName(String) - Method in class uk.ac.vamsas.objects.core.ApplicationData
Sets the value of field 'name'.
setName(String) - Method in class uk.ac.vamsas.objects.core.Input
Sets the value of field 'name'.
setName(String) - Method in class uk.ac.vamsas.objects.core.NodeType
Sets the value of field 'name'.
setName(String) - Method in class uk.ac.vamsas.objects.core.Param
Sets the value of field 'name'.
setName(String) - Method in class uk.ac.vamsas.objects.core.Property
Sets the value of field 'name'.
setName(String) - Method in class uk.ac.vamsas.objects.core.Score
Sets the value of field 'name'.
setName(String) - Method in class uk.ac.vamsas.objects.core.SequenceType
Sets the value of field 'name'.
setName(String) - Method in class uk.ac.vamsas.objects.utils.trees.BinaryNode
DOCUMENT ME!
setNewIdHash(Hashtable) - Method in class uk.ac.vamsas.client.VorbaIdFactory
Called by VorbaXmlBinder so the record of newly unmarshalled Vobject Ids is accessible to the Document's VorbaIdFactory instance.
setNewick(int, Newick) - Method in class uk.ac.vamsas.objects.core.Tree
 
setNewick(Newick[]) - Method in class uk.ac.vamsas.objects.core.Tree
 
setNewick(Vector) - Method in class uk.ac.vamsas.objects.core.Tree
Sets the value of '_newickList' by copying the given Vector.
setNewickAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.Tree
Deprecated.  
setNodespec(String) - Method in class uk.ac.vamsas.objects.core.Treenode
Sets the value of field 'nodespec'.
setObjRef(int, Object) - Method in class uk.ac.vamsas.objects.core.Input
 
setObjRef(Object[]) - Method in class uk.ac.vamsas.objects.core.Input
 
setObjRef(Vector) - Method in class uk.ac.vamsas.objects.core.Input
Sets the value of '_objRef' by copying the given Vector.
setObjRefAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.Input
Deprecated.  
setObjectref(Object) - Method in class uk.ac.vamsas.objects.core.Attachment
Sets the value of field 'objectref'.
setOnto(Object) - Method in class uk.ac.vamsas.objects.core.Mapping
Sets the value of field 'onto'.
setOrganization(String) - Method in class uk.ac.vamsas.client.UserHandle
 
setOrganization(String) - Method in class uk.ac.vamsas.objects.core.User
Sets the value of field 'organization'.
setParam(int, Param) - Method in class uk.ac.vamsas.objects.core.Entry
 
setParam(Param[]) - Method in class uk.ac.vamsas.objects.core.Entry
 
setParam(Vector) - Method in class uk.ac.vamsas.objects.core.Entry
Sets the value of '_paramList' by copying the given Vector.
setParamAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.Entry
Deprecated.  
setParent(BinaryNode) - Method in class uk.ac.vamsas.objects.utils.trees.BinaryNode
DOCUMENT ME!
setPassThru(boolean) - Method in class uk.ac.vamsas.client.simpleclient.SimplePickManager
 
setPlaceholder(boolean) - Method in class uk.ac.vamsas.objects.utils.trees.SequenceNode
DOCUMENT ME!
setPlatform(int) - Method in class org.apache.tools.zip.ZipEntry
Set the platform (UNIX or FAT).
setPos(int, Pos) - Method in class uk.ac.vamsas.objects.core.RangeType
 
setPos(Pos[]) - Method in class uk.ac.vamsas.objects.core.RangeType
 
setPos(Vector) - Method in class uk.ac.vamsas.objects.core.RangeType
Sets the value of '_posList' by copying the given Vector.
setPosAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.RangeType
Deprecated.  
setPosition(long) - Method in class uk.ac.vamsas.objects.core.AnnotationElement
Sets the value of field 'position'.
setProperty(int, Property) - Method in class uk.ac.vamsas.objects.core.Alignment
 
setProperty(Property[]) - Method in class uk.ac.vamsas.objects.core.Alignment
 
setProperty(Vector) - Method in class uk.ac.vamsas.objects.core.Alignment
Sets the value of '_propertyList' by copying the given Vector.
setProperty(int, Property) - Method in class uk.ac.vamsas.objects.core.DbRef
 
setProperty(Property[]) - Method in class uk.ac.vamsas.objects.core.DbRef
 
setProperty(Vector) - Method in class uk.ac.vamsas.objects.core.DbRef
Sets the value of '_propertyList' by copying the given Vector.
setProperty(int, Property) - Method in class uk.ac.vamsas.objects.core.Entry
 
setProperty(Property[]) - Method in class uk.ac.vamsas.objects.core.Entry
 
setProperty(Vector) - Method in class uk.ac.vamsas.objects.core.Entry
Sets the value of '_propertyList' by copying the given Vector.
setProperty(int, Property) - Method in class uk.ac.vamsas.objects.core.NodeType
 
setProperty(Property[]) - Method in class uk.ac.vamsas.objects.core.NodeType
 
setProperty(Vector) - Method in class uk.ac.vamsas.objects.core.NodeType
Sets the value of '_propertyList' by copying the given Vector.
setProperty(int, Property) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
 
setProperty(Property[]) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
 
setProperty(Vector) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Sets the value of '_propertyList' by copying the given Vector.
setProperty(int, Property) - Method in class uk.ac.vamsas.objects.core.SequenceType
 
setProperty(Property[]) - Method in class uk.ac.vamsas.objects.core.SequenceType
 
setProperty(Vector) - Method in class uk.ac.vamsas.objects.core.SequenceType
Sets the value of '_propertyList' by copying the given Vector.
setProperty(int, Property) - Method in class uk.ac.vamsas.objects.core.Tree
 
setProperty(Property[]) - Method in class uk.ac.vamsas.objects.core.Tree
 
setProperty(Vector) - Method in class uk.ac.vamsas.objects.core.Tree
Sets the value of '_propertyList' by copying the given Vector.
setPropertyAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.Alignment
Deprecated.  
setPropertyAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.DbRef
Deprecated.  
setPropertyAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.Entry
Deprecated.  
setPropertyAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.NodeType
Deprecated.  
setPropertyAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Deprecated.  
setPropertyAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.SequenceType
Deprecated.  
setPropertyAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.Tree
Deprecated.  
setProvenance(Provenance) - Method in class uk.ac.vamsas.objects.core.Alignment
Sets the value of field 'provenance'.
setProvenance(Provenance) - Method in class uk.ac.vamsas.objects.core.AlignmentAnnotation
Sets the value of field 'provenance'.
setProvenance(Provenance) - Method in class uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation
Sets the value of field 'provenance'.
setProvenance(Provenance) - Method in class uk.ac.vamsas.objects.core.DataSet
Sets the value of field 'provenance'.
setProvenance(Provenance) - Method in class uk.ac.vamsas.objects.core.DataSetAnnotations
Sets the value of field 'provenance'.
setProvenance(Provenance) - Method in class uk.ac.vamsas.objects.core.SequenceMapping
Sets the value of field 'provenance'.
setProvenance(Provenance) - Method in class uk.ac.vamsas.objects.core.Tree
Sets the value of field 'provenance'.
setProvenance(Provenance) - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Sets the value of field 'provenance'.
setRefid(Object) - Method in class uk.ac.vamsas.objects.core.AlignmentSequence
Sets the value of field 'refid'.
setRefs(int, Object) - Method in class uk.ac.vamsas.objects.core.ReferenceType
 
setRefs(Object[]) - Method in class uk.ac.vamsas.objects.core.ReferenceType
 
setRefs(Vector) - Method in class uk.ac.vamsas.objects.core.ReferenceType
Sets the value of '_refs' by copying the given Vector.
setRefsAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.ReferenceType
Deprecated.  
setRegisterable(boolean) - Method in class uk.ac.vamsas.client.Vobject
Called by __testInstanceForidField and the post-unmarshalling handler to indicate if Vobject will have a vorbaId.
setRight(BinaryNode) - Method in class uk.ac.vamsas.objects.utils.trees.BinaryNode
DOCUMENT ME!
setScore(int, Score) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
 
setScore(Score[]) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
 
setScore(Vector) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Sets the value of '_scoreList' by copying the given Vector.
setScoreAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Deprecated.  
setSeg(int, Seg) - Method in class uk.ac.vamsas.objects.core.RangeType
 
setSeg(Seg[]) - Method in class uk.ac.vamsas.objects.core.RangeType
 
setSeg(Vector) - Method in class uk.ac.vamsas.objects.core.RangeType
Sets the value of '_segList' by copying the given Vector.
setSegAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.RangeType
Deprecated.  
setSeqAEnd(int) - Method in class uk.ac.vamsas.objects.core.Range
Sets the value of field 'seqAEnd'.
setSeqAStart(int) - Method in class uk.ac.vamsas.objects.core.Range
Sets the value of field 'seqAStart'.
setSeqBEnd(int) - Method in class uk.ac.vamsas.objects.core.Range
Sets the value of field 'seqBEnd'.
setSeqBStart(int) - Method in class uk.ac.vamsas.objects.core.Range
Sets the value of field 'seqBStart'.
setSeqRef(int, Object) - Method in class uk.ac.vamsas.objects.core.DataSetAnnotations
 
setSeqRef(Object[]) - Method in class uk.ac.vamsas.objects.core.DataSetAnnotations
 
setSeqRef(Vector) - Method in class uk.ac.vamsas.objects.core.DataSetAnnotations
Sets the value of '_seqRef' by copying the given Vector.
setSeqRefAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.DataSetAnnotations
Deprecated.  
setSeqrefs(int, Object) - Method in class uk.ac.vamsas.objects.core.AlignmentAnnotation
 
setSeqrefs(Object[]) - Method in class uk.ac.vamsas.objects.core.AlignmentAnnotation
 
setSeqrefs(Vector) - Method in class uk.ac.vamsas.objects.core.AlignmentAnnotation
Sets the value of '_seqrefs' by copying the given Vector.
setSeqrefsAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.AlignmentAnnotation
Deprecated.  
setSequence(int, Sequence) - Method in class uk.ac.vamsas.objects.core.DataSet
 
setSequence(Sequence[]) - Method in class uk.ac.vamsas.objects.core.DataSet
 
setSequence(Vector) - Method in class uk.ac.vamsas.objects.core.DataSet
Sets the value of '_sequenceList' by copying the given Vector.
setSequence(String) - Method in class uk.ac.vamsas.objects.core.SequenceType
Sets the value of field 'sequence'.
setSequenceAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.DataSet
Deprecated.  
setSequenceMapping(int, SequenceMapping) - Method in class uk.ac.vamsas.objects.core.DataSet
 
setSequenceMapping(SequenceMapping[]) - Method in class uk.ac.vamsas.objects.core.DataSet
 
setSequenceMapping(Vector) - Method in class uk.ac.vamsas.objects.core.DataSet
Sets the value of '_sequenceMappingList' by copying the given Vector.
setSequenceMappingAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.DataSet
Deprecated.  
setSession(SessionHandle) - Method in class uk.ac.vamsas.client.VorbaIdFactory
TODO: decide if these are needed.
setSession(SessionHandle) - Method in class uk.ac.vamsas.client.simpleclient.IdFactory
 
setSessionManager(SimpleSessionManager) - Method in class uk.ac.vamsas.client.simpleclient.VamsasSession
 
setSessionUrn(String) - Method in class uk.ac.vamsas.client.SessionHandle
 
setSource(String) - Method in class uk.ac.vamsas.objects.core.DbRef
Sets the value of field 'source'.
setStart(long) - Method in class uk.ac.vamsas.objects.core.MapList
Sets the value of field 'start'.
setStart(int) - Method in class uk.ac.vamsas.objects.core.Seg
Sets the value of field 'start'.
setStart(long) - Method in class uk.ac.vamsas.objects.core.SequenceType
Sets the value of field 'start'.
setState() - Method in class uk.ac.vamsas.client.simpleclient.FileWatcher
updates internal record of file state when caller has intentionally modified subject.
setStatus(String) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Sets the value of field 'status'.
setTimeoutBeforeLastCycle(int) - Method in class uk.ac.vamsas.client.simpleclient.ClientSessionFileWatcherElement
Enable the time out if the timeout is greater than zero
setTitle(String) - Method in class uk.ac.vamsas.objects.core.Newick
Sets the value of field 'title'.
setTitle(String) - Method in class uk.ac.vamsas.objects.core.Tree
Sets the value of field 'title'.
setTo(long) - Method in class uk.ac.vamsas.objects.core.MapList
Sets the value of field 'to'.
setTree(int, Tree) - Method in class uk.ac.vamsas.objects.core.Alignment
 
setTree(Tree[]) - Method in class uk.ac.vamsas.objects.core.Alignment
 
setTree(Vector) - Method in class uk.ac.vamsas.objects.core.Alignment
Sets the value of '_treeList' by copying the given Vector.
setTree(int, Tree) - Method in class uk.ac.vamsas.objects.core.DataSet
 
setTree(Tree[]) - Method in class uk.ac.vamsas.objects.core.DataSet
 
setTree(Vector) - Method in class uk.ac.vamsas.objects.core.DataSet
Sets the value of '_treeList' by copying the given Vector.
setTree(int, Tree) - Method in class uk.ac.vamsas.objects.core.VAMSAS
 
setTree(Tree[]) - Method in class uk.ac.vamsas.objects.core.VAMSAS
 
setTree(Vector) - Method in class uk.ac.vamsas.objects.core.VAMSAS
Sets the value of '_treeList' by copying the given Vector.
setTreeAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.Alignment
Deprecated.  
setTreeAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.DataSet
Deprecated.  
setTreeAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.VAMSAS
Deprecated.  
setTreeId(int, Object) - Method in class uk.ac.vamsas.objects.core.Treenode
 
setTreeId(Object[]) - Method in class uk.ac.vamsas.objects.core.Treenode
 
setTreeId(Vector) - Method in class uk.ac.vamsas.objects.core.Treenode
Sets the value of '_treeId' by copying the given Vector.
setTreeIdAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.Treenode
Deprecated.  
setTreenode(int, Treenode) - Method in class uk.ac.vamsas.objects.core.Tree
 
setTreenode(Treenode[]) - Method in class uk.ac.vamsas.objects.core.Tree
 
setTreenode(Vector) - Method in class uk.ac.vamsas.objects.core.Tree
Sets the value of '_treenodeList' by copying the given Vector.
setTreenodeAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.Tree
Deprecated.  
setType(String) - Method in class uk.ac.vamsas.objects.core.Attachment
Sets the value of field 'type'.
setType(String) - Method in class uk.ac.vamsas.objects.core.Param
Sets the value of field 'type'.
setType(String) - Method in class uk.ac.vamsas.objects.core.Property
Sets the value of field 'type'.
setType(String) - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
Sets the value of field 'type'.
setURN(String) - Method in class uk.ac.vamsas.client.SessionUrn
Set the urn attribute create a URI from the provided String
setUnit(long) - Method in class uk.ac.vamsas.objects.core.MapRangeType
Sets the value of field 'unit'.
setUnixMode(int) - Method in class org.apache.tools.zip.ZipEntry
Sets Unix permissions in a way that is understood by Info-Zip's unzip command.
setUnsavedFlag() - Method in class uk.ac.vamsas.client.simpleclient.VamsasSession
called to indicate session document has been modified.
setUpdateHandler(IObjectUpdate) - Method in interface uk.ac.vamsas.client.IClient
Sets the update handler that will be called when any updates occur to objects of type rootObject.
setUpdateHandler(IObjectUpdate) - Method in class uk.ac.vamsas.client.simpleclient.SimpleClient
 
setUrn(String) - Method in class uk.ac.vamsas.objects.core.Instance
Sets the value of field 'urn'.
setUser(UserHandle) - Method in class uk.ac.vamsas.client.VorbaIdFactory
 
setUser(UserHandle) - Method in class uk.ac.vamsas.client.simpleclient.IdFactory
 
setUser(int, User) - Method in class uk.ac.vamsas.objects.core.ApplicationData
 
setUser(User[]) - Method in class uk.ac.vamsas.objects.core.ApplicationData
 
setUser(Vector) - Method in class uk.ac.vamsas.objects.core.ApplicationData
Sets the value of '_userList' by copying the given Vector.
setUser(String) - Method in class uk.ac.vamsas.objects.core.Entry
Sets the value of field 'user'.
setUserAppdata(byte[]) - Method in interface uk.ac.vamsas.client.IClientAppdata
set the User-specific application data
setUserAppdata(byte[]) - Method in class uk.ac.vamsas.client.simpleclient.SimpleClientAppdata
 
setUserAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.ApplicationData
Deprecated.  
setUserId(int) - Method in class org.apache.tools.zip.AsiExtraField
Set the user id.
setVAMSAS(int, VAMSAS) - Method in class uk.ac.vamsas.objects.core.VamsasDocument
 
setVAMSAS(VAMSAS[]) - Method in class uk.ac.vamsas.objects.core.VamsasDocument
 
setVAMSAS(Vector) - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Sets the value of '_VAMSASList' by copying the given Vector.
setVAMSASAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Deprecated.  
setV_parent(Vobject) - Method in class uk.ac.vamsas.client.Vobject
 
setValue(int, float) - Method in class uk.ac.vamsas.objects.core.AnnotationElement
 
setValue(float[]) - Method in class uk.ac.vamsas.objects.core.AnnotationElement
 
setValue(Vector) - Method in class uk.ac.vamsas.objects.core.AnnotationElement
Sets the value of '_valueList' by copying the given Vector.
setValueAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.AnnotationElement
Deprecated.  
setVamsasDocument(File) - Method in class uk.ac.vamsas.client.simpleclient.VamsasSession
create a new session with an existing vamsas Document - by copying it into the session.
setVamsasRoots(VAMSAS[]) - Method in interface uk.ac.vamsas.client.IClientDocument
set the VAMSAS roots in the document TODO: decide if objects are verified for provenance and VorbaIds by this call or when document is stored TODO: decide if this call should throw InvalidVamsasObject exceptions.
setVamsasRoots(VAMSAS[]) - Method in class uk.ac.vamsas.client.simpleclient.ClientDocument
update the document with new roots.
setVamsasRoots(VAMSAS[]) - Method in class uk.ac.vamsas.test.simpleclient.ClientDoc
update the document with new roots.
setVersion(String) - Method in class uk.ac.vamsas.client.ClientHandle
 
setVersion(String) - Method in class uk.ac.vamsas.objects.core.ApplicationData
Sets the value of field 'version'.
setVersion(String) - Method in class uk.ac.vamsas.objects.core.DbRef
Sets the value of field 'version'.
setVersion(String) - Method in class uk.ac.vamsas.objects.core.VamsasDocument
Sets the value of field 'version'.
setVorba(VorbaIdFactory) - Method in class uk.ac.vamsas.client.simpleclient.SimpleDocBinding
 
setVorba(VorbaIdFactory) - Method in class uk.ac.vamsas.client.simpleclient.VamsasArchive
 
setVorbaId(VorbaId) - Method in class uk.ac.vamsas.client.Vobject
used by the IClient implementation to generate unique Id based on client applications current namespace.
setVref(int, Vref) - Method in class uk.ac.vamsas.objects.core.NodeType
 
setVref(Vref[]) - Method in class uk.ac.vamsas.objects.core.NodeType
 
setVref(Vector) - Method in class uk.ac.vamsas.objects.core.NodeType
Sets the value of '_vrefList' by copying the given Vector.
setVrefAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.NodeType
Deprecated.  
setVxref(int, Vxref) - Method in class uk.ac.vamsas.objects.core.Sequence
 
setVxref(Vxref[]) - Method in class uk.ac.vamsas.objects.core.Sequence
 
setVxref(Vector) - Method in class uk.ac.vamsas.objects.core.Sequence
Sets the value of '_vxrefList' by copying the given Vector.
setVxrefAsReference(Vector) - Method in class uk.ac.vamsas.objects.core.Sequence
Deprecated.  
set__added_since_last_read(boolean) - Method in class uk.ac.vamsas.client.Vobject
 
set__stored_in_document(boolean) - Method in class uk.ac.vamsas.client.Vobject
for use by Vorba agent to reflect state of vamsas Vobject to client application.
set__updated_since_last_read(boolean) - Method in class uk.ac.vamsas.client.Vobject
Set internal flag to indicate this object was updated since the last document read
shiftFrom(int) - Method in class uk.ac.vamsas.objects.utils.MapList
shift from pos to To(pos)
shiftTo(int) - Method in class uk.ac.vamsas.objects.utils.MapList
inverse of shiftFrom - maps pos in To to a position in From
shutdown() - Method in interface uk.ac.vamsas.client.picking.IPickManager
Shutsdown the pick manager processes, terminating any connections to other clients.
shutdown() - Method in class uk.ac.vamsas.client.picking.SocketManager
 
shutdown() - Method in class uk.ac.vamsas.client.simpleclient.SimplePickManager
shutdown the pickmanager and remove all references to it
slog - Variable in class uk.ac.vamsas.client.simpleclient.VamsasSession
 
startWatcher() - Method in class uk.ac.vamsas.test.simpleclient.simpleapp.VamsasClient
spawn a new thread to start the VamsasClientWatcher.
startWatching() - Method in class uk.ac.vamsas.client.simpleclient.EventGeneratorThread
called to start the session watching thread which generates events
stopWatching() - Method in class uk.ac.vamsas.client.simpleclient.EventGeneratorThread
 
storeDocRequest(Lock) - Method in class uk.ac.vamsas.client.simpleclient.EventGeneratorThread
 
storeDocument(File) - Method in interface uk.ac.vamsas.client.IClient
Any application may call storeDocument to save a local copy of the current vamsas document including all application specific entries.
storeDocument(File) - Method in class uk.ac.vamsas.client.simpleclient.SimpleClient
 
storeFile - Variable in class uk.ac.vamsas.client.simpleclient.EventGeneratorThread
written to by client when its app calls storeDocument.
storeVAMSAS(Object) - Method in class uk.ac.vamsas.test.simpleclient.simpleapp.VamsasDatastore
put the alignment viewed by AlignViewport into cdoc.
storedocfile - Variable in class uk.ac.vamsas.client.simpleclient.VamsasSession
 

T

TYPES - Static variable in class uk.ac.vamsas.client.SessionUrn
The types of URI protocols we understand
TestApp - class uk.ac.vamsas.client.picking.TestApp.
Simple example of a (runnable) class that shows how to use the picking API.
TestApp() - Constructor for class uk.ac.vamsas.client.picking.TestApp
 
TestSessionURN - class uk.ac.vamsas.test.simpleclient.TestSessionURN.
Tests simple client sessionURN creation
TestSessionURN() - Constructor for class uk.ac.vamsas.test.simpleclient.TestSessionURN
 
Tree - class uk.ac.vamsas.objects.core.Tree.
Class Tree.
Tree() - Constructor for class uk.ac.vamsas.objects.core.Tree
 
TreeDescriptor - class uk.ac.vamsas.objects.core.descriptors.TreeDescriptor.
Class TreeDescriptor.
TreeDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.TreeDescriptor
 
Treenode - class uk.ac.vamsas.objects.core.Treenode.
node identity and mapping data between tree representations and vamsas document objects
Treenode() - Constructor for class uk.ac.vamsas.objects.core.Treenode
 
TreenodeDescriptor - class uk.ac.vamsas.objects.core.descriptors.TreenodeDescriptor.
Class TreenodeDescriptor.
TreenodeDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.TreenodeDescriptor
 
Trees - class uk.ac.vamsas.objects.utils.Trees.
 
Trees() - Constructor for class uk.ac.vamsas.objects.utils.Trees
 
testMap(MapList, int, int) - Static method in class uk.ac.vamsas.objects.utils.MapList
test routine.
tidyAwaySessionDocumentState() - Method in class uk.ac.vamsas.client.simpleclient.SimpleClient
garbage collect the ClientDocument instance and re-enable watchers.
toDosTime(Date) - Static method in class org.apache.tools.zip.ZipOutputStream
Convert a Date object to a DOS date/time field.
toDosTime(long) - Static method in class org.apache.tools.zip.ZipOutputStream
Convert a Date object to a DOS date/time field.
toShifts - Variable in class uk.ac.vamsas.objects.utils.MapList
 
toString() - Method in class uk.ac.vamsas.client.VorbaId
 
transferAppDataEntry(String) - Method in class uk.ac.vamsas.client.simpleclient.VamsasArchive
Convenience method to copy over the referred entry from the backup to the new version.
transferAppDataEntry(String, String) - Method in class uk.ac.vamsas.client.simpleclient.VamsasArchive
Transfers an AppDataReference from old to new vamsas archive, with a name change.
transferRemainingAppDatas() - Method in class uk.ac.vamsas.client.simpleclient.VamsasArchive
transfers any AppDataReferences existing in the old document that haven't already been transferred to the new one LATER: do the same for transfers requiring a namechange - more document dependent.
treeReport(Tree, boolean, PrintStream) - Static method in class uk.ac.vamsas.test.simpleclient.ArchiveReports
 
tryLock(File) - Static method in class uk.ac.vamsas.client.simpleclient.LockFactory
try to lock target

U

UnixStat - interface org.apache.tools.zip.UnixStat.
Constants from stat.h on Unix systems.
UnrecognizedExtraField - class org.apache.tools.zip.UnrecognizedExtraField.
Simple placeholder for all those extra fields we don't want to deal with.
UnrecognizedExtraField() - Constructor for class org.apache.tools.zip.UnrecognizedExtraField
 
Usage - Variable in class uk.ac.vamsas.test.ExampleApplication
 
User - class uk.ac.vamsas.objects.core.User.
Class User.
User() - Constructor for class uk.ac.vamsas.objects.core.User
 
UserDescriptor - class uk.ac.vamsas.objects.core.descriptors.UserDescriptor.
Class UserDescriptor.
UserDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.UserDescriptor
 
UserHandle - class uk.ac.vamsas.client.UserHandle.
Unique user identifier for a vamsas session.
UserHandle(String, String) - Constructor for class uk.ac.vamsas.client.UserHandle
 
uk.ac.vamsas.client - package uk.ac.vamsas.client
 
uk.ac.vamsas.client.picking - package uk.ac.vamsas.client.picking
 
uk.ac.vamsas.client.simpleclient - package uk.ac.vamsas.client.simpleclient
 
uk.ac.vamsas.objects - package uk.ac.vamsas.objects
 
uk.ac.vamsas.objects.core - package uk.ac.vamsas.objects.core
 
uk.ac.vamsas.objects.core.descriptors - package uk.ac.vamsas.objects.core.descriptors
 
uk.ac.vamsas.objects.utils - package uk.ac.vamsas.objects.utils
 
uk.ac.vamsas.objects.utils.document - package uk.ac.vamsas.objects.utils.document
 
uk.ac.vamsas.objects.utils.trees - package uk.ac.vamsas.objects.utils.trees
 
uk.ac.vamsas.test - package uk.ac.vamsas.test
 
uk.ac.vamsas.test.objects - package uk.ac.vamsas.test.objects
 
uk.ac.vamsas.test.simpleclient - package uk.ac.vamsas.test.simpleclient
 
uk.ac.vamsas.test.simpleclient.simpleapp - package uk.ac.vamsas.test.simpleclient.simpleapp
 
unLock() - Method in class uk.ac.vamsas.client.simpleclient.VamsasFile
explicitly unlocks vamsas file.
uniqueAppDataReference(VamsasDocument, String) - Static method in class uk.ac.vamsas.objects.utils.AppDataReference
safely creates a new appData reference
uniquify(SequenceType[]) - Static method in class uk.ac.vamsas.objects.utils.SeqSet
 
unlockFile() - Method in class uk.ac.vamsas.client.simpleclient.SessionFile
Explicitly release the SessionFile's lock.
unlockVamsasDocument() - Method in class uk.ac.vamsas.client.simpleclient.VamsasSession
Unlocks the vamsas archive session document after it has been closed.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.Alignment
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.AlignmentAnnotation
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.AlignmentSequence
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.AnnotationElement
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.AppData
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.ApplicationData
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.Attachment
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.Common
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.DataSet
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.DataSetAnnotations
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.DbRef
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.Entry
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.Glyph
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.Input
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.Instance
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.Link
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.Local
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.LockFile
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.Map
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.MapList
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.MapRangeType
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.MapType
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.Mapped
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.Mapping
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.Newick
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.NodeType
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.Param
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.Pos
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.Property
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.Provenance
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.Range
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.RangeAnnotation
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.ReferenceType
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.Score
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.Seg
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.Sequence
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.SequenceMapping
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.SequenceType
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.Tree
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.Treenode
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.User
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.VAMSAS
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.VamsasDocument
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.Vref
Method unmarshal.
unmarshal(Reader) - Static method in class uk.ac.vamsas.objects.core.Vxref
Method unmarshal.
unmarshalled(Object) - Method in class uk.ac.vamsas.client.VorbaXmlBinder
 
update(Vobject, IClientDocument) - Method in interface uk.ac.vamsas.client.IObjectUpdate
Method called by Vamsas Client Library for all updated objects that the handler is registered for.
update(Alignment) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(AlignmentAnnotation) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(AlignmentSequence) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(AlignmentSequenceAnnotation) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(AnnotationElement) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(AppData) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(ApplicationData) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(Common) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(DataSet) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(DataSetAnnotations) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(DbRef) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(Entry) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(Glyph) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(Input) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(Instance) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(Link) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(LockFile) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(Map) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(SequenceMapping) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(Newick) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(Param) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(Pos) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(Property) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(Provenance) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(RangeAnnotation) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(RangeType) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(Score) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(Seg) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(Sequence) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(SequenceType) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(Tree) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(User) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(VAMSAS) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(VamsasDocument) - Method in class uk.ac.vamsas.objects.EmptyDocumentUpdater
 
update(Alignment) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
update(AlignmentAnnotation) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
update(AlignmentSequence) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
update(AlignmentSequenceAnnotation) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
update(AnnotationElement) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
update(AppData) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
update(ApplicationData) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
update(Common) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
update(DataSet) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
update(DataSetAnnotations) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
update(DbRef) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
update(Entry) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
update(Glyph) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
update(Input) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
update(Instance) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
update(Link) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
update(LockFile) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
update(Map) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
update(SequenceMapping) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
update(Newick) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
update(Param) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
update(Pos) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
update(Property) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
update(Provenance) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
update(RangeAnnotation) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
update(RangeType) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
update(Score) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
update(Seg) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
update(Sequence) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
update(SequenceType) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
update(Tree) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
update(User) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
update(VAMSAS) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
update(VamsasDocument) - Method in interface uk.ac.vamsas.objects.IDocumentUpdater
 
updateAnAppdataEntry(VamsasArchive, AppData, SessionFile) - Method in class uk.ac.vamsas.client.simpleclient.SimpleClientAppdata
copy data from the appData jar file to an appropriately referenced jar or Data entry for the given ApplicationData Assumes the JarFile is properly closed.
updateDocument(IClientDocument) - Method in interface uk.ac.vamsas.client.IClient
Queue new Vorba objects for storage and propagation to other clients (via Event.DOCUMENT_UPDATE based notification of document change) New objects without provenance information will be given a default entry using the IClient's application, user (and session) handles Validity of IClientDocument object instances after this call is implementation dependent TODO: consider refactoring to remove the redundant IClientDocument parameter for this method
updateDocument(IClientDocument) - Method in class uk.ac.vamsas.client.simpleclient.SimpleClient
 
updateDocumentRoots() - Method in class uk.ac.vamsas.client.simpleclient.ClientDocument
 
updateDocumentRoots() - Method in class uk.ac.vamsas.test.simpleclient.ClientDoc
 
updateFrom(Lock, SessionFile) - Method in class uk.ac.vamsas.client.simpleclient.SessionFile
Replaces data in sessionFile with data from file handled by another sessionFile passes up any exceptions.
updateHashValue(Vobject) - Method in interface uk.ac.vamsas.client.IVorbaIdFactory
called when an object is touched by the vamsas library prior to writing to record last hash for the object's VorbaId
updateHashValue(Vobject) - Method in class uk.ac.vamsas.client.VorbaIdFactory
 
updateJalview(ClientDoc) - Method in class uk.ac.vamsas.test.simpleclient.simpleapp.VamsasClient
 
updateSessionDocument() - Method in class uk.ac.vamsas.client.simpleclient.ClientDocument
called by vamsas api to write updated document to session
updateToJalview() - Method in class uk.ac.vamsas.test.simpleclient.simpleapp.VamsasDatastore
 
updateVamsasDocument(ClientDoc) - Method in class uk.ac.vamsas.test.simpleclient.simpleapp.VamsasClient
called with a vamsas document which will be updated with new data from the app
urn - Variable in class uk.ac.vamsas.client.SessionUrn
 
usage() - Static method in class uk.ac.vamsas.test.simpleclient.ArchiveClient
 
user - Variable in class uk.ac.vamsas.client.simpleclient.SimpleClient
 
user - Static variable in class uk.ac.vamsas.test.objects.Core
complete any automatically completable entries in the dataset
usersData - Variable in class uk.ac.vamsas.client.simpleclient.SimpleClientAppdata
set by extractAppData

V

VAMSAS - class uk.ac.vamsas.objects.core.VAMSAS.
contains unassociated trees and a number of analysis sets
VAMSAS() - Constructor for class uk.ac.vamsas.objects.core.VAMSAS
 
VAMSASDOC - Static variable in class uk.ac.vamsas.client.simpleclient.VamsasArchiveReader
name of the jarEntry containing a well formatted vamsas XML Document
VAMSASDOCUMENT - Static variable in class uk.ac.vamsas.client.simpleclient.ArchiveUrn
a simple vamsas document urn prefix
VAMSASDOCUMENT - Static variable in class uk.ac.vamsas.client.simpleclient.SessionUrn
 
VAMSASDescriptor - class uk.ac.vamsas.objects.core.descriptors.VAMSASDescriptor.
Class VAMSASDescriptor.
VAMSASDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.VAMSASDescriptor
 
VAMSASXML - Static variable in class uk.ac.vamsas.client.simpleclient.VamsasArchiveReader
name of the jarEntry containing a root VAMSAS element, and containing a random sequence of VAMSAS DataSet elements
VAMSAS_OBJ - Static variable in class uk.ac.vamsas.client.simpleclient.VamsasSession
 
V_parent - Variable in class uk.ac.vamsas.client.Vobject
reference to containing object for this Vobject.
VamsasArchive - class uk.ac.vamsas.client.simpleclient.VamsasArchive.
Class for high-level io and Jar manipulation involved in creating or updating a vamsas archive (with backups).
VamsasArchive(File, boolean) - Constructor for class uk.ac.vamsas.client.simpleclient.VamsasArchive
Create a new vamsas archive File locks are made immediately to avoid contention
VamsasArchive(File, boolean, boolean) - Constructor for class uk.ac.vamsas.client.simpleclient.VamsasArchive
 
VamsasArchive(VamsasFile, boolean, boolean) - Constructor for class uk.ac.vamsas.client.simpleclient.VamsasArchive
Constructor for accessing Files under file-lock management (ie a session file)
VamsasArchive(VamsasFile) - Constructor for class uk.ac.vamsas.client.simpleclient.VamsasArchive
read and write to archive - will not overwrite original contents, and will always write an up to date vamsas document structure.
VamsasArchive(File, boolean, boolean, SessionFile) - Constructor for class uk.ac.vamsas.client.simpleclient.VamsasArchive
 
VamsasArchive - class uk.ac.vamsas.test.simpleclient.VamsasArchive.
 
VamsasArchive() - Constructor for class uk.ac.vamsas.test.simpleclient.VamsasArchive
 
VamsasArchiveReader - class uk.ac.vamsas.client.simpleclient.VamsasArchiveReader.
Basic methods for accessing an existing Vamsas Archive, and Jar entry names for creating new vamsas archives.
VamsasArchiveReader(File) - Constructor for class uk.ac.vamsas.client.simpleclient.VamsasArchiveReader
 
VamsasArchiveReader(Lock) - Constructor for class uk.ac.vamsas.client.simpleclient.VamsasArchiveReader
in an ideal world - this constructor will create a reader object for the locked file's random access stream.
VamsasClient - class uk.ac.vamsas.test.simpleclient.simpleapp.VamsasClient.
 
VamsasClient(File) - Constructor for class uk.ac.vamsas.test.simpleclient.simpleapp.VamsasClient
create a new vamsas client session from the archive at sessionPath.
VamsasClient.VamsasClientWatcher - class uk.ac.vamsas.test.simpleclient.simpleapp.VamsasClient.VamsasClientWatcher.
 
VamsasDatastore - class uk.ac.vamsas.test.simpleclient.simpleapp.VamsasDatastore.
 
VamsasDatastore(ClientDoc, Hashtable, IdentityHashMap, Entry) - Constructor for class uk.ac.vamsas.test.simpleclient.simpleapp.VamsasDatastore
 
VamsasDocument - class uk.ac.vamsas.objects.core.VamsasDocument.
Class VamsasDocument.
VamsasDocument() - Constructor for class uk.ac.vamsas.objects.core.VamsasDocument
 
VamsasDocumentDescriptor - class uk.ac.vamsas.objects.core.descriptors.VamsasDocumentDescriptor.
Class VamsasDocumentDescriptor.
VamsasDocumentDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.VamsasDocumentDescriptor
 
VamsasFile - class uk.ac.vamsas.client.simpleclient.VamsasFile.
low level vamsas document management routines analogous to ClientsFile Grew out of io tests on VamsasArchive class in uk.ac.vamsas.test.simpleclient.VamsasArchive This class is not thread safe.
VamsasFile(File) - Constructor for class uk.ac.vamsas.client.simpleclient.VamsasFile
Connect to an existing Vamsas document in a given sessionDir or create a new one.
VamsasFileWatcherElement - class uk.ac.vamsas.client.simpleclient.VamsasFileWatcherElement.
Element of the VamsasFileWatcherThread event generator chain.
VamsasFileWatcherElement(VamsasFile, WatcherCallBack) - Constructor for class uk.ac.vamsas.client.simpleclient.VamsasFileWatcherElement
create a new, enabled watch element
VamsasFileWatcherElement(VamsasFile, WatcherCallBack, boolean) - Constructor for class uk.ac.vamsas.client.simpleclient.VamsasFileWatcherElement
new watcher with flag to initially skip watching this sessionfile
VamsasFileWatcherThread - class uk.ac.vamsas.client.simpleclient.VamsasFileWatcherThread.
Watches a bunch of VamsasFile states, calling the associated event handler when anything changes.
VamsasFileWatcherThread(EventGeneratorThread) - Constructor for class uk.ac.vamsas.client.simpleclient.VamsasFileWatcherThread
 
VamsasSession - class uk.ac.vamsas.client.simpleclient.VamsasSession.
Does all the IO operations for a SimpleClient instance accessing a SimpleClient vamsas session.
VamsasSession(File) - Constructor for class uk.ac.vamsas.client.simpleclient.VamsasSession
sets up the vamsas session files and watchers in sessionDir1
VamsasSession(File, File) - Constructor for class uk.ac.vamsas.client.simpleclient.VamsasSession
sets up the vamsas session files and watchers in sessionDir1
VersionEntries - class uk.ac.vamsas.objects.utils.document.VersionEntries.
enumerates versions for the VamsasDocument.Version string provides version comparison methods TODO: LATER: associate schema versions with these strings
VersionEntries() - Constructor for class uk.ac.vamsas.objects.utils.document.VersionEntries
 
Vobject - class uk.ac.vamsas.client.Vobject.
Base class for all Vamsas objects extracted from an IClientDocument.
Vobject() - Constructor for class uk.ac.vamsas.client.Vobject
 
Vobjhash - class uk.ac.vamsas.client.Vobjhash.
Holds information about Vobj instances that is held over between different writes to the document.
Vobjhash(Vobject) - Constructor for class uk.ac.vamsas.client.Vobjhash
creates a record of the hash value for a vamsas document object
VorbaId - class uk.ac.vamsas.client.VorbaId.
The unique reference id for a Vamsas document Vobject, used by applications to refer to the vamsas Vobject within their own data space in the vamsas document.
VorbaId() - Constructor for class uk.ac.vamsas.client.VorbaId
 
VorbaIdFactory - class uk.ac.vamsas.client.VorbaIdFactory.
A VorbaIdFactory is constructed by an IClient instance.
VorbaIdFactory() - Constructor for class uk.ac.vamsas.client.VorbaIdFactory
 
VorbaXmlBinder - class uk.ac.vamsas.client.VorbaXmlBinder.
Implements the Vamsas Vobject ID machinery for translating between non-volatile XML IDs and Vobject references.
VorbaXmlBinder(IVorbaIdFactory, Vector, Hashtable, Hashtable, Vector) - Constructor for class uk.ac.vamsas.client.VorbaXmlBinder
 
Vref - class uk.ac.vamsas.objects.core.Vref.
Direct associations between this node and any vamsas objects
Vref() - Constructor for class uk.ac.vamsas.objects.core.Vref
 
VrefDescriptor - class uk.ac.vamsas.objects.core.descriptors.VrefDescriptor.
Class VrefDescriptor.
VrefDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.VrefDescriptor
 
Vxref - class uk.ac.vamsas.objects.core.Vxref.
explicitly named cross reference to other objects in the document.
Vxref() - Constructor for class uk.ac.vamsas.objects.core.Vxref
 
VxrefDescriptor - class uk.ac.vamsas.objects.core.descriptors.VxrefDescriptor.
Class VxrefDescriptor.
VxrefDescriptor() - Constructor for class uk.ac.vamsas.objects.core.descriptors.VxrefDescriptor
 
valid() - Method in class uk.ac.vamsas.test.simpleclient.ArchiveClient
 
validate() - Method in class uk.ac.vamsas.client.picking.Message
Test consistence of a Message class implementation.
validate() - Method in class uk.ac.vamsas.objects.core.Alignment
 
validate() - Method in class uk.ac.vamsas.objects.core.AlignmentAnnotation
 
validate() - Method in class uk.ac.vamsas.objects.core.AlignmentSequence
 
validate() - Method in class uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation
 
validate() - Method in class uk.ac.vamsas.objects.core.AnnotationElement
 
validate() - Method in class uk.ac.vamsas.objects.core.AppData
 
validate() - Method in class uk.ac.vamsas.objects.core.ApplicationData
 
validate() - Method in class uk.ac.vamsas.objects.core.Attachment
 
validate() - Method in class uk.ac.vamsas.objects.core.Common
 
validate() - Method in class uk.ac.vamsas.objects.core.DataSet
 
validate() - Method in class uk.ac.vamsas.objects.core.DataSetAnnotations
 
validate() - Method in class uk.ac.vamsas.objects.core.DbRef
 
validate() - Method in class uk.ac.vamsas.objects.core.Entry
 
validate() - Method in class uk.ac.vamsas.objects.core.Glyph
 
validate() - Method in class uk.ac.vamsas.objects.core.Input
 
validate() - Method in class uk.ac.vamsas.objects.core.Instance
 
validate() - Method in class uk.ac.vamsas.objects.core.Link
 
validate() - Method in class uk.ac.vamsas.objects.core.Local
 
validate() - Method in class uk.ac.vamsas.objects.core.LockFile
 
validate() - Method in class uk.ac.vamsas.objects.core.Map
 
validate() - Method in class uk.ac.vamsas.objects.core.MapList
 
validate() - Method in class uk.ac.vamsas.objects.core.MapRangeType
 
validate() - Method in class uk.ac.vamsas.objects.core.MapType
 
validate() - Method in class uk.ac.vamsas.objects.core.Mapped
 
validate() - Method in class uk.ac.vamsas.objects.core.Mapping
 
validate() - Method in class uk.ac.vamsas.objects.core.Newick
 
validate() - Method in class uk.ac.vamsas.objects.core.NodeType
 
validate() - Method in class uk.ac.vamsas.objects.core.Param
 
validate() - Method in class uk.ac.vamsas.objects.core.Pos
 
validate() - Method in class uk.ac.vamsas.objects.core.Property
 
validate() - Method in class uk.ac.vamsas.objects.core.Provenance
 
validate() - Method in class uk.ac.vamsas.objects.core.Range
 
validate() - Method in class uk.ac.vamsas.objects.core.RangeAnnotation
 
validate() - Method in class uk.ac.vamsas.objects.core.RangeType
 
validate() - Method in class uk.ac.vamsas.objects.core.ReferenceType
 
validate() - Method in class uk.ac.vamsas.objects.core.Score
 
validate() - Method in class uk.ac.vamsas.objects.core.Seg
 
validate() - Method in class uk.ac.vamsas.objects.core.Sequence
 
validate() - Method in class uk.ac.vamsas.objects.core.SequenceMapping
 
validate() - Method in class uk.ac.vamsas.objects.core.SequenceType
 
validate() - Method in class uk.ac.vamsas.objects.core.Tree
 
validate() - Method in class uk.ac.vamsas.objects.core.Treenode
 
validate() - Method in class uk.ac.vamsas.objects.core.User
 
validate() - Method in class uk.ac.vamsas.objects.core.VAMSAS
 
validate() - Method in class uk.ac.vamsas.objects.core.VamsasDocument
 
validate() - Method in class uk.ac.vamsas.objects.core.Vref
 
validate() - Method in class uk.ac.vamsas.objects.core.Vxref
 
validateMergedRoots() - Method in class uk.ac.vamsas.client.simpleclient.SimpleClientConfig
New VAMSAS roots added (merged) into the document will be validated before actually being added.
validateUpdatedRoots() - Method in class uk.ac.vamsas.client.simpleclient.SimpleClientConfig
existing VAMSAS roots that may have been modified will be validated before the updated document can be written.
vamsasObjects - Variable in class uk.ac.vamsas.client.ClientDocument
collection of uk.ac.vamsas.client.Vobject references
vamsasfile - Variable in class uk.ac.vamsas.client.simpleclient.EventGeneratorThread
the session's vamsasDocument
versions - Static variable in class uk.ac.vamsas.objects.utils.document.VersionEntries
 
vorba - Variable in class uk.ac.vamsas.client.simpleclient.SimpleDocBinding
 
vorba - Variable in class uk.ac.vamsas.client.simpleclient.VamsasArchive
 
vorbaId - Variable in class uk.ac.vamsas.client.Vobject
unique id for all vamsas objects allows unambiguous referencing to any Vobject in the vamsas document
vorbafactory - Variable in class uk.ac.vamsas.client.ClientDocument
 

W

WATCH_SLEEP - Variable in class uk.ac.vamsas.client.simpleclient.VamsasFileWatcherThread
time between checks for changes of state on the file
WATCH_SLEEP - Variable in class uk.ac.vamsas.client.simpleclient.VamsasSession
time between checking
WATCH_SLEEP - Static variable in class uk.ac.vamsas.test.simpleclient.ArchiveClient
 
WatcherCallBack - interface uk.ac.vamsas.client.simpleclient.WatcherCallBack.
Interface for VamsasFileWatcherElement call back events generated by the VamsasFileWatcherThread.
WatcherElement - class uk.ac.vamsas.client.simpleclient.WatcherElement.
 
WatcherElement(WatcherCallBack) - Constructor for class uk.ac.vamsas.client.simpleclient.WatcherElement
 
WriteClustalWAlignment(OutputStream, Alignment) - Static method in class uk.ac.vamsas.objects.utils.SeqAln
 
wait(int) - Method in class uk.ac.vamsas.client.simpleclient.EventGeneratorThread
 
want_to_store() - Method in class uk.ac.vamsas.client.simpleclient.EventGeneratorThread
client App requests offline storage of vamsas data.
watch(long) - Method in class uk.ac.vamsas.test.simpleclient.ArchiveClient
watch the document file for updates.
watchForChange - Variable in class uk.ac.vamsas.client.simpleclient.WatcherElement
set this to false to stop the thread
watchForChange - Variable in class uk.ac.vamsas.test.simpleclient.ArchiveClient
set this to false if watch loop should end immediately
watchThread - Variable in class uk.ac.vamsas.client.simpleclient.EventGeneratorThread
thread watching all the session's file objects
watcher - Variable in class uk.ac.vamsas.client.simpleclient.WatcherElement
 
write(byte[], int, int) - Method in class org.apache.tools.zip.ZipOutputStream
Writes bytes to ZIP entry.
write(int) - Method in class org.apache.tools.zip.ZipOutputStream
Writes a single byte to ZIP entry.
write(byte[], int, int) - Method in class uk.ac.vamsas.client.AppDataOutputStream
 
write(int) - Method in class uk.ac.vamsas.client.AppDataOutputStream
 
write(byte[]) - Method in class uk.ac.vamsas.client.AppDataOutputStream
 
write(byte[], int, int) - Method in class uk.ac.vamsas.client.simpleclient.LockedFileOutputStream
 
write(byte[]) - Method in class uk.ac.vamsas.client.simpleclient.LockedFileOutputStream
 
write(int) - Method in class uk.ac.vamsas.client.simpleclient.LockedFileOutputStream
 
writeAppdataFromStream(String, InputStream) - Method in class uk.ac.vamsas.client.simpleclient.VamsasArchive
write data from a stream into an appData reference.
writeCentralDirectoryEnd() - Method in class org.apache.tools.zip.ZipOutputStream
Writes the "End of central dir record".
writeCentralFileHeader(ZipEntry) - Method in class org.apache.tools.zip.ZipOutputStream
Writes the central file header entry.
writeDataDescriptor(ZipEntry) - Method in class org.apache.tools.zip.ZipOutputStream
Writes the data descriptor entry.
writeLocalFileHeader(ZipEntry) - Method in class org.apache.tools.zip.ZipOutputStream
Writes the local file header entry
writeOut(byte[]) - Method in class org.apache.tools.zip.ZipOutputStream
Write bytes to output or random access file.
writeOut(byte[], int, int) - Method in class org.apache.tools.zip.ZipOutputStream
Write bytes to output or random access file.
writeVamsasDocument(File, Lock) - Method in class uk.ac.vamsas.client.simpleclient.VamsasSession
write session as a new vamsas Document (this will overwrite any existing file without warning) TODO: test TODO: verify that lock should be released for vamsas document.
write_Fasta(OutputStream, SequenceType[]) - Static method in class uk.ac.vamsas.objects.utils.SeqSet
 
write_Fasta(OutputStream, SequenceType[], boolean) - Static method in class uk.ac.vamsas.objects.utils.SeqSet
 
write_Fasta(OutputStream, SequenceType[], int) - Static method in class uk.ac.vamsas.objects.utils.SeqSet
 
write_FastaSeq(OutputStream, SequenceType) - Static method in class uk.ac.vamsas.objects.utils.Seq
 
write_FastaSeq(OutputStream, SequenceType, int) - Static method in class uk.ac.vamsas.objects.utils.Seq
 
write_PirSeq(OutputStream, SequenceType, int) - Static method in class uk.ac.vamsas.objects.utils.Seq
 

Z

ZipEntry - class org.apache.tools.zip.ZipEntry.
Extension that adds better handling of extra fields and provides access to the internal and external file attributes.
ZipEntry(String) - Constructor for class org.apache.tools.zip.ZipEntry
Creates a new zip entry with the specified name.
ZipEntry(ZipEntry) - Constructor for class org.apache.tools.zip.ZipEntry
Creates a new zip entry with fields taken from the specified zip entry.
ZipEntry(ZipEntry) - Constructor for class org.apache.tools.zip.ZipEntry
Creates a new zip entry with fields taken from the specified zip entry.
ZipEntry() - Constructor for class org.apache.tools.zip.ZipEntry
 
ZipExtraField - interface org.apache.tools.zip.ZipExtraField.
General format of extra field data.
ZipFile - class org.apache.tools.zip.ZipFile.
Replacement for java.util.ZipFile.
ZipFile(File) - Constructor for class org.apache.tools.zip.ZipFile
Opens the given file for reading, assuming the platform's native encoding for file names.
ZipFile(String) - Constructor for class org.apache.tools.zip.ZipFile
Opens the given file for reading, assuming the platform's native encoding for file names.
ZipFile(String, String) - Constructor for class org.apache.tools.zip.ZipFile
Opens the given file for reading, assuming the specified encoding for file names.
ZipFile(File, String) - Constructor for class org.apache.tools.zip.ZipFile
Opens the given file for reading, assuming the specified encoding for file names.
ZipFile(RandomAccessFile) - Constructor for class org.apache.tools.zip.ZipFile
Read an archive from the given random access file
ZipFile(RandomAccessFile, String) - Constructor for class org.apache.tools.zip.ZipFile
Read an archive from the given random access file, assuming the specified encoding for file names.
ZipLong - class org.apache.tools.zip.ZipLong.
Utility class that represents a four byte integer with conversion rules for the big endian byte order of ZIP files.
ZipLong(long) - Constructor for class org.apache.tools.zip.ZipLong
Create instance from a number.
ZipLong(byte[]) - Constructor for class org.apache.tools.zip.ZipLong
Create instance from bytes.
ZipLong(byte[], int) - Constructor for class org.apache.tools.zip.ZipLong
Create instance from the four bytes starting at offset.
ZipOutputStream - class org.apache.tools.zip.ZipOutputStream.
Reimplementation of java.util.zip.ZipOutputStream that does handle the extended functionality of this package, especially internal/external file attributes and extra fields with different layouts for local file data and central directory entries.
ZipOutputStream(OutputStream) - Constructor for class org.apache.tools.zip.ZipOutputStream
Creates a new ZIP OutputStream filtering the underlying stream.
ZipOutputStream(File) - Constructor for class org.apache.tools.zip.ZipOutputStream
Creates a new ZIP OutputStream writing to a File.
ZipShort - class org.apache.tools.zip.ZipShort.
Utility class that represents a two byte integer with conversion rules for the big endian byte order of ZIP files.
ZipShort(int) - Constructor for class org.apache.tools.zip.ZipShort
Create instance from a number.
ZipShort(byte[]) - Constructor for class org.apache.tools.zip.ZipShort
Create instance from bytes.
ZipShort(byte[], int) - Constructor for class org.apache.tools.zip.ZipShort
Create instance from the two bytes starting at offset.
ZipTest - class uk.ac.vamsas.test.simpleclient.ZipTest.
really simple test to see if we can open an archive and test for the existence of an entry called vamssDocument.xml.
ZipTest() - Constructor for class uk.ac.vamsas.test.simpleclient.ZipTest
 

_

_LockSuffix - Static variable in class uk.ac.vamsas.client.simpleclient.FileLock
 
_VamsasRoots - Variable in class uk.ac.vamsas.test.simpleclient.ClientDoc
 
__added_since_last_read - Variable in class uk.ac.vamsas.client.Vobject
true if Vobject appeared in the document after the last access by this vamsas library instance
__callHash() - Method in class uk.ac.vamsas.client.Vobject
calls the castor-generated hashCode() method
__ensure_instance_ids() - Method in class uk.ac.vamsas.client.Vobject
ensure's internal id field corresponds to vorbaId and cascade through all fields referring to an instance of Vobject calling the same method on them.
__ensure_instance_ids(boolean) - Method in class uk.ac.vamsas.client.Vobject
 
__getInstanceIdField() - Method in class uk.ac.vamsas.client.Vobject
 
__getLHash() - Method in class uk.ac.vamsas.client.Vobject
get the LhashValue for this object
__last_hash - Variable in class uk.ac.vamsas.client.Vobject
memory of the last doHash() value computed for the Vobject
__setFinalHash(long) - Method in class uk.ac.vamsas.client.Vobject
compute the final LhashValue as a difference between checksum and the current base
__setInitHash(long) - Method in class uk.ac.vamsas.client.Vobject
set the base LhashValue for this object
__stored_in_document - Variable in class uk.ac.vamsas.client.Vobject
true if Vobject was stored in a vamsas Document or has been retrieved from it
__updated_since_last_read - Variable in class uk.ac.vamsas.client.Vobject
true if Vobject was updated since the vamsas library last read a Vobj with the same VorbaId from a document.
__visited - Variable in class uk.ac.vamsas.client.Vobject
 
__vorba - Variable in class uk.ac.vamsas.client.Vobject
the source of unique VorbaIds.
_getReadonly(VamsasArchiveReader) - Method in class uk.ac.vamsas.test.simpleclient.ArchiveClient
 
_print(StringBuffer, SequenceNode) - Method in class uk.ac.vamsas.objects.utils.trees.NewickFile
 
_registerObject(Vobject) - Method in class uk.ac.vamsas.client.ClientDocument
 
_session - Variable in class uk.ac.vamsas.client.simpleclient.SimpleClient
 
_validNewAppDataReference(String) - Method in class uk.ac.vamsas.client.simpleclient.VamsasArchive
Validates the AppDataReference: not null and not already written to archive.
_validatemergedroots - Variable in class uk.ac.vamsas.client.simpleclient.SimpleClientConfig
 
_validateupdatedroots - Variable in class uk.ac.vamsas.client.simpleclient.SimpleClientConfig
 

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