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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