From 156ad51b0a85ed5902f7f9ff051620c832acbea6 Mon Sep 17 00:00:00 2001 From: jprocter Date: Thu, 14 Dec 2006 17:08:32 +0000 Subject: [PATCH] refactored from org.vamsas to uk.ac.vamsas git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@261 be28352e-c001-0410-b1a7-c7978e42abec --- src/org/vamsas/client/ClientDocument.java | 52 - src/org/vamsas/client/ClientHandle.java | 97 -- src/org/vamsas/client/Events.java | 92 -- src/org/vamsas/client/IClient.java | 142 --- src/org/vamsas/client/IClientAppdata.java | 61 -- src/org/vamsas/client/IClientDocument.java | 99 -- src/org/vamsas/client/IClientFactory.java | 56 - src/org/vamsas/client/IObjectUpdate.java | 26 - src/org/vamsas/client/IVorbaIdFactory.java | 37 - src/org/vamsas/client/Iapp.java | 12 - .../vamsas/client/InvalidSessionUrnException.java | 38 - .../vamsas/client/NoDefaultSessionException.java | 46 - src/org/vamsas/client/SessionHandle.java | 38 - src/org/vamsas/client/SessionUrn.java | 40 - src/org/vamsas/client/UserHandle.java | 50 - src/org/vamsas/client/Vobject.java | 464 --------- src/org/vamsas/client/Vobjhash.java | 25 - src/org/vamsas/client/VorbaId.java | 73 -- src/org/vamsas/client/VorbaIdFactory.java | 84 -- src/org/vamsas/client/VorbaXmlBinder.java | 241 ----- src/org/vamsas/client/picking/PickEndPoint.java | 101 -- src/org/vamsas/client/picking/PickManager.java | 147 --- src/org/vamsas/client/picking/PickServer.java | 83 -- src/org/vamsas/client/picking/TestApp.java | 33 - .../client/simpleclient/AppDataInputStream.java | 53 - .../client/simpleclient/AppDataOutputStream.java | 86 -- src/org/vamsas/client/simpleclient/ArchiveUrn.java | 34 - .../vamsas/client/simpleclient/ClientDocument.java | 510 --------- .../vamsas/client/simpleclient/ClientsFile.java | 295 ------ .../client/simpleclient/EventGeneratorThread.java | 277 ----- src/org/vamsas/client/simpleclient/FileLock.java | 205 ---- .../vamsas/client/simpleclient/FileWatcher.java | 168 --- src/org/vamsas/client/simpleclient/IdFactory.java | 159 --- src/org/vamsas/client/simpleclient/ListFile.java | 25 - src/org/vamsas/client/simpleclient/Lock.java | 96 -- .../vamsas/client/simpleclient/LockFactory.java | 52 - .../client/simpleclient/LockTimeoutException.java | 29 - .../simpleclient/LockedFileOutputStream.java | 159 --- src/org/vamsas/client/simpleclient/NativeLock.java | 173 ---- .../vamsas/client/simpleclient/SessionFile.java | 215 ---- .../client/simpleclient/SessionFlagFile.java | 85 -- src/org/vamsas/client/simpleclient/SessionUrn.java | 40 - .../vamsas/client/simpleclient/SessionsFile.java | 342 ------ .../vamsas/client/simpleclient/SimpleClient.java | 416 -------- .../client/simpleclient/SimpleClientAppdata.java | 543 ---------- .../client/simpleclient/SimpleClientFactory.java | 262 ----- .../client/simpleclient/SimpleDocBinding.java | 138 --- .../vamsas/client/simpleclient/SimpleDocument.java | 28 - .../vamsas/client/simpleclient/VamsasArchive.java | 809 --------------- .../client/simpleclient/VamsasArchiveReader.java | 313 ------ src/org/vamsas/client/simpleclient/VamsasFile.java | 100 -- .../vamsas/client/simpleclient/VamsasSession.java | 312 ------ src/org/vamsas/objects/core/.castor.cdr | 3 - src/org/vamsas/objects/core/Alignment.java | 979 ------------------ .../vamsas/objects/core/AlignmentAnnotation.java | 249 ----- .../core/AlignmentAnnotationDescriptor.java | 255 ----- .../vamsas/objects/core/AlignmentDescriptor.java | 503 --------- src/org/vamsas/objects/core/AlignmentSequence.java | 385 ------- .../objects/core/AlignmentSequenceAnnotation.java | 256 ----- .../AlignmentSequenceAnnotationDescriptor.java | 255 ----- .../objects/core/AlignmentSequenceDescriptor.java | 282 ----- src/org/vamsas/objects/core/AnnotationElement.java | 673 ------------ .../objects/core/AnnotationElementDescriptor.java | 405 -------- src/org/vamsas/objects/core/AppData.java | 239 ----- src/org/vamsas/objects/core/AppDataDescriptor.java | 250 ----- src/org/vamsas/objects/core/ApplicationData.java | 572 ---------- .../objects/core/ApplicationDataDescriptor.java | 359 ------- src/org/vamsas/objects/core/Attachment.java | 330 ------ .../vamsas/objects/core/AttachmentDescriptor.java | 325 ------ src/org/vamsas/objects/core/Common.java | 141 --- src/org/vamsas/objects/core/CommonDescriptor.java | 167 --- src/org/vamsas/objects/core/DataSet.java | 850 --------------- .../vamsas/objects/core/DataSetAnnotations.java | 217 ---- .../objects/core/DataSetAnnotationsDescriptor.java | 249 ----- src/org/vamsas/objects/core/DataSetDescriptor.java | 385 ------- src/org/vamsas/objects/core/DbRef.java | 806 --------------- src/org/vamsas/objects/core/DbRefDescriptor.java | 430 -------- src/org/vamsas/objects/core/Entry.java | 803 -------------- src/org/vamsas/objects/core/EntryDescriptor.java | 471 --------- src/org/vamsas/objects/core/Glyph.java | 233 ----- src/org/vamsas/objects/core/GlyphDescriptor.java | 244 ----- src/org/vamsas/objects/core/Input.java | 219 ---- src/org/vamsas/objects/core/InputDescriptor.java | 247 ----- src/org/vamsas/objects/core/Instance.java | 179 ---- .../vamsas/objects/core/InstanceDescriptor.java | 213 ---- src/org/vamsas/objects/core/Link.java | 217 ---- src/org/vamsas/objects/core/LinkDescriptor.java | 240 ----- src/org/vamsas/objects/core/LockFile.java | 182 ---- .../vamsas/objects/core/LockFileDescriptor.java | 207 ---- src/org/vamsas/objects/core/Map.java | 151 --- src/org/vamsas/objects/core/MapDescriptor.java | 167 --- src/org/vamsas/objects/core/MapList.java | 404 -------- src/org/vamsas/objects/core/MapListDescriptor.java | 339 ------ src/org/vamsas/objects/core/Mapping.java | 186 ---- src/org/vamsas/objects/core/MappingDescriptor.java | 210 ---- src/org/vamsas/objects/core/Newick.java | 288 ------ src/org/vamsas/objects/core/NewickDescriptor.java | 315 ------ src/org/vamsas/objects/core/Param.java | 261 ----- src/org/vamsas/objects/core/ParamDescriptor.java | 285 ----- src/org/vamsas/objects/core/Pos.java | 204 ---- src/org/vamsas/objects/core/PosDescriptor.java | 213 ---- src/org/vamsas/objects/core/Property.java | 261 ----- .../vamsas/objects/core/PropertyDescriptor.java | 285 ----- src/org/vamsas/objects/core/Provenance.java | 306 ------ .../vamsas/objects/core/ProvenanceDescriptor.java | 210 ---- src/org/vamsas/objects/core/RangeAnnotation.java | 1093 -------------------- .../objects/core/RangeAnnotationDescriptor.java | 578 ----------- src/org/vamsas/objects/core/RangeType.java | 452 -------- .../vamsas/objects/core/RangeTypeDescriptor.java | 246 ----- src/org/vamsas/objects/core/Score.java | 240 ----- src/org/vamsas/objects/core/ScoreDescriptor.java | 249 ----- src/org/vamsas/objects/core/Seg.java | 331 ------ src/org/vamsas/objects/core/SegDescriptor.java | 297 ------ src/org/vamsas/objects/core/Sequence.java | 387 ------- .../vamsas/objects/core/SequenceDescriptor.java | 285 ----- src/org/vamsas/objects/core/SequenceType.java | 677 ------------ .../objects/core/SequenceTypeDescriptor.java | 446 -------- src/org/vamsas/objects/core/Tree.java | 600 ----------- src/org/vamsas/objects/core/TreeDescriptor.java | 390 ------- src/org/vamsas/objects/core/User.java | 212 ---- src/org/vamsas/objects/core/UserDescriptor.java | 252 ----- src/org/vamsas/objects/core/VAMSAS.java | 535 ---------- src/org/vamsas/objects/core/VAMSASDescriptor.java | 315 ------ src/org/vamsas/objects/core/VamsasDocument.java | 725 ------------- .../objects/core/VamsasDocumentDescriptor.java | 388 ------- src/org/vamsas/objects/utils/AppDataReference.java | 160 --- src/org/vamsas/objects/utils/DocumentStuff.java | 34 - src/org/vamsas/objects/utils/Format.java | 612 ----------- src/org/vamsas/objects/utils/GlyphDictionary.java | 23 - src/org/vamsas/objects/utils/ProvenanceStuff.java | 45 - src/org/vamsas/objects/utils/Seq.java | 131 --- src/org/vamsas/objects/utils/SeqAln.java | 238 ----- src/org/vamsas/objects/utils/SeqSet.java | 138 --- src/org/vamsas/objects/utils/SymbolDictionary.java | 19 - .../objects/utils/document/VersionEntries.java | 49 - src/org/vamsas/test/ExampleApplication.java | 160 --- src/org/vamsas/test/objects/Core.java | 81 -- .../vamsas/test/simpleclient/ArchiveClient.java | 292 ------ .../vamsas/test/simpleclient/ArchiveReader.java | 50 - .../vamsas/test/simpleclient/ArchiveReports.java | 186 ---- .../test/simpleclient/ArchiveStreamReader.java | 52 - .../vamsas/test/simpleclient/ArchiveWatcher.java | 105 -- .../vamsas/test/simpleclient/ArchiveWriter.java | 180 ---- src/org/vamsas/test/simpleclient/ClientDoc.java | 355 ------- .../vamsas/test/simpleclient/ClientsFileTest.java | 310 ------ .../vamsas/test/simpleclient/CommandProcessor.java | 65 -- .../vamsas/test/simpleclient/VamsasArchive.java | 205 ---- .../test/simpleclient/simpleapp/VamsasClient.java | 186 ---- .../simpleclient/simpleapp/VamsasDatastore.java | 333 ------ 149 files changed, 37873 deletions(-) delete mode 100644 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src/org/vamsas/test/simpleclient/VamsasArchive.java delete mode 100644 src/org/vamsas/test/simpleclient/simpleapp/VamsasClient.java delete mode 100644 src/org/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java diff --git a/src/org/vamsas/client/ClientDocument.java b/src/org/vamsas/client/ClientDocument.java deleted file mode 100644 index 3866a90..0000000 --- a/src/org/vamsas/client/ClientDocument.java +++ /dev/null @@ -1,52 +0,0 @@ -/* - * - */ -package org.vamsas.client; - -import java.util.Hashtable; - -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.vamsas.objects.core.VAMSAS; - -/** - * skeleton abstract class to allow client implementations - * access to vamsas.client.Vobject registry mechanism. - */ -public abstract class ClientDocument implements IClientDocument { - static Log log = LogFactory.getLog(ClientDocument.class); - - /** - * collection of org.vamsas.client.Vobject references - */ - protected Hashtable vamsasObjects; - protected IVorbaIdFactory vorbafactory; - - protected ClientDocument(Hashtable objects, IVorbaIdFactory factory) { - vamsasObjects = objects; - vorbafactory = factory; - } - - /** - * @see IClientHandle.registerObject(Vobject unregistered) - */ - protected VorbaId _registerObject(Vobject unregistered) { - // be ultra safe here because the user may be trying to mix different factories - if (unregistered.__vorba==null) - unregistered.__vorba = vorbafactory; - else - if (unregistered.__vorba!=vorbafactory) { - // LATER: decide if this is allowed - it isn't for the moment. - log.error("Attempt to overwrite info in a registered vorba Vobject (under a different IVorbaIdFactory) ! - Implementation fix needed."); - return null; - } else { - // probably didn't need to call registerObject. - log.debug("Redundant call to registerObject"); - } - // TODO: add default provenance. - // TODO: decide if we need to do call __ensure_instance_ids here - // TODO: check if __ensure_instance_ids works correctly with new 'visit flag' mechanism - unregistered.__ensure_instance_ids(); // call cascade method here : - return unregistered.getVorbaId(); - } -} diff --git a/src/org/vamsas/client/ClientHandle.java b/src/org/vamsas/client/ClientHandle.java deleted file mode 100644 index 76666f9..0000000 --- a/src/org/vamsas/client/ClientHandle.java +++ /dev/null @@ -1,97 +0,0 @@ -/* - */ -package org.vamsas.client; - -import java.io.Serializable; - -/** - * Uniquely describes a vamsas client application. - * @author jimp - */ -public class ClientHandle implements Serializable { - static final long serialVersionUID = 0; - /** - * @param clientName - * @param version - */ - public ClientHandle(String clientName, String version) { - super(); - this.clientName = clientName; - this.version = version; - this.setClientUrn("vamsas://"+clientName+":"+version+"/"); // TODO: decide on application handle ornthing (used to prefix new ids made by a particular application) - } - /** - * (non-unique) human readable vamsas client name - */ - String clientName; - - /** - * the unambiguous client identifier - * This may be rewritten by the Vorba object if - * other clients with the same name, version - * and user are involved in a session. - * - */ - String clientUrn; - - /** - * version modifier to tag application space - */ - String version; - - /** - * @return Returns the clientUrn. - */ - public String getClientUrn() { - return clientUrn; - } - - /** - * May become protected - should only be set by a Vorba object. - * @param clientUrn - * The clientUrn to set. - */ - public void setClientUrn(String clientUrn) { - this.clientUrn = clientUrn; - } - - /** - * @return Returns the version. - */ - public String getVersion() { - return version; - } - - /** - * @param version - * The version to set. - */ - public void setVersion(String version) { - this.version = version; - } - - - /** - * @return Returns the clientName. - */ - public String getClientName() { - return clientName; - } - - /** - * @param clientName - * The clientName to set. - */ - public void setClientName(String clientName) { - this.clientName = clientName; - } - - public boolean equals(Object that) { - if (that instanceof ClientHandle) - return this.equals((ClientHandle) that); - return false; - } - public boolean equals(ClientHandle that) { - return (clientName.equals(that.clientName) && version.equals(that.version) && clientUrn.equals(that.clientUrn)); - } -} diff --git a/src/org/vamsas/client/Events.java b/src/org/vamsas/client/Events.java deleted file mode 100644 index 4a91f5a..0000000 --- a/src/org/vamsas/client/Events.java +++ /dev/null @@ -1,92 +0,0 @@ -package org.vamsas.client; - -/** - * Enumerates the event types generated during the lifecycle of a Vamsas - * session. - * See the excel spreadsheet in VamsasClient/docs/VamsasSessionEventAnalysis.xls for - * some more information about when these are generated and how they should be - * handled. - * - */ - -public class Events { - /** - * Generated when a client has finished updating the document. - * Client which has completed an update should - * not receive the event. - * NewValue: org.vamsas.client.IClient for session. - */ - public static final String DOCUMENT_UPDATE = "org.vamsas.client.events.documentUpdateEvent"; - - /** - * Generated when a new vamsas document is created (perhaps from some existing - * Vamsas data) so an application may do its own data space initialization. - * Raised for a new application connecting to a vamsas document - * NewValue: org.vamsas.client.IClient for session. - * LATER: DOCUMENT_CREATE event may be redundant - */ - public static final String DOCUMENT_CREATE = "org.vamsas.client.events.documentCreateEvent"; - - /** - * Generated when a new vamsas client is attached to a session (Handle is - * passed) Note: the newly created client does not receive the event. - */ - public static final String CLIENT_CREATION = "org.vamsas.client.events.clientCreateEvent"; - - /** - * Generated when a vamsas client leaves a session (Handle is passed to all - * others). - */ - public static final String CLIENT_FINALIZATION = "org.vamsas.client.events.clientFinalizationEvent"; - - /** - * Generated prior to session Shutdown, after the last participating vamsas - * client has finalized. - * Probably only useful to IClientFactory implementations. - * NewValue: - */ - public static final String SESSION_SHUTDOWN = "org.vamsas.client.events.SessionShutdownEvent"; - - /** - * 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. - * Any client that handles this should call the - * IClient.getDocument(), update and then IClient.updateDocument in the same - * handler thread (the lock on the document is held until the handler exits). - * EventName: - * NewValue: org.vamsas.client.IClient for session. - */ - public static final String DOCUMENT_FINALIZEAPPDATA = "org.vamsas.client.events.DocumentFinalizeAppData"; - - /** - * Generated by Vorba stub for the sole remaining client instance in a session, - * when it makes a call to finalizeClient(). - * It is only raised if the session has been modified since the - * last call to storeDocument() by any application. - * LATER: copies of a document should be on a per-user basis for multi-user sessions. - * Sequence is as follows : 1. All other vamsas clients have - * called finalizeClient() 2. Final living client monitors closures, and - * realises that it is last. 3. Final client generates event to prompt - * associated application to inquire if the user wishes to save the document - * for future reference. - * * Any call to finalizeClient in a thread other than the registered - * EventListener will block until the RequestToClose handler has exited. - * NewValue: org.vamsas.client.IClient for session. - */ - public static final String DOCUMENT_REQUESTTOCLOSE = "org.vamas.client.DocumentRequestToCloseEvent"; - - public static java.util.Vector EventList = initList(); - - private static java.util.Vector initList() { - java.util.Vector vec = new java.util.Vector(); - vec.add((Object) DOCUMENT_UPDATE); - vec.add((Object) DOCUMENT_CREATE); - vec.add((Object) CLIENT_CREATION); - vec.add((Object) CLIENT_FINALIZATION); - vec.add((Object) SESSION_SHUTDOWN); - vec.add((Object) DOCUMENT_REQUESTTOCLOSE); - vec.add((Object) DOCUMENT_FINALIZEAPPDATA); - return vec; - } -} diff --git a/src/org/vamsas/client/IClient.java b/src/org/vamsas/client/IClient.java deleted file mode 100644 index aaf855f..0000000 --- a/src/org/vamsas/client/IClient.java +++ /dev/null @@ -1,142 +0,0 @@ -/** - * org.vamsas.client.IClient - * - */ -package org.vamsas.client; - -import java.beans.PropertyChangeListener; -import java.io.IOException; - -/** - * 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. - * (it's VORBA, not CORBA!) - * LATER: add exceptions for timeouts raised when there are problems accessing session data (because another application is hogging it). - * LATER: think about situations when two applications both want a ClientDocument at the same time - can one have read-only access (and be told that another is about to update) - */ - -public interface IClient { - - /** - * Self-documenting/describing info for the application to present - * to the user. - * LATER: formalise this for describing VAMSAS system, a particular - * Vorba client agent, and a particular session. - * @return string like VamsasClient v.1.1.1 (GPL) and whatever - */ - public String getAbout(); - - /** - * convenience method to get the SessionUrn as a string (for passing directly to a text box...). - * @return current SessionUrn - */ - public String getSessionUrn(); - /** - * Returns a valid URN for other applications to connect to - * the vamsas session. - * @return session handle for this session. - */ - public SessionHandle getSessionHandle(); - /** - * Included for applications with several ClientHandle - * identities. - * @return ClientHandle used to interact with - * other Vamsas applications. - */ - public ClientHandle getClientHandle(); - /** - * - * @return UserHandle used when interacting - * with other Vamsas applications. - */ - public UserHandle getUserHandle(); - /** - * Method called by client application on exit. - * Vorba will inform other clients if they exist. - * If this is the last application in the session - * then the session will be closed. - * Note: The application should be ready to handle - * 'RequestToCloseDocument' events from the Vorba - * agent in the latter case and so prompt the user - * to save the session locally. - * LATER: pick a better name ? - */ - public void finalizeClient(); - /** - * register handler for updates for the current session - */ - public void addDocumentUpdateHandler(PropertyChangeListener evt); - /** - * get vamsas document with - * user and app specific data - * IClientDocuments are not thread-safe. - * TODO: New exception for failed document lock. - * @throws IOException if lock is not obtainable for the document in the session - */ - public IClientDocument getClientDocument() throws IOException; - /** - * 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 - */ - public void updateDocument(IClientDocument newdoc); - /** - * Any application may call storeDocument to - * save a local copy of the current vamsas document - * including all application specific entries. - * - * @param location to write zip file - */ - public void storeDocument(java.io.File location); - /** - * Any application may call importDocument to merge a stored - * vamsasDocument into the current session. - * Note: use a IClientFactory's implementation to make sessions out of vamsas documnts - * LATER: VAMSAS: The IClient implementation will handle all ID 'relocations' - * @param location - */ - public void importDocument(java.io.File location); - /** - * Add a listener to a particular event chain. - * See org.vamsas.client.Events for allowed - * values for EventChain. - * The EventChain value is passed as the - * propertyName in the java.bean.PropertyChangeEvent - * LATER: extend class to form own vamsas Event/Listener model. - * @param EventChain Name of event. Blank/null registers handler for all events. - * @param evt - event handler function. - */ - public void addVorbaEventHandler(String EventChain, PropertyChangeListener evt); - /** - * Sets the update handler that will be called when any updates occur to objects of type rootObject. - * @param rootObject - * @param handler - */ - public void setUpdateHandler(IObjectUpdate handler); - public IObjectUpdate getUpdateHandler(Class rootObject); - public void removeUpdateHandler(Class rootObject); - public IObjectUpdate[] getUpdateHandlers(); - /** - * client application calls this to force the - * Vorba client to check for updates immediately. - * - */ - public void pollUpdate(); - - /** - * Client application calls this after any pre-session initialization - * (registering of Handlers, etc) - * Exceptions are raised for any failures. Any stateful calls to the session prior to - * this will result in an implicit call to joinSession - if that results in an exception - * then the VamsasClient should raise an Error. - * LATER: create VAMSAS exception hierarchy (in a language agnostic manner) - */ - public void joinSession() throws Exception; -} diff --git a/src/org/vamsas/client/IClientAppdata.java b/src/org/vamsas/client/IClientAppdata.java deleted file mode 100644 index 965a783..0000000 --- a/src/org/vamsas/client/IClientAppdata.java +++ /dev/null @@ -1,61 +0,0 @@ -/** - * - */ -package org.vamsas.client; - -import java.io.DataInput; -import java.io.DataOutput; - -/** - * Object for accessing Client and User specific data - * in an IClientDocument instance. - * - */ -public interface IClientAppdata { - /** - * @return true if Client's non-user specific application data is non-zero length. - */ - boolean hasClientAppdata(); - /** - * @return true if User's Client Application data is non-zero length - */ - boolean hasUserAppdata(); - /** - * - * @return byte array containing the Client's non-user specific application data - */ - byte[] getClientAppdata(); - /** - * - * @return byte array containing the Client's user specific application data - */ - byte[] getUserAppdata(); - /** - * set the non-User-specific application data - * @param data - the new non-user-specific data - */ - void setClientAppdata(byte[] data); - /** - * set the User-specific application data - * @param data - the new user-specific data - */ - void setUserAppdata(byte[] data); - /** - * @return non-user specific data output stream - */ - DataOutput getClientOutputStream(); - /** - * @return non-user specific data input stream - */ - DataInput getClientInputStream(); - /** - * - * @return user specific data output stream - */ - DataOutput getUserOutputStream(); - /** - * - * @return user specific data input stream - */ - DataInput getUserInputStream(); -} diff --git a/src/org/vamsas/client/IClientDocument.java b/src/org/vamsas/client/IClientDocument.java deleted file mode 100644 index 8db697f..0000000 --- a/src/org/vamsas/client/IClientDocument.java +++ /dev/null @@ -1,99 +0,0 @@ -/* - * Created on 13-Sep-2005 - * - * TODO To change the template for this generated file go to - * Window - Preferences - Java - Code Style - Code Templates - */ -package org.vamsas.client; - -import org.vamsas.objects.core.VAMSAS; - - -/** - * Defines the API for the Vamsas XML Document - * as accessed by a Vamsas SimpleClient Application. - * An instance of this interface is valid for a - * particular set of user, session and application - * handles. - * - * It initially represents a snapshot of the - * XML document at a particular time - queriable by - * reference or by retrieval of root objects. - * It provides methods to make new Vobject references, - * These are guaranteed to be unique amongst existing - * objects in the document, all other references created - * by this Vobject's instance and all other references - * constructed by any other vamsas agents in the session. - * TODO: LATER: finegrained access control for public/private user access - * Finegrained access control: Since a clientDocument is created for a particular - * UserHandle, there is scope for fine grain data access - * control based on user identity. - * A user may also want to make private notes, not - * available to other people using the same application - * in the same session. - * TODO: LATER: implement a more sophisticated query interface for quickly identifying new data in a vamsas document and manipulating existing objects - * @author jimp - */ -public interface IClientDocument { - - /** - * Get a single Vobject. - * @param id - * @return Vobject referred to by id or null if it doesn't exist. - */ - Vobject getObject(VorbaId id); - /** - * Get a list of objects. - * @param ids - * @return array of objects using a vector of VorbaId ids. - */ - Vobject[] getObjects(VorbaId[] ids); - /** - * Returns all root objects in document. All objects inherit - * from org.vamsas.client.Vobject and have valid VorbaIds and provenance entries. - * @return array of root Vamsas element objects. - */ - VAMSAS[] getVamsasRoots(); - /** - * 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. - * TODO: decide how this call deals with applications that 'forget' to include all VAMSAS roots (this is where reference counting/garbage collection happens) - * @param roots - */ - void setVamsasRoots(VAMSAS[] roots); - /** - * Adds a new VAMSAS root entry - * TODO: decide on same InvalidVamsasObject exceptions. - * TODO: decide if a 'removeVamsasRoot' method is really needed. - * @param newroot - */ - void addVamsasRoot(VAMSAS newroot); - /** - * Returns an Vobject with a valid VorbaId, and provenance element. - * The VorbaId is so the application may refer to it in - * its own dataspace. - * - * Note: An Vobject with valid VorbaId will not be reregistered. - * Advice: Calling this method for a high-level Vobject - * (such as org.vamsas.objects.core.VAMSAS) will - * register all its component objects too. - * - * @param unregistered unregistered vamsas Vobject - * @return VorbaId registered for vamsas Vobject - */ - VorbaId registerObject(Vobject unregistered); - /** - * Returns an array of objects, each with a valid VorbaId - * (and completed provenance entry). - * Note: An Vobject with valid VorbaId will not be reregistered. - * @param unregistered array of unregistered objects. - * @return array of VorbaIds for the registered objects - */ - VorbaId[] registerObjects(Vobject[] unregistered); - /** - * Get instance of Client and User specific vamsas document data access interface. - * @return Interface to Client and user specific application data - */ - IClientAppdata getClientAppdata(); -} \ No newline at end of file diff --git a/src/org/vamsas/client/IClientFactory.java b/src/org/vamsas/client/IClientFactory.java deleted file mode 100644 index f9a50b4..0000000 --- a/src/org/vamsas/client/IClientFactory.java +++ /dev/null @@ -1,56 +0,0 @@ -/* - * Created on 13-Sep-2005 - * - * TODO To change the template for this generated file go to - * Window - Preferences - Java - Code Style - Code Templates - */ -package org.vamsas.client; - -/** - * Defines methods for instantiating Vorba client application agents - * @author jimp - * - * (it's VORBA, not CORBA!) - */ - -public interface IClientFactory { - - /** - * Create a new Vorba Session - * @param applicationHandle is the application's VAMSAS handle string - * @throws NoDefaultSessionException if more than one session exists that the client may connect to - */ - IClient getIClient(ClientHandle applicationHandle) throws NoDefaultSessionException; - /** - * returns new Vorba for a given session. - * @param applicationHandle - * @param sessionUrn session to connect to (or null to create a new session) - * @return - */ - IClient getIClient(ClientHandle applicationHandle, String sessionUrn); - /** - * returns new vorba for a given session acting as a particular identity - * @param applicationHandle - * @param userId - * @param sessionUrn session to connect to (or null to create a new session) - * @return - */ - IClient getIClient(ClientHandle applicationHandle, UserHandle userId, String sessionUrn); - /** - * New session for application and specific user - * @param applicationHandle - * @param userId - * @return - * @throws NoDefaultSessionException if more than one session exists that the client may connect to - */ - IClient getIClient(ClientHandle applicationHandle, UserHandle userId) throws NoDefaultSessionException; - - /** - * enumerate the active sessions this IClientFactory instance knows about. - * Can be used by caller to pick a session on catching a NoDefaultSessionException. - * LATER: Define interface for discovering more information about a session (so it can be presented to a user in a meaningful way) - * @return possibly empty array of sessionUrn strings - */ - public String[] getCurrentSessions(); - -} diff --git a/src/org/vamsas/client/IObjectUpdate.java b/src/org/vamsas/client/IObjectUpdate.java deleted file mode 100644 index cda754d..0000000 --- a/src/org/vamsas/client/IObjectUpdate.java +++ /dev/null @@ -1,26 +0,0 @@ -package org.vamsas.client; - -/** - * Methods implemented by a Vamsas Application's Object Update handler - * @author vamsas - * Introduced November 2006 Vamsas Meeting - * TODO: verify this is sufficient for the per-object update event mechanism - */ -public interface IObjectUpdate { - /** - * Called by the library to find out which vamsas document object this update handler is interested in - * @return class that extends org.vamsas.Vobject - */ - Class getRootVobject(); - /** - * Called to test if this handler is to be called for updates to any Vobjects below the Root Vobject in the vamsas document. - * @return false means IObjectUpdate.update(updated, cdoc) will only be called with instances of type getRootVobject(). - */ - boolean handlesSubtreeUpdates(); - /** - * Method called by Vamsas Client Library for all updated objects that the handler is registered for. - * @param updated - * @param cdoc - */ - void update(org.vamsas.client.Vobject updated, org.vamsas.client.IClientDocument cdoc); -} diff --git a/src/org/vamsas/client/IVorbaIdFactory.java b/src/org/vamsas/client/IVorbaIdFactory.java deleted file mode 100644 index ea25e8e..0000000 --- a/src/org/vamsas/client/IVorbaIdFactory.java +++ /dev/null @@ -1,37 +0,0 @@ -/* - * Created on 14-Sep-2005 - * - * TODO To change the template for this generated file go to - * Window - Preferences - Java - Code Style - Code Templates - */ -package org.vamsas.client; - -/** - * @author jimp - * middleware interface for generating new VorbaId objects - * for a particular vamsas client based on the current - * session, user and client handle. Generally implemented - * by instances of the vamsas library api only. - */ -public interface IVorbaIdFactory { - /** - * construct a new id appropriate for this client in the vamsas session. - * @param vobject TODO - * - * @return valid VorbaId for session, or null if VorbaIdFactory not configured - * correctly. - */ - public abstract VorbaId makeVorbaId(Vobject vobject); - - public abstract SessionHandle getSessionHandle(); - - public abstract ClientHandle getClientHandle(); - - public abstract UserHandle getUserHandle(); - /** - * called when an object is touched by the vamsas library prior to writing - * to record last hash for the object's VorbaId - * @param vobject - */ - public abstract void updateHashValue(Vobject vobject); -} \ No newline at end of file diff --git a/src/org/vamsas/client/Iapp.java b/src/org/vamsas/client/Iapp.java deleted file mode 100644 index 381e22b..0000000 --- a/src/org/vamsas/client/Iapp.java +++ /dev/null @@ -1,12 +0,0 @@ -/** - * org.vamsas.client.Iapp - */ -package org.vamsas.client; -public interface Iapp { - /** - * Define core callback functionality that a fully - * fledged vamsas application Vobject must implement - * TODO: define some Application Callbacks and create use cases for them - */ - -}; diff --git a/src/org/vamsas/client/InvalidSessionUrnException.java b/src/org/vamsas/client/InvalidSessionUrnException.java deleted file mode 100644 index d1863a8..0000000 --- a/src/org/vamsas/client/InvalidSessionUrnException.java +++ /dev/null @@ -1,38 +0,0 @@ -package org.vamsas.client; - -public class InvalidSessionUrnException extends Exception { - - /** - * - */ - public InvalidSessionUrnException() { - super("Invalid Vamsas Session URN."); - // TODO Auto-generated constructor stub - } - - /** - * @param message - * @param cause - */ - public InvalidSessionUrnException(String message, Throwable cause) { - super(message, cause); - // TODO Auto-generated constructor stub - } - - /** - * @param message - */ - public InvalidSessionUrnException(String message) { - super("Invalid Vamsas Session URN: "+message); - // TODO Auto-generated constructor stub - } - - /** - * @param cause - */ - public InvalidSessionUrnException(Throwable cause) { - super(cause); - // TODO Auto-generated constructor stub - } - -} diff --git a/src/org/vamsas/client/NoDefaultSessionException.java b/src/org/vamsas/client/NoDefaultSessionException.java deleted file mode 100644 index bfee0e6..0000000 --- a/src/org/vamsas/client/NoDefaultSessionException.java +++ /dev/null @@ -1,46 +0,0 @@ -/** - * - */ -package org.vamsas.client; - -/** - * @author jimp - * Raised if an IClient instance is requested without - * specifying a particular vamsas session handle - * when more than one candidate session exists. - */ -public class NoDefaultSessionException extends Exception { - - /** - * - */ - public NoDefaultSessionException() { - super("No Default Session Defined"); - } - - /** - * @param message - */ - public NoDefaultSessionException(String message) { - super(message); - // TODO Auto-generated constructor stub - } - - /** - * @param cause - */ - public NoDefaultSessionException(Throwable cause) { - super(cause); - // TODO Auto-generated constructor stub - } - - /** - * @param message - * @param cause - */ - public NoDefaultSessionException(String message, Throwable cause) { - super(message, cause); - // TODO Auto-generated constructor stub - } - -} diff --git a/src/org/vamsas/client/SessionHandle.java b/src/org/vamsas/client/SessionHandle.java deleted file mode 100644 index 736fee3..0000000 --- a/src/org/vamsas/client/SessionHandle.java +++ /dev/null @@ -1,38 +0,0 @@ -/* - * Created on 12-Sep-2005 - * - */ -package org.vamsas.client; - -/** - * Uniquely locates a particular VAMSAS session. - * @author jimp - * - */ -public class SessionHandle { - - /** - * @param sessionUrn - */ - public SessionHandle(String sessionUrn) { - super(); - SessionUrn = sessionUrn; - } - /** - * @return Returns the sessionUrn. - */ - public String getSessionUrn() { - return SessionUrn; - } - /** - * @param sessionUrn The sessionUrn to set. - */ - public void setSessionUrn(String sessionUrn) { - SessionUrn = sessionUrn; - } - /** - * The path to the vamsas session file. - */ - String SessionUrn; - -} diff --git a/src/org/vamsas/client/SessionUrn.java b/src/org/vamsas/client/SessionUrn.java deleted file mode 100644 index 4eff113..0000000 --- a/src/org/vamsas/client/SessionUrn.java +++ /dev/null @@ -1,40 +0,0 @@ -/** - * - */ -package org.vamsas.client; - -import java.net.URI; -import java.util.Hashtable; -import java.util.Vector; - -/** - * @author jimp - * base class for vamsas session/document types - * uses java.net.URI internally for construction of URN - */ -public abstract class SessionUrn { - protected URI urn; - /** - * The types of URI protocols we understand - */ - protected static final Hashtable TYPES=new Hashtable(); - - /** - * construct urn for a locally stored session file - * @param type - * @param url - */ - protected SessionUrn(String type, java.net.URL url) { - if (!TYPES.containsKey(type.toLowerCase())) - throw new Error("Unknown "+this.getClass().getName()+" type '"+type+"' for URL '"+url+"'"); - try { - urn = URI.create(type+"://"+url.getPath()); - } catch (Exception e) { - // TODO: something better than throwing an error should be done here. - throw new Error(e); - } - } - public String getSessionUrn() { - return urn.toString(); - } -} diff --git a/src/org/vamsas/client/UserHandle.java b/src/org/vamsas/client/UserHandle.java deleted file mode 100644 index 8bfe16c..0000000 --- a/src/org/vamsas/client/UserHandle.java +++ /dev/null @@ -1,50 +0,0 @@ -/* - * Created on 12-Sep-2005 - * - * TODO To change the template for this generated file go to - * Window - Preferences - Java - Code Style - Code Templates - */ -package org.vamsas.client; - -/** - * Unique user identifier for a vamsas session. - * Used to write user provenance information, and - * track view/access control in multiuser sessions. - * @author jimp - */ -public class UserHandle { - /** - * @param fullName - * @param organization - */ - public UserHandle(String fullName, String organization) { - this.fullName = fullName; - Organization = organization; - } - String fullName; - String Organization; - /** - * @return Returns the fullName. - */ - public String getFullName() { - return fullName; - } - /** - * @param fullName The fullName to set. - */ - public void setFullName(String fullname) { - fullName = fullname; - } - /** - * @return Returns the organization. - */ - public String getOrganization() { - return Organization; - } - /** - * @param organization The organization to set. - */ - public void setOrganization(String organization) { - Organization = organization; - } -} diff --git a/src/org/vamsas/client/Vobject.java b/src/org/vamsas/client/Vobject.java deleted file mode 100644 index d7bd6eb..0000000 --- a/src/org/vamsas/client/Vobject.java +++ /dev/null @@ -1,464 +0,0 @@ -/** - * - */ -package org.vamsas.client; - -import java.lang.reflect.Field; -import java.lang.reflect.InvocationTargetException; -import java.lang.reflect.Method; -import java.util.Iterator; - -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.exolab.castor.mapping.FieldDescriptor; -import org.exolab.castor.mapping.FieldHandler; -import org.exolab.castor.xml.util.XMLClassDescriptorImpl; -import org.vamsas.test.simpleclient.VamsasArchive; - -/** - * Base class for all Vamsas objects extracted from an IClientDocument. An - * Vobject maybe registered or unregistered. - * - * @author jimp - * - */ -public abstract class Vobject { - static Log log = LogFactory.getLog(Vobject.class); - - /** - * true if Vobject was stored in a vamsas Document or has been retrieved from it - */ - protected boolean __stored_in_document = false; - /** - * true if Vobject was updated since the vamsas library last read a Vobj with the same VorbaId from a document. - */ - protected boolean __updated_since_last_read = false; - /** - * memory of the last doHash() value computed for the Vobject - * @see doHash() - */ - protected int __last_hash = 0; - /** - * set by testInstanceForIdField() if Vobject should have a VorbaId - */ - protected boolean registerable = false; - protected boolean __visited = false; - /** - * reference to containing object for this Vobject. - */ - protected Vobject V_parent=null; - /** - * unique id for all vamsas objects allows unambiguous referencing to any - * Vobject in the vamsas document - */ - protected VorbaId vorbaId = null; - - /** - * the source of unique VorbaIds. - */ - protected IVorbaIdFactory __vorba = null; - - /* (non-Javadoc) - * @see java.lang.Object#finalize() - */ - protected void finalize() throws Throwable { - V_parent=null; - __vorba=null; - vorbaId=null; - super.finalize(); - } - - /** - * - */ - protected Vobject() { - super(); - testInstanceForIdField(); - } - java.lang.reflect.Field ___id_field=null; // set to ease pain of reflection - /** - * set the isRegisterable flag based on the presence of a 'private String _id' field in - * the reflected class instance. - */ - private void testInstanceForIdField() { - // TODO: decide if 'id' is an appropriate reserved attribute name for the VorbaId - // look for the id field in all castor classes (should be an NCName string) - - Class thisclass=this.getClass(); - setRegisterable(false); - while (!thisclass.equals(Vobject.class)) { - try { - java.lang.reflect.Field fd = thisclass.getDeclaredField("_id"); - if (String.class.isAssignableFrom(fd.getType())) { - ___id_field=fd; - this.setRegisterable(true); - break; - } - } catch (SecurityException e) { - log.error("Unexpected Security Exception whilst finding id fields to set!",e); - } catch (NoSuchFieldException e) { - thisclass=thisclass.getSuperclass(); - } - } - } - // boolean __testedInstance=false; - /** - * update the Vobject instance's _id field, based on the contents of the - * VorbaId. Only call this if you mean to do it! - */ - protected void setInstanceIdField() { - /*if (!registerable && !__testedInstance) { - testInstanceForIdField(); - __testedInstance=true; - }*/ - if (registerable) { - if (__vorba != null) - try { - Method fd = this.getClass().getMethod("setId", new Class[] { String.class }); - fd.invoke((Object) this, new Object[] {new String(this.getVorbaId().id)}); - log.debug(this.getClass().getName()+" called setInstanceIdField!"); - } catch (InvocationTargetException e) { - log.error("SourceGeneration of " - + this.getClass().toString() - + "\n has resulted in an inaccessible 'setId' method!\nCannot set ID from the vorbaId Vobject.", e); - } - catch (IllegalAccessException e) { - log.error("SourceGeneration of " - + this.getClass().toString() - + "\n has resulted in an inaccessible 'setId' method!\nCannot set ID from the vorbaId Vobject.", e); - } catch (SecurityException e) { - log.error("Security access violation for "+this.getClass().toString(),e); - } catch (NoSuchMethodException e) { - log.warn(this.getClass().toString()+" was erroneously marked as a Vorba Vobject class (Implementation error?)"); - this.setRegisterable(false); - } - } else { - System.err.println("Client error. Trying to setInstanceIdField on a " - + this.getClass().toString() + " (which cannot be given a vorbaId)"); - } - } - - protected String __getInstanceIdField() { - /*if (!registerable && !__testedInstance) { - testInstanceForIdField(); - __testedInstance=true; - }*/ - if (registerable) { - if (__vorba != null) - try { - Method fd = this.getClass().getMethod("getId", (Class[]) null); - Object idstring = fd.invoke((Object) this, (Object[]) null); - log.debug(this.getClass().getName()+" called getInstanceIdField!"); - if (idstring!=null && idstring instanceof String) { - if (((String) idstring).length()>0) - return (String) idstring; - } - } catch (InvocationTargetException e) { - log.error("SourceGeneration of " - + this.getClass().toString() - + "\n has resulted in an inaccessible 'getId' method!\nCannot set ID from the vorbaId Vobject.", e); - } - catch (IllegalAccessException e) { - log.error("SourceGeneration of " - + this.getClass().toString() - + "\n has resulted in an inaccessible 'getId' method!\nCannot set ID from the vorbaId Vobject.", e); - } catch (SecurityException e) { - log.error("Security access violation for "+this.getClass().toString(),e); - } catch (NoSuchMethodException e) { - log.warn(this.getClass().toString()+" was erroneously marked as a Vorba Vobject class (Implementation error?)"); - this.setRegisterable(false); - } - } else { - System.err.println("Client error. Trying to getInstanceIdField on a " - + this.getClass().toString() + " (which cannot be given a vorbaId)"); - } - return null; - } - - /** - * calculate a hash for the Vobject with all housekeeping fields at standard - * values. (isRegisterable is an immutable attribute property) - * TODO: decide if __stored_in_document should be included in the hash or not. - * @return true if new hash different to last hash - */ - synchronized protected boolean doHash() { - long __old_hash = __last_hash; - __last_hash = 0; - Vobject _V_parent=V_parent; - V_parent=null; - VorbaId thisid = vorbaId; - IVorbaIdFactory factory = __vorba; - boolean stored = __stored_in_document; - boolean updated = __updated_since_last_read; - boolean visited = __visited; - java.lang.reflect.Field idfield = ___id_field; - ___id_field=null; - __updated_since_last_read=false; - vorbaId = null; - __vorba = null; - __visited=false; - // compute hash - __last_hash = this.hashCode(); - // reset houseskeeping variables - ___id_field=idfield; - vorbaId = thisid; - __vorba = factory; - __stored_in_document = stored; - __updated_since_last_read=updated; - V_parent=_V_parent; - __visited=visited; - return (__old_hash==0) || (__old_hash == __last_hash); - } - - /** - * 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. - * - * @return - */ - protected boolean merge(Vobject laterCopy) { - log.warn(this.getClass().getName()+".merge() not implemented."); - return true; - } - - /** - * - * @return true if Vobject is registered - */ - public boolean isRegistered() { - return (registerable) ? (vorbaId != null) : false; - } - - /** - * Method to get fixed reference for the Vobject in the vamsas document. - * - * @returns null if Vobject is neither registered or not associated with a - * properly instantiated VorbaIdFactory. - */ - public VorbaId getVorbaId() { - if (registerable && vorbaId == null) { - if (this.__stored_in_document) { - if (__vorba!=null) - vorbaId=org.vamsas.client.VorbaId.newId(this.__getInstanceIdField()); - } - // Try to use the associated factory. - if (__vorba != null) - if ((vorbaId = __vorba.makeVorbaId(this)) == null) - return null; // Factory not valid. - else { - this.setInstanceIdField(); - return vorbaId; - } - } - return vorbaId; - } - - /** - * used by the IClient implementation to generate unique Id based on client - * applications current namespace. - */ - protected void setVorbaId(VorbaId newid) { - vorbaId = newid; - } - - /** - * @return true if Vobject is present in Vamsas Document. - */ - public boolean is__stored_in_document() { - return __stored_in_document; - } - - /** - * @return true if this object has been updated in the currently stored document since the last time a Vobject with the same ID was read from a Vamsas Document - */ - public boolean is__updated_since_last_read() { - return __updated_since_last_read; - } - - /** - * Set internal flag to indicate this object was updated since the last document read - * @param __updated_since_last_read the __updated_since_last_read to set - */ - protected void set__updated_since_last_read(boolean __updated_since_last_read) { - this.__updated_since_last_read = __updated_since_last_read; - } - - /** - * for use by Vorba agent to reflect state of vamsas Vobject to client - * application. - * Setting stored_in_document on a registerable Vobject without a - * vorbaId will mean is will *never* get a vorbaId and - * horrible things will happen. - * @param __stored_in_document true if Vobject has been marshalled into current document. - */ - protected void set__stored_in_document(boolean __stored_in_document) { - this.__stored_in_document = __stored_in_document; - } - - /** - * __last_hash is the hash value computed when the Vobject was last checked - * against a IClientDocument generated by the Vobject's parent IClient - * instance. - * - * @return Returns the __last_hash. - */ - public int get__last_hash() { - return __last_hash; - } - - /** - * @return true if Vobject can have a vorbaId - */ - public boolean isRegisterable() { - return registerable; - } - - /** - * Called by __testInstanceForidField and the post-unmarshalling handler - * to indicate if Vobject will have a vorbaId. - * @param registerable - */ - protected void setRegisterable(boolean registerable) { - this.registerable = registerable; - } - /** - * 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. - * TODO: LATER: properly apply castors own field mechanisms to get at accessors - * TODO: FIX CYCLIC __ensure+instance_ids - * Implementation note for the todo: - * this works like a depth-first search over all vamsas objects in an vamsasDocument. - * __visited is the visited flag, any Vobj who's flag is of a different parity - * to the visited argument will be recursed on. - * note - the doHash() function used to be used as the 'visited' flag - - * this *is not* a valid heuristic, although it will work "most of the time". - * TODO: LATER? Add another method for setDefaultProvenanceField (in the spirit of setInstanceIdField) using the info from the __vorba.getClient/User/Session methods - */ - protected void __ensure_instance_ids() { - __ensure_instance_ids(!__visited); - } - protected void __ensure_instance_ids(boolean visited) { - if (__vorba==null) - throw new Error("Improperly intialised org.vamsas.client.Vobject - no VorbaFactory given."); - log.debug("doing "+this.getClass()+".__ensure_instance_ids()"); - if (!__stored_in_document && registerable) - setInstanceIdField(); - if (__visited==visited) - return; - __visited=visited; - __vorba.updateHashValue(this); - - Class descriptor = null; - XMLClassDescriptorImpl descimpl = null; - try { - // castor descriptor resolver magic - descriptor = this.getClass().getClassLoader().loadClass(this.getClass().getName()+"Descriptor"); - descimpl = (XMLClassDescriptorImpl) descriptor.getConstructor((Class[])null).newInstance((Object[])null); - } catch (Exception e) { - log.fatal("Source Generation Error!: Couldn't resolve descriptor for " - +this.getClass().getName() - +" was 'generate descriptors' set for castorbuilder.properties?"); - return; - } - FieldDescriptor fields[] = descimpl.getFields(); - for (int i=0,j=fields.length; i 0) { - nobj.setVorbaId(VorbaId.newId(idstring)); - if (objrefs.containsKey(nobj_id=nobj.getVorbaId()) && !objrefs.get(nobj.getVorbaId()).equals(nobj)) { - System.err.println("Serious problem : duplicate id '"+idstring+"' found! expect badness."); - // TODO: HANDLE duplicate XML ids correctly - } - objrefs.put(nobj_id, nobj); - } else { - // add to list of objects without a valid vorbaId - obj.add(nobj); - } - } else { - // TODO: add to list of objects without a valid vorbaId - obj.add(nobj); - } - - nobj.doHash(); - // check to see if new object was present in old object hash - if (oldobjhashes.containsKey(nobj.getVorbaId())) { - Vobjhash oldhash = (Vobjhash) oldobjhashes.get(nobj.getVorbaId()); - if (oldhash.isUpdated(nobj)) { - // mark the object as updated in this document read. - nobj.set__updated_since_last_read(true); - oldobjhashes.put(nobj_id, new Vobjhash(nobj)); - updatedobjs.addElement(nobj); - } - } - } - } catch (Exception e) { - return; - }; - - } - } - - /** - * writes the VamsasDocument to the given stream. - * TODO: ensure that (at least) default provenance entries are written for objects. - * @param outstream - * @param vorba valid VorbaIdFactory to construct any missing IDs - * @param doc - * @throws IOException - * @throws MarshalException - * @throws ValidationException - */ - public static void putVamsasDocument(PrintWriter outstream, VorbaIdFactory vorba, VamsasDocument doc) - throws IOException, MarshalException, ValidationException { - // Ensure references - if (vorba==null) - throw new Error("Null VorbaIdFactory Parameter"); - if (doc.__vorba==null) - doc.__vorba = vorba; - doc.__ensure_instance_ids(); // this may take a while. Do we allow for cyclic references ? - doc.marshal(outstream); - - } - /** - * creates new VorbaId references where necessary for newly unmarshalled objects - * @param unrefed - * @param objrefs - * @return false if any new object references were made - */ - private static boolean ensure_references(Vector unrefed, Hashtable objrefs) { - boolean sync=true; - if (unrefed.size()>0) { - sync=false; // document is out of sync - ids have been created. - java.util.Iterator newobj = unrefed.listIterator(); - while (newobj.hasNext()) { - Vobject o = (Vobject) newobj.next(); - // forces registration and id field update. - VorbaId id = o.getVorbaId(); - if (!objrefs.containsKey(id)) { - objrefs.put(id, o); - } else { - if (!objrefs.get(id).equals(o)) - throw new Error("Serious! Duplicate reference made by vorbaIdFactory!"); - } - } - } - return sync; - } - /** - * Unmarshals a vamsasDocument Vobject from a stream, registers - * unregistered objects, records existing VorbaIds, and completes - * the org.vamsas.client.Vobject housekeeping fields. - * For a valid unmarshalling, the array of returned objects also includes - * a sync parameter which is true if new VorbaIds - * were created. If sync is false, then the caller should ensure that the - * vamsasDocument is written back to disk to propagate the new VorbaIds. - * TODO: ensure that provenance is correct for newly registered objects - * as getVamsasObjects but will detect updated objects based on differing hash values - * obtained from the VorbaIdFactory's VorbaId, Vobject.get__last_Hash() pairs (if any) - * @param instream - the XML input stream - * @param factory - the SimpleClient's properly configured VorbaId factory to make new references. - * @param root the root element's org.vamsas.objects.core Vobject. - * @return null or {(Object) VamsasDocument Vobject, (Object) Hashtable of Vobject references, (Object) Boolean(sync), (Object) Vector of updated objects in document } - */ - public static Object[] getVamsasObjects(Reader instream, - VorbaIdFactory factory, Vobject root) { - Unmarshaller unmarshaller = new Unmarshaller(root); - unmarshaller.setIDResolver(new IDResolver() { - public Object resolve(String id) { - VorbaXmlBinder.log.warn("Warning - id " + id - + " is not found in the Vamsas XML!"); - return null; - } - }); - final Hashtable objrefs = new Hashtable(); - if (factory.extanthashv==null) - factory.extanthashv=new Hashtable(); - final Hashtable oobjhashes=factory.extanthashv; - final VorbaIdFactory vorbafactory = factory; - final Vector unrefedObj = new Vector(); - final Vector updatedObj = new Vector(); - unmarshaller.setUnmarshalListener(new VorbaXmlBinder(vorbafactory, unrefedObj, objrefs, oobjhashes, updatedObj)); - // Call the unmarshaller. - try { - while (instream.ready()) { - // TODO: mark objects in oobjhash prior to unmarshalling, to detect when objects have been lost through an update. - //tohere - Object obj = unmarshaller.unmarshal(instream); - boolean sync=ensure_references(unrefedObj, objrefs); - if (!(obj instanceof Vobject)) - return null; - vorbafactory.setNewIdHash(objrefs); // update the Document IO Handler's set of vorbaId<>Object bindings. - return new Object[] { obj, objrefs, new Boolean(sync),updatedObj}; - } - } catch (MarshalException e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } catch (ValidationException e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } catch (IOException e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } - return null; - } -} \ No newline at end of file diff --git a/src/org/vamsas/client/picking/PickEndPoint.java b/src/org/vamsas/client/picking/PickEndPoint.java deleted file mode 100644 index 7a464f1..0000000 --- a/src/org/vamsas/client/picking/PickEndPoint.java +++ /dev/null @@ -1,101 +0,0 @@ -package org.vamsas.client.picking; - -import java.io.*; -import java.net.*; - -class PickEndPoint extends Thread -{ - private Socket socket; - private int rPort; - private BufferedWriter os; - private BufferedReader in; - - private PickManager manager; - - PickEndPoint(PickManager manager, Socket s) - { - this.manager = manager; - socket = s; - } - - boolean openConnection() - { - try - { - // Create the socket if it doesn't already exist - if (socket == null) - socket = new Socket(InetAddress.getLocalHost(), PickServer.PORT); - - rPort = socket.getPort(); - socket.setKeepAlive(true); - - // Open the streams for reading/writing - os = new BufferedWriter(new OutputStreamWriter(socket.getOutputStream())); - in = new BufferedReader(new InputStreamReader(socket.getInputStream())); - - // Start the thread to listen for incoming messages - System.out.println("CLIENT: connection successful to port " - + socket.getPort() + " via port " + socket.getLocalPort()); - start(); - - return true; - } - catch (Exception e) - { - System.out.println("CLIENT: connection failed: " + e); - return false; - } - } - - void send(String str) - { - try - { - System.out.println("CLIENT: send " + str + " to " + rPort); - os.write(str); - - // We use a newline to terminate the message - os.newLine(); - os.flush(); - } - catch (Exception e) - { - System.out.println("CLIENT: failed to send"); - - // TODO: terminate the connection on a failed send or retry? - terminate(); - } - } - - // void receive() (threaded) - public void run() - { - try - { - while (true) - { - String str = in.readLine(); - System.out.println("CLIENT: recv " + str + " from " + rPort); - - manager.handleMessage(this, str); - } - } - catch (Exception e) - { - // Means the other end of the connection has (probably died) so we need - // terminate this endpoint (if this is server side) - System.out.println("CLIENT: read failed: " + e); - - terminate(); - } - } - - private void terminate() - { - try { socket.close(); } - catch (IOException e) {} - - System.out.println("CLIENT: closing connection to port " + socket.getPort()); - manager.removeEndPoint(this); - } -} \ No newline at end of file diff --git a/src/org/vamsas/client/picking/PickManager.java b/src/org/vamsas/client/picking/PickManager.java deleted file mode 100644 index c313e25..0000000 --- a/src/org/vamsas/client/picking/PickManager.java +++ /dev/null @@ -1,147 +0,0 @@ -package org.vamsas.client.picking; - -import java.net.*; -import java.util.*; -import java.util.logging.*; - -/** - * Manager class that maintains a list of connected clients in addition to - * attempting to run a server to listen for client connections. If the server - * initialization fails, then an attempt to connect (as a client) to another JVM - * that is already a server happens instead. - */ -public class PickManager -{ - private static Logger logger = Logger.getLogger("org.vamsas.client.picking"); - - // Maintains a list of client communication objects - each object represents - // a way of talking to either: - // the server - if this is client side (and in which case, the list will only contain one element - // the other clients - if this is server side - private LinkedList clients; - - private PickServer server; - - /** - * Constructs a new PickManager. This method will return immediately, while - * a looping thread runs that attempts to run the server or connect to an - * existing server. - */ - public PickManager() - { - server = new PickServer(this); - clients = new LinkedList(); - - new InitializeThread().start(); - } - - /** - * Attempts to establish a connection between two client endpoints. This - * method is called in two ways: 1) by the server when it receives a remote - * request (in which case the socket will already be established) and 2) by - * a client that is attempting to connect *to* the server. - * @param socket a socket endpoint for the connection - * @return true if the connection is successfully, false otherwise - */ - boolean addEndPoint(Socket socket) - { - PickEndPoint client = new PickEndPoint(this, socket); - - if (client.openConnection()) - { - clients.add(client); - logger.fine("List now contains " + clients.size() + " client(s)"); - return true; - } - - return false; - } - - /** - * Sends a message to other clients. - * @param str the message to send - */ - public void sendMessage(String str) - { - forwardMessage(null, str); - } - - /** - * Forwards (or sends) a message. When the server (client A) receives a - * message from client B, it must also forward it to clients C and D (etc), - * but mustn't forward it *back* to client B. - * @param origin the client endpoint that received the message (will be null - * if the message originates from this instance - * @param str the message to send - */ - private void forwardMessage(PickEndPoint origin, String str) - { - ListIterator itor = clients.listIterator(); - while (itor.hasNext()) - { - PickEndPoint client = (PickEndPoint) itor.next(); - - if (client != origin) - client.send(str); - } - } - - /** - * Handles a received message. If the manager is running in server mode, - * then it must ensure the message is also forwarded to the other clients. - * @param origin the client endpoint that received the message - * @str the message that was received - */ - void handleMessage(PickEndPoint origin, String str) - { - if (server.isServer()) - forwardMessage(origin, str); - - // TODO: pass message to VAMSAS API - } - - /** - * Removes a client connection from the list when its connection is no - * longer valid. - * @param client the client endpoint to remove - */ - void removeEndPoint(PickEndPoint client) - { - clients.remove(client); - logger.fine("List now contains " + clients.size() + " client(s)"); - - // If there's no endpoints left, then we've lost all connections and - // need to reinitialize - if (clients.size() == 0) - new InitializeThread().start(); - } - - /** - * Thread extension class to handle the actual initialization - */ - private class InitializeThread extends Thread - { - public void run() - { - logger.fine("Initializing connection..."); - boolean connected = false; - - // Loop until we can get a connection (one way or the other) - while (!connected) - { - // Sleep for a rnd time so we don't end up with all the VAMSAS - // apps trying to initialize servers at the same time - try { Thread.sleep((int)Math.random()); } - catch (InterruptedException e) {} - - // Attempt to open the server port... - if (server.isServer() || server.createServer()) - connected = true; - - // If it fails, then attempt to make a client connection... - else if (addEndPoint(null)) - connected = true; - } - } - } -} \ No newline at end of file diff --git a/src/org/vamsas/client/picking/PickServer.java b/src/org/vamsas/client/picking/PickServer.java deleted file mode 100644 index abef55e..0000000 --- a/src/org/vamsas/client/picking/PickServer.java +++ /dev/null @@ -1,83 +0,0 @@ -package org.vamsas.client.picking; - -import java.io.*; -import java.net.*; -import java.util.logging.*; - -/** - * Server class that listens for incoming connections on a predefined port. - */ -class PickServer extends Thread -{ - private static Logger logger = Logger.getLogger("org.vamsas.client.picking"); - - // The port number we'll listen on - static final int PORT = 53782; - - private ServerSocket serverSocket; - // Set to true once the server is established - private boolean isServer = false; - - private PickManager manager; - - /** - * Constructs a new instance of the server (but doesn't start it). - * @param manager a reference to the pick manager that owns this server - */ - PickServer(PickManager manager) - { - this.manager = manager; - } - - /** - * Returns true if this server instance is running. - * Return true if this server instance is running - */ - boolean isServer() - { return isServer; } - - /** - * Attempts to create the server by opening a server socket on the port. - * @return true if the server was created; false otherwise - */ - boolean createServer() - { - try - { - serverSocket = new ServerSocket(PORT); - start(); - - return isServer = true; - } - catch (IOException e) - { - logger.info("SERVER: " + e); - return false; - } - } - - /** - * Thread listening method - loops indefinitely listening for connections. - * When one is received, the socket object is passed to the manager so it - * can make a full client connection for further comms. - */ - public void run() - { - logger.fine("SERVER: listening on " + PORT + " - SERVER"); - - // Loop forever, accepting connectons from other clients - // TODO: add in the ability to terminate the server if a VAMSAS session - // is ended - while (true) - { - try - { - Socket socket = serverSocket.accept(); - logger.fine("SERVER: connection detected"); - - manager.addEndPoint(socket); - } - catch (IOException e) {} - } - } -} \ No newline at end of file diff --git a/src/org/vamsas/client/picking/TestApp.java b/src/org/vamsas/client/picking/TestApp.java deleted file mode 100644 index 96924b5..0000000 --- a/src/org/vamsas/client/picking/TestApp.java +++ /dev/null @@ -1,33 +0,0 @@ -package org.vamsas.client.picking; - -import java.util.logging.*; - -public class TestApp -{ - private static Logger logger = Logger.getLogger("org.vamsas.client.picking"); - - public static void main(String[] args) - throws Exception - { -// logger.setLevel(Level.INFO); - - TestApp app = new TestApp(); - - PickManager manager = new PickManager(); - - // Send 5 test messages... -// for (int i = 0; i < 5; i++) - while (true) - { - try { Thread.sleep((int) (Math.random()*20000)); } - catch (InterruptedException e) {} - - int rnd = (int) (Math.random()*100); - manager.sendMessage("" + rnd); - } - } - - public TestApp() - { - } -} \ No newline at end of file diff --git a/src/org/vamsas/client/simpleclient/AppDataInputStream.java b/src/org/vamsas/client/simpleclient/AppDataInputStream.java deleted file mode 100644 index 0785ed6..0000000 --- a/src/org/vamsas/client/simpleclient/AppDataInputStream.java +++ /dev/null @@ -1,53 +0,0 @@ -/** - * - */ -package org.vamsas.client.simpleclient; - -import java.io.DataInput; -import java.io.DataInputStream; -import java.io.IOException; -import java.io.InputStream; -import java.util.jar.JarInputStream; - -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; - -/** - * @author jimp - * LATER: this may not be a necessary or useful class to return from IClientAppdata get*InputStream() methods - */ -public class AppDataInputStream extends DataInputStream implements DataInput { - private Log log = LogFactory.getLog(AppDataInputStream.class); - private boolean isOpen = false; - /** - * Wrapper for writing to/from AppData Entries in a Vamsas Document. - */ - public AppDataInputStream(InputStream inputstream) { - super(inputstream); - isOpen=true; - } - - /* (non-Javadoc) - * @see java.io.FilterInputStream#close() - */ - public void close() throws IOException { - if (!isOpen) { - log.debug("close() called on closed AppDataInputStream."); - // throw new IOException("Attempt to close an already closed AppDataInputStream"); - } else { - isOpen=false; - } - } - - /** - * Will return zero if stream has been closed. - * @see java.io.FilterInputStream#available() - */ - public int available() throws IOException { - if (isOpen) - return super.available(); - else - return 0; - } - -} diff --git a/src/org/vamsas/client/simpleclient/AppDataOutputStream.java b/src/org/vamsas/client/simpleclient/AppDataOutputStream.java deleted file mode 100644 index db13652..0000000 --- a/src/org/vamsas/client/simpleclient/AppDataOutputStream.java +++ /dev/null @@ -1,86 +0,0 @@ -/** - * - */ -package org.vamsas.client.simpleclient; - -import java.io.DataOutputStream; -import java.io.IOException; -import java.io.OutputStream; - -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; - -/** - * @author jimp - * - */ -public class AppDataOutputStream extends DataOutputStream { - private Log log = LogFactory.getLog(AppDataOutputStream.class); - private boolean isOpen=true; - /** - * @param out - */ - public AppDataOutputStream(OutputStream out) { - super(out); - isOpen=true; - } - /* (non-Javadoc) - * @see java.io.DataOutputStream#flush() - */ - public void flush() throws IOException { - if (isOpen) - super.flush(); - else - log.warn("flush() called on closed AppDataOutputStream"); - } - /* (non-Javadoc) - * @see java.io.DataOutputStream#write(byte[], int, int) - */ - public synchronized void write(byte[] b, int off, int len) throws IOException { - if (isOpen) { - super.write(b, off, len); - } else { - log.debug("write(b,off,len) called on closed AppDataOutputStream"); - throw new IOException("Attempt to write to closed AppDataOutputStream"); - } - } - /* (non-Javadoc) - * @see java.io.DataOutputStream#write(int) - */ - public synchronized void write(int b) throws IOException { - if (isOpen) { - super.write(b); - } else { - log.debug("write(b) called on closed AppDataOutputStream"); - throw new IOException("Attempt to write to closed AppDataOutputStream"); - } - } - /** - * Sets an internal flag preventing further write operations - * to the AppData output stream and flushes any pending writes. - * @see java.io.FilterOutputStream#close() - */ - public void close() throws IOException { - isOpen=false; - super.flush(); - log.debug("AppDataOutputStream was closed."); - } - /* (non-Javadoc) - * @see java.io.FilterOutputStream#write(byte[]) - */ - public void write(byte[] b) throws IOException { - if (isOpen) { - super.write(b); - } else { - log.debug("write(b[]) called on closed AppDataOutputStream"); - throw new IOException("Attempt to write to closed AppDataOutputStream"); - } - } - /** - * @return true if stream is still Open. - */ - public boolean isOpen() { - return isOpen; - } - -} diff --git a/src/org/vamsas/client/simpleclient/ArchiveUrn.java b/src/org/vamsas/client/simpleclient/ArchiveUrn.java deleted file mode 100644 index 304e1f2..0000000 --- a/src/org/vamsas/client/simpleclient/ArchiveUrn.java +++ /dev/null @@ -1,34 +0,0 @@ -package org.vamsas.client.simpleclient; - -import java.io.File; -import java.net.MalformedURLException; - -/** - * Vamsas Document URN for files understood by ArchiveReader and - * written by VamsasArchive. - * vdoc://{Absolute path to file} - * @author jimp - * - */ -public class ArchiveUrn extends org.vamsas.client.SessionUrn { - /** - * a simple vamsas document urn prefix - */ - public static String VAMSASDOCUMENT="vdoc"; - static { - TYPES.put(ArchiveUrn.VAMSASDOCUMENT, ArchiveUrn.class); - } - - public ArchiveUrn(File docLocation) throws MalformedURLException { - super(VAMSASDOCUMENT, docLocation.getAbsoluteFile().toURL()); - } - - /** - * TODO: LATER: think about this again. - * @return File(urn.getPath()) - */ - public File asFile() { - return new File(urn.getPath()); - } - // TODO: add abstract 'handler' methods for resolving the URN to a particular class -} diff --git a/src/org/vamsas/client/simpleclient/ClientDocument.java b/src/org/vamsas/client/simpleclient/ClientDocument.java deleted file mode 100644 index 3b654f8..0000000 --- a/src/org/vamsas/client/simpleclient/ClientDocument.java +++ /dev/null @@ -1,510 +0,0 @@ -/* - * - */ -package org.vamsas.client.simpleclient; - -import java.io.IOException; -import java.util.Vector; - -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.vamsas.client.ClientHandle; -import org.vamsas.client.IClientAppdata; -import org.vamsas.client.IClientDocument; -import org.vamsas.client.UserHandle; -import org.vamsas.client.Vobject; -import org.vamsas.client.VorbaId; -import org.vamsas.objects.core.ApplicationData; -import org.vamsas.objects.core.User; -import org.vamsas.objects.core.VAMSAS; -import org.vamsas.objects.core.VamsasDocument; -import org.vamsas.objects.utils.AppDataReference; -import org.vamsas.test.objects.Core; - -/** - * Maintains a collection of vamsas objects, appdatas and states, and provides api for a SimpleClient's client. - * @author jimp - */ -public class ClientDocument extends org.vamsas.client.ClientDocument implements IClientDocument { - private static Log log = LogFactory.getLog(ClientDocument.class); - private VamsasDocument doc; - protected SimpleClient sclient; - protected VamsasArchive archive = null; - /** - * indicate if new data has been incorporated - */ - private boolean isModified = false; - /** - * Public method for internal use by SimpleClient. - * @return true if document has been modified. - */ - public boolean isModified() { - return isModified; - } - private Vector updatedObjects=null; - /** - * - * prepare Application-side dataset from the vamsas Document archive - * @param doc - the dataset - * @param docHandler - the sessionFile IO handler - * @param Factory - the source of current and new vorbaIds - * @param sclient - the simpleclient instance - */ - protected ClientDocument(VamsasDocument doc, VamsasArchive docHandler, IdFactory Factory, SimpleClient sclient) { - super(Factory.getVorbaIdHash(), Factory); - - - /** - * prepare Application-side dataset from the vamsas Document archive - */ - this.sclient = sclient; - archive = docHandler; - this.doc = doc; - updatedObjects=null; /// TODO: correct this line - } - - /* - * (non-Javadoc) - * - * @see org.vamsas.client.IClientDocument#getObject(org.vamsas.client.VorbaId) - */ - public Vobject getObject(VorbaId id) { - if (vamsasObjects==null) { - log.debug("getObject called on null objrefs list."); - return null; - } - if (vamsasObjects.containsKey(id)) - return (Vobject) vamsasObjects.get(id); - log.debug("Returning null Vobject reference for id "+id.getId()); - return null; - } - - /* - * (non-Javadoc) - * - * @see org.vamsas.client.IClientDocument#getObjects(org.vamsas.client.VorbaId[]) - */ - public Vobject[] getObjects(VorbaId[] ids) { - if (vamsasObjects==null) { - log.debug("getObject[] called on null vamsasObjects list."); - return null; - } - Vobject[] vo = new Vobject[ids.length]; - for (int i=0,j=ids.length; i-1) { - if (isValidUpdate(newr[k], original[i])) { - modified=true; - rts.add(newr[k]); - newr[k]=null; - } else { - // LATER: try harder to merge ducument roots. - log.warn("Couldn't merge new VAMSAS root "+newr[k].getId()); - newr[k] = null; // LATER: this means we ignore mangled roots. NOT GOOD - } - } else { - // add in order. - rts.add(original[i]); - } - } - // add remaining (new) roots - for (int i=0,j=newr.length; i0) { - - ObjectInputStream is = new ObjectInputStream(fileLock.getBufferedInputStream(true)); - Object o; - o=is.readObject(); - if (o!=null) { - try { - clients = (ClientHandle[]) o; - } - catch (Exception e) { - System.err.println("Garbage in the clientHandle list "+this.sessionFile); - } - } - } - return clients; - } catch (FileNotFoundException e) { - // TODO Auto-generated catch block - e.printStackTrace(System.err); - } catch (Exception e) { - e.printStackTrace(System.err); - } - } - return null; - } - /** - * get the clientList from the file. May return null if lock failed! - * @return clientList - */ - public ClientHandle[] retrieveClientList() { - if (lockFile()) { - ClientHandle[] clients = retrieveClientHandles(); - unlockFile(); - return clients; - } - return null; - } - /** - * get list from the locked ClientList. - * @param extantlock - * @return clientList or null if lock failed (or file was empty) - */ - public ClientHandle[] retrieveClientList(Lock extantlock) { - if (lockFile(extantlock)) { - ClientHandle[] clients = retrieveClientHandles(); - unlockFile(); - return clients; - } - return null; - } - /** - * adds clientHandle me to the clientList under an existing lock extantLock. - * @param me - * @param extantLock - * @return client index in list or 0 if lock was invalid or addClient operation failed. - */ - public int addClient(ClientHandle me, Lock extantLock) { - return addClient(me, true, extantLock); - } - - /** - * adds clientHandle me to the clientList under an existing lock. - * @param me - clientHandle - * @param disambig - if true then add will fail if an identical clientHandle already exists - * @param extantLock - existing lock - * @return client index in list or 0 if addClient (or the lock) failed. - */ - - public int addClient(ClientHandle me, boolean disambig, Lock extantLock) { - if (lockFile(extantLock)) { - syncnum = addClient(me, disambig); - unlockFile(); - return syncnum; - } - return 0; - } - - /** - * adds the ClientHandle to the list - if it is not unique, then the - * ClientHandle object is modified to make it unique in the list. returns the - * clientNumber for the client in the session. - * - * @param me - * @return - */ - - public int addClient(ClientHandle me) { - syncnum = addClient(me, true); - unlockFile(); - return syncnum; - } - - /** - * removes 'me' from the session ClientList without complaint if 'me' isn't in the clientList already. - * @param me client handle to be removed - * @param clientlock existing lock passed from watcher. - */ - public void removeClient(ClientHandle me, Lock clientlock) { - int mynum=-1; - if (lockFile(clientlock)) { - ClientHandle[] clients = retrieveClientHandles(); - if (clients != null) { - if ((syncnum<=0 || syncnum>clients.length) || clients[syncnum-1]!=me) { - for (int i = 0, j = clients.length; i < j; i++) - if (clients[i].equals(me)) { - mynum=i; - break; - } - } else { - mynum=syncnum-1; - } - if (mynum>-1) { - ClientHandle[] newlist = new ClientHandle[clients.length - 1]; - for (int k=0,i = 0, j = clients.length; i < j; i++) - if (i!=mynum) - newlist[k++] = clients[i]; - if (!putClientList(newlist)) - throw new Error("Failed to write new clientList!"); // failed to put the clientList to disk. - } - } - unlockFile(); - } else { - throw new Error("Couldn't get lock for "+((sessionFile==null) ? "Unitialised sessionFile in ClientsFile" : sessionFile.getAbsolutePath())); - } - } - /** - * Adds a ClientHandle to the ClientList file - optionally disambiguating - * the ClientHandle (modifes the URN). - * Note: Caller is left to release the lock on the ClientList. - * @param me - * @param disambiguate - - * flag indicating if the URN for me should be disambiguated to - * differentiate between sessions. - * @return index of clientHandle in new list, or -1-position of existing - * clientHandle (if disambiguate is true) - */ - protected int addClient(ClientHandle me, boolean disambiguate) { - int newclient = 0; - int tries=5; - while (tries-->0 && !lockFile()) - try { Thread.sleep(1); } catch (Exception e){}; - if (lockFile()) { - ClientHandle[] clients = retrieveClientHandles(); - if (me.getClientUrn()==null) { - // TODO: move this into ClientUrn as a standard form method. - me.setClientUrn("vamsas://"+me.getClientName()+":"+me.getVersion()+"/"); - } - if (clients == null) { - clients = new ClientHandle[1]; - clients[0] = me; - newclient = 1; - } else { - int k = 0; - for (int i = 0, j = clients.length; i < j; i++) { - if (clients[i].equals(me)) { - if (disambiguate) { - while (clients[i].equals(me)) { - me.setClientUrn(me.getClientUrn() + k++); // TODO: make a better - // disambiguation of - // urn. - } - } else { - // will not write the ambiguous clientHandle to disk, just return - // its index. - return -1 - i; - } - } - } - int i, j; - ClientHandle[] newlist = new ClientHandle[clients.length + 1]; - for (i = 0, j = clients.length; i < j; i++) - newlist[i] = clients[i]; - newlist[j] = me; - clients = newlist; - newclient = j+1; - } - if (!putClientList(clients)) - return 0; // failed to put the clientList to disk. - } - return newclient; - } - /** - * when set true - get FileNotFoundExceptions on WinXP when writing to locked stream after the backup has been made (via the backupFile method) - */ - boolean backup=false; - /** - * safely writes clients array to the file referred to by sessionFile. - * - * @param clients - * @return true if successful write. Throws Errors otherwise. - */ - protected boolean putClientList(ClientHandle[] clients) { - if (lockFile()) { - File templist=null; - if (!backup || (templist = backupSessionFile()) != null) { - int retries=3; - while (retries-->0) { - try { - ObjectOutputStream os = - new ObjectOutputStream(fileLock.getBufferedOutputStream(true)); - log.debug("About to write "+clients.length+" clientHandles to output stream."); - os.writeObject(clients); - os.close(); - // All done - remove the backup. - if (backup) - templist.delete(); - templist = null; - retries=-1; - } catch (Exception e) { - System.err - .println("Serious - problems writing to sessionFile."); - if (retries>0 && templist != null) { - System.err.println("Recovering from Backup in " - + templist.getAbsolutePath()); - templist.renameTo(fileLock.target); - } - e.printStackTrace(System.err); - } - } - if (retries>-2) { - System.err - .println("Serious - problems writing to sessionFile. Giving Up."); - return false; - } - } else { - throw new Error( - "Couldn't create backup of the clientList before writing to it!"); - } - } else { - throw new Error("Could not lock the clientList: " - + ((sessionFile == null) ? "Unitialized ClientsFile" - : " failed to get lock on " + sessionFile.getAbsolutePath())); - } - // successful! - return true; - } - - public void clearList() { - if (lockFile()) { - try { - FileOutputStream fout = fileLock.getFileOutputStream(true); - fout.flush(); - fout.close(); - } catch (Exception e) { - throw new Error("Problems trying to clear clientlist!",e); - - } - } - - } -} diff --git a/src/org/vamsas/client/simpleclient/EventGeneratorThread.java b/src/org/vamsas/client/simpleclient/EventGeneratorThread.java deleted file mode 100644 index d9aa1db..0000000 --- a/src/org/vamsas/client/simpleclient/EventGeneratorThread.java +++ /dev/null @@ -1,277 +0,0 @@ -package org.vamsas.client.simpleclient; - -import java.beans.PropertyChangeEvent; -import java.beans.PropertyChangeListener; -import java.beans.PropertyChangeSupport; -import java.util.Hashtable; - -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.vamsas.client.Events; - -/** - * monitors watcher objects and generates events. - */ -public class EventGeneratorThread extends Thread implements Runnable { - private static Log log = LogFactory.getLog(EventGeneratorThread.class); - private SimpleClient client; - private Hashtable handlers; // manager object - private VamsasSession session; - - /** - * list with all the clientHandles for the session - */ - protected FileWatcher clientfile=null; - /** - * the session's vamsasDocument - */ - protected FileWatcher vamsasfile=null; - /** - * written to by client when its app calls storeDocument. - */ - protected FileWatcher storeFile=null; - - private boolean watch=false; - - - EventGeneratorThread(VamsasSession s, SimpleClient _client, Hashtable eventhandlers) { - if (eventhandlers==null || s==null || _client==null) - throw new Error("Null arguments to EventGeneratorThread constructor."); - handlers = eventhandlers; - session = s; - client = _client; - setName(s.sessionDir.getName()); - initWatchers(); - } - - private void initWatchers() { - if (clientfile==null) - clientfile = session.getClientWatcher(); - if (vamsasfile ==null) - vamsasfile = session.getDocWatcher(); - if (storeFile == null) - storeFile = session.getStoreWatcher(); - clientfile.setState(); - vamsasfile.setState(); - storeFile.setState(); - } - boolean ownsf = false; - /** - * scans all watchers and fires changeEvents if necessary - * @return number of events generated. - */ - private int checkforEvents() { - Lock watchlock; - //TODO : leave slog.info messages for the events that occur. - int raised=0; - // could make this general - but for now keep simple - if ((watchlock=storeFile.getChangedState())!=null) { - // TODO: define the storeFile semaphore mechanism : file exists - all clients inform their apps, and then the client that wrote the file should delete the file (it should hold the lock to it). - if (storeFile.exists) { - PropertyChangeSupport h = (PropertyChangeSupport) handlers.get(Events.DOCUMENT_FINALIZEAPPDATA); - if (h!=null) { - log.debug("Triggering DOCUMENT_FINALIZEAPPDATA"); - raised++; - h.firePropertyChange(client.getSessionUrn(), null, client); - // expect client to - vamsasfile.setState(); - } - } - } - if ((watchlock=clientfile.getChangedState())!=null) { - // see what happened to the clientfile - compare our internal version with the one in the file, or just send the updated list out...? - // - /** - * Generated when a new vamsas client is attached to a session (Handle is - * passed) Note: the newly created client does not receive the event. - * - public static final String CLIENT_CREATION = "org.vamsas.client.events.clientCreateEvent"; - */ // as the test - /** - * Generated when a vamsas client leaves a session (Handle is passed to all - * others). - public static final String CLIENT_FINALIZATION = "org.vamsas.client.events.clientFinalizationEvent"; - */ // again - as the test. - raised++; - } - if ((watchlock=vamsasfile.getChangedState())!=null) { - - /** - * Generated when a client has finished updating the document. Passes - * applicationHandle of client so the updating client can recognise its own - * updates. - public static final String DOCUMENT_UPDATE = "org.vamsas.client.events.documentUpdateEvent"; - */ - // read apphandle from 'lastUpdate' session file. - // pass apphandle name to appHandler ? - - } - /** - * Generated when a new vamsas document is created (perhaps from some existing - * Vamsas data) so an application may do its own data space initialization. - * TODO: decide if this is called when an app is connected to a stored - * session... - public static final String DOCUMENT_CREATE = "org.vamsas.client.events.documentCreateEvent"; - */ - // check if this session's appInit flag is set - if not - generate event for this app. - // prolly don't need this at the moment - when an app does getDocument it can to the initing then. - - - /** - * Generated prior to session Shutdown, after the last participating vamsas - * client has finalized. - * TODO: decide on purpose of this ? is this for benefit of multi-session Apps only ? - public static final String SESSION_SHUTDOWN = "org.vamsas.client.events.SessionShutdownEvent"; - */ - - /** - * 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. Any client that handles this should call the - * IClient.getDocument(), update and then IClient.updateDocument in the same - * handler thread. - * EventName: - * NewValue: org.vamsas.client.IClient for session. - * - public static final String DOCUMENT_FINALIZEAPPDATA = "org.vamsas.client.events.DocumentFinalizeAppData"; -*/ - // watch for finalization semaphore (last finalised sessionFile). - - /** - * Generated by Vorba stub after the penultimate client makes a call to - * closeDocument(). Sequence is as follows : 1. All other vamsas clients have - * called closeDocument() 2. Final living client monitors closures, and - * realises that it is last. 3. Final client generates event to prompt - * associated application to inquire if the user wishes to save the document - * for future reference. - * * Any call to closeDocument in a thread other than the registered - * EventListener will block until the RequestToClose handler has exited. - * - */ - // public static final String DOCUMENT_REQUESTTOCLOSE = "org.vamas.client.DocumentRequestToCloseEvent"; - - return raised; - } - - private void initEvents() { - - } - /** - * Events raised by IClient and propagated to others in session - */ - - /** - * number of milliseconds between any file state check. - */ - long POLL_UNIT = 20; - protected void wait(int u) { - if (u<=0) - u=1; - long l = System.currentTimeMillis()+POLL_UNIT*u; - while (System.currentTimeMillis()0) { - sequence++; - } else { - idstring+="1/"; - sequence=1; - } - newidstring=idstring+Integer.toString(sequence); - } while (extantids.containsKey(newidstring)); - extantids.put(newidstring, vobject); // hash the Vobject by its new Id - VorbaId id = newId(newidstring); // VorbaId.hash()==newidstring.hash() so we can still recover vobject - return id; - } - - /* (non-Javadoc) - * @see org.vamsas.client.VorbaIdFactory#setSession(org.vamsas.client.SessionHandle) - */ - protected void setSession(SessionHandle sessionhandle) { - if (sessionhandle!=null) - session=sessionhandle; - else - log.warn("setSession(null) called."); - } - - /* (non-Javadoc) - * @see org.vamsas.client.VorbaIdFactory#getSessionHandle() - */ - public SessionHandle getSessionHandle() { - return session; - } - - /* (non-Javadoc) - * @see org.vamsas.client.VorbaIdFactory#setClient(org.vamsas.client.ClientHandle) - */ - protected void setClient(ClientHandle appHandle) { - if (appHandle!=null) - client = appHandle; - else - log.warn("setClient(null) called."); - } - - /* (non-Javadoc) - * @see org.vamsas.client.VorbaIdFactory#getClientHandle() - */ - public ClientHandle getClientHandle() { - return client; - } - - /* (non-Javadoc) - * @see org.vamsas.client.VorbaIdFactory#setUser(org.vamsas.client.UserHandle) - */ - protected void setUser(UserHandle userHandle) { - if (userHandle!=null) - user = userHandle; - else - log.warn("setUser(null) called."); - } - - /* (non-Javadoc) - * @see org.vamsas.client.VorbaIdFactory#getUserHandle() - */ - public UserHandle getUserHandle() { - return user; - } - /** - * Convenience method used for default behaviour in testing - * and any anonymous internal vamsasDocument unmarshalling - * @param clientname - * @return - */ - protected static IdFactory getDummyFactory(String clientname) { - if (clientname==null) - clientname="org.vamsas.client.simpleclient.IdFactory"; - return new IdFactory(new SessionHandle("dummy.session"), - new ClientHandle(clientname,VersionEntries.latestVersion()), - new UserHandle(clientname, "Arnold User's Inc.")); - } -} diff --git a/src/org/vamsas/client/simpleclient/ListFile.java b/src/org/vamsas/client/simpleclient/ListFile.java deleted file mode 100644 index 30956e9..0000000 --- a/src/org/vamsas/client/simpleclient/ListFile.java +++ /dev/null @@ -1,25 +0,0 @@ -/** - * - */ -package org.vamsas.client.simpleclient; - -import java.io.File; - - -/** - * 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) - */ -public class ListFile extends SessionFile { - - /** - * @param file - */ - public ListFile(File file) throws java.io.IOException { - super(file); - if (!this.sessionFile.exists()) - this.sessionFile.createNewFile(); - } - -} diff --git a/src/org/vamsas/client/simpleclient/Lock.java b/src/org/vamsas/client/simpleclient/Lock.java deleted file mode 100644 index d3a5889..0000000 --- a/src/org/vamsas/client/simpleclient/Lock.java +++ /dev/null @@ -1,96 +0,0 @@ -package org.vamsas.client.simpleclient; - -import java.io.BufferedInputStream; -import java.io.BufferedOutputStream; -import java.io.File; -import java.io.FileInputStream; -import java.io.FileOutputStream; -import java.io.IOException; -import java.io.OutputStream; -import java.io.RandomAccessFile; -import java.nio.channels.ByteChannel; -import java.nio.channels.FileChannel; -import java.nio.channels.ReadableByteChannel; - -import org.apache.commons.logging.LogFactory; - -/** - * transient object representing a file lock - * This lock should hold for all processes interacting in a session. - * @author jimp - */ - -public abstract class Lock { - protected org.apache.commons.logging.Log log = LogFactory.getLog(Lock.class); - File target = null; // The file that is being locked - protected RandomAccessFile rafile=null; - - /** - * creates a valid Lock (test with isLocked) - * if a lock could be obtained for lockfile - * @param lockfile - */ - protected Lock(java.io.File lockfile) { - target = lockfile; - } - /** - * - * @return true if lock is held on the target - */ - public abstract boolean isLocked(); - /** - * release lock and close all managed channels to file - * - */ - public abstract void release(); - /** - * optionally close the open random access channel on the file when releasing lock - * @param closeChannel - */ - public abstract void release(boolean closeChannel); - - /** - * gets Locked Stream for reading from - * @param atStart true to start reading at beginning of file. - * @return null if file not locked - * @throws IOException - */ - public abstract FileInputStream getFileInputStream(boolean atStart) throws IOException; - - /** - * gets Locked stream to write to - * FileInput always starts at the *end* of the file (after any truncation) - * @param clear true means file will be cleared to zero length - * @return null if file is not locked - * @throws IOException - */ - public abstract FileOutputStream getFileOutputStream(boolean clear) throws IOException; - /** - * return buffered output stream to locked file. - * @param clear - true means file is truncated to 0 length before writing - * @return - */ - public abstract BufferedOutputStream getBufferedOutputStream(boolean clear) throws IOException; - - protected void finalize() throws Throwable { - target=null; - } - /** - * return buffered input stream for locked file. - * @param atStart - true means read from begining of file - * @return null if file is not locked. - */ - public BufferedInputStream getBufferedInputStream(boolean atStart) throws IOException { - FileInputStream fis = getFileInputStream(atStart); - if (fis!=null) - return new BufferedInputStream(fis); - return null; - } - /** - * safe lock target length() function. - * @return -1 for non-lockable target, otherwise target's file length - */ - public abstract long length(); - public abstract RandomAccessFile getRaFile() throws IOException; - public abstract FileChannel getRaChannel() throws IOException; -} diff --git a/src/org/vamsas/client/simpleclient/LockFactory.java b/src/org/vamsas/client/simpleclient/LockFactory.java deleted file mode 100644 index 5fdde6c..0000000 --- a/src/org/vamsas/client/simpleclient/LockFactory.java +++ /dev/null @@ -1,52 +0,0 @@ -package org.vamsas.client.simpleclient; - -import java.io.File; - -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; - -public class LockFactory { - protected static Log log = LogFactory.getLog(LockFactory.class); - public static int locktype=0; // use file lock by default - public static String[] locktypes = {"file","native"}; - { - String lockt = System.getProperty("vamsas.locktype"); - if (lockt!=null) { - int i,j; - for (i=0, j=locktypes.length; i=j) { - String lt = "'"+locktypes[0]+"'"; - for (i=1; i0 && !fileLock.isLocked()); - if (!fileLock.isLocked()) - log.error("Failed to get lock for "+sessionFile); - // fileLock = new Lock(sessionFile); - return fileLock.isLocked(); - } - - /** - * Explicitly release the SessionFile's lock. - * - * @return true if lock was released. - */ - protected void unlockFile() { - if (fileLock != null) { - fileLock.release(); - fileLock = null; - } - } - - /** - * Makes a backup of the sessionFile. - * @return Backed up SessionFile or null if failed to make backup. - */ - protected File backupSessionFile() { - return backupSessionFile(null, sessionFile.getName(),".old", sessionFile.getParentFile()); - } - - protected File backupSessionFile(Lock extantLock, String backupPrefix, String backupSuffix, File backupDir) { - File tempfile=null; - if (lockFile(extantLock)) { - try { - tempfile = File.createTempFile(backupPrefix, backupSuffix, backupDir); - if (fileLock.length()>0) { - FileOutputStream tos = new FileOutputStream(tempfile); - ReadableByteChannel channel; - tos.getChannel().transferFrom(channel=fileLock.getRaChannel(), 0, - fileLock.length()); - tos.close(); - if (!channel.isOpen()) - throw new Error(tos.getChannel().getClass()+".transferFrom closes source channel!"); - if (!lockFile(extantLock)) - throw new Error("Lost lock for "+sessionFile.getName()+" after backup."); - - } - } catch (FileNotFoundException e1) { - log.warn("Can't create temp file for "+sessionFile.getName(),e1); - tempfile=null; - } catch (IOException e1) { - log.warn("Error when copying content to temp file for "+sessionFile.getName(),e1); - tempfile=null; - } - } - return tempfile; - } - /** - * Replaces data in sessionFile with data from file handled by another sessionFile - * passes up any exceptions. - * @param newData source for new data - */ - protected void updateFrom(Lock extantLock, SessionFile newData) throws IOException { - log.debug("Updating "+sessionFile.getAbsolutePath()+" from "+newData.sessionFile.getAbsolutePath()); - if (newData==null) - throw new IOException("Null newData object."); - if (newData.sessionFile==null) - throw new IOException("Null SessionFile in newData."); - - if (!lockFile(extantLock)) - throw new IOException("Failed to get write lock for "+sessionFile); - if (!newData.lockFile()) - throw new IOException("Failed to get lock for updateFrom "+newData.sessionFile); - RandomAccessFile nrafile = newData.fileLock.getRaFile(); - nrafile.seek(0); - RandomAccessFile trafile = fileLock.getRaFile(); - /*long tries=5000; - while (trafile==null && --tries>0) { - log.debug("Lost lock on "+sessionFile+"! Re-trying for a transfer."); - lockFile(); - trafile = fileLock.getRaFile(); - }*/ - trafile.seek(0); - trafile.getChannel().transferFrom(nrafile.getChannel(), 0, - nrafile.length()); - } - /** - * remove all trace of the sessionFile file - * - */ - protected void eraseExistence() { - unlockFile(); - if (sessionFile!=null) { - sessionFile.delete(); - sessionFile = null; - } - } - /* (non-Javadoc) - * @see org.vamsas.client.simpleclient.Lock#getBufferedInputStream(boolean) - */ - public BufferedInputStream getBufferedInputStream(boolean atStart) throws IOException { - lockFile(); - return fileLock.getBufferedInputStream(atStart); - } - - /* (non-Javadoc) - * @see org.vamsas.client.simpleclient.Lock#getBufferedOutputStream(boolean) - */ - public BufferedOutputStream getBufferedOutputStream(boolean clear) throws IOException { - lockFile(); - return fileLock.getBufferedOutputStream(clear); - } - - /* (non-Javadoc) - * @see org.vamsas.client.simpleclient.Lock#getFileInputStream(boolean) - */ - public FileInputStream getFileInputStream(boolean atStart) throws IOException { - lockFile(); - return fileLock.getFileInputStream(atStart); - } - - /* (non-Javadoc) - * @see org.vamsas.client.simpleclient.Lock#getFileOutputStream(boolean) - */ - public FileOutputStream getFileOutputStream(boolean clear) throws IOException { - lockFile(); - return fileLock.getFileOutputStream(clear); - } - -} diff --git a/src/org/vamsas/client/simpleclient/SessionFlagFile.java b/src/org/vamsas/client/simpleclient/SessionFlagFile.java deleted file mode 100644 index 7826fbc..0000000 --- a/src/org/vamsas/client/simpleclient/SessionFlagFile.java +++ /dev/null @@ -1,85 +0,0 @@ -package org.vamsas.client.simpleclient; - -import java.io.File; - -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; - -/** - * methods for setting and checking - * binary flags in a vamsas session directory. - * all methods apart from the constructor will - * throw a fatal error if the flagFile is not - * a valid java.io.File object. - * LATER: extract SessionFlag interface for generalizing the vamsas session code - * @author jimp - * - */ -public class SessionFlagFile { - private static Log log = LogFactory.getLog(SessionFlagFile.class); - protected File flagFile=null; - private void checkFlagFile() { - if (flagFile==null) { - log.fatal("Implementation error - uninitialized SessionFlagFile", - new Error("Implementation error - uninitialized SessionFlagFile")); - } - } - /** - * will log a warning if exceptions occur during flag creation. - * @return true if flag was set successfully - */ - public boolean setFlag() { - checkFlagFile(); - try { - if (flagFile.createNewFile()) { - log.debug("Set session flag "+flagFile); - } else { - log.debug("Session flag already set "+flagFile); - } - return true; - } - catch (Exception e) { - log.warn("Couldn't set session flag "+flagFile, e); - } - return false; - } - /** - * - * @return true if flag was cleared successfully - */ - public boolean clearFlag() { - checkFlagFile(); - if (flagFile.exists()) { - log.debug("clearing session flag "+flagFile); - if (!flagFile.delete()) { - log.warn("failed to clear session flag "+flagFile); - return false; - } - } else { - log.debug("clearFlag called for already cleared flag "+flagFile); - } - return true; - } - /** - * - * @return state of session flag - */ - public boolean checkFlag() { - checkFlagFile(); - if (flagFile.exists()) { - if (log.isDebugEnabled()) - log.debug("Flag '"+flagFile+"' is set."); - return true; - } - if (log.isDebugEnabled()) - log.debug("Flag '"+flagFile+"' is not set."); - return false; - } - /** - * @param flagFile - */ - public SessionFlagFile(File flagFile) { - super(); - this.flagFile = flagFile; - }; -} diff --git a/src/org/vamsas/client/simpleclient/SessionUrn.java b/src/org/vamsas/client/simpleclient/SessionUrn.java deleted file mode 100644 index 13b6f23..0000000 --- a/src/org/vamsas/client/simpleclient/SessionUrn.java +++ /dev/null @@ -1,40 +0,0 @@ -package org.vamsas.client.simpleclient; - -import java.io.File; -import java.net.MalformedURLException; - -/** - * SessionUrn for simpleclient sessions: - * simpleclient://{Absolute path to session directory} - * @author jimp - * - */ -public class SessionUrn extends org.vamsas.client.SessionUrn { - /** - * a simple client session urn prefix - */ - public static final String SIMPLECLIENT="simpleclient"; - public static String VAMSASDOCUMENT="vdoc"; - static { - TYPES.put(SIMPLECLIENT, SessionUrn.class); - TYPES.put(SessionUrn.VAMSASDOCUMENT, SessionUrn.class); - } - - public SessionUrn(File sessionLocation) throws MalformedURLException { - // TODO: LATER: implement switch to have vamsas document or simpleclient sessions for same constructor - super(SIMPLECLIENT, sessionLocation.getAbsoluteFile().toURL()); - //else - // super(VAMSASDOCUMENT, sessionLocation); - } - public SessionUrn(VamsasSession session) throws MalformedURLException { - super(SIMPLECLIENT, session.sessionDir.getAbsoluteFile().toURL()); - } - /** - * TODO: LATER: think about this again. - * @return File(urn.getPath()) - */ - public File asFile() { - return new File(urn.getPath()); - } - // TODO: add abstract 'handler' methods for resolving the URN to a particular class -} diff --git a/src/org/vamsas/client/simpleclient/SessionsFile.java b/src/org/vamsas/client/simpleclient/SessionsFile.java deleted file mode 100644 index eb80f45..0000000 --- a/src/org/vamsas/client/simpleclient/SessionsFile.java +++ /dev/null @@ -1,342 +0,0 @@ -/* EMBL - The European Bioinformatics institute -* MSD Group -* VAMSAS Project -* -* Copyright (c) 2005-2006 Thr European Bioinformatics Institute. All rights reserved. -* -* Redistribution and use in source and binary forms, with or without -* modification, are permitted provided that the following conditions -* are met: -* -* 1. Redistributions of source code must retain the above copyright -* notice, this list of conditions and the following disclaimer. -* -* 2. Redistributions in binary form must reproduce the above copyright -* notice, this list of conditions and the following disclaimer in -* the documentation and/or other materials provided with the -* distribution. -* -* 3. The name MSD must not be used to endorse or promote products -* derived from this software without prior written permission. For -* written permission, please contact msd-help@ebi.ac.uk -* -* 4. Products derived from this software may not be called "MSD" -* nor may "MSD" appear in their names without prior written -* permission of the MSD developers. -* -* 5. Redistributions of any form whatsoever must retain the following -* acknowledgment: -* "This product includes software developed by MSD -* (http://www.ebi.ac.uk/)" -* -* THIS SOFTWARE IS PROVIDED BY THE MSD GROUP ``AS IS'' AND ANY -* EXPRESSED OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR -* PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE ENSEMBL GROUP OR -* ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, -* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT -* NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) -* HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, -* STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) -* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED -* OF THE POSSIBILITY OF SUCH DAMAGE. -* -* The European Bioinformatics Institute may publish revised and/or new -* versions of this license with new releases of VAMSAS software. -*============================================================================== -* -* @author Pierre MARGUERITE -* -* Dec 13, 2006 - VamsasClientV4 -* -*/ - -package org.vamsas.client.simpleclient; - -import java.io.File; -import java.io.FileNotFoundException; -import java.io.FileOutputStream; -import java.io.ObjectInputStream; -import java.io.ObjectOutputStream; - - -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.vamsas.client.SessionHandle; - -/** - * @author Pierre MARGUERITE - * - * - */ -public class SessionsFile extends ListFile { - - private static Log log = LogFactory.getLog(SessionsFile.class); - /** - * when set true - get FileNotFoundExceptions on WinXP when writing to locked stream after the backup has been made (via the backupFile method) - */ - boolean backup=false; - /** - * number of my session in list - passed back when a session - * is added to list, and used (if valid) for quickly - * looking up presence of session handle in the list. - */ - private int syncnum = 1; - /** - * @param file - */ - public SessionsFile(File file) throws java.io.IOException { - super(file); - } - - - /** - * internal method for getting sessionsList - ensures a lock has been made but - * does not release it. - * - * @return list of clients - */ - private SessionHandle[] retrieveSessionHandles() { - if (lockFile()) { - try { - SessionHandle[] clients=null; - if (this.fileLock.length()>0) { - - ObjectInputStream is = new ObjectInputStream(this.fileLock.getBufferedInputStream(true)); - Object o; - o=is.readObject(); - if (o!=null) { - try { - clients = (SessionHandle[]) o; - } - catch (Exception e) { - log.error("Garbage in the clientHandle list "+this.sessionFile,e); - } - } - } - return clients; - } catch (FileNotFoundException e) { - // e.printStackTrace(System.err); - log.error(e); - } catch (Exception e) { - log.error(e); - //e.printStackTrace(System.err); - } - } - return null; - } - - /** - * get the SessionsList from the file. May return null if lock failed! - * @return sessionsList - */ - public SessionHandle[] retrieveSessionsList() { - if (lockFile()) { - SessionHandle[] clients = retrieveSessionHandles(); - unlockFile(); - return clients; - } - return null; - } - - /** - * get list from the locked ClientList. - * @param extantlock - * @return clientList or null if lock failed (or file was empty) - */ - public SessionHandle[] retrieveSessionsList(Lock extantlock) { - if (lockFile(extantlock)) { - SessionHandle[] clients = retrieveSessionHandles(); - unlockFile(); - return clients; - } - return null; - } - - - /** - * adds clientHandle me to the clientList under an existing lock extantLock. - * @param me - * @param extantLock - * @return client index in list or 0 if lock was invalid or addClient operation failed. - */ - public int addSession(SessionHandle me, Lock extantLock) { - return addSession(me, true, extantLock); - } - - /** - * adds SessionsHandle me to the sessionsList under an existing lock. - * @param me - sessionsHandle - * @param disambig - if true then add will fail if an identical clientHandle already exists - * @param extantLock - existing lock - * @return client index in list or 0 if addClient (or the lock) failed. - */ - - public int addSession(SessionHandle session, boolean disambig, Lock extantLock) { - if (lockFile(extantLock)) { - this.syncnum = addSession(session, disambig); - unlockFile(); - return this.syncnum; - } - return 0; - } - - /** - * removes the current session from the SessionsList without complaint if the session isn't in the sessionsList already. - * @param me client handle to be removed - * @param clientlock existing lock passed from watcher. - */ - public void removeSession(SessionHandle session, Lock clientlock) { - int mynum =-1; - if (lockFile(clientlock)) { - SessionHandle[] sessions = retrieveSessionHandles(); - if (sessions != null) { - if ((this.syncnum<=0 || this.syncnum>sessions.length) || sessions[this.syncnum-1]!=session) { - for (int i = 0, j = sessions.length; i < j; i++) - if (sessions[i].equals(session)) { - mynum=i; - break; - } - } else { - mynum=this.syncnum-1; - } - if (mynum>-1) { - SessionHandle[] newlist = new SessionHandle[sessions.length - 1]; - for (int k=0,i = 0, j = sessions.length; i < j; i++) - if (i!=mynum) - newlist[k++] = sessions[i]; - if (!putSessionsList(newlist)) - throw new Error("Failed to write new sessionsList!"); // failed to put the sessionList to disk. - } - } - unlockFile(); - } else { - throw new Error("Couldn't get lock for "+((sessionFile==null) ? "Unitialised sessionFile in SessionsFile" : this.sessionFile.getAbsolutePath())); - } - } - /** - * Adds a SessionHandle to the SessionList file - optionally disambiguating - * the SessionHandle (modifes the URN). - * Note: Caller is left to release the lock on the SessionList. - * @param me - * @param disambiguate - - * flag indicating if the URN for me should be disambiguated to - * differentiate between sessions. - * @return index of sessionHandle in new list, or -1-position of existing - * sessionHandle (if disambiguate is true) - */ - protected int addSession(SessionHandle session, boolean disambiguate) { - int newsession = 0; - int tries=5; - while (tries-->0 && !lockFile()) - try { Thread.sleep(1); } catch (Exception e){}; - if (lockFile()) { - SessionHandle[] sessions = retrieveSessionHandles(); - - if (sessions == null) { - sessions = new SessionHandle[1]; - sessions[0] = session; - newsession = 1; - } else { - int k = 0; - for (int i = 0, j = sessions.length; i < j; i++) { - if ( sessions[i].equals(session)) { - if (disambiguate) { - while (sessions[i].equals(session)) { - // me.setClientUrn(me.getClientUrn() + k++); // TODO: make a better - // disambiguation of - // urn. - } - } else { - // will not write the ambiguous clientHandle to disk, just return - // its index. - return -1 - i; - } - } - } - int i, j; - SessionHandle[] newlist = new SessionHandle[sessions.length + 1]; - for (i = 0, j = sessions.length; i < j; i++) - newlist[i] = sessions[i]; - newlist[j] = session; - sessions = newlist; - newsession = j+1; - } - if (!putSessionsList(sessions)) - return 0; // failed to put the clientList to disk. - } - return newsession; - } - - - /** - * safely writes sessions array to the file referred to by sessionFile. - * - * @param clients - * @return true if successful write. Throws Errors otherwise. - */ - protected boolean putSessionsList(SessionHandle[] clients) { - if (lockFile()) { - File templist=null; - if (!this.backup || (templist = backupSessionFile()) != null) { - int retries=3; - while (retries-->0) { - try { - ObjectOutputStream os = - new ObjectOutputStream(this.fileLock.getBufferedOutputStream(true)); - log.debug("About to write "+clients.length+" sessionHandles to output stream."); - os.writeObject(clients); - os.close(); - // All done - remove the backup. - if (this.backup) - templist.delete(); - templist = null; - retries=-1; - } catch (Exception e) { - // System.err - //.println("Serious - problems writing to sessionFile."); - log.error("Serious - problems writing to sessionFile.",e); - if (retries>0 && templist != null) { - // System.err.println("Recovering from Backup in " - // + templist.getAbsolutePath()); - log.error("Recovering from Backup in "+ templist.getAbsolutePath()); - templist.renameTo(this.fileLock.target); - } - //e.printStackTrace(System.err); - log.error(e); - } - } - if (retries>-2) { - // System.err - // .println("Serious - problems writing to sessionFile. Giving Up."); - log.error("Serious - problems writing to sessionFile. Giving Up."); - return false; - } - } else { - throw new Error( - "Couldn't create backup of the clientList before writing to it!"); - } - } else { - throw new Error("Could not lock the clientList: " - + ((this.sessionFile == null) ? "Unitialized ClientsFile" - : " failed to get lock on " + this.sessionFile.getAbsolutePath())); - } - // successful! - return true; - } - - public void clearList() { - if (lockFile()) { - try { - FileOutputStream fout = this.fileLock.getFileOutputStream(true); - fout.flush(); - fout.close(); - } catch (Exception e) { - throw new Error("Problems trying to clear clientlist!",e); - - } - } - - } -} diff --git a/src/org/vamsas/client/simpleclient/SimpleClient.java b/src/org/vamsas/client/simpleclient/SimpleClient.java deleted file mode 100644 index 2041c11..0000000 --- a/src/org/vamsas/client/simpleclient/SimpleClient.java +++ /dev/null @@ -1,416 +0,0 @@ -/* - * Created on 15-Sep-2005 - * - * TODO To change the template for this generated file go to - * Window - Preferences - Java - Code Style - Code Templates - */ -package org.vamsas.client.simpleclient; - -import java.beans.EventHandler; -import java.beans.PropertyChangeEvent; -import java.beans.PropertyChangeListener; -import java.beans.PropertyChangeSupport; -import java.io.BufferedReader; -import java.io.File; -import java.io.IOException; -import java.net.MalformedURLException; -import java.util.Hashtable; -import java.util.Vector; - -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.vamsas.client.ClientHandle; -import org.vamsas.client.Events; -import org.vamsas.client.IClient; -import org.vamsas.client.IClientDocument; -import org.vamsas.client.IObjectUpdate; -import org.vamsas.client.InvalidSessionUrnException; -import org.vamsas.client.SessionHandle; -import org.vamsas.client.UserHandle; -import org.vamsas.objects.core.ApplicationData; -import org.vamsas.objects.core.Entry; -import org.vamsas.objects.core.LockFile; -import org.vamsas.objects.core.VamsasDocument; -import org.vamsas.objects.utils.AppDataReference; -import org.vamsas.objects.utils.ProvenanceStuff; -import org.vamsas.objects.utils.document.VersionEntries; - -/** - * @author jimp - */ -public class SimpleClient implements IClient { - - private static Log log = LogFactory.getLog(SimpleClient.class); - - protected UserHandle user = null; - - protected SessionUrn session = null; - protected VamsasSession _session; - protected ClientHandle client = null; - protected EventGeneratorThread evgen = null; - protected ClientDocument cdocument = null; - /** - * object hash table that persists in each client holding vorbaIds and hash values after a document write - */ - protected Hashtable extantobjects=null; - /** - * construct a transient IdFactory instance - this should last only as long as the - * SimpleClient object holds the lock on the vamsas document being created/manipulated. - * @return - */ - private IdFactory makeVorbaIdFactory() { - return new IdFactory(getSessionHandle(), client, user); - } - - /** - * construct SimpleClient for user, client and VamsasSession directory - * use the SimpleClientFactory rather than this constructor directly. - * @param user - * @param client - * @param sess - */ - protected SimpleClient(UserHandle user, ClientHandle client, VamsasSession sess) throws InvalidSessionUrnException { - // TODO: validate user/client/session - _session = sess; - this.user = user; - this.client = client; - try { - session = new SessionUrn(_session); - } catch (MalformedURLException e) { - log.error("Couldn't form a valid SessionUrn object!",e); - throw new InvalidSessionUrnException(_session.toString()); - } - } - /** - * construct new session by importing objects from an existing vamsas document - * @param user - * @param client - * @param sess - * @param importingArchive - * @throws Exception IOExceptions for Session IO problems, and general Exception if importing document is invalid. - */ - protected SimpleClient(UserHandle user, ClientHandle client, VamsasSession sess, File importingArchive) throws Exception { - this(user, client, sess); - VamsasArchive sessdoc = _session.getVamsasDocument(); - try { - VamsasArchiveReader odoc = new VamsasArchiveReader(importingArchive); - SimpleDocument sdoc = new SimpleDocument(makeVorbaIdFactory()); - VamsasDocument doc = sdoc.getVamsasDocument(odoc); - sessdoc.putVamsasDocument(doc, sdoc.vorba); - sessdoc.closeArchive(); - } catch (Exception e) { - sessdoc.cancelArchive(); - // write a dummy archive - _session.slog.info("Exception when importing document data from "+importingArchive); - throw new Exception("Failed to import data from "+importingArchive, e); - } - } - - /* - * (non-Javadoc) - * LATER: check that build substitution variables are correct - * @see org.vamsas.client.IClient#getAbout() - */ - public String getAbout() { - return new String("VORBA SimpleClient version $version$ build $build$"); - } - - /* - * (non-Javadoc) - * - * @see org.vamsas.client.IClient#getSessionUrn() - */ - public String getSessionUrn() { - return session.getSessionUrn(); - } - - /* - * (non-Javadoc) - * - * @see org.vamsas.client.IClient#getSessionHandle() - */ - public SessionHandle getSessionHandle() { - // TODO: eliminate SessionHandle ? need to refactor interfaces. - SessionHandle sh = new SessionHandle(session.getSessionUrn()); - return sh; - } - - /* - * (non-Javadoc) - * - * @see org.vamsas.client.IClient#getClientHandle() - */ - public ClientHandle getClientHandle() { - return client; - } - - /* - * (non-Javadoc) - * - * @see org.vamsas.client.IClient#getUserHandle() - */ - public UserHandle getUserHandle() { - return user; - } - /** - * - * @return user field for a provenance entry - */ - protected String getProvenanceUser() { - return new String(user.getFullName()); - } - /** - * construct a provenance entry for this client with the specified action string. - * @param action - * @return properly completed provenance entry - */ - protected Entry getProvenanceEntry(String action) { - Entry prov = ProvenanceStuff.newProvenanceEntry(client.getClientUrn(), getProvenanceUser(), action); - return prov; - } - private Hashtable handlers = initHandlers(); - - private Vector listeners = new Vector(); - - /** - * make all the PropertyChangeSupport objects for the - * events described in org.vamsas.client.Event - * @return - */ - private static Hashtable initHandlers() { - Hashtable events = new Hashtable(); - java.util.Iterator evt = Events.EventList.iterator(); - while (evt.hasNext()) { - Object ths = evt.next(); - events.put(ths, (Object) new PropertyChangeSupport(ths)); - } - return events; - } - - /* - * (non-Javadoc) - * - * @see org.vamsas.client.IClient#addDocumentUpdateHandler(java.util.EventListener) - */ - public void addDocumentUpdateHandler(PropertyChangeListener evt) { - if (handlers.containsKey(Events.DOCUMENT_UPDATE)) { - Object handler; - ((PropertyChangeSupport) (handler = handlers.get(Events.DOCUMENT_UPDATE))) - .addPropertyChangeListener(evt); - listeners.add(handler); - listeners.add((Object) evt); - } - } - boolean finalized=false; - /* - * (non-Javadoc) - * - * @see org.vamsas.client.IClient#finalizeClient() - */ - public void finalizeClient() { - // TODO: determine if this is last client in session - // TODO: raise events like : ((lst_client && document.request.to.close), (client_finalization), ( - - // if (handlers.containsKey(Events.)) - // if (handlers.containsKey(Events.CLIENT_FINALIZATION)) - // deregister listeners. - // mark this instance as finalized - } - - /* - * (non-Javadoc) - * - * @see org.vamsas.client.IClient#getClientDocument() - */ - public IClientDocument getClientDocument() throws IOException { - if (cdocument!=null) { - // cdocument is non-nill if the ClientDocument.finalise() method hasn't been called. - return cdocument; - } - VamsasArchive va = null; - try { - // LATER: bail out if it takes too long to get the lock ? - va = _session.getVamsasDocument(); - } - catch (IOException e) { - throw new IOException("Failed to get lock on session document"); - } - VamsasDocument doc=null; - IdFactory vorba = null; - // TODO: reduce size of vorba ids generated from these parameters to IdFactory (mainly sessionHandle rationalization ?) - try { - va.setVorba(vorba=makeVorbaIdFactory()); - // if session currently holds data - read it in - or get a dummy - _session.slog.debug("Accessing document"); - doc = - va.getVamsasDocument(getProvenanceUser(), - "created new session document.", null); - if (doc!=null) - _session.slog.debug("Successfully retrieved document."); - else - log.error("Unexpectedly retrieved null document!"); - } - catch (Exception e) { - log.error("Failed to get session document for session directory '"+_session.sessionDir+"'", e); - throw new IOException("Failed to get session document for session directory '"+_session.sessionDir+"'"); - } - // Construct the IClientDocument instance - - ClientDocument cdoc = new ClientDocument(doc, va, vorba, this); - return cdoc; - } - - /* - * (non-Javadoc) - * @throws Errors for invalid newdoc parameter - * @see org.vamsas.client.IClient#updateDocument(org.vamsas.client.IClientDocument) - */ - public void updateDocument(IClientDocument newdoc) { - if (!(newdoc instanceof ClientDocument)) { - throw new Error("Invalid IClientDocument instance for SimpleClient."); - } - if (cdocument==null) - throw new Error("Client Error - updateDocument() called before getClientDocument()."); - if (newdoc!=cdocument) - throw new Error("Client Error - SimpleClient.updateDocument() can only take the IClientDocument instance returned from SimpleClient.getClientDocument()"); - if (!cdocument.isModified()) { - if (log.isDebugEnabled()) - log.debug("updateDocument for "+session.getSessionUrn()+" with unmodified IClientDocument."); - } else { - try { - if (!cdocument.updateSessionDocument()) { - log.warn("Session document did not update properly for session directory "+_session.sessionDir); - // cdocument.archive.cancelArchive(); // LATER: could be done - would need to prevent updateSessionDocument closing the archive. - _session.slog.warn("Session Document updated but may not be valid (false return from org.vamsas.simpleclient.ClientDocument.updateSessionDocument()"); - } - } - catch (IOException e) { - log.warn("IO Problems when updating document!",e); - _session.slog.error("IO problems when attempting to update document."); - } - } - // garbage collect the ClientDocument instance. - try { - cdocument.finalize(); - - } catch (Throwable e) { - log.error("Exception when trying to garbage collect ClientDocument for "+session.getSessionUrn(), e); - } - cdocument = null; // this is probably done by finalize - } - - /* - * (non-Javadoc) - * - * @see org.vamsas.client.IClient#storeDocument(java.io.File) - */ - public void storeDocument(File location) { - - // write storeDocument file to inform other clients that they should raise - Lock vamlock = evgen.want_to_store(); - // Events.DOCUMENT_FINALIZEAPPDATA - try { - _session.writeVamsasDocument(location, vamlock); - _session.clearUnsavedFlag(); - } catch (Exception e) { - log.warn("Exception whilst trying to store document in "+location,e); - } - - vamlock.release(); - } - - /* - * (non-Javadoc) - * - * @see org.vamsas.client.IClient#addVorbaEventHandler(java.lang.String, - * java.beans.PropertyChangeListener) - */ - public void addVorbaEventHandler(String EventChain, PropertyChangeListener evt) { - if (handlers.containsKey(EventChain)) { - Object handler; - ((PropertyChangeSupport) (handler = handlers.get(EventChain))) - .addPropertyChangeListener(evt); - listeners.add(handler); - listeners.add((Object) evt); - } - } - - /* (non-Javadoc) - * @see org.vamsas.client.IClient#pollUpdate() - */ - public void pollUpdate() { - - if (evgen==null) { - log.warn("pollUpdate called on incomplete SimpleClient object."); - return; - } - - if (!evgen.isAlive()) { - log.warn("pollUpdate called before joinSession() - trying to do this."); - try { - joinSession(); - } catch (Exception e) { - log.error("Unexpected exception on default call to joinSession",e); - } - } - - //TODO ensure event generator robustly handles these interrupts. - log.debug("interrrupting event generator."); - evgen.interrupt(); - log.debug("interrrupted event generator."); - } - - /* (non-Javadoc) - * @see org.vamsas.client.IClient#joinSession() - */ - public void joinSession() throws Exception { - // start the EventGenerator thread. - if (evgen==null) { - log.warn("joinSession called on incomplete SimpleClient object."); - return; - } - if (evgen.isAlive()) - throw new Error("Join session called twice for the same SimpleClient (IClient instance)."); - evgen.start(); - if (evgen.isAlive()) - log.debug("Started EventGenerator thread."); - else { - log.warn("Failed to start EventGenerator thread."); - throw new Exception("Failed to start event generator thread - client cannot be instantiated."); - } - if (evgen.countHandlersFor(Events.DOCUMENT_CREATE)>0) { - //TODO: is this application connecting to a newly created session document ? - //evgen.raise(Events.DOCUMENT_CREATE); - } - } - - - - /* (non-Javadoc) - * @see org.vamsas.client.IClient#importDocument(java.io.File) - */ - public void importDocument(File location) { - // TODO LATER: implement SimpleClient.importDocument() - log.error("importDocument is not yet implemented for a SimpleClient Session."); - } - - public IObjectUpdate getUpdateHandler(Class rootObject) { - // TODO Auto-generated method stub - return null; - } - - public IObjectUpdate[] getUpdateHandlers() { - // TODO Auto-generated method stub - return null; - } - - public void removeUpdateHandler(Class rootObject) { - // TODO Auto-generated method stub - - } - - public void setUpdateHandler(IObjectUpdate handler) { - // TODO Auto-generated method stub - - } -} diff --git a/src/org/vamsas/client/simpleclient/SimpleClientAppdata.java b/src/org/vamsas/client/simpleclient/SimpleClientAppdata.java deleted file mode 100644 index 84bc48a..0000000 --- a/src/org/vamsas/client/simpleclient/SimpleClientAppdata.java +++ /dev/null @@ -1,543 +0,0 @@ -/** - * - */ -package org.vamsas.client.simpleclient; - -import java.io.BufferedInputStream; -import java.io.BufferedOutputStream; -import java.io.ByteArrayInputStream; -import java.io.ByteArrayOutputStream; -import java.io.DataInput; -import java.io.DataInputStream; -import java.io.DataOutput; -import java.io.DataOutputStream; -import java.io.FileInputStream; -import java.io.IOException; -import java.io.InputStream; -import java.util.Vector; -import java.util.jar.JarEntry; -import java.util.jar.JarInputStream; -import java.util.jar.JarOutputStream; - -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.vamsas.client.IClientAppdata; -import org.vamsas.objects.core.AppData; -import org.vamsas.objects.core.ApplicationData; -import org.vamsas.objects.core.User; -import org.vamsas.objects.utils.AppDataReference; - -/** - * @author jimp - * Access interface to data chunks read from a VamsasArchiveReader stream - * (or byte buffer input stream) or written to a VamsasArchive stream. - * // TODO: get VamsasArchiveReader from sclient - */ -public class SimpleClientAppdata implements IClientAppdata { - private static Log log = LogFactory.getLog(SimpleClientAppdata.class); - /** - * has the session's document been accessed to get the AppData entrys? - */ - protected boolean accessedDocument = false; - /** - * has the user datablock been modified ? - * temporary file containing new user specific application data chunk - */ - SessionFile newUserData=null; - JarOutputStream newUserDataStream = null; - /** - * has the apps global datablock been modified ? - * temporary file containing new global application data chunk - */ - SessionFile newAppData=null; - JarOutputStream newAppDataStream=null; - /** - * set by extractAppData - */ - protected ApplicationData appsGlobal = null; - /** - * set by extractAppData - */ - protected User usersData = null; - - ClientDocument clientdoc; - /** - * 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. - * - need flag for switching between embedded and jar entry mode ? - always write a jar entry for a stream. - * - need code for rewind and overwriting if the set*Appdata methods are called more than once. - * - need flags for streams to except a call to set*Appdata when an output stream exists and is open. - * - need - * @param clientdoc The ClientDocument instance that this IClientAppData is accessing - */ - protected SimpleClientAppdata(ClientDocument clientdoc) { - if (clientdoc==null) { - log.fatal("Implementation error - Null ClientDocument for SimpleClientAppdata construction."); - throw new Error("Implementation error - Null ClientDocument for SimpleClientAppdata construction."); - } - this.clientdoc = clientdoc; - } - /** - * gets appropriate app data for the application, if it exists in this dataset - * Called by every accessor to ensure data has been retrieved from document. - */ - private void extractAppData(org.vamsas.objects.core.VamsasDocument doc) { - if (doc==null) { - log.debug("extractAppData called for null document object"); - return; - } - if (accessedDocument) { - return; - } - Vector apldataset = AppDataReference.getUserandApplicationsData( - doc, clientdoc.sclient.getUserHandle(), clientdoc.sclient.getClientHandle()); - accessedDocument = true; - if (apldataset!=null) { - if (apldataset.size()>0) { - AppData clientdat = (AppData) apldataset.get(0); - if (clientdat instanceof ApplicationData) { - appsGlobal = (ApplicationData) clientdat; - if (apldataset.size()>1) { - clientdat = (AppData) apldataset.get(1); - if (clientdat instanceof User) { - usersData = (User) clientdat; - } - if (apldataset.size()>2) - log.info("Ignoring additional ("+(apldataset.size()-2)+") AppDatas returned by document appdata query."); - } - } else { - log.warn("Unexpected entry in AppDataReference query: id="+clientdat.getVorbaId()+" type="+clientdat.getClass().getName()); - } - apldataset.removeAllElements(); // destroy references. - } - } - } - /** - * LATER: generalize this for different low-level session implementations (it may not always be a Jar) - * @param appdata - * @param docreader - * @return - */ - private JarInputStream getAppDataStream(AppData appdata, VamsasArchiveReader docreader) { - String entryRef = appdata.getDataReference(); - if (entryRef!=null) { - log.debug("Resolving appData reference +"+entryRef); - InputStream entry = docreader.getAppdataStream(entryRef); - if (entry!=null) { - if (entry instanceof JarInputStream) { - return (JarInputStream) entry; - } - log.warn("Implementation problem - docreader didn't return a JarInputStream entry."); - } - } else { - log.debug("GetAppDataStream called for an AppData without a data reference."); - } - return null; - } - /** - * yuk - size of buffer used for slurping appData JarEntry into a byte array. - */ - private final int _TRANSFER_BUFFER=4096*4; - - /** - * Resolve AppData object to a byte array. - * @param appdata - * @param archiveReader - * @return null or the application data as a byte array - */ - private byte[] getAppDataAsByteArray(AppData appdata, VamsasArchiveReader docreader) { - if (appdata.getData()==null) { - if (docreader==null) { - log.warn("Silently failing getAppDataAsByteArray with null docreader.",new Exception()); - return null; - } - // resolve and load data - JarInputStream entry = getAppDataStream(appdata, docreader); - ByteArrayOutputStream bytes = new ByteArrayOutputStream(); - try { - byte buff[] = new byte[_TRANSFER_BUFFER]; - int olen=0; - while (entry.available()>0) { - int len = entry.read(buff, olen, _TRANSFER_BUFFER); - bytes.write(buff, 0, len); - olen+=len; - } - buff=null; - } catch (Exception e) { - log.warn("Unexpected exception - probable truncation when accessing VamsasDocument entry "+appdata.getDataReference(), e); - } - if (bytes.size()>0) { - // LATER: deal with probable OutOfMemoryErrors here - log.debug("Got "+bytes.size()+" bytes from AppDataReference "+appdata.getDataReference()); - byte data[] = bytes.toByteArray(); - bytes = null; - return data; - } - return null; - } else { - log.debug("Returning inline AppData block for "+appdata.getVorbaId()); - return appdata.getData(); - } - } - /** - * internal method for getting a DataInputStream from an AppData object. - * @param appdata - * @param docreader - * @return data in object or null if no data is accessible - */ - private DataInput getAppDataAsDataInputStream(AppData appdata, VamsasArchiveReader docreader) { - if (appdata!=null && docreader!=null) { - String entryRef = appdata.getDataReference(); - if (entryRef!=null) { - log.debug("Resolving AppData reference for "+entryRef); - InputStream jstrm = docreader.getAppdataStream(entryRef); - if (jstrm!=null) - return new AppDataInputStream(jstrm); - else { - log.debug("Returning null input stream for unresolved reference ("+entryRef+") id="+appdata.getVorbaId()); - return null; - } - } else { - // return a byteArray input stream - byte[] data=appdata.getData(); - if (data.length>0) { - ByteArrayInputStream stream = new ByteArrayInputStream(data); - return new DataInputStream(stream); - } else { - log.debug("Returning null input stream for empty Appdata data block in id="+appdata.getVorbaId()); - return null; - } - } - } else { - log.debug("Returning null DataInputStream for appdata entry:"+appdata.getVorbaId()); - } - return null; - } - - /** - * internal method for getting ByteArray from AppData object - * @param clientOrUser - true for returning userData, otherwise return Client AppData. - * @return null or byte array - */ - private byte[] _getappdataByteArray(boolean clientOrUser) { - if (clientdoc==null) - throw new Error("Implementation error, Improperly initialized SimpleClientAppdata."); - byte[] data=null; - String appdName; - if (!clientOrUser) { - appdName = "Client's Appdata"; - } else { - appdName = "User's Appdata"; - } - log.debug("getting "+appdName+" as a byte array"); - extractAppData(clientdoc.getVamsasDocument()); - AppData object; - if (!clientOrUser) { - object = appsGlobal; - } else { - object = usersData; - } - if (object!=null) { - log.debug("Trying to resolve "+appdName+" object to byte array."); - data = getAppDataAsByteArray(object, clientdoc.getVamsasArchiveReader()); - } - if (data == null) - log.debug("Returning null for "+appdName+"ClientAppdata byte[] array"); - return data; - - } - - /** - * common method for Client and User AppData->InputStream accessor - * @param clientOrUser - the appData to resolve - false for client, true for user appdata. - * @return null or the DataInputStream desired. - */ - private DataInput _getappdataInputStream(boolean clientOrUser) { - if (clientdoc==null) - throw new Error("Implementation error, Improperly initialized SimpleClientAppdata."); - String appdName; - if (!clientOrUser) { - appdName = "Client's Appdata"; - } else { - appdName = "User's Appdata"; - } - if (log.isDebugEnabled()) - log.debug("getting "+appdName+" as an input stream."); - extractAppData(clientdoc.getVamsasDocument()); - AppData object; - if (!clientOrUser) { - object = appsGlobal; - } else { - object = usersData; - } - if (object!=null) { - log.debug("Trying to resolve ClientAppdata object to an input stream."); - return getAppDataAsDataInputStream(object, clientdoc.getVamsasArchiveReader()); - } - log.debug("getClientInputStream returning null."); - return null; - } - /* (non-Javadoc) - * @see org.vamsas.client.IClientAppdata#getClientAppdata() - */ - public byte[] getClientAppdata() { - return _getappdataByteArray(false); - } - /* (non-Javadoc) - * @see org.vamsas.client.IClientAppdata#getClientInputStream() - */ - public DataInput getClientInputStream() { - return _getappdataInputStream(false); - } - - /* (non-Javadoc) - * @see org.vamsas.client.IClientAppdata#getUserAppdata() - */ - public byte[] getUserAppdata() { - return _getappdataByteArray(true); - } - - /* (non-Javadoc) - * @see org.vamsas.client.IClientAppdata#getUserInputStream() - */ - public DataInput getUserInputStream() { - return _getappdataInputStream(true); - } - /** - * methods for writing new AppData entries. - */ - private DataOutput _getAppdataOutputStream(boolean clientOrUser) { - String apdname; - SessionFile apdfile=null; - if (!clientOrUser) { - apdname = "clientAppData"; - apdfile = newAppData; - } else { - apdname = "userAppData"; - apdfile = newUserData; - } - try { - if (apdfile==null) { - apdfile=clientdoc.sclient._session.getTempSessionFile(apdname,".jar"); - log.debug("Successfully made temp appData file for "+apdname); - } else { - // truncate to remove existing data. - apdfile.fileLock.getRaFile().setLength(0); - log.debug("Successfully truncated existing temp appData for "+apdname); - } - } catch (Exception e) { - log.error("Whilst opening temp file in directory "+clientdoc.sclient._session.sessionDir, e); - } - // we do not make another file for the new entry if one exists already - if (!clientOrUser) { - newAppData = apdfile; - } else { - newUserData = apdfile; - } - try { - apdfile.lockFile(); - // LATER: Refactor these local AppDatastream IO stuff to their own class. - JarOutputStream dstrm = - new JarOutputStream(apdfile.fileLock.getBufferedOutputStream(true)); - if (!clientOrUser) { - newAppDataStream = dstrm; - } else { - newUserDataStream = dstrm; - } - dstrm.putNextEntry(new JarEntry("appData_entry.dat")); - // LATER: there may be trouble ahead if an AppDataOutputStream is written to by one thread when another truncates the file. This situation should be prevented if possible - return new AppDataOutputStream(dstrm); - } - catch (Exception e) { - log.error("Whilst opening jar output stream for file "+apdfile.sessionFile); - } - // tidy up and return null - apdfile.unlockFile(); - return null; - } - /** - * 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. - * @param vdoc session Document handler - * @param appd the AppData whose block is being updated - * @param apdjar the new data in a Jar written by this class - */ - protected void updateAnAppdataEntry(VamsasArchive vdoc, AppData appd, SessionFile apdjar) throws IOException { - if (apdjar==null || apdjar.sessionFile==null || !apdjar.sessionFile.exists()) { - throw new IOException("No temporary Appdata to recover and transfer."); - } - if (vdoc==null) { - log.fatal("FATAL! NO DOCUMENT TO WRITE TO!"); - throw new IOException("FATAL! NO DOCUMENT TO WRITE TO!"); - } - log.debug("Recovering AppData entry from "+apdjar.sessionFile); - JarInputStream istrm = new JarInputStream(apdjar.getBufferedInputStream(true)); - JarEntry je=null; - while (istrm.available()>0 && (je=istrm.getNextJarEntry())!=null && !je.getName().equals("appData_entry.dat")) { - if (je!=null) - log.debug("Ignoring extraneous entry "+je.getName()); - } - if (istrm.available()>0 && je!=null) { - log.debug("Found appData_entry.dat in Jar"); - String ref = appd.getDataReference(); - if (ref==null) { - throw new IOException("Null AppData.DataReference passed."); - } - if (vdoc.writeAppdataFromStream(ref, istrm)) { - log.debug("Entry updated successfully."); - } else { - throw new IOException("writeAppdataFromStream did not return true - expect future badness."); // LATER - verify why this might occur. - } - } else { - throw new IOException("Couldn't find appData_entry.dat in temporary jar file "+apdjar.sessionFile.getAbsolutePath()); - } - istrm.close(); - } - /* (non-Javadoc) - * @see org.vamsas.client.IClientAppdata#getClientOutputStream() - */ - public DataOutput getClientOutputStream() { - if (clientdoc==null) - throw new Error("Implementation error, Improperly initialized SimpleClientAppdata."); - if (log.isDebugEnabled()) - log.debug("trying to getClientOutputStream for "+clientdoc.sclient.client.getClientUrn()); - return _getAppdataOutputStream(false); - } - - /* (non-Javadoc) - * @see org.vamsas.client.IClientAppdata#getUserOutputStream() - */ - public DataOutput getUserOutputStream() { - if (clientdoc==null) - throw new Error("Implementation error, Improperly initialized SimpleClientAppdata."); - if (log.isDebugEnabled()) - log.debug("trying to getUserOutputStream for (" - +clientdoc.sclient.getUserHandle().getFullName()+")"+clientdoc.sclient.client.getClientUrn()); - return _getAppdataOutputStream(true); - } - - /* (non-Javadoc) - * @see org.vamsas.client.IClientAppdata#hasClientAppdata() - */ - public boolean hasClientAppdata() { - if (clientdoc==null) - throw new Error("Implementation error, Improperly initialized SimpleClientAppdata."); - extractAppData(clientdoc.getVamsasDocument()); - // LATER - check validity of a DataReference before we return true - if ((appsGlobal!=null) && (appsGlobal.getDataReference()!=null || appsGlobal.getData()!=null)) - return true; - return false; - } - - /* (non-Javadoc) - * @see org.vamsas.client.IClientAppdata#hasUserAppdata() - */ - public boolean hasUserAppdata() { - if (clientdoc==null) - throw new Error("Implementation error, Improperly initialized SimpleClientAppdata."); - extractAppData(clientdoc.getVamsasDocument()); - // LATER - check validity of a DataReference before we return true - if ((appsGlobal!=null) && (appsGlobal.getDataReference()!=null || appsGlobal.getData()!=null)) - return true; - return false; - } - private boolean _writeAppDataStream(JarOutputStream ostrm, byte[] data) { - try { - if (data!=null && data.length>0) - ostrm.write(data); - ostrm.closeEntry(); - return true; - } - catch (Exception e) { - log.error("Serious! - IO error when writing AppDataStream to file "+newAppData.sessionFile, e); - } - return false; - } - /* (non-Javadoc) - * @see org.vamsas.client.IClientAppdata#setClientAppdata(byte[]) - */ - public void setClientAppdata(byte[] data) { - if (clientdoc==null) - throw new Error("Implementation error, Improperly initialized SimpleClientAppdata."); - _getAppdataOutputStream(false); - if (newAppDataStream==null) { - // LATER: define an exception for this ? - operation may fail even if file i/o not involved - log.error("Serious! - couldn't open new AppDataStream in session directory "+clientdoc.sclient._session.sessionDir); - } else { - _writeAppDataStream(newAppDataStream, data); - // LATER: deal with error case - do we make session read only, or what ? - } - } - - /* (non-Javadoc) - * @see org.vamsas.client.IClientAppdata#setUserAppdata(byte[]) - */ - public void setUserAppdata(byte[] data) { - if (clientdoc==null) - throw new Error("Implementation error, Improperly initialized SimpleClientAppdata."); - _getAppdataOutputStream(true); - if (newUserDataStream==null) { - // LATER: define an exception for this ? - operation may fail even if file i/o not involved - log.error("Serious! - couldn't open new UserDataStream in session directory "+clientdoc.sclient._session.sessionDir); - } else { - _writeAppDataStream(newUserDataStream, data); - // LATER: deal with error case - do we make session read only, or what ? - } - } - /** - * flush and close outstanding output streams. - * - do this before checking data length. - * @throws IOException - */ - protected void closeForWriting() throws IOException { - if (newAppDataStream!=null) { - newAppDataStream.flush(); - newAppDataStream.closeEntry(); - newAppDataStream.close(); - } - if (newUserDataStream!=null) { - newUserDataStream.flush(); - newUserDataStream.closeEntry(); - newUserDataStream.close(); - } - } - - - /** - * - * @return true if any AppData blocks have to be updated in session Jar - */ - protected boolean isModified() { - // LATER differentiate between core xml modification and Jar Entry modification. - if (newAppData.sessionFile.exists() || newUserData.sessionFile.exists()) - return true; - return false; - } - /* (non-Javadoc) - * @see java.lang.Object#finalize() - */ - protected void finalize() throws Throwable { - if (newAppDataStream!=null) { - newAppDataStream = null; - } - if (newAppDataStream!=null) { - newUserDataStream = null; - } - if (newAppData!=null) { - newAppData.eraseExistence(); - newAppData = null; - } - if (newUserData!=null) { - newUserData.eraseExistence(); - newUserData = null; - } - super.finalize(); - } - -} diff --git a/src/org/vamsas/client/simpleclient/SimpleClientFactory.java b/src/org/vamsas/client/simpleclient/SimpleClientFactory.java deleted file mode 100644 index 6f5509a..0000000 --- a/src/org/vamsas/client/simpleclient/SimpleClientFactory.java +++ /dev/null @@ -1,262 +0,0 @@ -/* -* VAMSAS Project -* - -* -* Dec 13, 2006 -* -*/ - -package org.vamsas.client.simpleclient; - -import java.io.File; - -import java.io.IOException; - - -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.vamsas.client.ClientHandle; -import org.vamsas.client.IClient; -import org.vamsas.client.IClientFactory; -import org.vamsas.client.InvalidSessionUrnException; -import org.vamsas.client.NoDefaultSessionException; -import org.vamsas.client.SessionHandle; -import org.vamsas.client.UserHandle; - -/** - * - * - */ -public class SimpleClientFactory implements IClientFactory { - - private static Log log = LogFactory.getLog(SimpleClientFactory.class); - - private File sessionArena = null; - - private String vamsasSubdirectoryName = ".vamsas"; - - private SessionsFile sessionFile = null; - private static final String SESSION_LIST="sessions.obj"; - - //private String[] currentlyAvailableDessions = null; - - /** - * default constructor - called by CreateClientFactory only. - * - *Inits the sessionarena to the directory .vamsas of the user home directory. - * - */ - public SimpleClientFactory() throws IOException - { - // sessionArena - - //retrieves user home directory - String userHomeDirectory = System.getProperty("user.home"); - if (userHomeDirectory == null || userHomeDirectory.length()<1) - { - new IOException("Unable to detect user home directory"); - } - String sessionArenaPath = userHomeDirectory.concat(File.separator.concat(this.vamsasSubdirectoryName)); - - this.initSessionArena(sessionArenaPath); - this.initFactoryObjects(); - } - - - /** - * Create a client factory that works with sessions at the given - * path. - * @param path path to directory called session arena, where will be created session directories and session files. - */ - public SimpleClientFactory(String path) throws IOException - { - this.initSessionArena(path); - } - /** - * Inits sessionArena to a given path. - * checks if path is valid. - * - * @param path path to a directory to use - * @throws IOException if the path is incorrect - */ - private void initSessionArena (String path) throws IOException - { - // Check path is valid and read/writeable. - File arenaFile = new File (path); - if (!arenaFile.exists()) - { - if (! arenaFile.mkdirs()) - { - this.sessionArena = null; - throw(new IOException("Unable to create a directory called "+path)); - } - } - if (arenaFile.exists() && arenaFile.isDirectory() && arenaFile.canRead() && arenaFile.canWrite()) - { - this.sessionArena = arenaFile; - } - else - { - this.sessionArena = null; - throw(new IOException("Cannot read and write to a directory called "+path)); - } - } - - /** - * construct SessionFile objects and watchers for each - */ - private void initFactoryObjects() throws IOException { - if (this.sessionFile!=null ) - throw new IOException("initFactoryObjects called for initialised ClientFactory object."); - this.sessionFile = new SessionsFile(new File(this.sessionArena,SESSION_LIST)); - - } - /** - * @see org.vamsas.client.IClientFactory#getCurrentSessions() - */ - public String[] getCurrentSessions() - { - String[] sessions = null; - if (this.sessionFile!=null ) - { - SessionHandle[] sessionHandles = this.sessionFile.retrieveSessionsList(); - if (sessionHandles != null) - { - sessions = new String[sessionHandles.length]; - for (int i = sessionHandles.length -1; i > 0; i--) - { - SessionHandle sessionHandle = sessionHandles[i]; - sessions [i] = sessionHandle.getSessionUrn(); - } - } - } - return sessions; - } - - - private void discoverSession() - { - - } - - /** - * @see org.vamsas.client.IClientFactory#getIClient(org.vamsas.client.ClientHandle) - * - * Creates a IClient object, using default UserHandle with system variables:"user.name" or "USERNAME")), - "host.name" or "HOSTNAME" - */ - public IClient getIClient(ClientHandle applicationHandle) - throws NoDefaultSessionException { - - return this.getIClient(applicationHandle, (UserHandle) null); - } - - /** - * @see org.vamsas.client.IClientFactory#getIClient(org.vamsas.client.ClientHandle, java.lang.String) - */ - public IClient getIClient(ClientHandle applicationHandle, String sessionUrn) { - // TODO Auto-generated method stub - return null; - } - - /** - * @see org.vamsas.client.IClientFactory#getIClient(org.vamsas.client.ClientHandle, org.vamsas.client.UserHandle, java.lang.String) - */ - public IClient getIClient(ClientHandle applicationHandle, UserHandle userId, - String sessionUrn) { - // TODO Auto-generated method stub - return null; - } - - /** - * @see org.vamsas.client.IClientFactory#getIClient(org.vamsas.client.ClientHandle, org.vamsas.client.UserHandle) - */ - public IClient getIClient(ClientHandle applicationHandle, UserHandle userId) - throws NoDefaultSessionException { - SimpleClient client = null; - if (this.sessionArena==null) - throw new Error("Improperly initialised SimpleClientFactory object - null sessionArena."); - - ClientHandle clientHandle =applicationHandle; - //create default clientHandle with "SimpleVamsasClientApp","0.1", - if (clientHandle == null) - clientHandle = new ClientHandle("SimpleVamsasClientApp","0.1"); - - //check if any available session(s) - String[] availableSessions = this.getCurrentSessions(); - if (availableSessions != null) - {//there are available sessions - if (availableSessions.length>1) - {//more than one session if available... can not choose - - //represents list of session as String - StringBuffer sessionURNs = new StringBuffer(""); - for (int i = 0; i< availableSessions.length ; i++) - { - sessionURNs.append(availableSessions[i]+" "); - } - throw new NoDefaultSessionException("Several sessions available, please pick one: "+sessionURNs); - } - - //check if only one session available. if yes, open it - if (availableSessions.length == 1) - { - //only one session available, open it. - return this.getIClient(clientHandle, availableSessions[0]); - } - } - //no session available - create a new one - - - try - { - //create sessionDirectory - File sessdir = File.createTempFile("sess", ".simpleclient", this.sessionArena); - log.debug("Creating new session directory"); - if (!(sessdir.delete() && sessdir.mkdir())) - throw new IOException("Could not make session directory "+sessdir); - //create session - VamsasSession vamsasSession = new VamsasSession(sessdir); - - this.getSessionFile().addSession(new SessionHandle(new SessionUrn(vamsasSession).getSessionUrn()), false); - if (userId == null) - { - //create a default userHandle - //with current OS user and hostname - userId = new UserHandle(System.getProperty("user.name", System.getProperty("USERNAME","Joe Doe")), - System.getProperty("host.name",System.getProperty("HOSTNAME", "Unknown") ));// clientName, clientVersion, sessionPath); - } - - - //create simple client - client = new SimpleClient(userId, clientHandle, vamsasSession); - } - catch (IOException e) - { - log.error("error while creating new IClient",e); - } - catch (InvalidSessionUrnException e) - { - log.error("Unable to create new IClient. The session urn is incorrect ",e); - } - - return client; - } - - - /** - * @return the sessionFile - */ - private SessionsFile getSessionFile() throws IOException - { - if (this.sessionFile == null) - { - this.sessionFile = new SessionsFile( new File (this.sessionArena, SESSION_LIST)); - } - return this.sessionFile; - } - - - -} diff --git a/src/org/vamsas/client/simpleclient/SimpleDocBinding.java b/src/org/vamsas/client/simpleclient/SimpleDocBinding.java deleted file mode 100644 index c0c8084..0000000 --- a/src/org/vamsas/client/simpleclient/SimpleDocBinding.java +++ /dev/null @@ -1,138 +0,0 @@ -package org.vamsas.client.simpleclient; - -import java.io.BufferedInputStream; -import java.io.IOException; -import java.io.InputStream; -import java.io.InputStreamReader; -import java.util.Vector; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.vamsas.client.Vobject; -import org.vamsas.client.VorbaIdFactory; -import org.vamsas.client.VorbaXmlBinder; -import org.vamsas.objects.core.VAMSAS; -import org.vamsas.objects.core.VamsasDocument; -import org.vamsas.objects.utils.AppDataReference; -import org.vamsas.objects.utils.DocumentStuff; -import org.vamsas.objects.utils.ProvenanceStuff; -import org.vamsas.objects.utils.document.VersionEntries; - -/** - * Base class for SimpleClient Vamsas Document Object Manipulation - * holds static vamsasDocument from XML routines and - * state objects for a particular unmarshalled Document instance. - * @author jimp - */ - - -public class SimpleDocBinding { - - protected VorbaIdFactory vorba; - protected static Log log = LogFactory.getLog(SimpleDocBinding.class); - - /** - * @return Returns the vorba. - */ - public VorbaIdFactory getVorba() { - return vorba; - } - - /** - * @param vorba The vorba to set. - */ - public void setVorba(VorbaIdFactory vorba) { - this.vorba = vorba; - } - - /** - * Uses VorbaXmlBinder to retrieve the VamsasDocument from the given stream - */ - public VamsasDocument getVamsasDocument(VamsasArchiveReader oReader) throws IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - if (oReader!=null) { - // check the factory - if (vorba==null) { - log.error("Invalid SimpleDocument construction - no VorbaIdFactory defined!"); - return null; - } - - if (oReader.isValid()) { - // Read vamsasDocument.xsd instance - InputStreamReader vdoc = new InputStreamReader(oReader.getVamsasDocumentStream()); - Object unmarsh[] = VorbaXmlBinder.getVamsasObjects(vdoc, vorba, new VamsasDocument()); - if (unmarsh==null) - log.fatal("Couldn't unmarshall document!"); - - Vobject vobjs = (Vobject) unmarsh[0]; - if (vobjs!=null) { - VamsasDocument doc=(VamsasDocument) vobjs; - if (doc!=null) - return doc; - } - log.debug("Found no VamsasDocument object in properly formatted Vamsas Archive."); - } else { - // deprecated data handler (vamsas.xsd instance) - InputStream vxmlis = oReader.getVamsasXmlStream(); - if (vxmlis!=null) { // Might be an old vamsas file. - BufferedInputStream ixml = new BufferedInputStream(oReader.getVamsasXmlStream()); - InputStreamReader vxml = new InputStreamReader(ixml); - Object unmarsh[] = VorbaXmlBinder.getVamsasObjects(vxml, vorba, new VAMSAS()); - - if (unmarsh==null) - log.fatal("Couldn't unmarshall document!"); - - VAMSAS root[]= new VAMSAS[] { null}; - root[0] = (VAMSAS) unmarsh[0]; - - if (root[0]==null) { - log.debug("Found no VAMSAS object in VamsasXML stream."); - } else { - log.debug("Making new VamsasDocument from VamsasXML stream."); - VamsasDocument doc = DocumentStuff.newVamsasDocument(root, - ProvenanceStuff.newProvenance( - vorba.getUserHandle().getFullName(), - "Vamsas Document constructed from vamsas.xml"), VersionEntries.ALPHA_VERSION); - // VAMSAS: decide on 'system' operations provenance form - // LATER: implement classes for translating Vorba properties into provenance user fields. - // VAMSAS: decide on machine readable info embedding in provenance should be done - root[0]=null; - root=null; - return doc; - } - } - } - } - // otherwise - there was no valid original document to read. - return null; - } - - /** - * Extract all jarEntries in an archive referenced by the vamsas document - * LATER: a family of methods for finding extraneous jarEntries , and invalid appDataReferences - * @param doc - * @param oReader - * @return array of the subset of JarEntry names that are referenced in doc - */ - public Vector getReferencedEntries(VamsasDocument doc, VamsasArchiveReader oReader) { - if (oReader==null) - return null; - if (doc==null) { - try { doc = getVamsasDocument(oReader); } - catch (Exception e) { log.warn("Failed to get document from "+oReader.jfile.getName()); }; - } - Vector docrefs = AppDataReference.getAppDataReferences(doc); - if (docrefs==null) - return null; - Vector entries = oReader.getExtraEntries(); - if (entries!=null && docrefs.size()>0) { - int i=0, j=entries.size(); - do { - if (!docrefs.contains(entries.get(i))) { - entries.remove(i); - j--; - } else - i++; - } while (iarchive - * @throws IOException - */ - public VamsasArchive(File archive, boolean overwrite, boolean vamsasdocument, SessionFile extantLock) throws IOException { - super(); - if (archive==null || (archive!=null && !(archive.getAbsoluteFile().getParentFile().canWrite() && (!archive.exists() || archive.canWrite())))) { - log.fatal("Expect Badness! -- Invalid parameters for VamsasArchive constructor:"+((archive!=null) - ? "File cannot be overwritten." : "Null Object not valid constructor parameter")); - return; - } - - this.vamsasdocument = vamsasdocument; - if (archive.exists() && !overwrite) { - this.original = archive; - if (extantLock!=null) { - this.odoclock = extantLock; - if (odoclock.fileLock==null || !odoclock.fileLock.isLocked()) - odoclock.lockFile(); - } else { - this.odoclock = new SessionFile(archive); - } - odoclock.lockFile(); // lock the file *immediatly* - this.archive = null; // archive will be a temp file when the open method is called - virginArchive=false; - try { - this.accessOriginal(); - } catch (IOException e) { - throw new IOException("Lock failed for existing archive"+archive); - } - } else { - this.original = null; - this.archive = archive; // archive is written in place. - if (extantLock!=null) - rchive=extantLock; - else - rchive = new SessionFile(archive); - rchive.lockFile(); - if (rchive.fileLock==null || !rchive.fileLock.isLocked()) - throw new IOException("Lock failed for new archive"+archive); - rchive.fileLock.getRaFile().setLength(0); // empty the archive. - virginArchive = true; - } - this.openArchive(); // open archive - } - /** - * open original archive file for exclusive (locked) reading. - * @throws IOException - */ - private void accessOriginal() throws IOException { - if (original!=null && original.exists()) { - if (odoclock==null) - odoclock = new SessionFile(original); - odoclock.lockFile(); - if (odoc == null) - odoc = new VamsasArchiveReader(original); - // this constructor is not implemented yet odoc = new VamsasArchiveReader(odoclock.fileLock); - } - } - - /** - * Add unique entry strings to internal JarEntries list. - * @param entry - * @return true if entry was unique and was added. - */ - private boolean addEntry(String entry) { - if (entries!=null) - entries=new Hashtable(); - if (entries.containsKey(entry)) - return false; - entries.put(entry, new Integer(entries.size())); - return true; - } - /** - * adds named entry to newarchive or returns false. - * @param entry - * @return true if entry was unique and could be added - * @throws IOException if entry name was invalid or a new entry could not be made on newarchive - */ - private boolean addValidEntry(String entry) throws IOException { - JarEntry je = new JarEntry(entry); - if (!addEntry(entry)) - return false; - newarchive.flush(); - newarchive.putNextEntry(je); - return true; - } - /** - * called by app to get name of backup if it was made. - * If this is called, the caller app *must* delete the backup themselves. - * @return null or a valid file object - */ - public File backupFile() { - - if (!virginArchive) { - makeBackup(); - donotdeletebackup=false; // external reference has been made. - return ((original!=null) ? originalBackup : null); - } - return null; - } - - /** - * Stops any current write to archive, and reverts to the backup if it exists. - * All existing locks on the original will be released. All backup files are removed. - */ - public boolean cancelArchive() { - if (newarchive!=null) { - try { - newarchive.closeEntry(); - newarchive.putNextEntry(new JarEntry("deleted")); - newarchive.closeEntry(); - newarchive.close(); - - } catch (Exception e) { - log.debug("Whilst closing newarchive",e); - }; - if (!virginArchive) { - // then there is something to recover. - try { - recoverBackup(); - } - catch (Exception e) { - log.warn("Problems when trying to cancel Archive "+archive.getAbsolutePath(), e); - return false; - } - } - - } else { - log.warn("Client Error: cancelArchive called before archive("+original.getAbsolutePath()+") has been opened!"); - } - closeAndReset(); // tidy up and release locks. - return true; - } - - /** - * only do this if you want to destroy the current file output stream - * - */ - private void closeAndReset() { - if (rchive!=null) { - rchive.unlockFile(); - rchive=null; - } - if (original!=null) { - if (odoc!=null) { - odoc.close(); - odoc=null; - } - if (archive!=null) - archive.delete(); - if (odoclock!=null) { - odoclock.unlockFile(); - odoclock = null; - } - } - removeBackup(); - newarchive=null; - original=null; - entries=null; - } - /** - * Tidies up and closes archive, removing any backups that were created. - * NOTE: It is up to the caller to delete the original archive backup obtained from backupFile() - * TODO: ensure all extant AppDataReference jar entries are transferred to new Jar - * TODO: provide convenient mechanism for generating new unique AppDataReferences and adding them to the document - */ - public void closeArchive() throws IOException { - if (newarchive!=null) { - newarchive.flush(); - newarchive.closeEntry(); - if (!isDocumentWritten()) - log.warn("Premature closure of archive '"+archive.getAbsolutePath()+"': No document has been written."); - newarchive.finish();// close(); // use newarchive.finish(); for a stream IO - newarchive.flush(); - // - updateOriginal(); - closeAndReset(); - } else { - log.warn("Attempt to close archive that has not been opened for writing."); - } - } - /** - * Opens and returns the applicationData output stream for the appdataReference string. - * @param appdataReference - * @return Output stream to write to - * @throws IOException - */ - public AppDataOutputStream getAppDataStream(String appdataReference) throws IOException { - if (newarchive==null) - throw new IOException("Attempt to write to closed VamsasArchive object."); - if (addValidEntry(appdataReference)) { - return new AppDataOutputStream(newarchive); - } - return null; - } - - /** - * - * @return JarEntry name for the vamsas XML stream in this archive - */ - protected String getDocumentJarEntry() { - if (vamsasdocument) - return VamsasArchiveReader.VAMSASDOC; - return VamsasArchiveReader.VAMSASXML; - } - /** - * Safely initializes the VAMSAS XML document Jar Entry. - * @return Writer to pass to the marshalling function. - * @throws IOException if a document entry has already been written. - */ - public PrintWriter getDocumentOutputStream() throws IOException { - if (newarchive==null) - openArchive(); - if (!isDocumentWritten()) { - try { - if (addValidEntry(getDocumentJarEntry())) - return new PrintWriter(new java.io.OutputStreamWriter(newarchive, "UTF-8")); - } catch (Exception e) { - log.warn("Problems opening XML document JarEntry stream",e); - } - } else { - throw new IOException("Vamsas Document output stream is already written."); - } - return null; - } - - /** - * 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. - * @return null if no original archive exists. - */ - public VamsasArchiveReader getOriginalArchiveReader() throws IOException { - if (!virginArchive) { - accessOriginal(); - return odoc; - } - return null; - } - /** - * returns original document's root vamsas elements. - * @return - * @throws IOException - * @throws org.exolab.castor.xml.MarshalException - * @throws org.exolab.castor.xml.ValidationException - */ - public Vobject[] getOriginalRoots() throws IOException, - org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return VamsasArchive.getOriginalRoots(this); - } - /** - * @return original document or a new empty document (with default provenance) - * @throws IOException - * @throws org.exolab.castor.xml.MarshalException - * @throws org.exolab.castor.xml.ValidationException - */ - public VamsasDocument getVamsasDocument() throws IOException, - org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return getVamsasDocument("org.vamsas.simpleclient.VamsasArchive", "Created new empty document", null); - } - /** - * Return the original document or a new empty document with initial provenance entry. - * @param provenance_user (null sets user to be the class name) - * @param provenance_action (null sets action to be 'created new document') - * @param version (null means use latest version) - * @return (original document or a new vamsas document with supplied provenance and version info) - * @throws IOException - * @throws org.exolab.castor.xml.MarshalException - * @throws org.exolab.castor.xml.ValidationException - */ - public VamsasDocument getVamsasDocument(String provenance_user, String provenance_action, String version) throws IOException, - org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - if (_doc!=null) - return _doc; - _doc = getOriginalVamsasDocument(this, getVorba()); - if (_doc!=null) - return _doc; - // validate parameters - if (provenance_user==null) - provenance_user = "org.vamsas.simpleclient.VamsasArchive"; - if (provenance_action == null) - provenance_action="Created new empty document"; - if (version==null) - version = VersionEntries.latestVersion(); - // Create a new document and return it - _doc = DocumentStuff.newVamsasDocument(new VAMSAS[] { new VAMSAS()}, - ProvenanceStuff.newProvenance(provenance_user, provenance_action), version); - return _doc; - } - /** - * @return Returns the current VorbaIdFactory for the archive. - */ - public VorbaIdFactory getVorba() { - if (vorba==null) - vorba = new SimpleDocument("simpleclient.VamsasArchive"); - return vorba.getVorba(); - } - /** - * @return true if Vamsas Document has been written to archive - */ - protected boolean isDocumentWritten() { - if (newarchive==null) - log.warn("isDocumentWritten() called for unopened archive."); - if (entries!=null) { - if (entries.containsKey(getDocumentJarEntry())) - return true; - } - return false; - } - private void makeBackup() { - if (!virginArchive) { - if (originalBackup==null && original!=null && original.exists()) { - try { - accessOriginal(); - originalBackup = odoclock.backupSessionFile(null, original.getName(), ".bak", original.getParentFile()); - } - catch (IOException e) { - log.warn("Problem whilst making a backup of original archive.",e); - } - } - } - } - /** - * opens the new archive ready for writing. If the new archive is replacing an existing one, - * then the existing archive will be locked, and the new archive written to a temporary file. - * The new archive will be put in place once close() is called. - * @param doclock LATER - pass existing lock on document, if it exists.... no need yet? - * @throws IOException - */ - private void openArchive() throws IOException { - - if (newarchive!=null) { - log.warn("openArchive() called multiple times."); - throw new IOException("Vamsas Archive '"+archive.getAbsolutePath()+"' is already open."); - } - if (archive==null && (virginArchive || original==null)) { - log.warn("openArchive called on uninitialised VamsasArchive object."); - throw new IOException("Badly initialised VamsasArchive object - no archive file specified."); - } - if (!virginArchive) { - // lock the original - accessOriginal(); - // make a temporary file to write to - archive = File.createTempFile(original.getName(), ".new",original.getParentFile()); - } else { - if (archive.exists()) - log.warn("New archive file name already in use! Possible lock failure imminent?"); - } - - if (rchive==null) - rchive = new SessionFile(archive); - if (!rchive.lockFile()) - throw new IOException("Failed to get lock on file "+archive); - // LATER: locked IO stream based access. - Manifest newmanifest = new Manifest(); - newarchive = new JarOutputStream(rchive.fileLock.getBufferedOutputStream(true), newmanifest); - //newarchive = new JarOutputStream(new BufferedOutputStream(new java.io.FileOutputStream(archive))); - entries = new Hashtable(); - } - public void putVamsasDocument(VamsasDocument doc) throws IOException, - org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - putVamsasDocument(doc, getVorba()); - } - /** - * - * @param doc - * @param vorba - * @return (vorbaId string, Vobjhash) pairs for last hash of each object in document - * @throws IOException - * @throws org.exolab.castor.xml.MarshalException - * @throws org.exolab.castor.xml.ValidationException - */ - public void putVamsasDocument(VamsasDocument doc, VorbaIdFactory vorba) throws IOException, - org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - if (vamsasdocument) - doc.setVersion(VersionEntries.latestVersion()); // LATER: ensure this does the correct thing. - VorbaXmlBinder.putVamsasDocument(getDocumentOutputStream(), vorba, doc); - } - - /** - * recovers the original file's contents from the (temporary) backup. - * @throws Exception if any SessionFile or file removal operations fail. - */ - private void recoverBackup() throws Exception { - if (originalBackup!=null) { - // backup has been made. - // revert from backup and delete it (changing backup filename) - if (rchive==null) { - rchive = new SessionFile(original); - } - SessionFile bckup = new SessionFile(originalBackup); - - rchive.updateFrom(null, bckup); // recover from backup file. - bckup.unlockFile(); - bckup=null; - removeBackup(); - } - } - - /** - * forget about any backup that was made - removing it first if it was only temporary. - */ - private void removeBackup() { - if (originalBackup!=null) { - log.debug("Removing backup in "+originalBackup.getAbsolutePath()); - if (!donotdeletebackup) - if (!originalBackup.delete()) - log.info("VamsasArchive couldn't remove temporary backup "+originalBackup.getAbsolutePath()); - originalBackup=null; - } - } - /** - * @param vorba the VorbaIdFactory to use for accessing vamsas objects. - */ - public void setVorba(VorbaIdFactory Vorba) { - if (Vorba!=null) { - if (vorba==null) - vorba = new SimpleDocument(Vorba); - else - vorba.setVorba(Vorba); - } else - getVorba(); - } - /** - * Convenience method to copy over the referred entry from the backup to the new version. - * Warning messages are raised if no backup exists or the - * entry doesn't exist in the backed-up original. - * Duplicate writes return true - but a warning message will also be raised. - * @param AppDataReference - * @return true if AppDataReference now exists in the new document - * @throws IOException - */ - public boolean transferAppDataEntry(String AppDataReference) throws IOException { - return transferAppDataEntry(AppDataReference, AppDataReference); - } - /** - * Validates the AppDataReference: not null and not already written to archive. - * @param AppDataReference - * @return true if valid. false if not - * @throws IOException for really broken references! - */ - protected boolean _validNewAppDataReference(String newAppDataReference) throws IOException { - // LATER: Specify valid AppDataReference form in all VamsasArchive handlers - if (newAppDataReference==null) - throw new IOException("null newAppDataReference!"); - if (entries.containsKey(newAppDataReference)) { - log.warn("Attempt to write '"+newAppDataReference+"' twice! - IGNORED"); - // LATER: fix me? warning message should raise an exception here. - return false; - } - return true; - } - /** - * Transfers an AppDataReference from old to new vamsas archive, with a name change. - * @see transferAppDataEntry(String AppDataReference) - * @param AppDataReference - * @param NewAppDataReference - AppDataReference in new Archive - * @return - * @throws IOException - */ - public boolean transferAppDataEntry(String AppDataReference, String NewAppDataReference) throws IOException { - if (original==null || !original.exists()) { - log.warn("No backup archive exists."); - return false; - } - if (AppDataReference==null) - throw new IOException("null AppDataReference!"); - - if (!_validNewAppDataReference(NewAppDataReference)) - return false; - - accessOriginal(); - - java.io.InputStream adstream = odoc.getAppdataStream(AppDataReference); - - if (adstream==null) { - log.warn("AppDataReference '"+AppDataReference+"' doesn't exist in backup archive."); - return false; - } - - java.io.OutputStream adout = getAppDataStream(NewAppDataReference); - // copy over the bytes - int written=-1; - long count=0; - byte[] buffer = new byte[_TRANSFER_BUFFER]; // conservative estimate of a sensible buffer - do { - if ((written = adstream.read(buffer))>-1) { - adout.write(buffer, 0, written); - log.debug("Transferring "+written+"."); - count+=written; - } - } while (written>-1); - log.debug("Sucessfully transferred AppData for '" - +AppDataReference+"' as '"+NewAppDataReference+"' ("+count+" bytes)"); - return true; - } - /** - * write data from a stream into an appData reference. - * @param AppDataReference - New AppDataReference not already written to archive - * @param adstream Source of data for appData reference - read until .read(buffer) returns -1 - * @return true on success. - * @throws IOException for file IO or invalid AppDataReference string - */ - public boolean writeAppdataFromStream(String AppDataReference, java.io.InputStream adstream) throws IOException { - if (!_validNewAppDataReference(AppDataReference)) { - log.warn("Invalid AppDataReference passed to writeAppdataFromStream"); - throw new IOException("Invalid AppDataReference! (null, or maybe non-unique)!"); - } - - if (AppDataReference==null) { - log.warn("null appdata passed."); - throw new IOException("Null AppDataReference"); - } - - java.io.OutputStream adout = getAppDataStream(AppDataReference); - // copy over the bytes - int written=-1; - long count=0; - byte[] buffer = new byte[_TRANSFER_BUFFER]; // conservative estimate of a sensible buffer - do { - if ((written = adstream.read(buffer))>-1) { - adout.write(buffer, 0, written); - log.debug("Transferring "+written+"."); - count+=written; - } - } while (written>-1); - return true; - } - /** - * 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. - * @return true if data was transferred. - */ - public boolean transferRemainingAppDatas() throws IOException { - boolean transfered=false; - if (original==null || !original.exists()) { - log.warn("No backup archive exists."); - return false; - } - accessOriginal(); - - if (getVorba()!=null) { - Vector originalRefs=null; - try { - originalRefs = vorba.getReferencedEntries(getVamsasDocument(), getOriginalArchiveReader()); - } catch (Exception e) { - log.warn("Problems accessing original document entries!",e); - } - if (originalRefs!=null) { - Iterator ref = originalRefs.iterator(); - while (ref.hasNext()) { - String oldentry = (String) ref.next(); - if (oldentry!=null && !entries.containsKey(oldentry)) { - log.debug("Transferring remaining entry '"+oldentry+"'"); - transfered |= transferAppDataEntry(oldentry); - } - } - } - } - return transfered; - } - /** - * called after archive is written to put file in its final place - */ - private void updateOriginal() { - if (!virginArchive) { - // make sure original document really is backed up and then overwrite it. - if (odoc!=null) { - // try to shut the odoc reader. - odoc.close(); - odoc = null; - } - // Make a backup if it isn't done already - makeBackup(); - try { - // copy new Archive data that was writen to a temporary file - odoclock.updateFrom(null, rchive); - } - catch (IOException e) { - // LATER: decide if leaving nastily named backup files around is necessary. - File backupFile=backupFile(); - if (backupFile!=null) - log.error("Problem updating archive from temporary file! - backup left in '" - +backupFile().getAbsolutePath()+"'",e); - else - log.error("Problems updating, and failed to even make a backup file. Ooops!", e); - } - // Tidy up if necessary. - removeBackup(); - } else { - - - } - } -} diff --git a/src/org/vamsas/client/simpleclient/VamsasArchiveReader.java b/src/org/vamsas/client/simpleclient/VamsasArchiveReader.java deleted file mode 100644 index 2df47f5..0000000 --- a/src/org/vamsas/client/simpleclient/VamsasArchiveReader.java +++ /dev/null @@ -1,313 +0,0 @@ -package org.vamsas.client.simpleclient; - -import java.io.File; -import java.io.IOException; -import java.io.InputStream; -import java.io.BufferedInputStream; -import java.io.FileInputStream; -import java.io.RandomAccessFile; -import java.util.Enumeration; -import java.util.Hashtable; -import java.util.Iterator; -import java.util.Vector; -import java.util.jar.JarEntry; -import java.util.jar.JarFile; -import java.util.jar.JarInputStream; -import java.util.jar.JarOutputStream; -import java.util.zip.ZipEntry; -import java.util.zip.ZipInputStream; - -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.vamsas.objects.utils.document.VersionEntries; -/** - * Basic methods for accessing an existing Vamsas Archive, - * and Jar entry names for creating new vamsas archives. - * - * @author jimp - * - */ -public class VamsasArchiveReader { - private static Log log = LogFactory.getLog(VamsasArchiveReader.class); - JarFile jfile=null; - boolean stream=false; // true if we are seeking on the stream. - RandomAccessFile rfile; - ZipInputStream jstream=null; - Hashtable strmentries = null; - private void streamInit() { - //throw new Error("VamsasArchiveReader(Stream) Not implemented!"); - if (!stream) { - log.debug("Skipping init for Jar Stream input."); - return; - } - strmentries = new Hashtable(); - log.debug("Jar Stream input Initialisation"); - try { - rfile.seek(0); - // no buffering - we need to be able to move around the random access stream. - jstream = new ZipInputStream(new FileInputStream(rfile.getFD())); // no manifest (probably) - if (jstream.available()==0) - log.warn("Can't read from JarInputStream (Locked stream!)"); - ZipEntry entry=null; - long pos=0; - do { - if ((entry=jstream.getNextEntry())!=null) { - if (strmentries.containsKey(entry.getName())) { - log.info("Only recording last of duplicate entries '"+entry.getName()+"'"); - } - strmentries.put(entry.getName(), new Long(pos++)); - jstream.closeEntry(); - } - } while (entry!=null); - } - catch (Exception e) { - log.warn("Exceptions during init!",e); - jstream=null; - } - } - - public VamsasArchiveReader(File vamsasfile) { - jfile=null; - if (vamsasfile.exists()) { - try { - jfile=new JarFile(vamsasfile); - } - catch (Exception e) { - log.debug("non-serious? couldn't open new JarFile on "+vamsasfile,e); - jfile=null; - } - } - - } - /** - * in an ideal world - this constructor will create a reader object - * for the locked file's random access stream. - * - * @param vamsaslock - */ - public VamsasArchiveReader(Lock vamsaslock) { - // LATER: implement or remove - if (vamsaslock==null || !vamsaslock.isLocked()) - throw new Error("IMPLEMENTATION ERROR: Cannot create a VamsasArchiveReader without a valid lock."); - // throw new Error("VamsasArchiveReading from locked IO stream not yet implemented."); - try { - rfile = vamsaslock.getRaFile(); - } catch (Exception e) { - log.warn("Unexpected IO Exception when accessing locked vamsas archive stream "+vamsaslock.target,e); - } - stream = true; - streamInit(); - if (jstream==null) - throw new Error("Failed to open archive from Locked random access stream."); - } - - /** - * the vamsas document version(s) handled by this Reader - */ - final public static String DOCUMENT_VERSION=VersionEntries.BETA_VERSION; - /** - * name of the jarEntry containing a well formatted vamsas XML Document - */ - - final public static String VAMSASDOC="vamsasDocument.xml"; - - /** - * name of the jarEntry containing a root VAMSAS element, and containing a - * random sequence of VAMSAS DataSet elements - */ - - final public static String VAMSASXML="vamsas.xml"; - /** - * seeks jstream to the given entry name and reads it. - * @param entryname - * @return - */ - private JarEntry seekEntry(String entryname) { - if (jstream==null) - return null; - if (!strmentries.containsKey(entryname)) - return null; - Long entrypos = (Long) strmentries.get(entryname); - if (entrypos==null) { - log.error("Null entry position for "+entryname); - return null; - } - try { - jstream=null; - rfile.seek(0); - jstream = new ZipInputStream(new FileInputStream(rfile.getFD())); - ZipEntry entry = null; - long epos = entrypos.longValue(); - do { - entry = jstream.getNextEntry(); - } while (entry!=null && --epos>=0); - // rfile.seek(entrypos.longValue()); - // make a Jar entry from a zip entry. - return new JarEntry(entry); - } - catch (Exception e) { - log.warn("Whilst seeking for "+entryname, e); - } - return null; - } - /** - * - * @return JarEntry for VamsasArchiveReader.VAMSASDOC - */ - protected JarEntry getVamsasDocumentEntry() { - return getJarEntry(VAMSASDOC); - } - /** - * - * @return JarEntry for VamsasArchiveReader.VAMSASXML - */ - protected JarEntry getVamsasXmlEntry() { - return getJarEntry(VAMSASXML); - } - /** - * Test for valid vamsas document archive - * @return true if getVamsasDocumentStream will return a stream likely to contain valid XML - */ - public boolean isValid() { - // TODO: check if VAMSASDOC is well formed (follows www.vamsas.ac.uk/schemas/vamsasDocument.xsd) and all appData references are resolvable - preferably as jar entries - if (jfile!=null || jstream!=null) - return (getVamsasDocumentEntry()!=null); - return false; - } - - - protected JarEntry getAppdataEntry(String AppdataRef) { - JarEntry entry; - if ((jfile==null && jstream==null) || !isValid() || (entry=getJarEntry(AppdataRef))==null) - return null; - - return entry; - } - - public InputStream getAppdataStream(String AppdataRef) { - JarEntry entry=getAppdataEntry(AppdataRef); - try { - if (entry!=null) - return getInputStream(entry); - } catch (IOException e) { - log.error("Failed when opening AppdataStream for "+AppdataRef, e); - } - return null; - } - /** - * get the VamsasDocument input stream, if it exists. - * @return null or valid input stream - */ - public InputStream getVamsasDocumentStream() { - InputStream vdoc; - if ((jfile==null && jstream==null) || !isValid()) - return null; - try { - vdoc = getInputStream(getVamsasDocumentEntry()); - } catch (IOException e) { - log.error("Whilst geting document stream",e); - vdoc=null; - } - return vdoc; - } - - /** - * get the VamsasXML input stream, if it exists. - * Note: Deprecated beyond our prealpha testing. - * @return null or valid input stream. - */ - - public InputStream getVamsasXmlStream() { - // log.warn("Deprecated call"); - JarEntry xmle=getVamsasXmlEntry(); - InputStream vdoc; - if (xmle==null) - return null; - try { - vdoc = getInputStream(xmle); - } catch (IOException e) { - log.error("Whilst getting VamsasXmlStream",e); - vdoc=null; - } - return vdoc; - } - - /** - * silently close the jar file. - * - */ - public void close() { - if (jfile!=null) { - try { - jfile.close(); - } catch (IOException e) { - log.error("Whilst closing JarFile "+jfile.getName(), e); - } - } - if (jstream!=null) { - try { - jstream.closeEntry(); - jstream=null; - // LATER: reference counting for random access file instances is necessary. - } - catch (Exception e) { - log.error("Whilst finishing reading from jar input stream",e); - } - } - } - - /** - * returns all entries not matching the filespec of a vamsas xml entry - * @return array of entries. - */ - public Vector getExtraEntries() { - if ((jfile==null && jstream==null)|| !isValid()) - return null; - Vector e = new Vector(); - if (jstream!=null) { - Enumeration entries = strmentries.keys(); - if (entries!=null && entries.hasMoreElements()) { - do { - JarEntry el = (JarEntry) entries.nextElement(); - if (!el.getName().equals(VAMSASDOC) && !el.getName().equals(VAMSASXML)) - e.add(new String(el.getName())); // avoid references - } while (entries.hasMoreElements()); - } - } else { - Enumeration entries = jfile.entries(); - if (entries!=null && entries.hasMoreElements()) { - do { - JarEntry el = (JarEntry) entries.nextElement(); - if (!el.getName().equals(VAMSASDOC) && !el.getName().equals(VAMSASXML)) - e.add(new String(el.getName())); // avoid references - } while (entries.hasMoreElements()); - } - return e; - } - return null; - } - - /* (non-Javadoc) - * @see java.util.jar.JarFile#getInputStream(java.util.zip.ZipEntry) - */ - private InputStream getInputStream(ZipEntry ze) throws IOException { - if (jfile!=null) - return jfile.getInputStream(ze); - if (jstream!=null) { - seekEntry(ze.getName()); - return new AppDataInputStream(jstream); - } - return null; - } - - /* (non-Javadoc) - * @see java.util.jar.JarFile#getJarEntry(java.lang.String) - */ - private JarEntry getJarEntry(String name) { - if (jfile!=null) - return jfile.getJarEntry(name); - if (jstream!=null) - return seekEntry(name); - return null; - } - } diff --git a/src/org/vamsas/client/simpleclient/VamsasFile.java b/src/org/vamsas/client/simpleclient/VamsasFile.java deleted file mode 100644 index 3dd2581..0000000 --- a/src/org/vamsas/client/simpleclient/VamsasFile.java +++ /dev/null @@ -1,100 +0,0 @@ - -package org.vamsas.client.simpleclient; - -import java.io.File; -import java.io.FileOutputStream; -import java.io.FileReader; -import java.io.IOException; -import java.io.InputStream; -import java.io.InputStreamReader; -import java.io.PrintWriter; -import java.util.Timer; -import java.util.jar.JarEntry; -import java.util.jar.JarFile; -import java.util.jar.JarInputStream; -import java.util.jar.JarOutputStream; - -import org.vamsas.objects.core.LockFileDescriptor; - -/** - * low level vamsas document management routines - * analogous to ClientsFile - * Grew out of io tests on VamsasArchive class in org.vamsas.test.simpleclient.VamsasArchive - * This class is not thread safe. - * @author jimp - * - */ -public class VamsasFile extends SessionFile { - /** - * - * Connect to an existing Vamsas document in a given sessionDir - * or create a new one. - * - * @param sessionDir - * @throws java.io.IOException - */ - public VamsasFile(File sessionFile) throws java.io.IOException { - super(sessionFile); - } - /** - * - * @return the VamsasFile - */ - public File getVamsasFile() { - return sessionFile; - } - /** - * Expand a previously stored session into the sessionDir - * @param sessionDir - * @param storedSession - - public VamsasFile(File sessionDir, JarFile storedSession) throws IOException { - // check if sessionDir is live or not - if (!sessionDir.exists()) { - sessionDir.mkdir(); - } - - { - // check its actually a writable directory - } - - File sfile = new File(sessionDir, "vamsas.jar"); - VamsasFile(sfile); - // if live - try to merge storedSession with sessionDir - // - will probably fail through duplicate Vobject references needing to be dereferenced. - // TODO: think of a way of specifying vorba_id scope for an application's references to allow merging of one vamsasDocument with another. - - } - */ - /** - * public interface for getting a lock. - * The lock object is internally referenced - * so the lock will persist even after the - * return value of the method goes out of scope. - * @return null if lock couldn't be got or a valid Lock object. - */ - public Lock getLock() { - if (lockFile()) - return fileLock; - return null; - } - /** - * - * @param extantLock - * @return null, extantLock or new Lock. - */ - public Lock getLock(Lock extantLock) { - if (lockFile(extantLock)) - return fileLock; - return null; - } - /** - * explicitly unlocks vamsas file. - * if you have called getLock() you *must* - * call this to release the lock. - */ - public void unLock() { - this.unlockFile(); - } - -} diff --git a/src/org/vamsas/client/simpleclient/VamsasSession.java b/src/org/vamsas/client/simpleclient/VamsasSession.java deleted file mode 100644 index a5359ad..0000000 --- a/src/org/vamsas/client/simpleclient/VamsasSession.java +++ /dev/null @@ -1,312 +0,0 @@ -package org.vamsas.client.simpleclient; - -import java.io.BufferedWriter; -import java.io.File; -import java.io.IOException; -import java.io.PrintStream; -import java.io.PrintWriter; -import java.io.RandomAccessFile; -import java.io.Writer; - -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.apache.log4j.Appender; -import org.apache.log4j.Logger; -import org.apache.log4j.FileAppender; -import org.vamsas.client.ClientHandle; -import org.vamsas.client.UserHandle; -/** - * Does all the IO operations for a SimpleClient instance accessing - * a SimpleClient vamsas session. - * - * Basically, it defines the various standard names for the files - * in the session directory (that maps to the sessionUrn), - * provides constructors for the file handlers and watchers of - * those file entities, and some higher level methods - * to check and change the state flags for the session. - * - * TODO: move the stuff below to the SimpleClientFactory documentation. - * much may not be valid now : - * Vamsas client is intialised with a path to create live session directories. - * This path may contain a vamsas.properties file - * that sets additional parameters (otherwise client - * just uses the one on the classpath). - * - * A vamsas session consists of : - * SessionDir - translates to urn of a live session. - * Contains: Vamsas Document (as a jar), Session client list file, - * both of which may be locked, and additional - * temporary versions of these files when write - * operations are taking place. - * - * Zip file entries - * - vamsasdocument.xml : core info - * one or more: - * - .version.sessionnumber.raw (string given in vamsasdocument.xml applicationData entry) - * - * Lockfile - * - filename given in the vamsasdocument.xml. Should be checked for validity by any client and rewritten if necessary. - * The lockfile can point to the jar itself. - * Mode of operation. - * Initially - documentHandler either: - * - creates a zip for a new session for the client - * - connect to an existing session zip - * 1. reads session urn file - * 2. waits for lock - * 3. examines session - decide whether to create new application data slice or connect to one stored in session. - * 4. writes info into session file - * 5. releases lock and generates local client events. - * 6. Creates Watcher thread to generate events. - * - * During the session - * - Update watcher checks for file change - - * - * Procedures for file based session message exchange - * - session document modification flag - * - */ - -public class VamsasSession { - /** - * indicator file for informing other processes that - * they should finalise their vamsas datasets for - * storing into a vamsas archive. - */ - public static final String CLOSEANDSAVE_FILE="stored.log"; - /** - * session file storing the last_stored_stat data - */ - public static final String MODIFIEDDOC_FILE="modified"; - - /** - * called to clear update flag after a successful offline storage event - */ - protected void clearUnsavedFlag() { - SessionFlagFile laststored = new SessionFlagFile(new File(sessionDir, MODIFIEDDOC_FILE)); - if (!laststored.clearFlag()) - log.warn("Unsaved flag was not cleared for "+sessionDir); - } - /** - * called to indicate session document has been modified. - * - */ - protected void setUnsavedFlag() { - SessionFlagFile laststored = new SessionFlagFile(new File(sessionDir, MODIFIEDDOC_FILE)); - if (!laststored.setFlag()) - log.warn("Couldn't set the Unsaved flag for "+sessionDir); - } - /** - * - * @return true if session document has been modified since last offline storage event - */ - protected boolean getUnsavedFlag() { - SessionFlagFile laststored = new SessionFlagFile(new File(sessionDir, MODIFIEDDOC_FILE)); - return laststored.checkFlag(); - } - /** - * log file location - */ - public static final String SESSION_LOG="Log.txt"; - private static Log log = LogFactory.getLog(VamsasSession.class); - protected Logger slog = Logger.getLogger("org.vamsas.client.SessionLog"); - /** - * setup the sessionLog using Log4j. - * @throws IOException - */ - private void initLog() throws IOException { - // LATER: make dedicated appender format for session log. - Appender app = slog.getAppender("SESSION_LOG"); - slog.addAppender(new FileAppender(app.getLayout(), new File(sessionDir, SESSION_LOG).getAbsolutePath())); - } - - /** - * the sessionDir is given as the session location for new clients. - */ - protected File sessionDir; - /** - * holds the list of attached clients - */ - ClientsFile clist; - public static final String CLIENT_LIST="Clients.obj"; - /** - * holds the data - */ - VamsasFile vamArchive; - public static final String VAMSAS_OBJ="VamDoc.jar"; - - /** - * sets up the vamsas session files and watchers in sessionDir - * @param sessionDir - */ - protected VamsasSession(File sessionDir) throws IOException { - if (sessionDir==null) - throw new Error("Null directory for VamsasSession."); - if (sessionDir.exists()) { - if (!sessionDir.isDirectory() || !sessionDir.canWrite() || !sessionDir.canRead()) - throw new IOException("Cannot access '"+sessionDir+"' as a read/writable Directory."); - if (checkSessionFiles(sessionDir)) { - // session files exist in the directory - this.sessionDir = sessionDir; - initSessionObjects(); - slog.debug("Initialising additional VamsasSession instance"); - log.debug("Attached to VamsasSession in "+sessionDir); - } - } else { - // start from scratch - if (!sessionDir.mkdir()) - throw new IOException("Failed to make VamsasSession directory in "+sessionDir); - this.sessionDir = sessionDir; - createSessionFiles(); - initSessionObjects(); - slog.debug("Session directory created."); - log.debug("Initialised VamsasSession in "+sessionDir); - } - } - /** - * tests presence of existing sessionfiles files in dir - * @param dir - * @return - */ - private boolean checkSessionFiles(File dir) throws IOException { - File c_file = new File(dir,CLIENT_LIST); - File v_doc = new File(dir,VAMSAS_OBJ); - if (c_file.exists() && v_doc.exists()) - return true; - return false; - } - /** - * create new empty files in dir - * - */ - private void createSessionFiles() throws IOException { - if (sessionDir==null) - throw new IOException("Invalid call to createSessionFiles() with null sessionDir"); - File c_file = new File(sessionDir,CLIENT_LIST); - File v_doc = new File(sessionDir,VAMSAS_OBJ); - if (c_file.createNewFile()) - log.debug("Created new ClientFile "+c_file); // don't care if this works or not - if (v_doc.createNewFile()) - log.debug("Created new Vamsas Session Document File "+v_doc); - } - /** - * construct SessionFile objects and watchers for each - */ - private void initSessionObjects() throws IOException { - if (clist!=null || vamArchive!=null) - throw new IOException("initSessionObjects called for initialised VamsasSession object."); - clist = new ClientsFile(new File(sessionDir,CLIENT_LIST)); - vamArchive = new VamsasFile(new File(sessionDir,VAMSAS_OBJ)); - initLog(); - } - /** - * make a new watcher object for the clientFile - * @return new ClientFile watcher instance - */ - public FileWatcher getClientWatcher() { - return new FileWatcher(clist.sessionFile); - } - FileWatcher session_doc_watcher=null; - /** - * make a new watcher object for the vamsas Document - * @return new ClientFile watcher instance - */ - public FileWatcher getDocWatcher() { - if (session_doc_watcher==null) - return session_doc_watcher = new FileWatcher(vamArchive.sessionFile); - return new FileWatcher(vamArchive.sessionFile); - } - FileWatcher store_doc_file=null; - /** - * make a new watcher object for the messages file - * (thread safe - keeps a reference to the first watcher) - * @return new watcher instance - */ - public FileWatcher getStoreWatcher() { - if (store_doc_file==null) - return store_doc_file = new FileWatcher(new File(CLOSEANDSAVE_FILE)); - return new FileWatcher(new File(CLOSEANDSAVE_FILE)); - - } - /** - * write to the StoreWatcher file to indicate that a storeDocumentRequest has been made. - * The local client's storeWatcher FileWatcher object is updated so the initial change is not registered. - * @param client - * @param user - * @return - */ - public void addStoreDocumentRequest(ClientHandle client, UserHandle user) throws IOException { - SessionFile sfw = new SessionFile(new File(sessionDir, CLOSEANDSAVE_FILE)); - while (!sfw.lockFile()) - log.debug("Trying to get lock for "+CLOSEANDSAVE_FILE); - RandomAccessFile sfwfile=sfw.fileLock.getRaFile(); - sfwfile.setLength(0); // wipe out any old info. - // TODO: rationalise what gets written to this file (ie do we want other clients to read the id of the requestor?) - sfwfile.writeUTF(client.getClientUrn()+":"+user.getFullName()+"@"+user.getOrganization()); - sfw.unlockFile(); - if (store_doc_file!=null) - store_doc_file.setState(); - slog.info("FinalizeAppData request from "+user.getFullName()+" using "+client.getClientUrn()+""); - } - /** - * create a new session with an existing vamsas Document - by copying it into the session. - * @param archive - */ - public void setVamsasDocument(File archive) throws IOException { - log.debug("Transferring vamsas data from "+archive+" to session:"+vamArchive.sessionFile); - SessionFile xtantdoc = new SessionFile(archive); - vamArchive.updateFrom(null, xtantdoc); - // LATER: decide if session archive provenance should be updated to reflect access. - // TODO: soon! do a proper import objects from external file - log.debug("Transfer complete."); - } - /** - * 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. - * @param destarchive - */ - protected void writeVamsasDocument(File destarchive, Lock extlock) throws IOException { - log.debug("Transferring vamsas data from "+vamArchive.sessionFile+" to session:"+destarchive); - SessionFile newdoc = new SessionFile(destarchive); - if (extlock==null && !vamArchive.lockFile()) - while (!vamArchive.lockFile()) - log.info("Trying to get lock for "+vamArchive.sessionFile); - // TODO: LATER: decide if session archive provenance should be written in vamsasDocument file for this export. - newdoc.updateFrom(extlock, vamArchive); - // LATER: LATER: fix use of updateFrom for file systems where locks cannot be made (because they don't have a lockManager, ie NFS/Unix, etc). - vamArchive.unLock(); - newdoc.unlockFile(); - log.debug("Transfer complete."); - } - - /** - * Creates a VamsasArchive Vobject for accessing and updating document - * Note: this will lock the Vamsas Document for exclusive access to the client. - * @return session vamsas document - * @throws IOException if locks fail or vamsas document read fails. - */ - protected VamsasArchive getVamsasDocument() throws IOException { - // TODO: check we haven't already done this once - if (!vamArchive.lockFile()) - throw new IOException("Failed to get lock for vamsas archive."); - - VamsasArchive va = new VamsasArchive(vamArchive.sessionFile, false, true, vamArchive); - - return va; - } - /** - * create a uniquely named file in the session Directory - * @see java.io.File.createTempFile - * @param pref Prefix for name - * @param suff Suffix for name - * @return SessionFile object configured for the new file (of length zero) - * @throws IOException - */ - protected SessionFile getTempSessionFile(String pref, String suff) throws IOException { - File tfile = File.createTempFile(pref,suff,sessionDir); - SessionFile tempFile = new SessionFile(tfile); - return tempFile; - } -} - - diff --git a/src/org/vamsas/objects/core/.castor.cdr b/src/org/vamsas/objects/core/.castor.cdr deleted file mode 100644 index 8ec2cf3..0000000 --- a/src/org/vamsas/objects/core/.castor.cdr +++ /dev/null @@ -1,3 +0,0 @@ --- listing properties -- -org.vamsas.objects.core.LockFile=org.vamsas.objects.core.LockFileDescr... -org.vamsas.objects.core.VamsasDocument=org.vamsas.objects.core.VamsasDocumen... diff --git a/src/org/vamsas/objects/core/Alignment.java b/src/org/vamsas/objects/core/Alignment.java deleted file mode 100644 index bf70f4e..0000000 --- a/src/org/vamsas/objects/core/Alignment.java +++ /dev/null @@ -1,979 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Alignment. - * - * @version $Revision$ $Date$ - */ -public class Alignment extends org.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _gapChar - */ - private java.lang.String _gapChar; - - /** - * Field _aligned - */ - private boolean _aligned; - - /** - * keeps track of state for field: _aligned - */ - private boolean _has_aligned; - - /** - * Primary Key for vamsas object referencing - * - */ - private java.lang.String _id; - - /** - * Field _modifiable - */ - private java.lang.String _modifiable; - - /** - * This is annotation over the coordinate frame - * defined by all the columns in the alignment. - * - */ - private java.util.Vector _alignmentAnnotationList; - - /** - * Field _treeList - */ - private java.util.Vector _treeList; - - /** - * Field _alignmentSequenceList - */ - private java.util.Vector _alignmentSequenceList; - - /** - * typical properties may be additional - * alignment score objects - */ - private java.util.Vector _propertyList; - - /** - * Field _provenance - */ - private org.vamsas.objects.core.Provenance _provenance; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Alignment() - { - super(); - _alignmentAnnotationList = new Vector(); - _treeList = new Vector(); - _alignmentSequenceList = new Vector(); - _propertyList = new Vector(); - } //-- org.vamsas.objects.core.Alignment() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addAlignmentAnnotation - * - * - * - * @param vAlignmentAnnotation - */ - public void addAlignmentAnnotation(org.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation) - throws java.lang.IndexOutOfBoundsException - { - _alignmentAnnotationList.addElement(vAlignmentAnnotation); - } //-- void addAlignmentAnnotation(org.vamsas.objects.core.AlignmentAnnotation) - - /** - * Method addAlignmentAnnotation - * - * - * - * @param index - * @param vAlignmentAnnotation - */ - public void addAlignmentAnnotation(int index, org.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation) - throws java.lang.IndexOutOfBoundsException - { - _alignmentAnnotationList.insertElementAt(vAlignmentAnnotation, index); - } //-- void addAlignmentAnnotation(int, org.vamsas.objects.core.AlignmentAnnotation) - - /** - * Method addAlignmentSequence - * - * - * - * @param vAlignmentSequence - */ - public void addAlignmentSequence(org.vamsas.objects.core.AlignmentSequence vAlignmentSequence) - throws java.lang.IndexOutOfBoundsException - { - _alignmentSequenceList.addElement(vAlignmentSequence); - } //-- void addAlignmentSequence(org.vamsas.objects.core.AlignmentSequence) - - /** - * Method addAlignmentSequence - * - * - * - * @param index - * @param vAlignmentSequence - */ - public void addAlignmentSequence(int index, org.vamsas.objects.core.AlignmentSequence vAlignmentSequence) - throws java.lang.IndexOutOfBoundsException - { - _alignmentSequenceList.insertElementAt(vAlignmentSequence, index); - } //-- void addAlignmentSequence(int, org.vamsas.objects.core.AlignmentSequence) - - /** - * Method addProperty - * - * - * - * @param vProperty - */ - public void addProperty(org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - _propertyList.addElement(vProperty); - } //-- void addProperty(org.vamsas.objects.core.Property) - - /** - * Method addProperty - * - * - * - * @param index - * @param vProperty - */ - public void addProperty(int index, org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - _propertyList.insertElementAt(vProperty, index); - } //-- void addProperty(int, org.vamsas.objects.core.Property) - - /** - * Method addTree - * - * - * - * @param vTree - */ - public void addTree(org.vamsas.objects.core.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - _treeList.addElement(vTree); - } //-- void addTree(org.vamsas.objects.core.Tree) - - /** - * Method addTree - * - * - * - * @param index - * @param vTree - */ - public void addTree(int index, org.vamsas.objects.core.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - _treeList.insertElementAt(vTree, index); - } //-- void addTree(int, org.vamsas.objects.core.Tree) - - /** - * Method deleteAligned - * - */ - public void deleteAligned() - { - this._has_aligned= false; - } //-- void deleteAligned() - - /** - * Method enumerateAlignmentAnnotation - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateAlignmentAnnotation() - { - return _alignmentAnnotationList.elements(); - } //-- java.util.Enumeration enumerateAlignmentAnnotation() - - /** - * Method enumerateAlignmentSequence - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateAlignmentSequence() - { - return _alignmentSequenceList.elements(); - } //-- java.util.Enumeration enumerateAlignmentSequence() - - /** - * Method enumerateProperty - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateProperty() - { - return _propertyList.elements(); - } //-- java.util.Enumeration enumerateProperty() - - /** - * Method enumerateTree - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateTree() - { - return _treeList.elements(); - } //-- java.util.Enumeration enumerateTree() - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof Alignment) { - - Alignment temp = (Alignment)obj; - if (this._gapChar != null) { - if (temp._gapChar == null) return false; - else if (!(this._gapChar.equals(temp._gapChar))) - return false; - } - else if (temp._gapChar != null) - return false; - if (this._aligned != temp._aligned) - return false; - if (this._has_aligned != temp._has_aligned) - return false; - if (this._id != null) { - if (temp._id == null) return false; - else if (!(this._id.equals(temp._id))) - return false; - } - else if (temp._id != null) - return false; - if (this._modifiable != null) { - if (temp._modifiable == null) return false; - else if (!(this._modifiable.equals(temp._modifiable))) - return false; - } - else if (temp._modifiable != null) - return false; - if (this._alignmentAnnotationList != null) { - if (temp._alignmentAnnotationList == null) return false; - else if (!(this._alignmentAnnotationList.equals(temp._alignmentAnnotationList))) - return false; - } - else if (temp._alignmentAnnotationList != null) - return false; - if (this._treeList != null) { - if (temp._treeList == null) return false; - else if (!(this._treeList.equals(temp._treeList))) - return false; - } - else if (temp._treeList != null) - return false; - if (this._alignmentSequenceList != null) { - if (temp._alignmentSequenceList == null) return false; - else if (!(this._alignmentSequenceList.equals(temp._alignmentSequenceList))) - return false; - } - else if (temp._alignmentSequenceList != null) - return false; - if (this._propertyList != null) { - if (temp._propertyList == null) return false; - else if (!(this._propertyList.equals(temp._propertyList))) - return false; - } - else if (temp._propertyList != null) - return false; - if (this._provenance != null) { - if (temp._provenance == null) return false; - else if (!(this._provenance.equals(temp._provenance))) - return false; - } - else if (temp._provenance != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'aligned'. - * - * @return boolean - * @return the value of field 'aligned'. - */ - public boolean getAligned() - { - return this._aligned; - } //-- boolean getAligned() - - /** - * Method getAlignmentAnnotation - * - * - * - * @param index - * @return AlignmentAnnotation - */ - public org.vamsas.objects.core.AlignmentAnnotation getAlignmentAnnotation(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _alignmentAnnotationList.size())) { - throw new IndexOutOfBoundsException("getAlignmentAnnotation: Index value '"+index+"' not in range [0.."+_alignmentAnnotationList.size()+ "]"); - } - - return (org.vamsas.objects.core.AlignmentAnnotation) _alignmentAnnotationList.elementAt(index); - } //-- org.vamsas.objects.core.AlignmentAnnotation getAlignmentAnnotation(int) - - /** - * Method getAlignmentAnnotation - * - * - * - * @return AlignmentAnnotation - */ - public org.vamsas.objects.core.AlignmentAnnotation[] getAlignmentAnnotation() - { - int size = _alignmentAnnotationList.size(); - org.vamsas.objects.core.AlignmentAnnotation[] mArray = new org.vamsas.objects.core.AlignmentAnnotation[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.AlignmentAnnotation) _alignmentAnnotationList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.AlignmentAnnotation[] getAlignmentAnnotation() - - /** - * Method getAlignmentAnnotationCount - * - * - * - * @return int - */ - public int getAlignmentAnnotationCount() - { - return _alignmentAnnotationList.size(); - } //-- int getAlignmentAnnotationCount() - - /** - * Method getAlignmentSequence - * - * - * - * @param index - * @return AlignmentSequence - */ - public org.vamsas.objects.core.AlignmentSequence getAlignmentSequence(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _alignmentSequenceList.size())) { - throw new IndexOutOfBoundsException("getAlignmentSequence: Index value '"+index+"' not in range [0.."+_alignmentSequenceList.size()+ "]"); - } - - return (org.vamsas.objects.core.AlignmentSequence) _alignmentSequenceList.elementAt(index); - } //-- org.vamsas.objects.core.AlignmentSequence getAlignmentSequence(int) - - /** - * Method getAlignmentSequence - * - * - * - * @return AlignmentSequence - */ - public org.vamsas.objects.core.AlignmentSequence[] getAlignmentSequence() - { - int size = _alignmentSequenceList.size(); - org.vamsas.objects.core.AlignmentSequence[] mArray = new org.vamsas.objects.core.AlignmentSequence[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.AlignmentSequence) _alignmentSequenceList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.AlignmentSequence[] getAlignmentSequence() - - /** - * Method getAlignmentSequenceCount - * - * - * - * @return int - */ - public int getAlignmentSequenceCount() - { - return _alignmentSequenceList.size(); - } //-- int getAlignmentSequenceCount() - - /** - * Returns the value of field 'gapChar'. - * - * @return String - * @return the value of field 'gapChar'. - */ - public java.lang.String getGapChar() - { - return this._gapChar; - } //-- java.lang.String getGapChar() - - /** - * Returns the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * - * @return String - * @return the value of field 'id'. - */ - public java.lang.String getId() - { - return this._id; - } //-- java.lang.String getId() - - /** - * Returns the value of field 'modifiable'. - * - * @return String - * @return the value of field 'modifiable'. - */ - public java.lang.String getModifiable() - { - return this._modifiable; - } //-- java.lang.String getModifiable() - - /** - * Method getProperty - * - * - * - * @param index - * @return Property - */ - public org.vamsas.objects.core.Property getProperty(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _propertyList.size())) { - throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]"); - } - - return (org.vamsas.objects.core.Property) _propertyList.elementAt(index); - } //-- org.vamsas.objects.core.Property getProperty(int) - - /** - * Method getProperty - * - * - * - * @return Property - */ - public org.vamsas.objects.core.Property[] getProperty() - { - int size = _propertyList.size(); - org.vamsas.objects.core.Property[] mArray = new org.vamsas.objects.core.Property[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Property) _propertyList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Property[] getProperty() - - /** - * Method getPropertyCount - * - * - * - * @return int - */ - public int getPropertyCount() - { - return _propertyList.size(); - } //-- int getPropertyCount() - - /** - * Returns the value of field 'provenance'. - * - * @return Provenance - * @return the value of field 'provenance'. - */ - public org.vamsas.objects.core.Provenance getProvenance() - { - return this._provenance; - } //-- org.vamsas.objects.core.Provenance getProvenance() - - /** - * Method getTree - * - * - * - * @param index - * @return Tree - */ - public org.vamsas.objects.core.Tree getTree(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _treeList.size())) { - throw new IndexOutOfBoundsException("getTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]"); - } - - return (org.vamsas.objects.core.Tree) _treeList.elementAt(index); - } //-- org.vamsas.objects.core.Tree getTree(int) - - /** - * Method getTree - * - * - * - * @return Tree - */ - public org.vamsas.objects.core.Tree[] getTree() - { - int size = _treeList.size(); - org.vamsas.objects.core.Tree[] mArray = new org.vamsas.objects.core.Tree[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Tree) _treeList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Tree[] getTree() - - /** - * Method getTreeCount - * - * - * - * @return int - */ - public int getTreeCount() - { - return _treeList.size(); - } //-- int getTreeCount() - - /** - * Method hasAligned - * - * - * - * @return boolean - */ - public boolean hasAligned() - { - return this._has_aligned; - } //-- boolean hasAligned() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method removeAlignmentAnnotation - * - * - * - * @param index - * @return AlignmentAnnotation - */ - public org.vamsas.objects.core.AlignmentAnnotation removeAlignmentAnnotation(int index) - { - java.lang.Object obj = _alignmentAnnotationList.elementAt(index); - _alignmentAnnotationList.removeElementAt(index); - return (org.vamsas.objects.core.AlignmentAnnotation) obj; - } //-- org.vamsas.objects.core.AlignmentAnnotation removeAlignmentAnnotation(int) - - /** - * Method removeAlignmentSequence - * - * - * - * @param index - * @return AlignmentSequence - */ - public org.vamsas.objects.core.AlignmentSequence removeAlignmentSequence(int index) - { - java.lang.Object obj = _alignmentSequenceList.elementAt(index); - _alignmentSequenceList.removeElementAt(index); - return (org.vamsas.objects.core.AlignmentSequence) obj; - } //-- org.vamsas.objects.core.AlignmentSequence removeAlignmentSequence(int) - - /** - * Method removeAllAlignmentAnnotation - * - */ - public void removeAllAlignmentAnnotation() - { - _alignmentAnnotationList.removeAllElements(); - } //-- void removeAllAlignmentAnnotation() - - /** - * Method removeAllAlignmentSequence - * - */ - public void removeAllAlignmentSequence() - { - _alignmentSequenceList.removeAllElements(); - } //-- void removeAllAlignmentSequence() - - /** - * Method removeAllProperty - * - */ - public void removeAllProperty() - { - _propertyList.removeAllElements(); - } //-- void removeAllProperty() - - /** - * Method removeAllTree - * - */ - public void removeAllTree() - { - _treeList.removeAllElements(); - } //-- void removeAllTree() - - /** - * Method removeProperty - * - * - * - * @param index - * @return Property - */ - public org.vamsas.objects.core.Property removeProperty(int index) - { - java.lang.Object obj = _propertyList.elementAt(index); - _propertyList.removeElementAt(index); - return (org.vamsas.objects.core.Property) obj; - } //-- org.vamsas.objects.core.Property removeProperty(int) - - /** - * Method removeTree - * - * - * - * @param index - * @return Tree - */ - public org.vamsas.objects.core.Tree removeTree(int index) - { - java.lang.Object obj = _treeList.elementAt(index); - _treeList.removeElementAt(index); - return (org.vamsas.objects.core.Tree) obj; - } //-- org.vamsas.objects.core.Tree removeTree(int) - - /** - * Sets the value of field 'aligned'. - * - * @param aligned the value of field 'aligned'. - */ - public void setAligned(boolean aligned) - { - this._aligned = aligned; - this._has_aligned = true; - } //-- void setAligned(boolean) - - /** - * Method setAlignmentAnnotation - * - * - * - * @param index - * @param vAlignmentAnnotation - */ - public void setAlignmentAnnotation(int index, org.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _alignmentAnnotationList.size())) { - throw new IndexOutOfBoundsException("setAlignmentAnnotation: Index value '"+index+"' not in range [0.."+_alignmentAnnotationList.size()+ "]"); - } - _alignmentAnnotationList.setElementAt(vAlignmentAnnotation, index); - } //-- void setAlignmentAnnotation(int, org.vamsas.objects.core.AlignmentAnnotation) - - /** - * Method setAlignmentAnnotation - * - * - * - * @param alignmentAnnotationArray - */ - public void setAlignmentAnnotation(org.vamsas.objects.core.AlignmentAnnotation[] alignmentAnnotationArray) - { - //-- copy array - _alignmentAnnotationList.removeAllElements(); - for (int i = 0; i < alignmentAnnotationArray.length; i++) { - _alignmentAnnotationList.addElement(alignmentAnnotationArray[i]); - } - } //-- void setAlignmentAnnotation(org.vamsas.objects.core.AlignmentAnnotation) - - /** - * Method setAlignmentSequence - * - * - * - * @param index - * @param vAlignmentSequence - */ - public void setAlignmentSequence(int index, org.vamsas.objects.core.AlignmentSequence vAlignmentSequence) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _alignmentSequenceList.size())) { - throw new IndexOutOfBoundsException("setAlignmentSequence: Index value '"+index+"' not in range [0.."+_alignmentSequenceList.size()+ "]"); - } - _alignmentSequenceList.setElementAt(vAlignmentSequence, index); - } //-- void setAlignmentSequence(int, org.vamsas.objects.core.AlignmentSequence) - - /** - * Method setAlignmentSequence - * - * - * - * @param alignmentSequenceArray - */ - public void setAlignmentSequence(org.vamsas.objects.core.AlignmentSequence[] alignmentSequenceArray) - { - //-- copy array - _alignmentSequenceList.removeAllElements(); - for (int i = 0; i < alignmentSequenceArray.length; i++) { - _alignmentSequenceList.addElement(alignmentSequenceArray[i]); - } - } //-- void setAlignmentSequence(org.vamsas.objects.core.AlignmentSequence) - - /** - * Sets the value of field 'gapChar'. - * - * @param gapChar the value of field 'gapChar'. - */ - public void setGapChar(java.lang.String gapChar) - { - this._gapChar = gapChar; - } //-- void setGapChar(java.lang.String) - - /** - * Sets the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * - * @param id the value of field 'id'. - */ - public void setId(java.lang.String id) - { - this._id = id; - } //-- void setId(java.lang.String) - - /** - * Sets the value of field 'modifiable'. - * - * @param modifiable the value of field 'modifiable'. - */ - public void setModifiable(java.lang.String modifiable) - { - this._modifiable = modifiable; - } //-- void setModifiable(java.lang.String) - - /** - * Method setProperty - * - * - * - * @param index - * @param vProperty - */ - public void setProperty(int index, org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _propertyList.size())) { - throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]"); - } - _propertyList.setElementAt(vProperty, index); - } //-- void setProperty(int, org.vamsas.objects.core.Property) - - /** - * Method setProperty - * - * - * - * @param propertyArray - */ - public void setProperty(org.vamsas.objects.core.Property[] propertyArray) - { - //-- copy array - _propertyList.removeAllElements(); - for (int i = 0; i < propertyArray.length; i++) { - _propertyList.addElement(propertyArray[i]); - } - } //-- void setProperty(org.vamsas.objects.core.Property) - - /** - * Sets the value of field 'provenance'. - * - * @param provenance the value of field 'provenance'. - */ - public void setProvenance(org.vamsas.objects.core.Provenance provenance) - { - this._provenance = provenance; - } //-- void setProvenance(org.vamsas.objects.core.Provenance) - - /** - * Method setTree - * - * - * - * @param index - * @param vTree - */ - public void setTree(int index, org.vamsas.objects.core.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _treeList.size())) { - throw new IndexOutOfBoundsException("setTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]"); - } - _treeList.setElementAt(vTree, index); - } //-- void setTree(int, org.vamsas.objects.core.Tree) - - /** - * Method setTree - * - * - * - * @param treeArray - */ - public void setTree(org.vamsas.objects.core.Tree[] treeArray) - { - //-- copy array - _treeList.removeAllElements(); - for (int i = 0; i < treeArray.length; i++) { - _treeList.addElement(treeArray[i]); - } - } //-- void setTree(org.vamsas.objects.core.Tree) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Alignment - */ - public static org.vamsas.objects.core.Alignment unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Alignment) Unmarshaller.unmarshal(org.vamsas.objects.core.Alignment.class, reader); - } //-- org.vamsas.objects.core.Alignment unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/AlignmentAnnotation.java b/src/org/vamsas/objects/core/AlignmentAnnotation.java deleted file mode 100644 index 3fb9dfc..0000000 --- a/src/org/vamsas/objects/core/AlignmentAnnotation.java +++ /dev/null @@ -1,249 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * This is annotation over the coordinate frame - * defined by all the columns in the alignment. - * - * - * @version $Revision$ $Date$ - */ -public class AlignmentAnnotation extends org.vamsas.objects.core.RangeAnnotation -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * TODO: decide if this flag is - * redundant - when true it would suggest that - * the annotationElement values together form a - * graph - */ - private boolean _graph; - - /** - * keeps track of state for field: _graph - */ - private boolean _has_graph; - - /** - * Field _provenance - */ - private org.vamsas.objects.core.Provenance _provenance; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AlignmentAnnotation() - { - super(); - } //-- org.vamsas.objects.core.AlignmentAnnotation() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method deleteGraph - * - */ - public void deleteGraph() - { - this._has_graph= false; - } //-- void deleteGraph() - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof AlignmentAnnotation) { - - AlignmentAnnotation temp = (AlignmentAnnotation)obj; - if (this._graph != temp._graph) - return false; - if (this._has_graph != temp._has_graph) - return false; - if (this._provenance != null) { - if (temp._provenance == null) return false; - else if (!(this._provenance.equals(temp._provenance))) - return false; - } - else if (temp._provenance != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'graph'. The field 'graph' has - * the following description: TODO: decide if this flag is - * redundant - when true it would suggest that - * the annotationElement values together form a - * graph - * - * @return boolean - * @return the value of field 'graph'. - */ - public boolean getGraph() - { - return this._graph; - } //-- boolean getGraph() - - /** - * Returns the value of field 'provenance'. - * - * @return Provenance - * @return the value of field 'provenance'. - */ - public org.vamsas.objects.core.Provenance getProvenance() - { - return this._provenance; - } //-- org.vamsas.objects.core.Provenance getProvenance() - - /** - * Method hasGraph - * - * - * - * @return boolean - */ - public boolean hasGraph() - { - return this._has_graph; - } //-- boolean hasGraph() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Sets the value of field 'graph'. The field 'graph' has the - * following description: TODO: decide if this flag is - * redundant - when true it would suggest that - * the annotationElement values together form a - * graph - * - * @param graph the value of field 'graph'. - */ - public void setGraph(boolean graph) - { - this._graph = graph; - this._has_graph = true; - } //-- void setGraph(boolean) - - /** - * Sets the value of field 'provenance'. - * - * @param provenance the value of field 'provenance'. - */ - public void setProvenance(org.vamsas.objects.core.Provenance provenance) - { - this._provenance = provenance; - } //-- void setProvenance(org.vamsas.objects.core.Provenance) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return RangeType - */ - public static org.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.AlignmentAnnotation) Unmarshaller.unmarshal(org.vamsas.objects.core.AlignmentAnnotation.class, reader); - } //-- org.vamsas.objects.core.RangeType unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/AlignmentAnnotationDescriptor.java b/src/org/vamsas/objects/core/AlignmentAnnotationDescriptor.java deleted file mode 100644 index fb81a9a..0000000 --- a/src/org/vamsas/objects/core/AlignmentAnnotationDescriptor.java +++ /dev/null @@ -1,255 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class AlignmentAnnotationDescriptor. - * - * @version $Revision$ $Date$ - */ -public class AlignmentAnnotationDescriptor extends org.vamsas.objects.core.RangeAnnotationDescriptor { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AlignmentAnnotationDescriptor() - { - super(); - setExtendsWithoutFlatten(new org.vamsas.objects.core.RangeAnnotationDescriptor()); - nsURI = "http://www.vamsas.org"; - xmlName = "AlignmentAnnotation"; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _graph - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_graph", "graph", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AlignmentAnnotation target = (AlignmentAnnotation) object; - if(!target.hasGraph()) - return null; - return (target.getGraph() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AlignmentAnnotation target = (AlignmentAnnotation) object; - // ignore null values for non optional primitives - if (value == null) return; - - target.setGraph( ((java.lang.Boolean)value).booleanValue()); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _graph - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - BooleanValidator typeValidator = new BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _provenance - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AlignmentAnnotation target = (AlignmentAnnotation) object; - return target.getProvenance(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AlignmentAnnotation target = (AlignmentAnnotation) object; - target.setProvenance( (org.vamsas.objects.core.Provenance) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Provenance(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _provenance - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.objects.core.AlignmentAnnotationDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return super.getExtends(); - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - if (identity == null) - return super.getIdentity(); - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.AlignmentAnnotation.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/AlignmentDescriptor.java b/src/org/vamsas/objects/core/AlignmentDescriptor.java deleted file mode 100644 index 4804a61..0000000 --- a/src/org/vamsas/objects/core/AlignmentDescriptor.java +++ /dev/null @@ -1,503 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class AlignmentDescriptor. - * - * @version $Revision$ $Date$ - */ -public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AlignmentDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "Alignment"; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _gapChar - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_gapChar", "gapChar", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Alignment target = (Alignment) object; - return target.getGapChar(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Alignment target = (Alignment) object; - target.setGapChar( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _gapChar - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _aligned - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_aligned", "aligned", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Alignment target = (Alignment) object; - if(!target.hasAligned()) - return null; - return (target.getAligned() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Alignment target = (Alignment) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteAligned(); - return; - } - target.setAligned( ((java.lang.Boolean)value).booleanValue()); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _aligned - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - BooleanValidator typeValidator = new BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); - this.identity = desc; - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Alignment target = (Alignment) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Alignment target = (Alignment) object; - target.setId( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new java.lang.String(); - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _modifiable - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_modifiable", "modifiable", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Alignment target = (Alignment) object; - return target.getModifiable(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Alignment target = (Alignment) object; - target.setModifiable( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _modifiable - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _alignmentAnnotationList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.AlignmentAnnotation.class, "_alignmentAnnotationList", "AlignmentAnnotation", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Alignment target = (Alignment) object; - return target.getAlignmentAnnotation(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Alignment target = (Alignment) object; - target.addAlignmentAnnotation( (org.vamsas.objects.core.AlignmentAnnotation) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.AlignmentAnnotation(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _alignmentAnnotationList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _treeList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Tree.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Alignment target = (Alignment) object; - return target.getTree(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Alignment target = (Alignment) object; - target.addTree( (org.vamsas.objects.core.Tree) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Tree(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _treeList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _alignmentSequenceList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.AlignmentSequence.class, "_alignmentSequenceList", "alignmentSequence", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Alignment target = (Alignment) object; - return target.getAlignmentSequence(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Alignment target = (Alignment) object; - target.addAlignmentSequence( (org.vamsas.objects.core.AlignmentSequence) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.AlignmentSequence(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _alignmentSequenceList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _propertyList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Property.class, "_propertyList", "property", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Alignment target = (Alignment) object; - return target.getProperty(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Alignment target = (Alignment) object; - target.addProperty( (org.vamsas.objects.core.Property) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Property(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _propertyList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _provenance - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Alignment target = (Alignment) object; - return target.getProvenance(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Alignment target = (Alignment) object; - target.setProvenance( (org.vamsas.objects.core.Provenance) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Provenance(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _provenance - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.objects.core.AlignmentDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return null; - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.Alignment.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/AlignmentSequence.java b/src/org/vamsas/objects/core/AlignmentSequence.java deleted file mode 100644 index 3a0a72e..0000000 --- a/src/org/vamsas/objects/core/AlignmentSequence.java +++ /dev/null @@ -1,385 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class AlignmentSequence. - * - * @version $Revision$ $Date$ - */ -public class AlignmentSequence extends org.vamsas.objects.core.SequenceType -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Primary Key for vamsas object - * referencing - */ - private java.lang.String _id; - - /** - * Dataset Sequence from which - * this alignment sequence is taken from - * - */ - private java.lang.Object _refid; - - /** - * Field _alignmentSequenceAnnotationList - */ - private java.util.Vector _alignmentSequenceAnnotationList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AlignmentSequence() - { - super(); - _alignmentSequenceAnnotationList = new Vector(); - } //-- org.vamsas.objects.core.AlignmentSequence() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addAlignmentSequenceAnnotation - * - * - * - * @param vAlignmentSequenceAnnotation - */ - public void addAlignmentSequenceAnnotation(org.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation) - throws java.lang.IndexOutOfBoundsException - { - _alignmentSequenceAnnotationList.addElement(vAlignmentSequenceAnnotation); - } //-- void addAlignmentSequenceAnnotation(org.vamsas.objects.core.AlignmentSequenceAnnotation) - - /** - * Method addAlignmentSequenceAnnotation - * - * - * - * @param index - * @param vAlignmentSequenceAnnotation - */ - public void addAlignmentSequenceAnnotation(int index, org.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation) - throws java.lang.IndexOutOfBoundsException - { - _alignmentSequenceAnnotationList.insertElementAt(vAlignmentSequenceAnnotation, index); - } //-- void addAlignmentSequenceAnnotation(int, org.vamsas.objects.core.AlignmentSequenceAnnotation) - - /** - * Method enumerateAlignmentSequenceAnnotation - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateAlignmentSequenceAnnotation() - { - return _alignmentSequenceAnnotationList.elements(); - } //-- java.util.Enumeration enumerateAlignmentSequenceAnnotation() - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof AlignmentSequence) { - - AlignmentSequence temp = (AlignmentSequence)obj; - if (this._id != null) { - if (temp._id == null) return false; - else if (!(this._id.equals(temp._id))) - return false; - } - else if (temp._id != null) - return false; - if (this._refid != null) { - if (temp._refid == null) return false; - else if (!(this._refid.equals(temp._refid))) - return false; - } - else if (temp._refid != null) - return false; - if (this._alignmentSequenceAnnotationList != null) { - if (temp._alignmentSequenceAnnotationList == null) return false; - else if (!(this._alignmentSequenceAnnotationList.equals(temp._alignmentSequenceAnnotationList))) - return false; - } - else if (temp._alignmentSequenceAnnotationList != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Method getAlignmentSequenceAnnotation - * - * - * - * @param index - * @return AlignmentSequenceAnnotation - */ - public org.vamsas.objects.core.AlignmentSequenceAnnotation getAlignmentSequenceAnnotation(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _alignmentSequenceAnnotationList.size())) { - throw new IndexOutOfBoundsException("getAlignmentSequenceAnnotation: Index value '"+index+"' not in range [0.."+_alignmentSequenceAnnotationList.size()+ "]"); - } - - return (org.vamsas.objects.core.AlignmentSequenceAnnotation) _alignmentSequenceAnnotationList.elementAt(index); - } //-- org.vamsas.objects.core.AlignmentSequenceAnnotation getAlignmentSequenceAnnotation(int) - - /** - * Method getAlignmentSequenceAnnotation - * - * - * - * @return AlignmentSequenceAnnotation - */ - public org.vamsas.objects.core.AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation() - { - int size = _alignmentSequenceAnnotationList.size(); - org.vamsas.objects.core.AlignmentSequenceAnnotation[] mArray = new org.vamsas.objects.core.AlignmentSequenceAnnotation[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.AlignmentSequenceAnnotation) _alignmentSequenceAnnotationList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation() - - /** - * Method getAlignmentSequenceAnnotationCount - * - * - * - * @return int - */ - public int getAlignmentSequenceAnnotationCount() - { - return _alignmentSequenceAnnotationList.size(); - } //-- int getAlignmentSequenceAnnotationCount() - - /** - * Returns the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * @return String - * @return the value of field 'id'. - */ - public java.lang.String getId() - { - return this._id; - } //-- java.lang.String getId() - - /** - * Returns the value of field 'refid'. The field 'refid' has - * the following description: Dataset Sequence from which - * this alignment sequence is taken from - * - * - * @return Object - * @return the value of field 'refid'. - */ - public java.lang.Object getRefid() - { - return this._refid; - } //-- java.lang.Object getRefid() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method removeAlignmentSequenceAnnotation - * - * - * - * @param index - * @return AlignmentSequenceAnnotation - */ - public org.vamsas.objects.core.AlignmentSequenceAnnotation removeAlignmentSequenceAnnotation(int index) - { - java.lang.Object obj = _alignmentSequenceAnnotationList.elementAt(index); - _alignmentSequenceAnnotationList.removeElementAt(index); - return (org.vamsas.objects.core.AlignmentSequenceAnnotation) obj; - } //-- org.vamsas.objects.core.AlignmentSequenceAnnotation removeAlignmentSequenceAnnotation(int) - - /** - * Method removeAllAlignmentSequenceAnnotation - * - */ - public void removeAllAlignmentSequenceAnnotation() - { - _alignmentSequenceAnnotationList.removeAllElements(); - } //-- void removeAllAlignmentSequenceAnnotation() - - /** - * Method setAlignmentSequenceAnnotation - * - * - * - * @param index - * @param vAlignmentSequenceAnnotation - */ - public void setAlignmentSequenceAnnotation(int index, org.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _alignmentSequenceAnnotationList.size())) { - throw new IndexOutOfBoundsException("setAlignmentSequenceAnnotation: Index value '"+index+"' not in range [0.."+_alignmentSequenceAnnotationList.size()+ "]"); - } - _alignmentSequenceAnnotationList.setElementAt(vAlignmentSequenceAnnotation, index); - } //-- void setAlignmentSequenceAnnotation(int, org.vamsas.objects.core.AlignmentSequenceAnnotation) - - /** - * Method setAlignmentSequenceAnnotation - * - * - * - * @param alignmentSequenceAnnotationArray - */ - public void setAlignmentSequenceAnnotation(org.vamsas.objects.core.AlignmentSequenceAnnotation[] alignmentSequenceAnnotationArray) - { - //-- copy array - _alignmentSequenceAnnotationList.removeAllElements(); - for (int i = 0; i < alignmentSequenceAnnotationArray.length; i++) { - _alignmentSequenceAnnotationList.addElement(alignmentSequenceAnnotationArray[i]); - } - } //-- void setAlignmentSequenceAnnotation(org.vamsas.objects.core.AlignmentSequenceAnnotation) - - /** - * Sets the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * @param id the value of field 'id'. - */ - public void setId(java.lang.String id) - { - this._id = id; - } //-- void setId(java.lang.String) - - /** - * Sets the value of field 'refid'. The field 'refid' has the - * following description: Dataset Sequence from which - * this alignment sequence is taken from - * - * - * @param refid the value of field 'refid'. - */ - public void setRefid(java.lang.Object refid) - { - this._refid = refid; - } //-- void setRefid(java.lang.Object) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return SequenceType - */ - public static org.vamsas.objects.core.SequenceType unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.AlignmentSequence) Unmarshaller.unmarshal(org.vamsas.objects.core.AlignmentSequence.class, reader); - } //-- org.vamsas.objects.core.SequenceType unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/AlignmentSequenceAnnotation.java b/src/org/vamsas/objects/core/AlignmentSequenceAnnotation.java deleted file mode 100644 index 0f229af..0000000 --- a/src/org/vamsas/objects/core/AlignmentSequenceAnnotation.java +++ /dev/null @@ -1,256 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class AlignmentSequenceAnnotation. - * - * @version $Revision$ $Date$ - */ -public class AlignmentSequenceAnnotation extends org.vamsas.objects.core.RangeAnnotation -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * TODO: - * decide if this flag is - * redundant - when true it - * would suggest that the - * annotationElement values - * together form a graph - * - */ - private boolean _graph; - - /** - * keeps track of state for field: _graph - */ - private boolean _has_graph; - - /** - * Field _provenance - */ - private org.vamsas.objects.core.Provenance _provenance; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AlignmentSequenceAnnotation() - { - super(); - } //-- org.vamsas.objects.core.AlignmentSequenceAnnotation() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method deleteGraph - * - */ - public void deleteGraph() - { - this._has_graph= false; - } //-- void deleteGraph() - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof AlignmentSequenceAnnotation) { - - AlignmentSequenceAnnotation temp = (AlignmentSequenceAnnotation)obj; - if (this._graph != temp._graph) - return false; - if (this._has_graph != temp._has_graph) - return false; - if (this._provenance != null) { - if (temp._provenance == null) return false; - else if (!(this._provenance.equals(temp._provenance))) - return false; - } - else if (temp._provenance != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'graph'. The field 'graph' has - * the following description: TODO: - * decide if this flag is - * redundant - when true it - * would suggest that the - * annotationElement values - * together form a graph - * - * - * @return boolean - * @return the value of field 'graph'. - */ - public boolean getGraph() - { - return this._graph; - } //-- boolean getGraph() - - /** - * Returns the value of field 'provenance'. - * - * @return Provenance - * @return the value of field 'provenance'. - */ - public org.vamsas.objects.core.Provenance getProvenance() - { - return this._provenance; - } //-- org.vamsas.objects.core.Provenance getProvenance() - - /** - * Method hasGraph - * - * - * - * @return boolean - */ - public boolean hasGraph() - { - return this._has_graph; - } //-- boolean hasGraph() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Sets the value of field 'graph'. The field 'graph' has the - * following description: TODO: - * decide if this flag is - * redundant - when true it - * would suggest that the - * annotationElement values - * together form a graph - * - * - * @param graph the value of field 'graph'. - */ - public void setGraph(boolean graph) - { - this._graph = graph; - this._has_graph = true; - } //-- void setGraph(boolean) - - /** - * Sets the value of field 'provenance'. - * - * @param provenance the value of field 'provenance'. - */ - public void setProvenance(org.vamsas.objects.core.Provenance provenance) - { - this._provenance = provenance; - } //-- void setProvenance(org.vamsas.objects.core.Provenance) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return RangeType - */ - public static org.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.AlignmentSequenceAnnotation) Unmarshaller.unmarshal(org.vamsas.objects.core.AlignmentSequenceAnnotation.class, reader); - } //-- org.vamsas.objects.core.RangeType unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/AlignmentSequenceAnnotationDescriptor.java b/src/org/vamsas/objects/core/AlignmentSequenceAnnotationDescriptor.java deleted file mode 100644 index a4aa126..0000000 --- a/src/org/vamsas/objects/core/AlignmentSequenceAnnotationDescriptor.java +++ /dev/null @@ -1,255 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class AlignmentSequenceAnnotationDescriptor. - * - * @version $Revision$ $Date$ - */ -public class AlignmentSequenceAnnotationDescriptor extends org.vamsas.objects.core.RangeAnnotationDescriptor { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AlignmentSequenceAnnotationDescriptor() - { - super(); - setExtendsWithoutFlatten(new org.vamsas.objects.core.RangeAnnotationDescriptor()); - nsURI = "http://www.vamsas.org"; - xmlName = "AlignmentSequenceAnnotation"; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _graph - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_graph", "graph", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AlignmentSequenceAnnotation target = (AlignmentSequenceAnnotation) object; - if(!target.hasGraph()) - return null; - return (target.getGraph() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AlignmentSequenceAnnotation target = (AlignmentSequenceAnnotation) object; - // ignore null values for non optional primitives - if (value == null) return; - - target.setGraph( ((java.lang.Boolean)value).booleanValue()); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _graph - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - BooleanValidator typeValidator = new BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _provenance - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AlignmentSequenceAnnotation target = (AlignmentSequenceAnnotation) object; - return target.getProvenance(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AlignmentSequenceAnnotation target = (AlignmentSequenceAnnotation) object; - target.setProvenance( (org.vamsas.objects.core.Provenance) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Provenance(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _provenance - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.objects.core.AlignmentSequenceAnnotationDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return super.getExtends(); - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - if (identity == null) - return super.getIdentity(); - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.AlignmentSequenceAnnotation.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/AlignmentSequenceDescriptor.java b/src/org/vamsas/objects/core/AlignmentSequenceDescriptor.java deleted file mode 100644 index afbe5cd..0000000 --- a/src/org/vamsas/objects/core/AlignmentSequenceDescriptor.java +++ /dev/null @@ -1,282 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class AlignmentSequenceDescriptor. - * - * @version $Revision$ $Date$ - */ -public class AlignmentSequenceDescriptor extends org.vamsas.objects.core.SequenceTypeDescriptor { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AlignmentSequenceDescriptor() - { - super(); - setExtendsWithoutFlatten(new org.vamsas.objects.core.SequenceTypeDescriptor()); - nsURI = "http://www.vamsas.org"; - xmlName = "alignmentSequence"; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); - this.identity = desc; - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AlignmentSequence target = (AlignmentSequence) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AlignmentSequence target = (AlignmentSequence) object; - target.setId( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new java.lang.String(); - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _refid - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_refid", "refid", org.exolab.castor.xml.NodeType.Attribute); - desc.setReference(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AlignmentSequence target = (AlignmentSequence) object; - return target.getRefid(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AlignmentSequence target = (AlignmentSequence) object; - target.setRefid( (java.lang.Object) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new java.lang.Object(); - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _refid - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _alignmentSequenceAnnotationList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.AlignmentSequenceAnnotation.class, "_alignmentSequenceAnnotationList", "AlignmentSequenceAnnotation", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AlignmentSequence target = (AlignmentSequence) object; - return target.getAlignmentSequenceAnnotation(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AlignmentSequence target = (AlignmentSequence) object; - target.addAlignmentSequenceAnnotation( (org.vamsas.objects.core.AlignmentSequenceAnnotation) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.AlignmentSequenceAnnotation(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _alignmentSequenceAnnotationList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.objects.core.AlignmentSequenceDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return super.getExtends(); - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - if (identity == null) - return super.getIdentity(); - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.AlignmentSequence.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/AnnotationElement.java b/src/org/vamsas/objects/core/AnnotationElement.java deleted file mode 100644 index b2ed9c5..0000000 --- a/src/org/vamsas/objects/core/AnnotationElement.java +++ /dev/null @@ -1,673 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class AnnotationElement. - * - * @version $Revision$ $Date$ - */ -public class AnnotationElement extends org.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * position with respect to the coordinate frame defined by a - * rangeType specification - */ - private int _position; - - /** - * keeps track of state for field: _position - */ - private boolean _has_position; - - /** - * true means the annotation element appears between the - * specified position and the next - */ - private boolean _after = false; - - /** - * keeps track of state for field: _after - */ - private boolean _has_after; - - /** - * Primary Key for vamsas object referencing - */ - private java.lang.String _id; - - /** - * Free text at this position - */ - private java.lang.String _description; - - /** - * Discrete symbol - possibly graphically represented - * - */ - private java.util.Vector _glyphList; - - /** - * Ordered set of float values - an application may treat - * the values together as a vector with common support for a - * set of - * annotation elements - but this is, again, not validated so - * applications - * should deal gracefully with varying numbers of dimensions - * - */ - private java.util.Vector _valueList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AnnotationElement() - { - super(); - _glyphList = new Vector(); - _valueList = new Vector(); - } //-- org.vamsas.objects.core.AnnotationElement() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addGlyph - * - * - * - * @param vGlyph - */ - public void addGlyph(org.vamsas.objects.core.Glyph vGlyph) - throws java.lang.IndexOutOfBoundsException - { - _glyphList.addElement(vGlyph); - } //-- void addGlyph(org.vamsas.objects.core.Glyph) - - /** - * Method addGlyph - * - * - * - * @param index - * @param vGlyph - */ - public void addGlyph(int index, org.vamsas.objects.core.Glyph vGlyph) - throws java.lang.IndexOutOfBoundsException - { - _glyphList.insertElementAt(vGlyph, index); - } //-- void addGlyph(int, org.vamsas.objects.core.Glyph) - - /** - * Method addValue - * - * - * - * @param vValue - */ - public void addValue(float vValue) - throws java.lang.IndexOutOfBoundsException - { - _valueList.addElement(new java.lang.Float(vValue)); - } //-- void addValue(float) - - /** - * Method addValue - * - * - * - * @param index - * @param vValue - */ - public void addValue(int index, float vValue) - throws java.lang.IndexOutOfBoundsException - { - _valueList.insertElementAt(new java.lang.Float(vValue), index); - } //-- void addValue(int, float) - - /** - * Method deleteAfter - * - */ - public void deleteAfter() - { - this._has_after= false; - } //-- void deleteAfter() - - /** - * Method deletePosition - * - */ - public void deletePosition() - { - this._has_position= false; - } //-- void deletePosition() - - /** - * Method enumerateGlyph - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateGlyph() - { - return _glyphList.elements(); - } //-- java.util.Enumeration enumerateGlyph() - - /** - * Method enumerateValue - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateValue() - { - return _valueList.elements(); - } //-- java.util.Enumeration enumerateValue() - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof AnnotationElement) { - - AnnotationElement temp = (AnnotationElement)obj; - if (this._position != temp._position) - return false; - if (this._has_position != temp._has_position) - return false; - if (this._after != temp._after) - return false; - if (this._has_after != temp._has_after) - return false; - if (this._id != null) { - if (temp._id == null) return false; - else if (!(this._id.equals(temp._id))) - return false; - } - else if (temp._id != null) - return false; - if (this._description != null) { - if (temp._description == null) return false; - else if (!(this._description.equals(temp._description))) - return false; - } - else if (temp._description != null) - return false; - if (this._glyphList != null) { - if (temp._glyphList == null) return false; - else if (!(this._glyphList.equals(temp._glyphList))) - return false; - } - else if (temp._glyphList != null) - return false; - if (this._valueList != null) { - if (temp._valueList == null) return false; - else if (!(this._valueList.equals(temp._valueList))) - return false; - } - else if (temp._valueList != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'after'. The field 'after' has - * the following description: true means the annotation element - * appears between the - * specified position and the next - * - * @return boolean - * @return the value of field 'after'. - */ - public boolean getAfter() - { - return this._after; - } //-- boolean getAfter() - - /** - * Returns the value of field 'description'. The field - * 'description' has the following description: Free text at - * this position - * - * @return String - * @return the value of field 'description'. - */ - public java.lang.String getDescription() - { - return this._description; - } //-- java.lang.String getDescription() - - /** - * Method getGlyph - * - * - * - * @param index - * @return Glyph - */ - public org.vamsas.objects.core.Glyph getGlyph(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _glyphList.size())) { - throw new IndexOutOfBoundsException("getGlyph: Index value '"+index+"' not in range [0.."+_glyphList.size()+ "]"); - } - - return (org.vamsas.objects.core.Glyph) _glyphList.elementAt(index); - } //-- org.vamsas.objects.core.Glyph getGlyph(int) - - /** - * Method getGlyph - * - * - * - * @return Glyph - */ - public org.vamsas.objects.core.Glyph[] getGlyph() - { - int size = _glyphList.size(); - org.vamsas.objects.core.Glyph[] mArray = new org.vamsas.objects.core.Glyph[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Glyph) _glyphList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Glyph[] getGlyph() - - /** - * Method getGlyphCount - * - * - * - * @return int - */ - public int getGlyphCount() - { - return _glyphList.size(); - } //-- int getGlyphCount() - - /** - * Returns the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * @return String - * @return the value of field 'id'. - */ - public java.lang.String getId() - { - return this._id; - } //-- java.lang.String getId() - - /** - * Returns the value of field 'position'. The field 'position' - * has the following description: position with respect to the - * coordinate frame defined by a - * rangeType specification - * - * @return int - * @return the value of field 'position'. - */ - public int getPosition() - { - return this._position; - } //-- int getPosition() - - /** - * Method getValue - * - * - * - * @param index - * @return float - */ - public float getValue(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _valueList.size())) { - throw new IndexOutOfBoundsException("getValue: Index value '"+index+"' not in range [0.."+_valueList.size()+ "]"); - } - - return ((java.lang.Float)_valueList.elementAt(index)).floatValue(); - } //-- float getValue(int) - - /** - * Method getValue - * - * - * - * @return float - */ - public float[] getValue() - { - int size = _valueList.size(); - float[] mArray = new float[size]; - for (int index = 0; index < size; index++) { - mArray[index] = ((java.lang.Float)_valueList.elementAt(index)).floatValue(); - } - return mArray; - } //-- float[] getValue() - - /** - * Method getValueCount - * - * - * - * @return int - */ - public int getValueCount() - { - return _valueList.size(); - } //-- int getValueCount() - - /** - * Method hasAfter - * - * - * - * @return boolean - */ - public boolean hasAfter() - { - return this._has_after; - } //-- boolean hasAfter() - - /** - * Method hasPosition - * - * - * - * @return boolean - */ - public boolean hasPosition() - { - return this._has_position; - } //-- boolean hasPosition() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method removeAllGlyph - * - */ - public void removeAllGlyph() - { - _glyphList.removeAllElements(); - } //-- void removeAllGlyph() - - /** - * Method removeAllValue - * - */ - public void removeAllValue() - { - _valueList.removeAllElements(); - } //-- void removeAllValue() - - /** - * Method removeGlyph - * - * - * - * @param index - * @return Glyph - */ - public org.vamsas.objects.core.Glyph removeGlyph(int index) - { - java.lang.Object obj = _glyphList.elementAt(index); - _glyphList.removeElementAt(index); - return (org.vamsas.objects.core.Glyph) obj; - } //-- org.vamsas.objects.core.Glyph removeGlyph(int) - - /** - * Method removeValue - * - * - * - * @param index - * @return float - */ - public float removeValue(int index) - { - java.lang.Object obj = _valueList.elementAt(index); - _valueList.removeElementAt(index); - return ((java.lang.Float)obj).floatValue(); - } //-- float removeValue(int) - - /** - * Sets the value of field 'after'. The field 'after' has the - * following description: true means the annotation element - * appears between the - * specified position and the next - * - * @param after the value of field 'after'. - */ - public void setAfter(boolean after) - { - this._after = after; - this._has_after = true; - } //-- void setAfter(boolean) - - /** - * Sets the value of field 'description'. The field - * 'description' has the following description: Free text at - * this position - * - * @param description the value of field 'description'. - */ - public void setDescription(java.lang.String description) - { - this._description = description; - } //-- void setDescription(java.lang.String) - - /** - * Method setGlyph - * - * - * - * @param index - * @param vGlyph - */ - public void setGlyph(int index, org.vamsas.objects.core.Glyph vGlyph) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _glyphList.size())) { - throw new IndexOutOfBoundsException("setGlyph: Index value '"+index+"' not in range [0.."+_glyphList.size()+ "]"); - } - _glyphList.setElementAt(vGlyph, index); - } //-- void setGlyph(int, org.vamsas.objects.core.Glyph) - - /** - * Method setGlyph - * - * - * - * @param glyphArray - */ - public void setGlyph(org.vamsas.objects.core.Glyph[] glyphArray) - { - //-- copy array - _glyphList.removeAllElements(); - for (int i = 0; i < glyphArray.length; i++) { - _glyphList.addElement(glyphArray[i]); - } - } //-- void setGlyph(org.vamsas.objects.core.Glyph) - - /** - * Sets the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * @param id the value of field 'id'. - */ - public void setId(java.lang.String id) - { - this._id = id; - } //-- void setId(java.lang.String) - - /** - * Sets the value of field 'position'. The field 'position' has - * the following description: position with respect to the - * coordinate frame defined by a - * rangeType specification - * - * @param position the value of field 'position'. - */ - public void setPosition(int position) - { - this._position = position; - this._has_position = true; - } //-- void setPosition(int) - - /** - * Method setValue - * - * - * - * @param index - * @param vValue - */ - public void setValue(int index, float vValue) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _valueList.size())) { - throw new IndexOutOfBoundsException("setValue: Index value '"+index+"' not in range [0.."+_valueList.size()+ "]"); - } - _valueList.setElementAt(new java.lang.Float(vValue), index); - } //-- void setValue(int, float) - - /** - * Method setValue - * - * - * - * @param valueArray - */ - public void setValue(float[] valueArray) - { - //-- copy array - _valueList.removeAllElements(); - for (int i = 0; i < valueArray.length; i++) { - _valueList.addElement(new java.lang.Float(valueArray[i])); - } - } //-- void setValue(float) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return AnnotationElement - */ - public static org.vamsas.objects.core.AnnotationElement unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.AnnotationElement) Unmarshaller.unmarshal(org.vamsas.objects.core.AnnotationElement.class, reader); - } //-- org.vamsas.objects.core.AnnotationElement unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/AnnotationElementDescriptor.java b/src/org/vamsas/objects/core/AnnotationElementDescriptor.java deleted file mode 100644 index cc7bb65..0000000 --- a/src/org/vamsas/objects/core/AnnotationElementDescriptor.java +++ /dev/null @@ -1,405 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class AnnotationElementDescriptor. - * - * @version $Revision$ $Date$ - */ -public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AnnotationElementDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "annotationElement"; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _position - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_position", "position", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AnnotationElement target = (AnnotationElement) object; - if(!target.hasPosition()) - return null; - return new java.lang.Integer(target.getPosition()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AnnotationElement target = (AnnotationElement) object; - // ignore null values for non optional primitives - if (value == null) return; - - target.setPosition( ((java.lang.Integer)value).intValue()); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _position - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - IntegerValidator typeValidator = new IntegerValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _after - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_after", "after", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AnnotationElement target = (AnnotationElement) object; - if(!target.hasAfter()) - return null; - return (target.getAfter() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AnnotationElement target = (AnnotationElement) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteAfter(); - return; - } - target.setAfter( ((java.lang.Boolean)value).booleanValue()); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _after - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - BooleanValidator typeValidator = new BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); - this.identity = desc; - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AnnotationElement target = (AnnotationElement) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AnnotationElement target = (AnnotationElement) object; - target.setId( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new java.lang.String(); - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _description - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AnnotationElement target = (AnnotationElement) object; - return target.getDescription(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AnnotationElement target = (AnnotationElement) object; - target.setDescription( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _description - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _glyphList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Glyph.class, "_glyphList", "glyph", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AnnotationElement target = (AnnotationElement) object; - return target.getGlyph(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AnnotationElement target = (AnnotationElement) object; - target.addGlyph( (org.vamsas.objects.core.Glyph) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Glyph(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _glyphList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _valueList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class, "_valueList", "value", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AnnotationElement target = (AnnotationElement) object; - return target.getValue(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AnnotationElement target = (AnnotationElement) object; - // ignore null values for non optional primitives - if (value == null) return; - - target.addValue( ((java.lang.Float)value).floatValue()); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _valueList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - FloatValidator typeValidator = new FloatValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.objects.core.AnnotationElementDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return null; - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.AnnotationElement.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/AppData.java b/src/org/vamsas/objects/core/AppData.java deleted file mode 100644 index 168bc6b..0000000 --- a/src/org/vamsas/objects/core/AppData.java +++ /dev/null @@ -1,239 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class AppData. - * - * @version $Revision$ $Date$ - */ -public class AppData extends org.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Internal choice value storage - */ - private java.lang.Object _choiceValue; - - /** - * Field _data - */ - private byte[] _data; - - /** - * Field _dataReference - */ - private java.lang.String _dataReference; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AppData() - { - super(); - } //-- org.vamsas.objects.core.AppData() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof AppData) { - - AppData temp = (AppData)obj; - if (this._choiceValue != null) { - if (temp._choiceValue == null) return false; - else if (!(this._choiceValue.equals(temp._choiceValue))) - return false; - } - else if (temp._choiceValue != null) - return false; - if (this._data != null) { - if (temp._data == null) return false; - else if (!(this._data.equals(temp._data))) - return false; - } - else if (temp._data != null) - return false; - if (this._dataReference != null) { - if (temp._dataReference == null) return false; - else if (!(this._dataReference.equals(temp._dataReference))) - return false; - } - else if (temp._dataReference != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'choiceValue'. The field - * 'choiceValue' has the following description: Internal choice - * value storage - * - * @return Object - * @return the value of field 'choiceValue'. - */ - public java.lang.Object getChoiceValue() - { - return this._choiceValue; - } //-- java.lang.Object getChoiceValue() - - /** - * Returns the value of field 'data'. - * - * @return byte - * @return the value of field 'data'. - */ - public byte[] getData() - { - return this._data; - } //-- byte[] getData() - - /** - * Returns the value of field 'dataReference'. - * - * @return String - * @return the value of field 'dataReference'. - */ - public java.lang.String getDataReference() - { - return this._dataReference; - } //-- java.lang.String getDataReference() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Sets the value of field 'data'. - * - * @param data the value of field 'data'. - */ - public void setData(byte[] data) - { - this._data = data; - this._choiceValue = data; - } //-- void setData(byte) - - /** - * Sets the value of field 'dataReference'. - * - * @param dataReference the value of field 'dataReference'. - */ - public void setDataReference(java.lang.String dataReference) - { - this._dataReference = dataReference; - this._choiceValue = dataReference; - } //-- void setDataReference(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return AppData - */ - public static org.vamsas.objects.core.AppData unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.AppData) Unmarshaller.unmarshal(org.vamsas.objects.core.AppData.class, reader); - } //-- org.vamsas.objects.core.AppData unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/AppDataDescriptor.java b/src/org/vamsas/objects/core/AppDataDescriptor.java deleted file mode 100644 index d0eeab9..0000000 --- a/src/org/vamsas/objects/core/AppDataDescriptor.java +++ /dev/null @@ -1,250 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class AppDataDescriptor. - * - * @version $Revision$ $Date$ - */ -public class AppDataDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AppDataDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "appData"; - - //-- set grouping compositor - setCompositorAsChoice(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- initialize element descriptors - - //-- _data - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(byte[].class, "_data", "data", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AppData target = (AppData) object; - return target.getData(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AppData target = (AppData) object; - target.setData( (byte[]) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _data - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _dataReference - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dataReference", "dataReference", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - AppData target = (AppData) object; - return target.getDataReference(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - AppData target = (AppData) object; - target.setDataReference( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _dataReference - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.objects.core.AppDataDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return null; - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.AppData.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/ApplicationData.java b/src/org/vamsas/objects/core/ApplicationData.java deleted file mode 100644 index 76f44be..0000000 --- a/src/org/vamsas/objects/core/ApplicationData.java +++ /dev/null @@ -1,572 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class ApplicationData. - * - * @version $Revision$ $Date$ - */ -public class ApplicationData extends org.vamsas.objects.core.AppData -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Version string describing the application specific - * data storage version used - */ - private java.lang.String _version; - - /** - * Canonical name of application - */ - private java.lang.String _name; - - /** - * Field _userList - */ - private java.util.Vector _userList; - - /** - * Field _common - */ - private org.vamsas.objects.core.Common _common; - - /** - * Field _instanceList - */ - private java.util.Vector _instanceList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public ApplicationData() - { - super(); - _userList = new Vector(); - _instanceList = new Vector(); - } //-- org.vamsas.objects.core.ApplicationData() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addInstance - * - * - * - * @param vInstance - */ - public void addInstance(org.vamsas.objects.core.Instance vInstance) - throws java.lang.IndexOutOfBoundsException - { - _instanceList.addElement(vInstance); - } //-- void addInstance(org.vamsas.objects.core.Instance) - - /** - * Method addInstance - * - * - * - * @param index - * @param vInstance - */ - public void addInstance(int index, org.vamsas.objects.core.Instance vInstance) - throws java.lang.IndexOutOfBoundsException - { - _instanceList.insertElementAt(vInstance, index); - } //-- void addInstance(int, org.vamsas.objects.core.Instance) - - /** - * Method addUser - * - * - * - * @param vUser - */ - public void addUser(org.vamsas.objects.core.User vUser) - throws java.lang.IndexOutOfBoundsException - { - _userList.addElement(vUser); - } //-- void addUser(org.vamsas.objects.core.User) - - /** - * Method addUser - * - * - * - * @param index - * @param vUser - */ - public void addUser(int index, org.vamsas.objects.core.User vUser) - throws java.lang.IndexOutOfBoundsException - { - _userList.insertElementAt(vUser, index); - } //-- void addUser(int, org.vamsas.objects.core.User) - - /** - * Method enumerateInstance - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateInstance() - { - return _instanceList.elements(); - } //-- java.util.Enumeration enumerateInstance() - - /** - * Method enumerateUser - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateUser() - { - return _userList.elements(); - } //-- java.util.Enumeration enumerateUser() - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof ApplicationData) { - - ApplicationData temp = (ApplicationData)obj; - if (this._version != null) { - if (temp._version == null) return false; - else if (!(this._version.equals(temp._version))) - return false; - } - else if (temp._version != null) - return false; - if (this._name != null) { - if (temp._name == null) return false; - else if (!(this._name.equals(temp._name))) - return false; - } - else if (temp._name != null) - return false; - if (this._userList != null) { - if (temp._userList == null) return false; - else if (!(this._userList.equals(temp._userList))) - return false; - } - else if (temp._userList != null) - return false; - if (this._common != null) { - if (temp._common == null) return false; - else if (!(this._common.equals(temp._common))) - return false; - } - else if (temp._common != null) - return false; - if (this._instanceList != null) { - if (temp._instanceList == null) return false; - else if (!(this._instanceList.equals(temp._instanceList))) - return false; - } - else if (temp._instanceList != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'common'. - * - * @return Common - * @return the value of field 'common'. - */ - public org.vamsas.objects.core.Common getCommon() - { - return this._common; - } //-- org.vamsas.objects.core.Common getCommon() - - /** - * Method getInstance - * - * - * - * @param index - * @return Instance - */ - public org.vamsas.objects.core.Instance getInstance(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _instanceList.size())) { - throw new IndexOutOfBoundsException("getInstance: Index value '"+index+"' not in range [0.."+_instanceList.size()+ "]"); - } - - return (org.vamsas.objects.core.Instance) _instanceList.elementAt(index); - } //-- org.vamsas.objects.core.Instance getInstance(int) - - /** - * Method getInstance - * - * - * - * @return Instance - */ - public org.vamsas.objects.core.Instance[] getInstance() - { - int size = _instanceList.size(); - org.vamsas.objects.core.Instance[] mArray = new org.vamsas.objects.core.Instance[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Instance) _instanceList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Instance[] getInstance() - - /** - * Method getInstanceCount - * - * - * - * @return int - */ - public int getInstanceCount() - { - return _instanceList.size(); - } //-- int getInstanceCount() - - /** - * Returns the value of field 'name'. The field 'name' has the - * following description: Canonical name of application - * - * @return String - * @return the value of field 'name'. - */ - public java.lang.String getName() - { - return this._name; - } //-- java.lang.String getName() - - /** - * Method getUser - * - * - * - * @param index - * @return User - */ - public org.vamsas.objects.core.User getUser(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _userList.size())) { - throw new IndexOutOfBoundsException("getUser: Index value '"+index+"' not in range [0.."+_userList.size()+ "]"); - } - - return (org.vamsas.objects.core.User) _userList.elementAt(index); - } //-- org.vamsas.objects.core.User getUser(int) - - /** - * Method getUser - * - * - * - * @return User - */ - public org.vamsas.objects.core.User[] getUser() - { - int size = _userList.size(); - org.vamsas.objects.core.User[] mArray = new org.vamsas.objects.core.User[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.User) _userList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.User[] getUser() - - /** - * Method getUserCount - * - * - * - * @return int - */ - public int getUserCount() - { - return _userList.size(); - } //-- int getUserCount() - - /** - * Returns the value of field 'version'. The field 'version' - * has the following description: Version string describing the - * application specific - * data storage version used - * - * @return String - * @return the value of field 'version'. - */ - public java.lang.String getVersion() - { - return this._version; - } //-- java.lang.String getVersion() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method removeAllInstance - * - */ - public void removeAllInstance() - { - _instanceList.removeAllElements(); - } //-- void removeAllInstance() - - /** - * Method removeAllUser - * - */ - public void removeAllUser() - { - _userList.removeAllElements(); - } //-- void removeAllUser() - - /** - * Method removeInstance - * - * - * - * @param index - * @return Instance - */ - public org.vamsas.objects.core.Instance removeInstance(int index) - { - java.lang.Object obj = _instanceList.elementAt(index); - _instanceList.removeElementAt(index); - return (org.vamsas.objects.core.Instance) obj; - } //-- org.vamsas.objects.core.Instance removeInstance(int) - - /** - * Method removeUser - * - * - * - * @param index - * @return User - */ - public org.vamsas.objects.core.User removeUser(int index) - { - java.lang.Object obj = _userList.elementAt(index); - _userList.removeElementAt(index); - return (org.vamsas.objects.core.User) obj; - } //-- org.vamsas.objects.core.User removeUser(int) - - /** - * Sets the value of field 'common'. - * - * @param common the value of field 'common'. - */ - public void setCommon(org.vamsas.objects.core.Common common) - { - this._common = common; - } //-- void setCommon(org.vamsas.objects.core.Common) - - /** - * Method setInstance - * - * - * - * @param index - * @param vInstance - */ - public void setInstance(int index, org.vamsas.objects.core.Instance vInstance) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _instanceList.size())) { - throw new IndexOutOfBoundsException("setInstance: Index value '"+index+"' not in range [0.."+_instanceList.size()+ "]"); - } - _instanceList.setElementAt(vInstance, index); - } //-- void setInstance(int, org.vamsas.objects.core.Instance) - - /** - * Method setInstance - * - * - * - * @param instanceArray - */ - public void setInstance(org.vamsas.objects.core.Instance[] instanceArray) - { - //-- copy array - _instanceList.removeAllElements(); - for (int i = 0; i < instanceArray.length; i++) { - _instanceList.addElement(instanceArray[i]); - } - } //-- void setInstance(org.vamsas.objects.core.Instance) - - /** - * Sets the value of field 'name'. The field 'name' has the - * following description: Canonical name of application - * - * @param name the value of field 'name'. - */ - public void setName(java.lang.String name) - { - this._name = name; - } //-- void setName(java.lang.String) - - /** - * Method setUser - * - * - * - * @param index - * @param vUser - */ - public void setUser(int index, org.vamsas.objects.core.User vUser) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _userList.size())) { - throw new IndexOutOfBoundsException("setUser: Index value '"+index+"' not in range [0.."+_userList.size()+ "]"); - } - _userList.setElementAt(vUser, index); - } //-- void setUser(int, org.vamsas.objects.core.User) - - /** - * Method setUser - * - * - * - * @param userArray - */ - public void setUser(org.vamsas.objects.core.User[] userArray) - { - //-- copy array - _userList.removeAllElements(); - for (int i = 0; i < userArray.length; i++) { - _userList.addElement(userArray[i]); - } - } //-- void setUser(org.vamsas.objects.core.User) - - /** - * Sets the value of field 'version'. The field 'version' has - * the following description: Version string describing the - * application specific - * data storage version used - * - * @param version the value of field 'version'. - */ - public void setVersion(java.lang.String version) - { - this._version = version; - } //-- void setVersion(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return AppData - */ - public static org.vamsas.objects.core.AppData unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.ApplicationData) Unmarshaller.unmarshal(org.vamsas.objects.core.ApplicationData.class, reader); - } //-- org.vamsas.objects.core.AppData unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/ApplicationDataDescriptor.java b/src/org/vamsas/objects/core/ApplicationDataDescriptor.java deleted file mode 100644 index 894e945..0000000 --- a/src/org/vamsas/objects/core/ApplicationDataDescriptor.java +++ /dev/null @@ -1,359 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class ApplicationDataDescriptor. - * - * @version $Revision$ $Date$ - */ -public class ApplicationDataDescriptor extends org.vamsas.objects.core.AppDataDescriptor { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public ApplicationDataDescriptor() - { - super(); - setExtendsWithoutFlatten(new org.vamsas.objects.core.AppDataDescriptor()); - nsURI = "http://www.vamsas.org"; - xmlName = "ApplicationData"; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _version - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "version", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - ApplicationData target = (ApplicationData) object; - return target.getVersion(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - ApplicationData target = (ApplicationData) object; - target.setVersion( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _version - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _name - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - ApplicationData target = (ApplicationData) object; - return target.getName(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - ApplicationData target = (ApplicationData) object; - target.setName( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _name - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _userList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.User.class, "_userList", "User", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - ApplicationData target = (ApplicationData) object; - return target.getUser(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - ApplicationData target = (ApplicationData) object; - target.addUser( (org.vamsas.objects.core.User) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.User(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _userList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _common - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Common.class, "_common", "Common", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - ApplicationData target = (ApplicationData) object; - return target.getCommon(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - ApplicationData target = (ApplicationData) object; - target.setCommon( (org.vamsas.objects.core.Common) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Common(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _common - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _instanceList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Instance.class, "_instanceList", "Instance", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - ApplicationData target = (ApplicationData) object; - return target.getInstance(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - ApplicationData target = (ApplicationData) object; - target.addInstance( (org.vamsas.objects.core.Instance) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Instance(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _instanceList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.objects.core.ApplicationDataDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return super.getExtends(); - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - if (identity == null) - return super.getIdentity(); - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.ApplicationData.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/Attachment.java b/src/org/vamsas/objects/core/Attachment.java deleted file mode 100644 index 9bf14c2..0000000 --- a/src/org/vamsas/objects/core/Attachment.java +++ /dev/null @@ -1,330 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Attachment. - * - * @version $Revision$ $Date$ - */ -public class Attachment extends org.vamsas.objects.core.AppData -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * true implies data will be decompresses with Zip - * before presenting to application - */ - private boolean _compressed = false; - - /** - * keeps track of state for field: _compressed - */ - private boolean _has_compressed; - - /** - * Type of arbitrary data - TODO: decide format - use - * (extended) MIME types ? - */ - private java.lang.String _type; - - /** - * Object the arbitrary data is associated with - * - */ - private java.lang.Object _objectref; - - /** - * Primary Key for vamsas object referencing - * - */ - private java.lang.String _id; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Attachment() - { - super(); - } //-- org.vamsas.objects.core.Attachment() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method deleteCompressed - * - */ - public void deleteCompressed() - { - this._has_compressed= false; - } //-- void deleteCompressed() - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof Attachment) { - - Attachment temp = (Attachment)obj; - if (this._compressed != temp._compressed) - return false; - if (this._has_compressed != temp._has_compressed) - return false; - if (this._type != null) { - if (temp._type == null) return false; - else if (!(this._type.equals(temp._type))) - return false; - } - else if (temp._type != null) - return false; - if (this._objectref != null) { - if (temp._objectref == null) return false; - else if (!(this._objectref.equals(temp._objectref))) - return false; - } - else if (temp._objectref != null) - return false; - if (this._id != null) { - if (temp._id == null) return false; - else if (!(this._id.equals(temp._id))) - return false; - } - else if (temp._id != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'compressed'. The field - * 'compressed' has the following description: true implies - * data will be decompresses with Zip - * before presenting to application - * - * @return boolean - * @return the value of field 'compressed'. - */ - public boolean getCompressed() - { - return this._compressed; - } //-- boolean getCompressed() - - /** - * Returns the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * - * @return String - * @return the value of field 'id'. - */ - public java.lang.String getId() - { - return this._id; - } //-- java.lang.String getId() - - /** - * Returns the value of field 'objectref'. The field - * 'objectref' has the following description: Object the - * arbitrary data is associated with - * - * - * @return Object - * @return the value of field 'objectref'. - */ - public java.lang.Object getObjectref() - { - return this._objectref; - } //-- java.lang.Object getObjectref() - - /** - * Returns the value of field 'type'. The field 'type' has the - * following description: Type of arbitrary data - TODO: decide - * format - use - * (extended) MIME types ? - * - * @return String - * @return the value of field 'type'. - */ - public java.lang.String getType() - { - return this._type; - } //-- java.lang.String getType() - - /** - * Method hasCompressed - * - * - * - * @return boolean - */ - public boolean hasCompressed() - { - return this._has_compressed; - } //-- boolean hasCompressed() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Sets the value of field 'compressed'. The field 'compressed' - * has the following description: true implies data will be - * decompresses with Zip - * before presenting to application - * - * @param compressed the value of field 'compressed'. - */ - public void setCompressed(boolean compressed) - { - this._compressed = compressed; - this._has_compressed = true; - } //-- void setCompressed(boolean) - - /** - * Sets the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * - * @param id the value of field 'id'. - */ - public void setId(java.lang.String id) - { - this._id = id; - } //-- void setId(java.lang.String) - - /** - * Sets the value of field 'objectref'. The field 'objectref' - * has the following description: Object the arbitrary data is - * associated with - * - * - * @param objectref the value of field 'objectref'. - */ - public void setObjectref(java.lang.Object objectref) - { - this._objectref = objectref; - } //-- void setObjectref(java.lang.Object) - - /** - * Sets the value of field 'type'. The field 'type' has the - * following description: Type of arbitrary data - TODO: decide - * format - use - * (extended) MIME types ? - * - * @param type the value of field 'type'. - */ - public void setType(java.lang.String type) - { - this._type = type; - } //-- void setType(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return AppData - */ - public static org.vamsas.objects.core.AppData unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Attachment) Unmarshaller.unmarshal(org.vamsas.objects.core.Attachment.class, reader); - } //-- org.vamsas.objects.core.AppData unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/AttachmentDescriptor.java b/src/org/vamsas/objects/core/AttachmentDescriptor.java deleted file mode 100644 index e2669da..0000000 --- a/src/org/vamsas/objects/core/AttachmentDescriptor.java +++ /dev/null @@ -1,325 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class AttachmentDescriptor. - * - * @version $Revision$ $Date$ - */ -public class AttachmentDescriptor extends org.vamsas.objects.core.AppDataDescriptor { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AttachmentDescriptor() - { - super(); - setExtendsWithoutFlatten(new org.vamsas.objects.core.AppDataDescriptor()); - nsURI = "http://www.vamsas.org"; - xmlName = "Attachment"; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _compressed - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_compressed", "compressed", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Attachment target = (Attachment) object; - if(!target.hasCompressed()) - return null; - return (target.getCompressed() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Attachment target = (Attachment) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteCompressed(); - return; - } - target.setCompressed( ((java.lang.Boolean)value).booleanValue()); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _compressed - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - BooleanValidator typeValidator = new BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _type - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Attachment target = (Attachment) object; - return target.getType(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Attachment target = (Attachment) object; - target.setType( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _type - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _objectref - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_objectref", "objectref", org.exolab.castor.xml.NodeType.Attribute); - desc.setReference(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Attachment target = (Attachment) object; - return target.getObjectref(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Attachment target = (Attachment) object; - target.setObjectref( (java.lang.Object) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new java.lang.Object(); - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _objectref - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); - this.identity = desc; - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Attachment target = (Attachment) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Attachment target = (Attachment) object; - target.setId( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new java.lang.String(); - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } //-- org.vamsas.objects.core.AttachmentDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return super.getExtends(); - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - if (identity == null) - return super.getIdentity(); - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.Attachment.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/Common.java b/src/org/vamsas/objects/core/Common.java deleted file mode 100644 index 3fdab82..0000000 --- a/src/org/vamsas/objects/core/Common.java +++ /dev/null @@ -1,141 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Common. - * - * @version $Revision$ $Date$ - */ -public class Common extends org.vamsas.objects.core.AppData -implements java.io.Serializable -{ - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Common() - { - super(); - } //-- org.vamsas.objects.core.Common() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof Common) { - - Common temp = (Common)obj; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return AppData - */ - public static org.vamsas.objects.core.AppData unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Common) Unmarshaller.unmarshal(org.vamsas.objects.core.Common.class, reader); - } //-- org.vamsas.objects.core.AppData unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/CommonDescriptor.java b/src/org/vamsas/objects/core/CommonDescriptor.java deleted file mode 100644 index c7bc7e0..0000000 --- a/src/org/vamsas/objects/core/CommonDescriptor.java +++ /dev/null @@ -1,167 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class CommonDescriptor. - * - * @version $Revision$ $Date$ - */ -public class CommonDescriptor extends org.vamsas.objects.core.AppDataDescriptor { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public CommonDescriptor() - { - super(); - setExtendsWithoutFlatten(new org.vamsas.objects.core.AppDataDescriptor()); - nsURI = "http://www.vamsas.org"; - xmlName = "Common"; - } //-- org.vamsas.objects.core.CommonDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return super.getExtends(); - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - if (identity == null) - return super.getIdentity(); - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.Common.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/DataSet.java b/src/org/vamsas/objects/core/DataSet.java deleted file mode 100644 index e6d064e..0000000 --- a/src/org/vamsas/objects/core/DataSet.java +++ /dev/null @@ -1,850 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class DataSet. - * - * @version $Revision$ $Date$ - */ -public class DataSet extends org.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Primary Key for vamsas object referencing - */ - private java.lang.String _id; - - /** - * Field _sequenceList - */ - private java.util.Vector _sequenceList; - - /** - * Field _dataSetAnnotationsList - */ - private java.util.Vector _dataSetAnnotationsList; - - /** - * Field _alignmentList - */ - private java.util.Vector _alignmentList; - - /** - * Field _treeList - */ - private java.util.Vector _treeList; - - /** - * Field _provenance - */ - private org.vamsas.objects.core.Provenance _provenance; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public DataSet() - { - super(); - _sequenceList = new Vector(); - _dataSetAnnotationsList = new Vector(); - _alignmentList = new Vector(); - _treeList = new Vector(); - } //-- org.vamsas.objects.core.DataSet() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addAlignment - * - * - * - * @param vAlignment - */ - public void addAlignment(org.vamsas.objects.core.Alignment vAlignment) - throws java.lang.IndexOutOfBoundsException - { - _alignmentList.addElement(vAlignment); - } //-- void addAlignment(org.vamsas.objects.core.Alignment) - - /** - * Method addAlignment - * - * - * - * @param index - * @param vAlignment - */ - public void addAlignment(int index, org.vamsas.objects.core.Alignment vAlignment) - throws java.lang.IndexOutOfBoundsException - { - _alignmentList.insertElementAt(vAlignment, index); - } //-- void addAlignment(int, org.vamsas.objects.core.Alignment) - - /** - * Method addDataSetAnnotations - * - * - * - * @param vDataSetAnnotations - */ - public void addDataSetAnnotations(org.vamsas.objects.core.DataSetAnnotations vDataSetAnnotations) - throws java.lang.IndexOutOfBoundsException - { - _dataSetAnnotationsList.addElement(vDataSetAnnotations); - } //-- void addDataSetAnnotations(org.vamsas.objects.core.DataSetAnnotations) - - /** - * Method addDataSetAnnotations - * - * - * - * @param index - * @param vDataSetAnnotations - */ - public void addDataSetAnnotations(int index, org.vamsas.objects.core.DataSetAnnotations vDataSetAnnotations) - throws java.lang.IndexOutOfBoundsException - { - _dataSetAnnotationsList.insertElementAt(vDataSetAnnotations, index); - } //-- void addDataSetAnnotations(int, org.vamsas.objects.core.DataSetAnnotations) - - /** - * Method addSequence - * - * - * - * @param vSequence - */ - public void addSequence(org.vamsas.objects.core.Sequence vSequence) - throws java.lang.IndexOutOfBoundsException - { - _sequenceList.addElement(vSequence); - } //-- void addSequence(org.vamsas.objects.core.Sequence) - - /** - * Method addSequence - * - * - * - * @param index - * @param vSequence - */ - public void addSequence(int index, org.vamsas.objects.core.Sequence vSequence) - throws java.lang.IndexOutOfBoundsException - { - _sequenceList.insertElementAt(vSequence, index); - } //-- void addSequence(int, org.vamsas.objects.core.Sequence) - - /** - * Method addTree - * - * - * - * @param vTree - */ - public void addTree(org.vamsas.objects.core.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - _treeList.addElement(vTree); - } //-- void addTree(org.vamsas.objects.core.Tree) - - /** - * Method addTree - * - * - * - * @param index - * @param vTree - */ - public void addTree(int index, org.vamsas.objects.core.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - _treeList.insertElementAt(vTree, index); - } //-- void addTree(int, org.vamsas.objects.core.Tree) - - /** - * Method enumerateAlignment - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateAlignment() - { - return _alignmentList.elements(); - } //-- java.util.Enumeration enumerateAlignment() - - /** - * Method enumerateDataSetAnnotations - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateDataSetAnnotations() - { - return _dataSetAnnotationsList.elements(); - } //-- java.util.Enumeration enumerateDataSetAnnotations() - - /** - * Method enumerateSequence - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateSequence() - { - return _sequenceList.elements(); - } //-- java.util.Enumeration enumerateSequence() - - /** - * Method enumerateTree - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateTree() - { - return _treeList.elements(); - } //-- java.util.Enumeration enumerateTree() - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof DataSet) { - - DataSet temp = (DataSet)obj; - if (this._id != null) { - if (temp._id == null) return false; - else if (!(this._id.equals(temp._id))) - return false; - } - else if (temp._id != null) - return false; - if (this._sequenceList != null) { - if (temp._sequenceList == null) return false; - else if (!(this._sequenceList.equals(temp._sequenceList))) - return false; - } - else if (temp._sequenceList != null) - return false; - if (this._dataSetAnnotationsList != null) { - if (temp._dataSetAnnotationsList == null) return false; - else if (!(this._dataSetAnnotationsList.equals(temp._dataSetAnnotationsList))) - return false; - } - else if (temp._dataSetAnnotationsList != null) - return false; - if (this._alignmentList != null) { - if (temp._alignmentList == null) return false; - else if (!(this._alignmentList.equals(temp._alignmentList))) - return false; - } - else if (temp._alignmentList != null) - return false; - if (this._treeList != null) { - if (temp._treeList == null) return false; - else if (!(this._treeList.equals(temp._treeList))) - return false; - } - else if (temp._treeList != null) - return false; - if (this._provenance != null) { - if (temp._provenance == null) return false; - else if (!(this._provenance.equals(temp._provenance))) - return false; - } - else if (temp._provenance != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Method getAlignment - * - * - * - * @param index - * @return Alignment - */ - public org.vamsas.objects.core.Alignment getAlignment(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _alignmentList.size())) { - throw new IndexOutOfBoundsException("getAlignment: Index value '"+index+"' not in range [0.."+_alignmentList.size()+ "]"); - } - - return (org.vamsas.objects.core.Alignment) _alignmentList.elementAt(index); - } //-- org.vamsas.objects.core.Alignment getAlignment(int) - - /** - * Method getAlignment - * - * - * - * @return Alignment - */ - public org.vamsas.objects.core.Alignment[] getAlignment() - { - int size = _alignmentList.size(); - org.vamsas.objects.core.Alignment[] mArray = new org.vamsas.objects.core.Alignment[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Alignment) _alignmentList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Alignment[] getAlignment() - - /** - * Method getAlignmentCount - * - * - * - * @return int - */ - public int getAlignmentCount() - { - return _alignmentList.size(); - } //-- int getAlignmentCount() - - /** - * Method getDataSetAnnotations - * - * - * - * @param index - * @return DataSetAnnotations - */ - public org.vamsas.objects.core.DataSetAnnotations getDataSetAnnotations(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _dataSetAnnotationsList.size())) { - throw new IndexOutOfBoundsException("getDataSetAnnotations: Index value '"+index+"' not in range [0.."+_dataSetAnnotationsList.size()+ "]"); - } - - return (org.vamsas.objects.core.DataSetAnnotations) _dataSetAnnotationsList.elementAt(index); - } //-- org.vamsas.objects.core.DataSetAnnotations getDataSetAnnotations(int) - - /** - * Method getDataSetAnnotations - * - * - * - * @return DataSetAnnotations - */ - public org.vamsas.objects.core.DataSetAnnotations[] getDataSetAnnotations() - { - int size = _dataSetAnnotationsList.size(); - org.vamsas.objects.core.DataSetAnnotations[] mArray = new org.vamsas.objects.core.DataSetAnnotations[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.DataSetAnnotations) _dataSetAnnotationsList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.DataSetAnnotations[] getDataSetAnnotations() - - /** - * Method getDataSetAnnotationsCount - * - * - * - * @return int - */ - public int getDataSetAnnotationsCount() - { - return _dataSetAnnotationsList.size(); - } //-- int getDataSetAnnotationsCount() - - /** - * Returns the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * @return String - * @return the value of field 'id'. - */ - public java.lang.String getId() - { - return this._id; - } //-- java.lang.String getId() - - /** - * Returns the value of field 'provenance'. - * - * @return Provenance - * @return the value of field 'provenance'. - */ - public org.vamsas.objects.core.Provenance getProvenance() - { - return this._provenance; - } //-- org.vamsas.objects.core.Provenance getProvenance() - - /** - * Method getSequence - * - * - * - * @param index - * @return Sequence - */ - public org.vamsas.objects.core.Sequence getSequence(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _sequenceList.size())) { - throw new IndexOutOfBoundsException("getSequence: Index value '"+index+"' not in range [0.."+_sequenceList.size()+ "]"); - } - - return (org.vamsas.objects.core.Sequence) _sequenceList.elementAt(index); - } //-- org.vamsas.objects.core.Sequence getSequence(int) - - /** - * Method getSequence - * - * - * - * @return Sequence - */ - public org.vamsas.objects.core.Sequence[] getSequence() - { - int size = _sequenceList.size(); - org.vamsas.objects.core.Sequence[] mArray = new org.vamsas.objects.core.Sequence[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Sequence) _sequenceList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Sequence[] getSequence() - - /** - * Method getSequenceCount - * - * - * - * @return int - */ - public int getSequenceCount() - { - return _sequenceList.size(); - } //-- int getSequenceCount() - - /** - * Method getTree - * - * - * - * @param index - * @return Tree - */ - public org.vamsas.objects.core.Tree getTree(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _treeList.size())) { - throw new IndexOutOfBoundsException("getTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]"); - } - - return (org.vamsas.objects.core.Tree) _treeList.elementAt(index); - } //-- org.vamsas.objects.core.Tree getTree(int) - - /** - * Method getTree - * - * - * - * @return Tree - */ - public org.vamsas.objects.core.Tree[] getTree() - { - int size = _treeList.size(); - org.vamsas.objects.core.Tree[] mArray = new org.vamsas.objects.core.Tree[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Tree) _treeList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Tree[] getTree() - - /** - * Method getTreeCount - * - * - * - * @return int - */ - public int getTreeCount() - { - return _treeList.size(); - } //-- int getTreeCount() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method removeAlignment - * - * - * - * @param index - * @return Alignment - */ - public org.vamsas.objects.core.Alignment removeAlignment(int index) - { - java.lang.Object obj = _alignmentList.elementAt(index); - _alignmentList.removeElementAt(index); - return (org.vamsas.objects.core.Alignment) obj; - } //-- org.vamsas.objects.core.Alignment removeAlignment(int) - - /** - * Method removeAllAlignment - * - */ - public void removeAllAlignment() - { - _alignmentList.removeAllElements(); - } //-- void removeAllAlignment() - - /** - * Method removeAllDataSetAnnotations - * - */ - public void removeAllDataSetAnnotations() - { - _dataSetAnnotationsList.removeAllElements(); - } //-- void removeAllDataSetAnnotations() - - /** - * Method removeAllSequence - * - */ - public void removeAllSequence() - { - _sequenceList.removeAllElements(); - } //-- void removeAllSequence() - - /** - * Method removeAllTree - * - */ - public void removeAllTree() - { - _treeList.removeAllElements(); - } //-- void removeAllTree() - - /** - * Method removeDataSetAnnotations - * - * - * - * @param index - * @return DataSetAnnotations - */ - public org.vamsas.objects.core.DataSetAnnotations removeDataSetAnnotations(int index) - { - java.lang.Object obj = _dataSetAnnotationsList.elementAt(index); - _dataSetAnnotationsList.removeElementAt(index); - return (org.vamsas.objects.core.DataSetAnnotations) obj; - } //-- org.vamsas.objects.core.DataSetAnnotations removeDataSetAnnotations(int) - - /** - * Method removeSequence - * - * - * - * @param index - * @return Sequence - */ - public org.vamsas.objects.core.Sequence removeSequence(int index) - { - java.lang.Object obj = _sequenceList.elementAt(index); - _sequenceList.removeElementAt(index); - return (org.vamsas.objects.core.Sequence) obj; - } //-- org.vamsas.objects.core.Sequence removeSequence(int) - - /** - * Method removeTree - * - * - * - * @param index - * @return Tree - */ - public org.vamsas.objects.core.Tree removeTree(int index) - { - java.lang.Object obj = _treeList.elementAt(index); - _treeList.removeElementAt(index); - return (org.vamsas.objects.core.Tree) obj; - } //-- org.vamsas.objects.core.Tree removeTree(int) - - /** - * Method setAlignment - * - * - * - * @param index - * @param vAlignment - */ - public void setAlignment(int index, org.vamsas.objects.core.Alignment vAlignment) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _alignmentList.size())) { - throw new IndexOutOfBoundsException("setAlignment: Index value '"+index+"' not in range [0.."+_alignmentList.size()+ "]"); - } - _alignmentList.setElementAt(vAlignment, index); - } //-- void setAlignment(int, org.vamsas.objects.core.Alignment) - - /** - * Method setAlignment - * - * - * - * @param alignmentArray - */ - public void setAlignment(org.vamsas.objects.core.Alignment[] alignmentArray) - { - //-- copy array - _alignmentList.removeAllElements(); - for (int i = 0; i < alignmentArray.length; i++) { - _alignmentList.addElement(alignmentArray[i]); - } - } //-- void setAlignment(org.vamsas.objects.core.Alignment) - - /** - * Method setDataSetAnnotations - * - * - * - * @param index - * @param vDataSetAnnotations - */ - public void setDataSetAnnotations(int index, org.vamsas.objects.core.DataSetAnnotations vDataSetAnnotations) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _dataSetAnnotationsList.size())) { - throw new IndexOutOfBoundsException("setDataSetAnnotations: Index value '"+index+"' not in range [0.."+_dataSetAnnotationsList.size()+ "]"); - } - _dataSetAnnotationsList.setElementAt(vDataSetAnnotations, index); - } //-- void setDataSetAnnotations(int, org.vamsas.objects.core.DataSetAnnotations) - - /** - * Method setDataSetAnnotations - * - * - * - * @param dataSetAnnotationsArray - */ - public void setDataSetAnnotations(org.vamsas.objects.core.DataSetAnnotations[] dataSetAnnotationsArray) - { - //-- copy array - _dataSetAnnotationsList.removeAllElements(); - for (int i = 0; i < dataSetAnnotationsArray.length; i++) { - _dataSetAnnotationsList.addElement(dataSetAnnotationsArray[i]); - } - } //-- void setDataSetAnnotations(org.vamsas.objects.core.DataSetAnnotations) - - /** - * Sets the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * @param id the value of field 'id'. - */ - public void setId(java.lang.String id) - { - this._id = id; - } //-- void setId(java.lang.String) - - /** - * Sets the value of field 'provenance'. - * - * @param provenance the value of field 'provenance'. - */ - public void setProvenance(org.vamsas.objects.core.Provenance provenance) - { - this._provenance = provenance; - } //-- void setProvenance(org.vamsas.objects.core.Provenance) - - /** - * Method setSequence - * - * - * - * @param index - * @param vSequence - */ - public void setSequence(int index, org.vamsas.objects.core.Sequence vSequence) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _sequenceList.size())) { - throw new IndexOutOfBoundsException("setSequence: Index value '"+index+"' not in range [0.."+_sequenceList.size()+ "]"); - } - _sequenceList.setElementAt(vSequence, index); - } //-- void setSequence(int, org.vamsas.objects.core.Sequence) - - /** - * Method setSequence - * - * - * - * @param sequenceArray - */ - public void setSequence(org.vamsas.objects.core.Sequence[] sequenceArray) - { - //-- copy array - _sequenceList.removeAllElements(); - for (int i = 0; i < sequenceArray.length; i++) { - _sequenceList.addElement(sequenceArray[i]); - } - } //-- void setSequence(org.vamsas.objects.core.Sequence) - - /** - * Method setTree - * - * - * - * @param index - * @param vTree - */ - public void setTree(int index, org.vamsas.objects.core.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _treeList.size())) { - throw new IndexOutOfBoundsException("setTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]"); - } - _treeList.setElementAt(vTree, index); - } //-- void setTree(int, org.vamsas.objects.core.Tree) - - /** - * Method setTree - * - * - * - * @param treeArray - */ - public void setTree(org.vamsas.objects.core.Tree[] treeArray) - { - //-- copy array - _treeList.removeAllElements(); - for (int i = 0; i < treeArray.length; i++) { - _treeList.addElement(treeArray[i]); - } - } //-- void setTree(org.vamsas.objects.core.Tree) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return DataSet - */ - public static org.vamsas.objects.core.DataSet unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.DataSet) Unmarshaller.unmarshal(org.vamsas.objects.core.DataSet.class, reader); - } //-- org.vamsas.objects.core.DataSet unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/DataSetAnnotations.java b/src/org/vamsas/objects/core/DataSetAnnotations.java deleted file mode 100644 index 1d5552a..0000000 --- a/src/org/vamsas/objects/core/DataSetAnnotations.java +++ /dev/null @@ -1,217 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class DataSetAnnotations. - * - * @version $Revision$ $Date$ - */ -public class DataSetAnnotations extends org.vamsas.objects.core.RangeAnnotation -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * annotation is associated with a - * particular dataset sequence - */ - private java.lang.Object _seqRef; - - /** - * Field _provenance - */ - private org.vamsas.objects.core.Provenance _provenance; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public DataSetAnnotations() - { - super(); - } //-- org.vamsas.objects.core.DataSetAnnotations() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof DataSetAnnotations) { - - DataSetAnnotations temp = (DataSetAnnotations)obj; - if (this._seqRef != null) { - if (temp._seqRef == null) return false; - else if (!(this._seqRef.equals(temp._seqRef))) - return false; - } - else if (temp._seqRef != null) - return false; - if (this._provenance != null) { - if (temp._provenance == null) return false; - else if (!(this._provenance.equals(temp._provenance))) - return false; - } - else if (temp._provenance != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'provenance'. - * - * @return Provenance - * @return the value of field 'provenance'. - */ - public org.vamsas.objects.core.Provenance getProvenance() - { - return this._provenance; - } //-- org.vamsas.objects.core.Provenance getProvenance() - - /** - * Returns the value of field 'seqRef'. The field 'seqRef' has - * the following description: annotation is associated with a - * particular dataset sequence - * - * @return Object - * @return the value of field 'seqRef'. - */ - public java.lang.Object getSeqRef() - { - return this._seqRef; - } //-- java.lang.Object getSeqRef() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Sets the value of field 'provenance'. - * - * @param provenance the value of field 'provenance'. - */ - public void setProvenance(org.vamsas.objects.core.Provenance provenance) - { - this._provenance = provenance; - } //-- void setProvenance(org.vamsas.objects.core.Provenance) - - /** - * Sets the value of field 'seqRef'. The field 'seqRef' has the - * following description: annotation is associated with a - * particular dataset sequence - * - * @param seqRef the value of field 'seqRef'. - */ - public void setSeqRef(java.lang.Object seqRef) - { - this._seqRef = seqRef; - } //-- void setSeqRef(java.lang.Object) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return RangeType - */ - public static org.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.DataSetAnnotations) Unmarshaller.unmarshal(org.vamsas.objects.core.DataSetAnnotations.class, reader); - } //-- org.vamsas.objects.core.RangeType unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/DataSetAnnotationsDescriptor.java b/src/org/vamsas/objects/core/DataSetAnnotationsDescriptor.java deleted file mode 100644 index a8b2741..0000000 --- a/src/org/vamsas/objects/core/DataSetAnnotationsDescriptor.java +++ /dev/null @@ -1,249 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class DataSetAnnotationsDescriptor. - * - * @version $Revision$ $Date$ - */ -public class DataSetAnnotationsDescriptor extends org.vamsas.objects.core.RangeAnnotationDescriptor { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public DataSetAnnotationsDescriptor() - { - super(); - setExtendsWithoutFlatten(new org.vamsas.objects.core.RangeAnnotationDescriptor()); - nsURI = "http://www.vamsas.org"; - xmlName = "DataSetAnnotations"; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _seqRef - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_seqRef", "seqRef", org.exolab.castor.xml.NodeType.Attribute); - desc.setReference(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - DataSetAnnotations target = (DataSetAnnotations) object; - return target.getSeqRef(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DataSetAnnotations target = (DataSetAnnotations) object; - target.setSeqRef( (java.lang.Object) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new java.lang.Object(); - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _seqRef - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _provenance - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - DataSetAnnotations target = (DataSetAnnotations) object; - return target.getProvenance(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DataSetAnnotations target = (DataSetAnnotations) object; - target.setProvenance( (org.vamsas.objects.core.Provenance) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Provenance(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _provenance - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.objects.core.DataSetAnnotationsDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return super.getExtends(); - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - if (identity == null) - return super.getIdentity(); - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.DataSetAnnotations.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/DataSetDescriptor.java b/src/org/vamsas/objects/core/DataSetDescriptor.java deleted file mode 100644 index 7e342bc..0000000 --- a/src/org/vamsas/objects/core/DataSetDescriptor.java +++ /dev/null @@ -1,385 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class DataSetDescriptor. - * - * @version $Revision$ $Date$ - */ -public class DataSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public DataSetDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "DataSet"; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); - this.identity = desc; - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - DataSet target = (DataSet) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DataSet target = (DataSet) object; - target.setId( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new java.lang.String(); - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _sequenceList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Sequence.class, "_sequenceList", "Sequence", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - DataSet target = (DataSet) object; - return target.getSequence(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DataSet target = (DataSet) object; - target.addSequence( (org.vamsas.objects.core.Sequence) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Sequence(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _sequenceList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _dataSetAnnotationsList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.DataSetAnnotations.class, "_dataSetAnnotationsList", "DataSetAnnotations", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - DataSet target = (DataSet) object; - return target.getDataSetAnnotations(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DataSet target = (DataSet) object; - target.addDataSetAnnotations( (org.vamsas.objects.core.DataSetAnnotations) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.DataSetAnnotations(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _dataSetAnnotationsList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _alignmentList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Alignment.class, "_alignmentList", "Alignment", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - DataSet target = (DataSet) object; - return target.getAlignment(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DataSet target = (DataSet) object; - target.addAlignment( (org.vamsas.objects.core.Alignment) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Alignment(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _alignmentList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _treeList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Tree.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - DataSet target = (DataSet) object; - return target.getTree(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DataSet target = (DataSet) object; - target.addTree( (org.vamsas.objects.core.Tree) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Tree(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _treeList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _provenance - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - DataSet target = (DataSet) object; - return target.getProvenance(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DataSet target = (DataSet) object; - target.setProvenance( (org.vamsas.objects.core.Provenance) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Provenance(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _provenance - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.objects.core.DataSetDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return null; - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.DataSet.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/DbRef.java b/src/org/vamsas/objects/core/DbRef.java deleted file mode 100644 index 3be5671..0000000 --- a/src/org/vamsas/objects/core/DbRef.java +++ /dev/null @@ -1,806 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Store a list of database references - * for this sequence record - with optional mapping - * from database sequence to the given sequence record - * - * @version $Revision$ $Date$ - */ -public class DbRef extends org.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * TODO Database Naming - * Convention: either start using LSID (so - * change type to URI) or leave this as an - * uncontrolled/unspecified string ID - * - */ - private java.lang.String _source; - - /** - * Version must be specified - - * - */ - private java.lang.String _version; - - /** - * TODO: make some specification - * of the database field from which this - * accessionId is taken from - should that be a - * special property of the dbRef object ? - * - */ - private java.lang.String _accessionId; - - /** - * Primary Key for vamsas object - * referencing - */ - private java.lang.String _id; - - /** - * From: Offset to first - * position in dataset sequence record that - * this database entry maps to To: Offset - * to last position in dataset sequence - * record that this database entry maps to - * Start: Offset to first last position in - * database entry that first (or offset) - * position in sequence maps to End: Offset - * to last position in database entry that - * last (offset) position in sequence maps - * to - */ - private java.util.Vector _mapList; - - /** - * Field _linkList - */ - private java.util.Vector _linkList; - - /** - * Field _propertyList - */ - private java.util.Vector _propertyList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public DbRef() - { - super(); - _mapList = new Vector(); - _linkList = new Vector(); - _propertyList = new Vector(); - } //-- org.vamsas.objects.core.DbRef() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addLink - * - * - * - * @param vLink - */ - public void addLink(org.vamsas.objects.core.Link vLink) - throws java.lang.IndexOutOfBoundsException - { - _linkList.addElement(vLink); - } //-- void addLink(org.vamsas.objects.core.Link) - - /** - * Method addLink - * - * - * - * @param index - * @param vLink - */ - public void addLink(int index, org.vamsas.objects.core.Link vLink) - throws java.lang.IndexOutOfBoundsException - { - _linkList.insertElementAt(vLink, index); - } //-- void addLink(int, org.vamsas.objects.core.Link) - - /** - * Method addMap - * - * - * - * @param vMap - */ - public void addMap(org.vamsas.objects.core.Map vMap) - throws java.lang.IndexOutOfBoundsException - { - _mapList.addElement(vMap); - } //-- void addMap(org.vamsas.objects.core.Map) - - /** - * Method addMap - * - * - * - * @param index - * @param vMap - */ - public void addMap(int index, org.vamsas.objects.core.Map vMap) - throws java.lang.IndexOutOfBoundsException - { - _mapList.insertElementAt(vMap, index); - } //-- void addMap(int, org.vamsas.objects.core.Map) - - /** - * Method addProperty - * - * - * - * @param vProperty - */ - public void addProperty(org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - _propertyList.addElement(vProperty); - } //-- void addProperty(org.vamsas.objects.core.Property) - - /** - * Method addProperty - * - * - * - * @param index - * @param vProperty - */ - public void addProperty(int index, org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - _propertyList.insertElementAt(vProperty, index); - } //-- void addProperty(int, org.vamsas.objects.core.Property) - - /** - * Method enumerateLink - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateLink() - { - return _linkList.elements(); - } //-- java.util.Enumeration enumerateLink() - - /** - * Method enumerateMap - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateMap() - { - return _mapList.elements(); - } //-- java.util.Enumeration enumerateMap() - - /** - * Method enumerateProperty - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateProperty() - { - return _propertyList.elements(); - } //-- java.util.Enumeration enumerateProperty() - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof DbRef) { - - DbRef temp = (DbRef)obj; - if (this._source != null) { - if (temp._source == null) return false; - else if (!(this._source.equals(temp._source))) - return false; - } - else if (temp._source != null) - return false; - if (this._version != null) { - if (temp._version == null) return false; - else if (!(this._version.equals(temp._version))) - return false; - } - else if (temp._version != null) - return false; - if (this._accessionId != null) { - if (temp._accessionId == null) return false; - else if (!(this._accessionId.equals(temp._accessionId))) - return false; - } - else if (temp._accessionId != null) - return false; - if (this._id != null) { - if (temp._id == null) return false; - else if (!(this._id.equals(temp._id))) - return false; - } - else if (temp._id != null) - return false; - if (this._mapList != null) { - if (temp._mapList == null) return false; - else if (!(this._mapList.equals(temp._mapList))) - return false; - } - else if (temp._mapList != null) - return false; - if (this._linkList != null) { - if (temp._linkList == null) return false; - else if (!(this._linkList.equals(temp._linkList))) - return false; - } - else if (temp._linkList != null) - return false; - if (this._propertyList != null) { - if (temp._propertyList == null) return false; - else if (!(this._propertyList.equals(temp._propertyList))) - return false; - } - else if (temp._propertyList != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'accessionId'. The field - * 'accessionId' has the following description: TODO: make some - * specification - * of the database field from which this - * accessionId is taken from - should that be a - * special property of the dbRef object ? - * - * - * @return String - * @return the value of field 'accessionId'. - */ - public java.lang.String getAccessionId() - { - return this._accessionId; - } //-- java.lang.String getAccessionId() - - /** - * Returns the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * @return String - * @return the value of field 'id'. - */ - public java.lang.String getId() - { - return this._id; - } //-- java.lang.String getId() - - /** - * Method getLink - * - * - * - * @param index - * @return Link - */ - public org.vamsas.objects.core.Link getLink(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _linkList.size())) { - throw new IndexOutOfBoundsException("getLink: Index value '"+index+"' not in range [0.."+_linkList.size()+ "]"); - } - - return (org.vamsas.objects.core.Link) _linkList.elementAt(index); - } //-- org.vamsas.objects.core.Link getLink(int) - - /** - * Method getLink - * - * - * - * @return Link - */ - public org.vamsas.objects.core.Link[] getLink() - { - int size = _linkList.size(); - org.vamsas.objects.core.Link[] mArray = new org.vamsas.objects.core.Link[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Link) _linkList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Link[] getLink() - - /** - * Method getLinkCount - * - * - * - * @return int - */ - public int getLinkCount() - { - return _linkList.size(); - } //-- int getLinkCount() - - /** - * Method getMap - * - * - * - * @param index - * @return Map - */ - public org.vamsas.objects.core.Map getMap(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _mapList.size())) { - throw new IndexOutOfBoundsException("getMap: Index value '"+index+"' not in range [0.."+_mapList.size()+ "]"); - } - - return (org.vamsas.objects.core.Map) _mapList.elementAt(index); - } //-- org.vamsas.objects.core.Map getMap(int) - - /** - * Method getMap - * - * - * - * @return Map - */ - public org.vamsas.objects.core.Map[] getMap() - { - int size = _mapList.size(); - org.vamsas.objects.core.Map[] mArray = new org.vamsas.objects.core.Map[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Map) _mapList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Map[] getMap() - - /** - * Method getMapCount - * - * - * - * @return int - */ - public int getMapCount() - { - return _mapList.size(); - } //-- int getMapCount() - - /** - * Method getProperty - * - * - * - * @param index - * @return Property - */ - public org.vamsas.objects.core.Property getProperty(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _propertyList.size())) { - throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]"); - } - - return (org.vamsas.objects.core.Property) _propertyList.elementAt(index); - } //-- org.vamsas.objects.core.Property getProperty(int) - - /** - * Method getProperty - * - * - * - * @return Property - */ - public org.vamsas.objects.core.Property[] getProperty() - { - int size = _propertyList.size(); - org.vamsas.objects.core.Property[] mArray = new org.vamsas.objects.core.Property[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Property) _propertyList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Property[] getProperty() - - /** - * Method getPropertyCount - * - * - * - * @return int - */ - public int getPropertyCount() - { - return _propertyList.size(); - } //-- int getPropertyCount() - - /** - * Returns the value of field 'source'. The field 'source' has - * the following description: TODO Database Naming - * Convention: either start using LSID (so - * change type to URI) or leave this as an - * uncontrolled/unspecified string ID - * - * - * @return String - * @return the value of field 'source'. - */ - public java.lang.String getSource() - { - return this._source; - } //-- java.lang.String getSource() - - /** - * Returns the value of field 'version'. The field 'version' - * has the following description: Version must be specified - - * - * - * @return String - * @return the value of field 'version'. - */ - public java.lang.String getVersion() - { - return this._version; - } //-- java.lang.String getVersion() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method removeAllLink - * - */ - public void removeAllLink() - { - _linkList.removeAllElements(); - } //-- void removeAllLink() - - /** - * Method removeAllMap - * - */ - public void removeAllMap() - { - _mapList.removeAllElements(); - } //-- void removeAllMap() - - /** - * Method removeAllProperty - * - */ - public void removeAllProperty() - { - _propertyList.removeAllElements(); - } //-- void removeAllProperty() - - /** - * Method removeLink - * - * - * - * @param index - * @return Link - */ - public org.vamsas.objects.core.Link removeLink(int index) - { - java.lang.Object obj = _linkList.elementAt(index); - _linkList.removeElementAt(index); - return (org.vamsas.objects.core.Link) obj; - } //-- org.vamsas.objects.core.Link removeLink(int) - - /** - * Method removeMap - * - * - * - * @param index - * @return Map - */ - public org.vamsas.objects.core.Map removeMap(int index) - { - java.lang.Object obj = _mapList.elementAt(index); - _mapList.removeElementAt(index); - return (org.vamsas.objects.core.Map) obj; - } //-- org.vamsas.objects.core.Map removeMap(int) - - /** - * Method removeProperty - * - * - * - * @param index - * @return Property - */ - public org.vamsas.objects.core.Property removeProperty(int index) - { - java.lang.Object obj = _propertyList.elementAt(index); - _propertyList.removeElementAt(index); - return (org.vamsas.objects.core.Property) obj; - } //-- org.vamsas.objects.core.Property removeProperty(int) - - /** - * Sets the value of field 'accessionId'. The field - * 'accessionId' has the following description: TODO: make some - * specification - * of the database field from which this - * accessionId is taken from - should that be a - * special property of the dbRef object ? - * - * - * @param accessionId the value of field 'accessionId'. - */ - public void setAccessionId(java.lang.String accessionId) - { - this._accessionId = accessionId; - } //-- void setAccessionId(java.lang.String) - - /** - * Sets the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * @param id the value of field 'id'. - */ - public void setId(java.lang.String id) - { - this._id = id; - } //-- void setId(java.lang.String) - - /** - * Method setLink - * - * - * - * @param index - * @param vLink - */ - public void setLink(int index, org.vamsas.objects.core.Link vLink) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _linkList.size())) { - throw new IndexOutOfBoundsException("setLink: Index value '"+index+"' not in range [0.."+_linkList.size()+ "]"); - } - _linkList.setElementAt(vLink, index); - } //-- void setLink(int, org.vamsas.objects.core.Link) - - /** - * Method setLink - * - * - * - * @param linkArray - */ - public void setLink(org.vamsas.objects.core.Link[] linkArray) - { - //-- copy array - _linkList.removeAllElements(); - for (int i = 0; i < linkArray.length; i++) { - _linkList.addElement(linkArray[i]); - } - } //-- void setLink(org.vamsas.objects.core.Link) - - /** - * Method setMap - * - * - * - * @param index - * @param vMap - */ - public void setMap(int index, org.vamsas.objects.core.Map vMap) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _mapList.size())) { - throw new IndexOutOfBoundsException("setMap: Index value '"+index+"' not in range [0.."+_mapList.size()+ "]"); - } - _mapList.setElementAt(vMap, index); - } //-- void setMap(int, org.vamsas.objects.core.Map) - - /** - * Method setMap - * - * - * - * @param mapArray - */ - public void setMap(org.vamsas.objects.core.Map[] mapArray) - { - //-- copy array - _mapList.removeAllElements(); - for (int i = 0; i < mapArray.length; i++) { - _mapList.addElement(mapArray[i]); - } - } //-- void setMap(org.vamsas.objects.core.Map) - - /** - * Method setProperty - * - * - * - * @param index - * @param vProperty - */ - public void setProperty(int index, org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _propertyList.size())) { - throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]"); - } - _propertyList.setElementAt(vProperty, index); - } //-- void setProperty(int, org.vamsas.objects.core.Property) - - /** - * Method setProperty - * - * - * - * @param propertyArray - */ - public void setProperty(org.vamsas.objects.core.Property[] propertyArray) - { - //-- copy array - _propertyList.removeAllElements(); - for (int i = 0; i < propertyArray.length; i++) { - _propertyList.addElement(propertyArray[i]); - } - } //-- void setProperty(org.vamsas.objects.core.Property) - - /** - * Sets the value of field 'source'. The field 'source' has the - * following description: TODO Database Naming - * Convention: either start using LSID (so - * change type to URI) or leave this as an - * uncontrolled/unspecified string ID - * - * - * @param source the value of field 'source'. - */ - public void setSource(java.lang.String source) - { - this._source = source; - } //-- void setSource(java.lang.String) - - /** - * Sets the value of field 'version'. The field 'version' has - * the following description: Version must be specified - - * - * - * @param version the value of field 'version'. - */ - public void setVersion(java.lang.String version) - { - this._version = version; - } //-- void setVersion(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return DbRef - */ - public static org.vamsas.objects.core.DbRef unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.DbRef) Unmarshaller.unmarshal(org.vamsas.objects.core.DbRef.class, reader); - } //-- org.vamsas.objects.core.DbRef unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/DbRefDescriptor.java b/src/org/vamsas/objects/core/DbRefDescriptor.java deleted file mode 100644 index fdb9238..0000000 --- a/src/org/vamsas/objects/core/DbRefDescriptor.java +++ /dev/null @@ -1,430 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class DbRefDescriptor. - * - * @version $Revision$ $Date$ - */ -public class DbRefDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public DbRefDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "dbRef"; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _source - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_source", "source", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - DbRef target = (DbRef) object; - return target.getSource(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DbRef target = (DbRef) object; - target.setSource( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _source - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _version - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "version", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - DbRef target = (DbRef) object; - return target.getVersion(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DbRef target = (DbRef) object; - target.setVersion( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _version - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _accessionId - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_accessionId", "accessionId", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - DbRef target = (DbRef) object; - return target.getAccessionId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DbRef target = (DbRef) object; - target.setAccessionId( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _accessionId - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); - this.identity = desc; - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - DbRef target = (DbRef) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DbRef target = (DbRef) object; - target.setId( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new java.lang.String(); - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _mapList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Map.class, "_mapList", "map", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - DbRef target = (DbRef) object; - return target.getMap(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DbRef target = (DbRef) object; - target.addMap( (org.vamsas.objects.core.Map) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Map(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _mapList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _linkList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Link.class, "_linkList", "link", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - DbRef target = (DbRef) object; - return target.getLink(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DbRef target = (DbRef) object; - target.addLink( (org.vamsas.objects.core.Link) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Link(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _linkList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _propertyList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Property.class, "_propertyList", "property", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - DbRef target = (DbRef) object; - return target.getProperty(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - DbRef target = (DbRef) object; - target.addProperty( (org.vamsas.objects.core.Property) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Property(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _propertyList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.objects.core.DbRefDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return null; - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.DbRef.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/Entry.java b/src/org/vamsas/objects/core/Entry.java deleted file mode 100644 index dcf3c5e..0000000 --- a/src/org/vamsas/objects/core/Entry.java +++ /dev/null @@ -1,803 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Entry. - * - * @version $Revision$ $Date$ - */ -public class Entry extends org.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Primary Key for vamsas object referencing - * - */ - private java.lang.String _id; - - /** - * Who - */ - private java.lang.String _user; - - /** - * With which application - */ - private java.lang.String _app; - - /** - * Did what - */ - private java.lang.String _action; - - /** - * When - */ - private org.exolab.castor.types.Date _date; - - /** - * additional information - */ - private java.util.Vector _propertyList; - - /** - * parameter for the action - */ - private java.util.Vector _paramList; - - /** - * bioinformatic objects input to action - * - */ - private java.util.Vector _inputList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Entry() - { - super(); - _propertyList = new Vector(); - _paramList = new Vector(); - _inputList = new Vector(); - } //-- org.vamsas.objects.core.Entry() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addInput - * - * - * - * @param vInput - */ - public void addInput(org.vamsas.objects.core.Input vInput) - throws java.lang.IndexOutOfBoundsException - { - _inputList.addElement(vInput); - } //-- void addInput(org.vamsas.objects.core.Input) - - /** - * Method addInput - * - * - * - * @param index - * @param vInput - */ - public void addInput(int index, org.vamsas.objects.core.Input vInput) - throws java.lang.IndexOutOfBoundsException - { - _inputList.insertElementAt(vInput, index); - } //-- void addInput(int, org.vamsas.objects.core.Input) - - /** - * Method addParam - * - * - * - * @param vParam - */ - public void addParam(org.vamsas.objects.core.Param vParam) - throws java.lang.IndexOutOfBoundsException - { - _paramList.addElement(vParam); - } //-- void addParam(org.vamsas.objects.core.Param) - - /** - * Method addParam - * - * - * - * @param index - * @param vParam - */ - public void addParam(int index, org.vamsas.objects.core.Param vParam) - throws java.lang.IndexOutOfBoundsException - { - _paramList.insertElementAt(vParam, index); - } //-- void addParam(int, org.vamsas.objects.core.Param) - - /** - * Method addProperty - * - * - * - * @param vProperty - */ - public void addProperty(org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - _propertyList.addElement(vProperty); - } //-- void addProperty(org.vamsas.objects.core.Property) - - /** - * Method addProperty - * - * - * - * @param index - * @param vProperty - */ - public void addProperty(int index, org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - _propertyList.insertElementAt(vProperty, index); - } //-- void addProperty(int, org.vamsas.objects.core.Property) - - /** - * Method enumerateInput - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateInput() - { - return _inputList.elements(); - } //-- java.util.Enumeration enumerateInput() - - /** - * Method enumerateParam - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateParam() - { - return _paramList.elements(); - } //-- java.util.Enumeration enumerateParam() - - /** - * Method enumerateProperty - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateProperty() - { - return _propertyList.elements(); - } //-- java.util.Enumeration enumerateProperty() - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof Entry) { - - Entry temp = (Entry)obj; - if (this._id != null) { - if (temp._id == null) return false; - else if (!(this._id.equals(temp._id))) - return false; - } - else if (temp._id != null) - return false; - if (this._user != null) { - if (temp._user == null) return false; - else if (!(this._user.equals(temp._user))) - return false; - } - else if (temp._user != null) - return false; - if (this._app != null) { - if (temp._app == null) return false; - else if (!(this._app.equals(temp._app))) - return false; - } - else if (temp._app != null) - return false; - if (this._action != null) { - if (temp._action == null) return false; - else if (!(this._action.equals(temp._action))) - return false; - } - else if (temp._action != null) - return false; - if (this._date != null) { - if (temp._date == null) return false; - else if (!(this._date.equals(temp._date))) - return false; - } - else if (temp._date != null) - return false; - if (this._propertyList != null) { - if (temp._propertyList == null) return false; - else if (!(this._propertyList.equals(temp._propertyList))) - return false; - } - else if (temp._propertyList != null) - return false; - if (this._paramList != null) { - if (temp._paramList == null) return false; - else if (!(this._paramList.equals(temp._paramList))) - return false; - } - else if (temp._paramList != null) - return false; - if (this._inputList != null) { - if (temp._inputList == null) return false; - else if (!(this._inputList.equals(temp._inputList))) - return false; - } - else if (temp._inputList != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'action'. The field 'action' has - * the following description: Did what - * - * @return String - * @return the value of field 'action'. - */ - public java.lang.String getAction() - { - return this._action; - } //-- java.lang.String getAction() - - /** - * Returns the value of field 'app'. The field 'app' has the - * following description: With which application - * - * @return String - * @return the value of field 'app'. - */ - public java.lang.String getApp() - { - return this._app; - } //-- java.lang.String getApp() - - /** - * Returns the value of field 'date'. The field 'date' has the - * following description: When - * - * @return Date - * @return the value of field 'date'. - */ - public org.exolab.castor.types.Date getDate() - { - return this._date; - } //-- org.exolab.castor.types.Date getDate() - - /** - * Returns the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * - * @return String - * @return the value of field 'id'. - */ - public java.lang.String getId() - { - return this._id; - } //-- java.lang.String getId() - - /** - * Method getInput - * - * - * - * @param index - * @return Input - */ - public org.vamsas.objects.core.Input getInput(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _inputList.size())) { - throw new IndexOutOfBoundsException("getInput: Index value '"+index+"' not in range [0.."+_inputList.size()+ "]"); - } - - return (org.vamsas.objects.core.Input) _inputList.elementAt(index); - } //-- org.vamsas.objects.core.Input getInput(int) - - /** - * Method getInput - * - * - * - * @return Input - */ - public org.vamsas.objects.core.Input[] getInput() - { - int size = _inputList.size(); - org.vamsas.objects.core.Input[] mArray = new org.vamsas.objects.core.Input[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Input) _inputList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Input[] getInput() - - /** - * Method getInputCount - * - * - * - * @return int - */ - public int getInputCount() - { - return _inputList.size(); - } //-- int getInputCount() - - /** - * Method getParam - * - * - * - * @param index - * @return Param - */ - public org.vamsas.objects.core.Param getParam(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _paramList.size())) { - throw new IndexOutOfBoundsException("getParam: Index value '"+index+"' not in range [0.."+_paramList.size()+ "]"); - } - - return (org.vamsas.objects.core.Param) _paramList.elementAt(index); - } //-- org.vamsas.objects.core.Param getParam(int) - - /** - * Method getParam - * - * - * - * @return Param - */ - public org.vamsas.objects.core.Param[] getParam() - { - int size = _paramList.size(); - org.vamsas.objects.core.Param[] mArray = new org.vamsas.objects.core.Param[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Param) _paramList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Param[] getParam() - - /** - * Method getParamCount - * - * - * - * @return int - */ - public int getParamCount() - { - return _paramList.size(); - } //-- int getParamCount() - - /** - * Method getProperty - * - * - * - * @param index - * @return Property - */ - public org.vamsas.objects.core.Property getProperty(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _propertyList.size())) { - throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]"); - } - - return (org.vamsas.objects.core.Property) _propertyList.elementAt(index); - } //-- org.vamsas.objects.core.Property getProperty(int) - - /** - * Method getProperty - * - * - * - * @return Property - */ - public org.vamsas.objects.core.Property[] getProperty() - { - int size = _propertyList.size(); - org.vamsas.objects.core.Property[] mArray = new org.vamsas.objects.core.Property[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Property) _propertyList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Property[] getProperty() - - /** - * Method getPropertyCount - * - * - * - * @return int - */ - public int getPropertyCount() - { - return _propertyList.size(); - } //-- int getPropertyCount() - - /** - * Returns the value of field 'user'. The field 'user' has the - * following description: Who - * - * @return String - * @return the value of field 'user'. - */ - public java.lang.String getUser() - { - return this._user; - } //-- java.lang.String getUser() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method removeAllInput - * - */ - public void removeAllInput() - { - _inputList.removeAllElements(); - } //-- void removeAllInput() - - /** - * Method removeAllParam - * - */ - public void removeAllParam() - { - _paramList.removeAllElements(); - } //-- void removeAllParam() - - /** - * Method removeAllProperty - * - */ - public void removeAllProperty() - { - _propertyList.removeAllElements(); - } //-- void removeAllProperty() - - /** - * Method removeInput - * - * - * - * @param index - * @return Input - */ - public org.vamsas.objects.core.Input removeInput(int index) - { - java.lang.Object obj = _inputList.elementAt(index); - _inputList.removeElementAt(index); - return (org.vamsas.objects.core.Input) obj; - } //-- org.vamsas.objects.core.Input removeInput(int) - - /** - * Method removeParam - * - * - * - * @param index - * @return Param - */ - public org.vamsas.objects.core.Param removeParam(int index) - { - java.lang.Object obj = _paramList.elementAt(index); - _paramList.removeElementAt(index); - return (org.vamsas.objects.core.Param) obj; - } //-- org.vamsas.objects.core.Param removeParam(int) - - /** - * Method removeProperty - * - * - * - * @param index - * @return Property - */ - public org.vamsas.objects.core.Property removeProperty(int index) - { - java.lang.Object obj = _propertyList.elementAt(index); - _propertyList.removeElementAt(index); - return (org.vamsas.objects.core.Property) obj; - } //-- org.vamsas.objects.core.Property removeProperty(int) - - /** - * Sets the value of field 'action'. The field 'action' has the - * following description: Did what - * - * @param action the value of field 'action'. - */ - public void setAction(java.lang.String action) - { - this._action = action; - } //-- void setAction(java.lang.String) - - /** - * Sets the value of field 'app'. The field 'app' has the - * following description: With which application - * - * @param app the value of field 'app'. - */ - public void setApp(java.lang.String app) - { - this._app = app; - } //-- void setApp(java.lang.String) - - /** - * Sets the value of field 'date'. The field 'date' has the - * following description: When - * - * @param date the value of field 'date'. - */ - public void setDate(org.exolab.castor.types.Date date) - { - this._date = date; - } //-- void setDate(org.exolab.castor.types.Date) - - /** - * Sets the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * - * @param id the value of field 'id'. - */ - public void setId(java.lang.String id) - { - this._id = id; - } //-- void setId(java.lang.String) - - /** - * Method setInput - * - * - * - * @param index - * @param vInput - */ - public void setInput(int index, org.vamsas.objects.core.Input vInput) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _inputList.size())) { - throw new IndexOutOfBoundsException("setInput: Index value '"+index+"' not in range [0.."+_inputList.size()+ "]"); - } - _inputList.setElementAt(vInput, index); - } //-- void setInput(int, org.vamsas.objects.core.Input) - - /** - * Method setInput - * - * - * - * @param inputArray - */ - public void setInput(org.vamsas.objects.core.Input[] inputArray) - { - //-- copy array - _inputList.removeAllElements(); - for (int i = 0; i < inputArray.length; i++) { - _inputList.addElement(inputArray[i]); - } - } //-- void setInput(org.vamsas.objects.core.Input) - - /** - * Method setParam - * - * - * - * @param index - * @param vParam - */ - public void setParam(int index, org.vamsas.objects.core.Param vParam) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _paramList.size())) { - throw new IndexOutOfBoundsException("setParam: Index value '"+index+"' not in range [0.."+_paramList.size()+ "]"); - } - _paramList.setElementAt(vParam, index); - } //-- void setParam(int, org.vamsas.objects.core.Param) - - /** - * Method setParam - * - * - * - * @param paramArray - */ - public void setParam(org.vamsas.objects.core.Param[] paramArray) - { - //-- copy array - _paramList.removeAllElements(); - for (int i = 0; i < paramArray.length; i++) { - _paramList.addElement(paramArray[i]); - } - } //-- void setParam(org.vamsas.objects.core.Param) - - /** - * Method setProperty - * - * - * - * @param index - * @param vProperty - */ - public void setProperty(int index, org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _propertyList.size())) { - throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]"); - } - _propertyList.setElementAt(vProperty, index); - } //-- void setProperty(int, org.vamsas.objects.core.Property) - - /** - * Method setProperty - * - * - * - * @param propertyArray - */ - public void setProperty(org.vamsas.objects.core.Property[] propertyArray) - { - //-- copy array - _propertyList.removeAllElements(); - for (int i = 0; i < propertyArray.length; i++) { - _propertyList.addElement(propertyArray[i]); - } - } //-- void setProperty(org.vamsas.objects.core.Property) - - /** - * Sets the value of field 'user'. The field 'user' has the - * following description: Who - * - * @param user the value of field 'user'. - */ - public void setUser(java.lang.String user) - { - this._user = user; - } //-- void setUser(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Entry - */ - public static org.vamsas.objects.core.Entry unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Entry) Unmarshaller.unmarshal(org.vamsas.objects.core.Entry.class, reader); - } //-- org.vamsas.objects.core.Entry unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/EntryDescriptor.java b/src/org/vamsas/objects/core/EntryDescriptor.java deleted file mode 100644 index 0426fa4..0000000 --- a/src/org/vamsas/objects/core/EntryDescriptor.java +++ /dev/null @@ -1,471 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class EntryDescriptor. - * - * @version $Revision$ $Date$ - */ -public class EntryDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public EntryDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "entry"; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); - this.identity = desc; - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Entry target = (Entry) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Entry target = (Entry) object; - target.setId( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new java.lang.String(); - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _user - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_user", "User", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Entry target = (Entry) object; - return target.getUser(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Entry target = (Entry) object; - target.setUser( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _user - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _app - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_app", "App", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Entry target = (Entry) object; - return target.getApp(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Entry target = (Entry) object; - target.setApp( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _app - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _action - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_action", "Action", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Entry target = (Entry) object; - return target.getAction(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Entry target = (Entry) object; - target.setAction( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _action - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _date - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.exolab.castor.types.Date.class, "_date", "Date", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Entry target = (Entry) object; - return target.getDate(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Entry target = (Entry) object; - target.setDate( (org.exolab.castor.types.Date) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.exolab.castor.types.Date(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _date - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - DateTimeValidator typeValidator = new DateTimeValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _propertyList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Property.class, "_propertyList", "property", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Entry target = (Entry) object; - return target.getProperty(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Entry target = (Entry) object; - target.addProperty( (org.vamsas.objects.core.Property) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Property(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _propertyList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _paramList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Param.class, "_paramList", "param", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Entry target = (Entry) object; - return target.getParam(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Entry target = (Entry) object; - target.addParam( (org.vamsas.objects.core.Param) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Param(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _paramList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _inputList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Input.class, "_inputList", "input", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Entry target = (Entry) object; - return target.getInput(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Entry target = (Entry) object; - target.addInput( (org.vamsas.objects.core.Input) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Input(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _inputList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.objects.core.EntryDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return null; - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.Entry.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/Glyph.java b/src/org/vamsas/objects/core/Glyph.java deleted file mode 100644 index f5d9362..0000000 --- a/src/org/vamsas/objects/core/Glyph.java +++ /dev/null @@ -1,233 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Discrete symbol - possibly graphically represented - * - * - * @version $Revision$ $Date$ - */ -public class Glyph extends org.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * internal content storage - */ - private java.lang.String _content = ""; - - /** - * specifies the symbol dictionary for this - * glyph - eg utf8 (the default), aasecstr_3 or - * kd_hydrophobicity - the content is not validated so - * applications must ensure they gracefully deal with - * invalid entries here - */ - private java.lang.String _dict = "utf8"; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Glyph() - { - super(); - setContent(""); - setDict("utf8"); - } //-- org.vamsas.objects.core.Glyph() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof Glyph) { - - Glyph temp = (Glyph)obj; - if (this._content != null) { - if (temp._content == null) return false; - else if (!(this._content.equals(temp._content))) - return false; - } - else if (temp._content != null) - return false; - if (this._dict != null) { - if (temp._dict == null) return false; - else if (!(this._dict.equals(temp._dict))) - return false; - } - else if (temp._dict != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'content'. The field 'content' - * has the following description: internal content storage - * - * @return String - * @return the value of field 'content'. - */ - public java.lang.String getContent() - { - return this._content; - } //-- java.lang.String getContent() - - /** - * Returns the value of field 'dict'. The field 'dict' has the - * following description: specifies the symbol dictionary for - * this - * glyph - eg utf8 (the default), aasecstr_3 or - * kd_hydrophobicity - the content is not validated so - * applications must ensure they gracefully deal with - * invalid entries here - * - * @return String - * @return the value of field 'dict'. - */ - public java.lang.String getDict() - { - return this._dict; - } //-- java.lang.String getDict() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Sets the value of field 'content'. The field 'content' has - * the following description: internal content storage - * - * @param content the value of field 'content'. - */ - public void setContent(java.lang.String content) - { - this._content = content; - } //-- void setContent(java.lang.String) - - /** - * Sets the value of field 'dict'. The field 'dict' has the - * following description: specifies the symbol dictionary for - * this - * glyph - eg utf8 (the default), aasecstr_3 or - * kd_hydrophobicity - the content is not validated so - * applications must ensure they gracefully deal with - * invalid entries here - * - * @param dict the value of field 'dict'. - */ - public void setDict(java.lang.String dict) - { - this._dict = dict; - } //-- void setDict(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Glyph - */ - public static org.vamsas.objects.core.Glyph unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Glyph) Unmarshaller.unmarshal(org.vamsas.objects.core.Glyph.class, reader); - } //-- org.vamsas.objects.core.Glyph unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/GlyphDescriptor.java b/src/org/vamsas/objects/core/GlyphDescriptor.java deleted file mode 100644 index e1d6966..0000000 --- a/src/org/vamsas/objects/core/GlyphDescriptor.java +++ /dev/null @@ -1,244 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class GlyphDescriptor. - * - * @version $Revision$ $Date$ - */ -public class GlyphDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public GlyphDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "glyph"; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- _content - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Glyph target = (Glyph) object; - return target.getContent(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Glyph target = (Glyph) object; - target.setContent( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - addFieldDescriptor(desc); - - //-- validation code for: _content - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize attribute descriptors - - //-- _dict - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dict", "dict", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Glyph target = (Glyph) object; - return target.getDict(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Glyph target = (Glyph) object; - target.setDict( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _dict - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } //-- org.vamsas.objects.core.GlyphDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return null; - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.Glyph.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/Input.java b/src/org/vamsas/objects/core/Input.java deleted file mode 100644 index 4743d67..0000000 --- a/src/org/vamsas/objects/core/Input.java +++ /dev/null @@ -1,219 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Input. - * - * @version $Revision$ $Date$ - */ -public class Input extends org.vamsas.objects.core.RangeType -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _name - */ - private java.lang.String _name; - - /** - * Reference Frame for rangeType specfication - * - */ - private java.lang.Object _objRef; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Input() - { - super(); - } //-- org.vamsas.objects.core.Input() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof Input) { - - Input temp = (Input)obj; - if (this._name != null) { - if (temp._name == null) return false; - else if (!(this._name.equals(temp._name))) - return false; - } - else if (temp._name != null) - return false; - if (this._objRef != null) { - if (temp._objRef == null) return false; - else if (!(this._objRef.equals(temp._objRef))) - return false; - } - else if (temp._objRef != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'name'. - * - * @return String - * @return the value of field 'name'. - */ - public java.lang.String getName() - { - return this._name; - } //-- java.lang.String getName() - - /** - * Returns the value of field 'objRef'. The field 'objRef' has - * the following description: Reference Frame for rangeType - * specfication - * - * - * @return Object - * @return the value of field 'objRef'. - */ - public java.lang.Object getObjRef() - { - return this._objRef; - } //-- java.lang.Object getObjRef() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Sets the value of field 'name'. - * - * @param name the value of field 'name'. - */ - public void setName(java.lang.String name) - { - this._name = name; - } //-- void setName(java.lang.String) - - /** - * Sets the value of field 'objRef'. The field 'objRef' has the - * following description: Reference Frame for rangeType - * specfication - * - * - * @param objRef the value of field 'objRef'. - */ - public void setObjRef(java.lang.Object objRef) - { - this._objRef = objRef; - } //-- void setObjRef(java.lang.Object) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return RangeType - */ - public static org.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Input) Unmarshaller.unmarshal(org.vamsas.objects.core.Input.class, reader); - } //-- org.vamsas.objects.core.RangeType unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/InputDescriptor.java b/src/org/vamsas/objects/core/InputDescriptor.java deleted file mode 100644 index 56cc4b5..0000000 --- a/src/org/vamsas/objects/core/InputDescriptor.java +++ /dev/null @@ -1,247 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class InputDescriptor. - * - * @version $Revision$ $Date$ - */ -public class InputDescriptor extends org.vamsas.objects.core.RangeTypeDescriptor { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public InputDescriptor() - { - super(); - setExtendsWithoutFlatten(new org.vamsas.objects.core.RangeTypeDescriptor()); - nsURI = "http://www.vamsas.org"; - xmlName = "input"; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _name - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Input target = (Input) object; - return target.getName(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Input target = (Input) object; - target.setName( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _name - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _objRef - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_objRef", "objRef", org.exolab.castor.xml.NodeType.Attribute); - desc.setReference(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Input target = (Input) object; - return target.getObjRef(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Input target = (Input) object; - target.setObjRef( (java.lang.Object) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new java.lang.Object(); - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _objRef - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } //-- org.vamsas.objects.core.InputDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return super.getExtends(); - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - if (identity == null) - return super.getIdentity(); - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.Input.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/Instance.java b/src/org/vamsas/objects/core/Instance.java deleted file mode 100644 index 037d035..0000000 --- a/src/org/vamsas/objects/core/Instance.java +++ /dev/null @@ -1,179 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Instance. - * - * @version $Revision$ $Date$ - */ -public class Instance extends org.vamsas.objects.core.AppData -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _urn - */ - private java.lang.String _urn; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Instance() - { - super(); - } //-- org.vamsas.objects.core.Instance() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof Instance) { - - Instance temp = (Instance)obj; - if (this._urn != null) { - if (temp._urn == null) return false; - else if (!(this._urn.equals(temp._urn))) - return false; - } - else if (temp._urn != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'urn'. - * - * @return String - * @return the value of field 'urn'. - */ - public java.lang.String getUrn() - { - return this._urn; - } //-- java.lang.String getUrn() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Sets the value of field 'urn'. - * - * @param urn the value of field 'urn'. - */ - public void setUrn(java.lang.String urn) - { - this._urn = urn; - } //-- void setUrn(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return AppData - */ - public static org.vamsas.objects.core.AppData unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Instance) Unmarshaller.unmarshal(org.vamsas.objects.core.Instance.class, reader); - } //-- org.vamsas.objects.core.AppData unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/InstanceDescriptor.java b/src/org/vamsas/objects/core/InstanceDescriptor.java deleted file mode 100644 index 0fdec55..0000000 --- a/src/org/vamsas/objects/core/InstanceDescriptor.java +++ /dev/null @@ -1,213 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class InstanceDescriptor. - * - * @version $Revision$ $Date$ - */ -public class InstanceDescriptor extends org.vamsas.objects.core.AppDataDescriptor { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public InstanceDescriptor() - { - super(); - setExtendsWithoutFlatten(new org.vamsas.objects.core.AppDataDescriptor()); - nsURI = "http://www.vamsas.org"; - xmlName = "Instance"; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _urn - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_urn", "urn", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Instance target = (Instance) object; - return target.getUrn(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Instance target = (Instance) object; - target.setUrn( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _urn - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } //-- org.vamsas.objects.core.InstanceDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return super.getExtends(); - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - if (identity == null) - return super.getIdentity(); - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.Instance.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/Link.java b/src/org/vamsas/objects/core/Link.java deleted file mode 100644 index 1330cff..0000000 --- a/src/org/vamsas/objects/core/Link.java +++ /dev/null @@ -1,217 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Link. - * - * @version $Revision$ $Date$ - */ -public class Link extends org.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * internal content storage - */ - private java.lang.String _content = ""; - - /** - * The URI - */ - private java.lang.String _href; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Link() - { - super(); - setContent(""); - } //-- org.vamsas.objects.core.Link() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof Link) { - - Link temp = (Link)obj; - if (this._content != null) { - if (temp._content == null) return false; - else if (!(this._content.equals(temp._content))) - return false; - } - else if (temp._content != null) - return false; - if (this._href != null) { - if (temp._href == null) return false; - else if (!(this._href.equals(temp._href))) - return false; - } - else if (temp._href != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'content'. The field 'content' - * has the following description: internal content storage - * - * @return String - * @return the value of field 'content'. - */ - public java.lang.String getContent() - { - return this._content; - } //-- java.lang.String getContent() - - /** - * Returns the value of field 'href'. The field 'href' has the - * following description: The URI - * - * @return String - * @return the value of field 'href'. - */ - public java.lang.String getHref() - { - return this._href; - } //-- java.lang.String getHref() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Sets the value of field 'content'. The field 'content' has - * the following description: internal content storage - * - * @param content the value of field 'content'. - */ - public void setContent(java.lang.String content) - { - this._content = content; - } //-- void setContent(java.lang.String) - - /** - * Sets the value of field 'href'. The field 'href' has the - * following description: The URI - * - * @param href the value of field 'href'. - */ - public void setHref(java.lang.String href) - { - this._href = href; - } //-- void setHref(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Link - */ - public static org.vamsas.objects.core.Link unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Link) Unmarshaller.unmarshal(org.vamsas.objects.core.Link.class, reader); - } //-- org.vamsas.objects.core.Link unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/LinkDescriptor.java b/src/org/vamsas/objects/core/LinkDescriptor.java deleted file mode 100644 index 659278d..0000000 --- a/src/org/vamsas/objects/core/LinkDescriptor.java +++ /dev/null @@ -1,240 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class LinkDescriptor. - * - * @version $Revision$ $Date$ - */ -public class LinkDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public LinkDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "link"; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- _content - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Link target = (Link) object; - return target.getContent(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Link target = (Link) object; - target.setContent( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - addFieldDescriptor(desc); - - //-- validation code for: _content - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize attribute descriptors - - //-- _href - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_href", "href", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Link target = (Link) object; - return target.getHref(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Link target = (Link) object; - target.setHref( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new java.lang.String(); - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _href - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } //-- org.vamsas.objects.core.LinkDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return null; - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.Link.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/LockFile.java b/src/org/vamsas/objects/core/LockFile.java deleted file mode 100644 index a26bbe2..0000000 --- a/src/org/vamsas/objects/core/LockFile.java +++ /dev/null @@ -1,182 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class LockFile. - * - * @version $Revision$ $Date$ - */ -public class LockFile extends org.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * internal content storage - */ - private java.lang.String _content = ""; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public LockFile() - { - super(); - setContent(""); - } //-- org.vamsas.objects.core.LockFile() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof LockFile) { - - LockFile temp = (LockFile)obj; - if (this._content != null) { - if (temp._content == null) return false; - else if (!(this._content.equals(temp._content))) - return false; - } - else if (temp._content != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'content'. The field 'content' - * has the following description: internal content storage - * - * @return String - * @return the value of field 'content'. - */ - public java.lang.String getContent() - { - return this._content; - } //-- java.lang.String getContent() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Sets the value of field 'content'. The field 'content' has - * the following description: internal content storage - * - * @param content the value of field 'content'. - */ - public void setContent(java.lang.String content) - { - this._content = content; - } //-- void setContent(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return LockFile - */ - public static org.vamsas.objects.core.LockFile unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.LockFile) Unmarshaller.unmarshal(org.vamsas.objects.core.LockFile.class, reader); - } //-- org.vamsas.objects.core.LockFile unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/LockFileDescriptor.java b/src/org/vamsas/objects/core/LockFileDescriptor.java deleted file mode 100644 index b837f28..0000000 --- a/src/org/vamsas/objects/core/LockFileDescriptor.java +++ /dev/null @@ -1,207 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class LockFileDescriptor. - * - * @version $Revision$ $Date$ - */ -public class LockFileDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public LockFileDescriptor() - { - super(); - nsURI = "http://www.vamsas.ac.uk/vamsasDocument"; - xmlName = "LockFile"; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- _content - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - LockFile target = (LockFile) object; - return target.getContent(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - LockFile target = (LockFile) object; - target.setContent( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - addFieldDescriptor(desc); - - //-- validation code for: _content - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize attribute descriptors - - //-- initialize element descriptors - - } //-- org.vamsas.objects.core.LockFileDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return null; - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.LockFile.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/Map.java b/src/org/vamsas/objects/core/Map.java deleted file mode 100644 index 38bab4b..0000000 --- a/src/org/vamsas/objects/core/Map.java +++ /dev/null @@ -1,151 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * From: Offset to first - * position in dataset sequence record that - * this database entry maps to To: Offset - * to last position in dataset sequence - * record that this database entry maps to - * Start: Offset to first last position in - * database entry that first (or offset) - * position in sequence maps to End: Offset - * to last position in database entry that - * last (offset) position in sequence maps - * to - * - * @version $Revision$ $Date$ - */ -public class Map extends org.vamsas.objects.core.MapList -implements java.io.Serializable -{ - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Map() - { - super(); - } //-- org.vamsas.objects.core.Map() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof Map) { - - Map temp = (Map)obj; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return MapList - */ - public static org.vamsas.objects.core.MapList unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Map) Unmarshaller.unmarshal(org.vamsas.objects.core.Map.class, reader); - } //-- org.vamsas.objects.core.MapList unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/MapDescriptor.java b/src/org/vamsas/objects/core/MapDescriptor.java deleted file mode 100644 index a4c5123..0000000 --- a/src/org/vamsas/objects/core/MapDescriptor.java +++ /dev/null @@ -1,167 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class MapDescriptor. - * - * @version $Revision$ $Date$ - */ -public class MapDescriptor extends org.vamsas.objects.core.MapListDescriptor { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public MapDescriptor() - { - super(); - setExtendsWithoutFlatten(new org.vamsas.objects.core.MapListDescriptor()); - nsURI = "http://www.vamsas.org"; - xmlName = "map"; - } //-- org.vamsas.objects.core.MapDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return super.getExtends(); - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - if (identity == null) - return super.getIdentity(); - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.Map.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/MapList.java b/src/org/vamsas/objects/core/MapList.java deleted file mode 100644 index 608ee58..0000000 --- a/src/org/vamsas/objects/core/MapList.java +++ /dev/null @@ -1,404 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class MapList. - * - * @version $Revision$ $Date$ - */ -public class MapList extends org.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Offset to first position in dataset sequence record that - * start - * position on 'onto' maps to - */ - private int _from = 0; - - /** - * keeps track of state for field: _from - */ - private boolean _has_from; - - /** - * Offset to last position in dataset sequence record that end - * position on 'onto' maps to - */ - private int _to = 0; - - /** - * keeps track of state for field: _to - */ - private boolean _has_to; - - /** - * Offset to first position in database entry that first (or - * offset) - * position in sequence maps to - */ - private int _start; - - /** - * keeps track of state for field: _start - */ - private boolean _has_start; - - /** - * Offset to last position in database entry that last (offset) - * position in sequence maps to - */ - private int _end; - - /** - * keeps track of state for field: _end - */ - private boolean _has_end; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public MapList() - { - super(); - } //-- org.vamsas.objects.core.MapList() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method deleteEnd - * - */ - public void deleteEnd() - { - this._has_end= false; - } //-- void deleteEnd() - - /** - * Method deleteFrom - * - */ - public void deleteFrom() - { - this._has_from= false; - } //-- void deleteFrom() - - /** - * Method deleteStart - * - */ - public void deleteStart() - { - this._has_start= false; - } //-- void deleteStart() - - /** - * Method deleteTo - * - */ - public void deleteTo() - { - this._has_to= false; - } //-- void deleteTo() - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof MapList) { - - MapList temp = (MapList)obj; - if (this._from != temp._from) - return false; - if (this._has_from != temp._has_from) - return false; - if (this._to != temp._to) - return false; - if (this._has_to != temp._has_to) - return false; - if (this._start != temp._start) - return false; - if (this._has_start != temp._has_start) - return false; - if (this._end != temp._end) - return false; - if (this._has_end != temp._has_end) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'end'. The field 'end' has the - * following description: Offset to last position in database - * entry that last (offset) - * position in sequence maps to - * - * @return int - * @return the value of field 'end'. - */ - public int getEnd() - { - return this._end; - } //-- int getEnd() - - /** - * Returns the value of field 'from'. The field 'from' has the - * following description: Offset to first position in dataset - * sequence record that start - * position on 'onto' maps to - * - * @return int - * @return the value of field 'from'. - */ - public int getFrom() - { - return this._from; - } //-- int getFrom() - - /** - * Returns the value of field 'start'. The field 'start' has - * the following description: Offset to first position in - * database entry that first (or offset) - * position in sequence maps to - * - * @return int - * @return the value of field 'start'. - */ - public int getStart() - { - return this._start; - } //-- int getStart() - - /** - * Returns the value of field 'to'. The field 'to' has the - * following description: Offset to last position in dataset - * sequence record that end - * position on 'onto' maps to - * - * @return int - * @return the value of field 'to'. - */ - public int getTo() - { - return this._to; - } //-- int getTo() - - /** - * Method hasEnd - * - * - * - * @return boolean - */ - public boolean hasEnd() - { - return this._has_end; - } //-- boolean hasEnd() - - /** - * Method hasFrom - * - * - * - * @return boolean - */ - public boolean hasFrom() - { - return this._has_from; - } //-- boolean hasFrom() - - /** - * Method hasStart - * - * - * - * @return boolean - */ - public boolean hasStart() - { - return this._has_start; - } //-- boolean hasStart() - - /** - * Method hasTo - * - * - * - * @return boolean - */ - public boolean hasTo() - { - return this._has_to; - } //-- boolean hasTo() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Sets the value of field 'end'. The field 'end' has the - * following description: Offset to last position in database - * entry that last (offset) - * position in sequence maps to - * - * @param end the value of field 'end'. - */ - public void setEnd(int end) - { - this._end = end; - this._has_end = true; - } //-- void setEnd(int) - - /** - * Sets the value of field 'from'. The field 'from' has the - * following description: Offset to first position in dataset - * sequence record that start - * position on 'onto' maps to - * - * @param from the value of field 'from'. - */ - public void setFrom(int from) - { - this._from = from; - this._has_from = true; - } //-- void setFrom(int) - - /** - * Sets the value of field 'start'. The field 'start' has the - * following description: Offset to first position in database - * entry that first (or offset) - * position in sequence maps to - * - * @param start the value of field 'start'. - */ - public void setStart(int start) - { - this._start = start; - this._has_start = true; - } //-- void setStart(int) - - /** - * Sets the value of field 'to'. The field 'to' has the - * following description: Offset to last position in dataset - * sequence record that end - * position on 'onto' maps to - * - * @param to the value of field 'to'. - */ - public void setTo(int to) - { - this._to = to; - this._has_to = true; - } //-- void setTo(int) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return MapList - */ - public static org.vamsas.objects.core.MapList unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.MapList) Unmarshaller.unmarshal(org.vamsas.objects.core.MapList.class, reader); - } //-- org.vamsas.objects.core.MapList unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/MapListDescriptor.java b/src/org/vamsas/objects/core/MapListDescriptor.java deleted file mode 100644 index 4d46e41..0000000 --- a/src/org/vamsas/objects/core/MapListDescriptor.java +++ /dev/null @@ -1,339 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class MapListDescriptor. - * - * @version $Revision$ $Date$ - */ -public class MapListDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public MapListDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "mapList"; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _from - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_from", "from", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - MapList target = (MapList) object; - if(!target.hasFrom()) - return null; - return new java.lang.Integer(target.getFrom()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - MapList target = (MapList) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteFrom(); - return; - } - target.setFrom( ((java.lang.Integer)value).intValue()); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _from - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - IntegerValidator typeValidator = new IntegerValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _to - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_to", "to", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - MapList target = (MapList) object; - if(!target.hasTo()) - return null; - return new java.lang.Integer(target.getTo()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - MapList target = (MapList) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteTo(); - return; - } - target.setTo( ((java.lang.Integer)value).intValue()); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _to - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - IntegerValidator typeValidator = new IntegerValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _start - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - MapList target = (MapList) object; - if(!target.hasStart()) - return null; - return new java.lang.Integer(target.getStart()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - MapList target = (MapList) object; - // ignore null values for non optional primitives - if (value == null) return; - - target.setStart( ((java.lang.Integer)value).intValue()); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _start - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - IntegerValidator typeValidator = new IntegerValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _end - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - MapList target = (MapList) object; - if(!target.hasEnd()) - return null; - return new java.lang.Integer(target.getEnd()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - MapList target = (MapList) object; - // ignore null values for non optional primitives - if (value == null) return; - - target.setEnd( ((java.lang.Integer)value).intValue()); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _end - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - IntegerValidator typeValidator = new IntegerValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } //-- org.vamsas.objects.core.MapListDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return null; - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.MapList.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/Mapping.java b/src/org/vamsas/objects/core/Mapping.java deleted file mode 100644 index e68ad1d..0000000 --- a/src/org/vamsas/objects/core/Mapping.java +++ /dev/null @@ -1,186 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Mapping. - * - * @version $Revision$ $Date$ - */ -public class Mapping extends org.vamsas.objects.core.MapList -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * object to which the mapping is being mapped - * - */ - private java.lang.Object _onto; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Mapping() - { - super(); - } //-- org.vamsas.objects.core.Mapping() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof Mapping) { - - Mapping temp = (Mapping)obj; - if (this._onto != null) { - if (temp._onto == null) return false; - else if (!(this._onto.equals(temp._onto))) - return false; - } - else if (temp._onto != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'onto'. The field 'onto' has the - * following description: object to which the mapping is being - * mapped - * - * - * @return Object - * @return the value of field 'onto'. - */ - public java.lang.Object getOnto() - { - return this._onto; - } //-- java.lang.Object getOnto() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Sets the value of field 'onto'. The field 'onto' has the - * following description: object to which the mapping is being - * mapped - * - * - * @param onto the value of field 'onto'. - */ - public void setOnto(java.lang.Object onto) - { - this._onto = onto; - } //-- void setOnto(java.lang.Object) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return MapList - */ - public static org.vamsas.objects.core.MapList unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Mapping) Unmarshaller.unmarshal(org.vamsas.objects.core.Mapping.class, reader); - } //-- org.vamsas.objects.core.MapList unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/MappingDescriptor.java b/src/org/vamsas/objects/core/MappingDescriptor.java deleted file mode 100644 index 95a6cbb..0000000 --- a/src/org/vamsas/objects/core/MappingDescriptor.java +++ /dev/null @@ -1,210 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class MappingDescriptor. - * - * @version $Revision$ $Date$ - */ -public class MappingDescriptor extends org.vamsas.objects.core.MapListDescriptor { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public MappingDescriptor() - { - super(); - setExtendsWithoutFlatten(new org.vamsas.objects.core.MapListDescriptor()); - nsURI = "http://www.vamsas.org"; - xmlName = "mapping"; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _onto - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_onto", "onto", org.exolab.castor.xml.NodeType.Attribute); - desc.setReference(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Mapping target = (Mapping) object; - return target.getOnto(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Mapping target = (Mapping) object; - target.setOnto( (java.lang.Object) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new java.lang.Object(); - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _onto - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } //-- org.vamsas.objects.core.MappingDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return super.getExtends(); - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - if (identity == null) - return super.getIdentity(); - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.Mapping.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/Newick.java b/src/org/vamsas/objects/core/Newick.java deleted file mode 100644 index 2c60f61..0000000 --- a/src/org/vamsas/objects/core/Newick.java +++ /dev/null @@ -1,288 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Newick. - * - * @version $Revision$ $Date$ - */ -public class Newick extends org.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * internal content storage - */ - private java.lang.String _content = ""; - - /** - * Field _title - */ - private java.lang.String _title; - - /** - * Primary Key for vamsas object referencing - * - */ - private java.lang.String _id; - - /** - * Field _modifiable - */ - private java.lang.String _modifiable; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Newick() - { - super(); - setContent(""); - } //-- org.vamsas.objects.core.Newick() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof Newick) { - - Newick temp = (Newick)obj; - if (this._content != null) { - if (temp._content == null) return false; - else if (!(this._content.equals(temp._content))) - return false; - } - else if (temp._content != null) - return false; - if (this._title != null) { - if (temp._title == null) return false; - else if (!(this._title.equals(temp._title))) - return false; - } - else if (temp._title != null) - return false; - if (this._id != null) { - if (temp._id == null) return false; - else if (!(this._id.equals(temp._id))) - return false; - } - else if (temp._id != null) - return false; - if (this._modifiable != null) { - if (temp._modifiable == null) return false; - else if (!(this._modifiable.equals(temp._modifiable))) - return false; - } - else if (temp._modifiable != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'content'. The field 'content' - * has the following description: internal content storage - * - * @return String - * @return the value of field 'content'. - */ - public java.lang.String getContent() - { - return this._content; - } //-- java.lang.String getContent() - - /** - * Returns the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * - * @return String - * @return the value of field 'id'. - */ - public java.lang.String getId() - { - return this._id; - } //-- java.lang.String getId() - - /** - * Returns the value of field 'modifiable'. - * - * @return String - * @return the value of field 'modifiable'. - */ - public java.lang.String getModifiable() - { - return this._modifiable; - } //-- java.lang.String getModifiable() - - /** - * Returns the value of field 'title'. - * - * @return String - * @return the value of field 'title'. - */ - public java.lang.String getTitle() - { - return this._title; - } //-- java.lang.String getTitle() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Sets the value of field 'content'. The field 'content' has - * the following description: internal content storage - * - * @param content the value of field 'content'. - */ - public void setContent(java.lang.String content) - { - this._content = content; - } //-- void setContent(java.lang.String) - - /** - * Sets the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * - * @param id the value of field 'id'. - */ - public void setId(java.lang.String id) - { - this._id = id; - } //-- void setId(java.lang.String) - - /** - * Sets the value of field 'modifiable'. - * - * @param modifiable the value of field 'modifiable'. - */ - public void setModifiable(java.lang.String modifiable) - { - this._modifiable = modifiable; - } //-- void setModifiable(java.lang.String) - - /** - * Sets the value of field 'title'. - * - * @param title the value of field 'title'. - */ - public void setTitle(java.lang.String title) - { - this._title = title; - } //-- void setTitle(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Newick - */ - public static org.vamsas.objects.core.Newick unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Newick) Unmarshaller.unmarshal(org.vamsas.objects.core.Newick.class, reader); - } //-- org.vamsas.objects.core.Newick unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/NewickDescriptor.java b/src/org/vamsas/objects/core/NewickDescriptor.java deleted file mode 100644 index d56a141..0000000 --- a/src/org/vamsas/objects/core/NewickDescriptor.java +++ /dev/null @@ -1,315 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class NewickDescriptor. - * - * @version $Revision$ $Date$ - */ -public class NewickDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public NewickDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "newick"; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- _content - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Newick target = (Newick) object; - return target.getContent(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Newick target = (Newick) object; - target.setContent( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - addFieldDescriptor(desc); - - //-- validation code for: _content - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize attribute descriptors - - //-- _title - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Newick target = (Newick) object; - return target.getTitle(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Newick target = (Newick) object; - target.setTitle( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _title - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); - this.identity = desc; - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Newick target = (Newick) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Newick target = (Newick) object; - target.setId( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new java.lang.String(); - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _modifiable - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_modifiable", "modifiable", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Newick target = (Newick) object; - return target.getModifiable(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Newick target = (Newick) object; - target.setModifiable( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _modifiable - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } //-- org.vamsas.objects.core.NewickDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return null; - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.Newick.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/Param.java b/src/org/vamsas/objects/core/Param.java deleted file mode 100644 index b7c2ab5..0000000 --- a/src/org/vamsas/objects/core/Param.java +++ /dev/null @@ -1,261 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Param. - * - * @version $Revision$ $Date$ - */ -public class Param extends org.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * internal content storage - */ - private java.lang.String _content = ""; - - /** - * Field _name - */ - private java.lang.String _name; - - /** - * The type specifies how the property will be parsed. - * Empty property strings are allowed, and can be used to - * prototype the - * input to a document. TODO: specify allowed types - */ - private java.lang.String _type; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Param() - { - super(); - setContent(""); - } //-- org.vamsas.objects.core.Param() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof Param) { - - Param temp = (Param)obj; - if (this._content != null) { - if (temp._content == null) return false; - else if (!(this._content.equals(temp._content))) - return false; - } - else if (temp._content != null) - return false; - if (this._name != null) { - if (temp._name == null) return false; - else if (!(this._name.equals(temp._name))) - return false; - } - else if (temp._name != null) - return false; - if (this._type != null) { - if (temp._type == null) return false; - else if (!(this._type.equals(temp._type))) - return false; - } - else if (temp._type != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'content'. The field 'content' - * has the following description: internal content storage - * - * @return String - * @return the value of field 'content'. - */ - public java.lang.String getContent() - { - return this._content; - } //-- java.lang.String getContent() - - /** - * Returns the value of field 'name'. - * - * @return String - * @return the value of field 'name'. - */ - public java.lang.String getName() - { - return this._name; - } //-- java.lang.String getName() - - /** - * Returns the value of field 'type'. The field 'type' has the - * following description: The type specifies how the property - * will be parsed. - * Empty property strings are allowed, and can be used to - * prototype the - * input to a document. TODO: specify allowed types - * - * @return String - * @return the value of field 'type'. - */ - public java.lang.String getType() - { - return this._type; - } //-- java.lang.String getType() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Sets the value of field 'content'. The field 'content' has - * the following description: internal content storage - * - * @param content the value of field 'content'. - */ - public void setContent(java.lang.String content) - { - this._content = content; - } //-- void setContent(java.lang.String) - - /** - * Sets the value of field 'name'. - * - * @param name the value of field 'name'. - */ - public void setName(java.lang.String name) - { - this._name = name; - } //-- void setName(java.lang.String) - - /** - * Sets the value of field 'type'. The field 'type' has the - * following description: The type specifies how the property - * will be parsed. - * Empty property strings are allowed, and can be used to - * prototype the - * input to a document. TODO: specify allowed types - * - * @param type the value of field 'type'. - */ - public void setType(java.lang.String type) - { - this._type = type; - } //-- void setType(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Param - */ - public static org.vamsas.objects.core.Param unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Param) Unmarshaller.unmarshal(org.vamsas.objects.core.Param.class, reader); - } //-- org.vamsas.objects.core.Param unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/ParamDescriptor.java b/src/org/vamsas/objects/core/ParamDescriptor.java deleted file mode 100644 index d049192..0000000 --- a/src/org/vamsas/objects/core/ParamDescriptor.java +++ /dev/null @@ -1,285 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class ParamDescriptor. - * - * @version $Revision$ $Date$ - */ -public class ParamDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public ParamDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "param"; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- _content - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Param target = (Param) object; - return target.getContent(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Param target = (Param) object; - target.setContent( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - addFieldDescriptor(desc); - - //-- validation code for: _content - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize attribute descriptors - - //-- _name - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Param target = (Param) object; - return target.getName(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Param target = (Param) object; - target.setName( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _name - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _type - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Param target = (Param) object; - return target.getType(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Param target = (Param) object; - target.setType( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _type - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } //-- org.vamsas.objects.core.ParamDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return null; - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.Param.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/Pos.java b/src/org/vamsas/objects/core/Pos.java deleted file mode 100644 index 5053f98..0000000 --- a/src/org/vamsas/objects/core/Pos.java +++ /dev/null @@ -1,204 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * a position within the associated object's coordinate system - * - * - * @version $Revision$ $Date$ - */ -public class Pos extends org.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _i - */ - private int _i; - - /** - * keeps track of state for field: _i - */ - private boolean _has_i; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Pos() - { - super(); - } //-- org.vamsas.objects.core.Pos() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method deleteI - * - */ - public void deleteI() - { - this._has_i= false; - } //-- void deleteI() - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof Pos) { - - Pos temp = (Pos)obj; - if (this._i != temp._i) - return false; - if (this._has_i != temp._has_i) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'i'. - * - * @return int - * @return the value of field 'i'. - */ - public int getI() - { - return this._i; - } //-- int getI() - - /** - * Method hasI - * - * - * - * @return boolean - */ - public boolean hasI() - { - return this._has_i; - } //-- boolean hasI() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Sets the value of field 'i'. - * - * @param i the value of field 'i'. - */ - public void setI(int i) - { - this._i = i; - this._has_i = true; - } //-- void setI(int) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Pos - */ - public static org.vamsas.objects.core.Pos unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Pos) Unmarshaller.unmarshal(org.vamsas.objects.core.Pos.class, reader); - } //-- org.vamsas.objects.core.Pos unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/PosDescriptor.java b/src/org/vamsas/objects/core/PosDescriptor.java deleted file mode 100644 index fdfffc7..0000000 --- a/src/org/vamsas/objects/core/PosDescriptor.java +++ /dev/null @@ -1,213 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class PosDescriptor. - * - * @version $Revision$ $Date$ - */ -public class PosDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public PosDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "pos"; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _i - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_i", "i", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Pos target = (Pos) object; - if(!target.hasI()) - return null; - return new java.lang.Integer(target.getI()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Pos target = (Pos) object; - // ignore null values for non optional primitives - if (value == null) return; - - target.setI( ((java.lang.Integer)value).intValue()); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _i - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - IntegerValidator typeValidator= new IntegerValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } //-- org.vamsas.objects.core.PosDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return null; - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.Pos.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/Property.java b/src/org/vamsas/objects/core/Property.java deleted file mode 100644 index fb4aacc..0000000 --- a/src/org/vamsas/objects/core/Property.java +++ /dev/null @@ -1,261 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Property. - * - * @version $Revision$ $Date$ - */ -public class Property extends org.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * internal content storage - */ - private java.lang.String _content = ""; - - /** - * Field _name - */ - private java.lang.String _name; - - /** - * The type specifies how the property will be parsed. - * Empty property strings are allowed, and can be used to - * prototype the - * input to a document. TODO: specify allowed types - */ - private java.lang.String _type; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Property() - { - super(); - setContent(""); - } //-- org.vamsas.objects.core.Property() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof Property) { - - Property temp = (Property)obj; - if (this._content != null) { - if (temp._content == null) return false; - else if (!(this._content.equals(temp._content))) - return false; - } - else if (temp._content != null) - return false; - if (this._name != null) { - if (temp._name == null) return false; - else if (!(this._name.equals(temp._name))) - return false; - } - else if (temp._name != null) - return false; - if (this._type != null) { - if (temp._type == null) return false; - else if (!(this._type.equals(temp._type))) - return false; - } - else if (temp._type != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'content'. The field 'content' - * has the following description: internal content storage - * - * @return String - * @return the value of field 'content'. - */ - public java.lang.String getContent() - { - return this._content; - } //-- java.lang.String getContent() - - /** - * Returns the value of field 'name'. - * - * @return String - * @return the value of field 'name'. - */ - public java.lang.String getName() - { - return this._name; - } //-- java.lang.String getName() - - /** - * Returns the value of field 'type'. The field 'type' has the - * following description: The type specifies how the property - * will be parsed. - * Empty property strings are allowed, and can be used to - * prototype the - * input to a document. TODO: specify allowed types - * - * @return String - * @return the value of field 'type'. - */ - public java.lang.String getType() - { - return this._type; - } //-- java.lang.String getType() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Sets the value of field 'content'. The field 'content' has - * the following description: internal content storage - * - * @param content the value of field 'content'. - */ - public void setContent(java.lang.String content) - { - this._content = content; - } //-- void setContent(java.lang.String) - - /** - * Sets the value of field 'name'. - * - * @param name the value of field 'name'. - */ - public void setName(java.lang.String name) - { - this._name = name; - } //-- void setName(java.lang.String) - - /** - * Sets the value of field 'type'. The field 'type' has the - * following description: The type specifies how the property - * will be parsed. - * Empty property strings are allowed, and can be used to - * prototype the - * input to a document. TODO: specify allowed types - * - * @param type the value of field 'type'. - */ - public void setType(java.lang.String type) - { - this._type = type; - } //-- void setType(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Property - */ - public static org.vamsas.objects.core.Property unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Property) Unmarshaller.unmarshal(org.vamsas.objects.core.Property.class, reader); - } //-- org.vamsas.objects.core.Property unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/PropertyDescriptor.java b/src/org/vamsas/objects/core/PropertyDescriptor.java deleted file mode 100644 index bb80022..0000000 --- a/src/org/vamsas/objects/core/PropertyDescriptor.java +++ /dev/null @@ -1,285 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class PropertyDescriptor. - * - * @version $Revision$ $Date$ - */ -public class PropertyDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public PropertyDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "property"; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- _content - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Property target = (Property) object; - return target.getContent(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Property target = (Property) object; - target.setContent( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - addFieldDescriptor(desc); - - //-- validation code for: _content - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize attribute descriptors - - //-- _name - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Property target = (Property) object; - return target.getName(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Property target = (Property) object; - target.setName( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _name - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _type - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Property target = (Property) object; - return target.getType(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Property target = (Property) object; - target.setType( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _type - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } //-- org.vamsas.objects.core.PropertyDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return null; - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.Property.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/Provenance.java b/src/org/vamsas/objects/core/Provenance.java deleted file mode 100644 index e1f6b85..0000000 --- a/src/org/vamsas/objects/core/Provenance.java +++ /dev/null @@ -1,306 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Provenance. - * - * @version $Revision$ $Date$ - */ -public class Provenance extends org.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _entryList - */ - private java.util.Vector _entryList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Provenance() - { - super(); - _entryList = new Vector(); - } //-- org.vamsas.objects.core.Provenance() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addEntry - * - * - * - * @param vEntry - */ - public void addEntry(org.vamsas.objects.core.Entry vEntry) - throws java.lang.IndexOutOfBoundsException - { - _entryList.addElement(vEntry); - } //-- void addEntry(org.vamsas.objects.core.Entry) - - /** - * Method addEntry - * - * - * - * @param index - * @param vEntry - */ - public void addEntry(int index, org.vamsas.objects.core.Entry vEntry) - throws java.lang.IndexOutOfBoundsException - { - _entryList.insertElementAt(vEntry, index); - } //-- void addEntry(int, org.vamsas.objects.core.Entry) - - /** - * Method enumerateEntry - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateEntry() - { - return _entryList.elements(); - } //-- java.util.Enumeration enumerateEntry() - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof Provenance) { - - Provenance temp = (Provenance)obj; - if (this._entryList != null) { - if (temp._entryList == null) return false; - else if (!(this._entryList.equals(temp._entryList))) - return false; - } - else if (temp._entryList != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Method getEntry - * - * - * - * @param index - * @return Entry - */ - public org.vamsas.objects.core.Entry getEntry(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _entryList.size())) { - throw new IndexOutOfBoundsException("getEntry: Index value '"+index+"' not in range [0.."+_entryList.size()+ "]"); - } - - return (org.vamsas.objects.core.Entry) _entryList.elementAt(index); - } //-- org.vamsas.objects.core.Entry getEntry(int) - - /** - * Method getEntry - * - * - * - * @return Entry - */ - public org.vamsas.objects.core.Entry[] getEntry() - { - int size = _entryList.size(); - org.vamsas.objects.core.Entry[] mArray = new org.vamsas.objects.core.Entry[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Entry) _entryList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Entry[] getEntry() - - /** - * Method getEntryCount - * - * - * - * @return int - */ - public int getEntryCount() - { - return _entryList.size(); - } //-- int getEntryCount() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method removeAllEntry - * - */ - public void removeAllEntry() - { - _entryList.removeAllElements(); - } //-- void removeAllEntry() - - /** - * Method removeEntry - * - * - * - * @param index - * @return Entry - */ - public org.vamsas.objects.core.Entry removeEntry(int index) - { - java.lang.Object obj = _entryList.elementAt(index); - _entryList.removeElementAt(index); - return (org.vamsas.objects.core.Entry) obj; - } //-- org.vamsas.objects.core.Entry removeEntry(int) - - /** - * Method setEntry - * - * - * - * @param index - * @param vEntry - */ - public void setEntry(int index, org.vamsas.objects.core.Entry vEntry) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _entryList.size())) { - throw new IndexOutOfBoundsException("setEntry: Index value '"+index+"' not in range [0.."+_entryList.size()+ "]"); - } - _entryList.setElementAt(vEntry, index); - } //-- void setEntry(int, org.vamsas.objects.core.Entry) - - /** - * Method setEntry - * - * - * - * @param entryArray - */ - public void setEntry(org.vamsas.objects.core.Entry[] entryArray) - { - //-- copy array - _entryList.removeAllElements(); - for (int i = 0; i < entryArray.length; i++) { - _entryList.addElement(entryArray[i]); - } - } //-- void setEntry(org.vamsas.objects.core.Entry) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Provenance - */ - public static org.vamsas.objects.core.Provenance unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Provenance) Unmarshaller.unmarshal(org.vamsas.objects.core.Provenance.class, reader); - } //-- org.vamsas.objects.core.Provenance unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/ProvenanceDescriptor.java b/src/org/vamsas/objects/core/ProvenanceDescriptor.java deleted file mode 100644 index a76c8ab..0000000 --- a/src/org/vamsas/objects/core/ProvenanceDescriptor.java +++ /dev/null @@ -1,210 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class ProvenanceDescriptor. - * - * @version $Revision$ $Date$ - */ -public class ProvenanceDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public ProvenanceDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "Provenance"; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- initialize element descriptors - - //-- _entryList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Entry.class, "_entryList", "entry", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Provenance target = (Provenance) object; - return target.getEntry(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Provenance target = (Provenance) object; - target.addEntry( (org.vamsas.objects.core.Entry) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Entry(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _entryList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.objects.core.ProvenanceDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return null; - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.Provenance.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/RangeAnnotation.java b/src/org/vamsas/objects/core/RangeAnnotation.java deleted file mode 100644 index 0dda140..0000000 --- a/src/org/vamsas/objects/core/RangeAnnotation.java +++ /dev/null @@ -1,1093 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Annotation for a rangeSpec - values can be attached for the - * whole - * specification, and to each position within the spec. following - * the orientation - * specified by the ordered set of rangeSpec (pos, seg) elements. - * - * @version $Revision$ $Date$ - */ -public class RangeAnnotation extends org.vamsas.objects.core.RangeType -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Primary Key for vamsas object referencing - * - */ - private java.lang.String _id; - - /** - * Field _modifiable - */ - private java.lang.String _modifiable; - - /** - * Annotation with the same non-empty group name are grouped - * together - */ - private java.lang.String _group = ""; - - /** - * A Das Feature has both a type and a Type ID. We go the - * route of requiring the type string to be taken from a - * controlled - * vocabulary if an application expects others to make sense - * of it. The - * type may qualified - so uniprot:CHAIN is a valid type name, - * and - * considered distinct from someotherDB:CHAIN - */ - private java.lang.String _type; - - /** - * Short, meaningful name for the annotation - if this - * is absent, then the type string should be used in its - * place. - * - */ - private java.lang.String _label; - - /** - * Human readable description of the annotation - * - */ - private java.lang.String _description; - - /** - * TODO: specify this - we have considered taking the GO - * evidence codes as a model for assessing a measure of - * quality to an - * annotation. - */ - private java.lang.String _status; - - /** - * Annotation Element position maps to ordered positions - * defined by the sequence of rangeType pos positions or - * concatenated - * seg start/end segments. - */ - private java.util.Vector _annotationElementList; - - /** - * Ordered set of optionally named float values for the - * whole annotation - */ - private java.util.Vector _scoreList; - - /** - * Field _linkList - */ - private java.util.Vector _linkList; - - /** - * Note:These are mutable so an application should check - * them each time. - */ - private java.util.Vector _propertyList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public RangeAnnotation() - { - super(); - setGroup(""); - _annotationElementList = new Vector(); - _scoreList = new Vector(); - _linkList = new Vector(); - _propertyList = new Vector(); - } //-- org.vamsas.objects.core.RangeAnnotation() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addAnnotationElement - * - * - * - * @param vAnnotationElement - */ - public void addAnnotationElement(org.vamsas.objects.core.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException - { - _annotationElementList.addElement(vAnnotationElement); - } //-- void addAnnotationElement(org.vamsas.objects.core.AnnotationElement) - - /** - * Method addAnnotationElement - * - * - * - * @param index - * @param vAnnotationElement - */ - public void addAnnotationElement(int index, org.vamsas.objects.core.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException - { - _annotationElementList.insertElementAt(vAnnotationElement, index); - } //-- void addAnnotationElement(int, org.vamsas.objects.core.AnnotationElement) - - /** - * Method addLink - * - * - * - * @param vLink - */ - public void addLink(org.vamsas.objects.core.Link vLink) - throws java.lang.IndexOutOfBoundsException - { - _linkList.addElement(vLink); - } //-- void addLink(org.vamsas.objects.core.Link) - - /** - * Method addLink - * - * - * - * @param index - * @param vLink - */ - public void addLink(int index, org.vamsas.objects.core.Link vLink) - throws java.lang.IndexOutOfBoundsException - { - _linkList.insertElementAt(vLink, index); - } //-- void addLink(int, org.vamsas.objects.core.Link) - - /** - * Method addProperty - * - * - * - * @param vProperty - */ - public void addProperty(org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - _propertyList.addElement(vProperty); - } //-- void addProperty(org.vamsas.objects.core.Property) - - /** - * Method addProperty - * - * - * - * @param index - * @param vProperty - */ - public void addProperty(int index, org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - _propertyList.insertElementAt(vProperty, index); - } //-- void addProperty(int, org.vamsas.objects.core.Property) - - /** - * Method addScore - * - * - * - * @param vScore - */ - public void addScore(org.vamsas.objects.core.Score vScore) - throws java.lang.IndexOutOfBoundsException - { - _scoreList.addElement(vScore); - } //-- void addScore(org.vamsas.objects.core.Score) - - /** - * Method addScore - * - * - * - * @param index - * @param vScore - */ - public void addScore(int index, org.vamsas.objects.core.Score vScore) - throws java.lang.IndexOutOfBoundsException - { - _scoreList.insertElementAt(vScore, index); - } //-- void addScore(int, org.vamsas.objects.core.Score) - - /** - * Method enumerateAnnotationElement - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateAnnotationElement() - { - return _annotationElementList.elements(); - } //-- java.util.Enumeration enumerateAnnotationElement() - - /** - * Method enumerateLink - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateLink() - { - return _linkList.elements(); - } //-- java.util.Enumeration enumerateLink() - - /** - * Method enumerateProperty - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateProperty() - { - return _propertyList.elements(); - } //-- java.util.Enumeration enumerateProperty() - - /** - * Method enumerateScore - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateScore() - { - return _scoreList.elements(); - } //-- java.util.Enumeration enumerateScore() - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof RangeAnnotation) { - - RangeAnnotation temp = (RangeAnnotation)obj; - if (this._id != null) { - if (temp._id == null) return false; - else if (!(this._id.equals(temp._id))) - return false; - } - else if (temp._id != null) - return false; - if (this._modifiable != null) { - if (temp._modifiable == null) return false; - else if (!(this._modifiable.equals(temp._modifiable))) - return false; - } - else if (temp._modifiable != null) - return false; - if (this._group != null) { - if (temp._group == null) return false; - else if (!(this._group.equals(temp._group))) - return false; - } - else if (temp._group != null) - return false; - if (this._type != null) { - if (temp._type == null) return false; - else if (!(this._type.equals(temp._type))) - return false; - } - else if (temp._type != null) - return false; - if (this._label != null) { - if (temp._label == null) return false; - else if (!(this._label.equals(temp._label))) - return false; - } - else if (temp._label != null) - return false; - if (this._description != null) { - if (temp._description == null) return false; - else if (!(this._description.equals(temp._description))) - return false; - } - else if (temp._description != null) - return false; - if (this._status != null) { - if (temp._status == null) return false; - else if (!(this._status.equals(temp._status))) - return false; - } - else if (temp._status != null) - return false; - if (this._annotationElementList != null) { - if (temp._annotationElementList == null) return false; - else if (!(this._annotationElementList.equals(temp._annotationElementList))) - return false; - } - else if (temp._annotationElementList != null) - return false; - if (this._scoreList != null) { - if (temp._scoreList == null) return false; - else if (!(this._scoreList.equals(temp._scoreList))) - return false; - } - else if (temp._scoreList != null) - return false; - if (this._linkList != null) { - if (temp._linkList == null) return false; - else if (!(this._linkList.equals(temp._linkList))) - return false; - } - else if (temp._linkList != null) - return false; - if (this._propertyList != null) { - if (temp._propertyList == null) return false; - else if (!(this._propertyList.equals(temp._propertyList))) - return false; - } - else if (temp._propertyList != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Method getAnnotationElement - * - * - * - * @param index - * @return AnnotationElement - */ - public org.vamsas.objects.core.AnnotationElement getAnnotationElement(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _annotationElementList.size())) { - throw new IndexOutOfBoundsException("getAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]"); - } - - return (org.vamsas.objects.core.AnnotationElement) _annotationElementList.elementAt(index); - } //-- org.vamsas.objects.core.AnnotationElement getAnnotationElement(int) - - /** - * Method getAnnotationElement - * - * - * - * @return AnnotationElement - */ - public org.vamsas.objects.core.AnnotationElement[] getAnnotationElement() - { - int size = _annotationElementList.size(); - org.vamsas.objects.core.AnnotationElement[] mArray = new org.vamsas.objects.core.AnnotationElement[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.AnnotationElement) _annotationElementList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.AnnotationElement[] getAnnotationElement() - - /** - * Method getAnnotationElementCount - * - * - * - * @return int - */ - public int getAnnotationElementCount() - { - return _annotationElementList.size(); - } //-- int getAnnotationElementCount() - - /** - * Returns the value of field 'description'. The field - * 'description' has the following description: Human readable - * description of the annotation - * - * - * @return String - * @return the value of field 'description'. - */ - public java.lang.String getDescription() - { - return this._description; - } //-- java.lang.String getDescription() - - /** - * Returns the value of field 'group'. The field 'group' has - * the following description: Annotation with the same - * non-empty group name are grouped - * together - * - * @return String - * @return the value of field 'group'. - */ - public java.lang.String getGroup() - { - return this._group; - } //-- java.lang.String getGroup() - - /** - * Returns the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * - * @return String - * @return the value of field 'id'. - */ - public java.lang.String getId() - { - return this._id; - } //-- java.lang.String getId() - - /** - * Returns the value of field 'label'. The field 'label' has - * the following description: Short, meaningful name for the - * annotation - if this - * is absent, then the type string should be used in its - * place. - * - * - * @return String - * @return the value of field 'label'. - */ - public java.lang.String getLabel() - { - return this._label; - } //-- java.lang.String getLabel() - - /** - * Method getLink - * - * - * - * @param index - * @return Link - */ - public org.vamsas.objects.core.Link getLink(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _linkList.size())) { - throw new IndexOutOfBoundsException("getLink: Index value '"+index+"' not in range [0.."+_linkList.size()+ "]"); - } - - return (org.vamsas.objects.core.Link) _linkList.elementAt(index); - } //-- org.vamsas.objects.core.Link getLink(int) - - /** - * Method getLink - * - * - * - * @return Link - */ - public org.vamsas.objects.core.Link[] getLink() - { - int size = _linkList.size(); - org.vamsas.objects.core.Link[] mArray = new org.vamsas.objects.core.Link[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Link) _linkList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Link[] getLink() - - /** - * Method getLinkCount - * - * - * - * @return int - */ - public int getLinkCount() - { - return _linkList.size(); - } //-- int getLinkCount() - - /** - * Returns the value of field 'modifiable'. - * - * @return String - * @return the value of field 'modifiable'. - */ - public java.lang.String getModifiable() - { - return this._modifiable; - } //-- java.lang.String getModifiable() - - /** - * Method getProperty - * - * - * - * @param index - * @return Property - */ - public org.vamsas.objects.core.Property getProperty(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _propertyList.size())) { - throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]"); - } - - return (org.vamsas.objects.core.Property) _propertyList.elementAt(index); - } //-- org.vamsas.objects.core.Property getProperty(int) - - /** - * Method getProperty - * - * - * - * @return Property - */ - public org.vamsas.objects.core.Property[] getProperty() - { - int size = _propertyList.size(); - org.vamsas.objects.core.Property[] mArray = new org.vamsas.objects.core.Property[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Property) _propertyList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Property[] getProperty() - - /** - * Method getPropertyCount - * - * - * - * @return int - */ - public int getPropertyCount() - { - return _propertyList.size(); - } //-- int getPropertyCount() - - /** - * Method getScore - * - * - * - * @param index - * @return Score - */ - public org.vamsas.objects.core.Score getScore(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _scoreList.size())) { - throw new IndexOutOfBoundsException("getScore: Index value '"+index+"' not in range [0.."+_scoreList.size()+ "]"); - } - - return (org.vamsas.objects.core.Score) _scoreList.elementAt(index); - } //-- org.vamsas.objects.core.Score getScore(int) - - /** - * Method getScore - * - * - * - * @return Score - */ - public org.vamsas.objects.core.Score[] getScore() - { - int size = _scoreList.size(); - org.vamsas.objects.core.Score[] mArray = new org.vamsas.objects.core.Score[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Score) _scoreList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Score[] getScore() - - /** - * Method getScoreCount - * - * - * - * @return int - */ - public int getScoreCount() - { - return _scoreList.size(); - } //-- int getScoreCount() - - /** - * Returns the value of field 'status'. The field 'status' has - * the following description: TODO: specify this - we have - * considered taking the GO - * evidence codes as a model for assessing a measure of - * quality to an - * annotation. - * - * @return String - * @return the value of field 'status'. - */ - public java.lang.String getStatus() - { - return this._status; - } //-- java.lang.String getStatus() - - /** - * Returns the value of field 'type'. The field 'type' has the - * following description: A Das Feature has both a type and a - * Type ID. We go the - * route of requiring the type string to be taken from a - * controlled - * vocabulary if an application expects others to make sense - * of it. The - * type may qualified - so uniprot:CHAIN is a valid type name, - * and - * considered distinct from someotherDB:CHAIN - * - * @return String - * @return the value of field 'type'. - */ - public java.lang.String getType() - { - return this._type; - } //-- java.lang.String getType() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method removeAllAnnotationElement - * - */ - public void removeAllAnnotationElement() - { - _annotationElementList.removeAllElements(); - } //-- void removeAllAnnotationElement() - - /** - * Method removeAllLink - * - */ - public void removeAllLink() - { - _linkList.removeAllElements(); - } //-- void removeAllLink() - - /** - * Method removeAllProperty - * - */ - public void removeAllProperty() - { - _propertyList.removeAllElements(); - } //-- void removeAllProperty() - - /** - * Method removeAllScore - * - */ - public void removeAllScore() - { - _scoreList.removeAllElements(); - } //-- void removeAllScore() - - /** - * Method removeAnnotationElement - * - * - * - * @param index - * @return AnnotationElement - */ - public org.vamsas.objects.core.AnnotationElement removeAnnotationElement(int index) - { - java.lang.Object obj = _annotationElementList.elementAt(index); - _annotationElementList.removeElementAt(index); - return (org.vamsas.objects.core.AnnotationElement) obj; - } //-- org.vamsas.objects.core.AnnotationElement removeAnnotationElement(int) - - /** - * Method removeLink - * - * - * - * @param index - * @return Link - */ - public org.vamsas.objects.core.Link removeLink(int index) - { - java.lang.Object obj = _linkList.elementAt(index); - _linkList.removeElementAt(index); - return (org.vamsas.objects.core.Link) obj; - } //-- org.vamsas.objects.core.Link removeLink(int) - - /** - * Method removeProperty - * - * - * - * @param index - * @return Property - */ - public org.vamsas.objects.core.Property removeProperty(int index) - { - java.lang.Object obj = _propertyList.elementAt(index); - _propertyList.removeElementAt(index); - return (org.vamsas.objects.core.Property) obj; - } //-- org.vamsas.objects.core.Property removeProperty(int) - - /** - * Method removeScore - * - * - * - * @param index - * @return Score - */ - public org.vamsas.objects.core.Score removeScore(int index) - { - java.lang.Object obj = _scoreList.elementAt(index); - _scoreList.removeElementAt(index); - return (org.vamsas.objects.core.Score) obj; - } //-- org.vamsas.objects.core.Score removeScore(int) - - /** - * Method setAnnotationElement - * - * - * - * @param index - * @param vAnnotationElement - */ - public void setAnnotationElement(int index, org.vamsas.objects.core.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _annotationElementList.size())) { - throw new IndexOutOfBoundsException("setAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]"); - } - _annotationElementList.setElementAt(vAnnotationElement, index); - } //-- void setAnnotationElement(int, org.vamsas.objects.core.AnnotationElement) - - /** - * Method setAnnotationElement - * - * - * - * @param annotationElementArray - */ - public void setAnnotationElement(org.vamsas.objects.core.AnnotationElement[] annotationElementArray) - { - //-- copy array - _annotationElementList.removeAllElements(); - for (int i = 0; i < annotationElementArray.length; i++) { - _annotationElementList.addElement(annotationElementArray[i]); - } - } //-- void setAnnotationElement(org.vamsas.objects.core.AnnotationElement) - - /** - * Sets the value of field 'description'. The field - * 'description' has the following description: Human readable - * description of the annotation - * - * - * @param description the value of field 'description'. - */ - public void setDescription(java.lang.String description) - { - this._description = description; - } //-- void setDescription(java.lang.String) - - /** - * Sets the value of field 'group'. The field 'group' has the - * following description: Annotation with the same non-empty - * group name are grouped - * together - * - * @param group the value of field 'group'. - */ - public void setGroup(java.lang.String group) - { - this._group = group; - } //-- void setGroup(java.lang.String) - - /** - * Sets the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * - * @param id the value of field 'id'. - */ - public void setId(java.lang.String id) - { - this._id = id; - } //-- void setId(java.lang.String) - - /** - * Sets the value of field 'label'. The field 'label' has the - * following description: Short, meaningful name for the - * annotation - if this - * is absent, then the type string should be used in its - * place. - * - * - * @param label the value of field 'label'. - */ - public void setLabel(java.lang.String label) - { - this._label = label; - } //-- void setLabel(java.lang.String) - - /** - * Method setLink - * - * - * - * @param index - * @param vLink - */ - public void setLink(int index, org.vamsas.objects.core.Link vLink) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _linkList.size())) { - throw new IndexOutOfBoundsException("setLink: Index value '"+index+"' not in range [0.."+_linkList.size()+ "]"); - } - _linkList.setElementAt(vLink, index); - } //-- void setLink(int, org.vamsas.objects.core.Link) - - /** - * Method setLink - * - * - * - * @param linkArray - */ - public void setLink(org.vamsas.objects.core.Link[] linkArray) - { - //-- copy array - _linkList.removeAllElements(); - for (int i = 0; i < linkArray.length; i++) { - _linkList.addElement(linkArray[i]); - } - } //-- void setLink(org.vamsas.objects.core.Link) - - /** - * Sets the value of field 'modifiable'. - * - * @param modifiable the value of field 'modifiable'. - */ - public void setModifiable(java.lang.String modifiable) - { - this._modifiable = modifiable; - } //-- void setModifiable(java.lang.String) - - /** - * Method setProperty - * - * - * - * @param index - * @param vProperty - */ - public void setProperty(int index, org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _propertyList.size())) { - throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]"); - } - _propertyList.setElementAt(vProperty, index); - } //-- void setProperty(int, org.vamsas.objects.core.Property) - - /** - * Method setProperty - * - * - * - * @param propertyArray - */ - public void setProperty(org.vamsas.objects.core.Property[] propertyArray) - { - //-- copy array - _propertyList.removeAllElements(); - for (int i = 0; i < propertyArray.length; i++) { - _propertyList.addElement(propertyArray[i]); - } - } //-- void setProperty(org.vamsas.objects.core.Property) - - /** - * Method setScore - * - * - * - * @param index - * @param vScore - */ - public void setScore(int index, org.vamsas.objects.core.Score vScore) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _scoreList.size())) { - throw new IndexOutOfBoundsException("setScore: Index value '"+index+"' not in range [0.."+_scoreList.size()+ "]"); - } - _scoreList.setElementAt(vScore, index); - } //-- void setScore(int, org.vamsas.objects.core.Score) - - /** - * Method setScore - * - * - * - * @param scoreArray - */ - public void setScore(org.vamsas.objects.core.Score[] scoreArray) - { - //-- copy array - _scoreList.removeAllElements(); - for (int i = 0; i < scoreArray.length; i++) { - _scoreList.addElement(scoreArray[i]); - } - } //-- void setScore(org.vamsas.objects.core.Score) - - /** - * Sets the value of field 'status'. The field 'status' has the - * following description: TODO: specify this - we have - * considered taking the GO - * evidence codes as a model for assessing a measure of - * quality to an - * annotation. - * - * @param status the value of field 'status'. - */ - public void setStatus(java.lang.String status) - { - this._status = status; - } //-- void setStatus(java.lang.String) - - /** - * Sets the value of field 'type'. The field 'type' has the - * following description: A Das Feature has both a type and a - * Type ID. We go the - * route of requiring the type string to be taken from a - * controlled - * vocabulary if an application expects others to make sense - * of it. The - * type may qualified - so uniprot:CHAIN is a valid type name, - * and - * considered distinct from someotherDB:CHAIN - * - * @param type the value of field 'type'. - */ - public void setType(java.lang.String type) - { - this._type = type; - } //-- void setType(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return RangeType - */ - public static org.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.RangeAnnotation) Unmarshaller.unmarshal(org.vamsas.objects.core.RangeAnnotation.class, reader); - } //-- org.vamsas.objects.core.RangeType unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/RangeAnnotationDescriptor.java b/src/org/vamsas/objects/core/RangeAnnotationDescriptor.java deleted file mode 100644 index 39bb29a..0000000 --- a/src/org/vamsas/objects/core/RangeAnnotationDescriptor.java +++ /dev/null @@ -1,578 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class RangeAnnotationDescriptor. - * - * @version $Revision$ $Date$ - */ -public class RangeAnnotationDescriptor extends org.vamsas.objects.core.RangeTypeDescriptor { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public RangeAnnotationDescriptor() - { - super(); - setExtendsWithoutFlatten(new org.vamsas.objects.core.RangeTypeDescriptor()); - nsURI = "http://www.vamsas.org"; - xmlName = "rangeAnnotation"; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); - this.identity = desc; - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - RangeAnnotation target = (RangeAnnotation) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - RangeAnnotation target = (RangeAnnotation) object; - target.setId( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new java.lang.String(); - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _modifiable - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_modifiable", "modifiable", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - RangeAnnotation target = (RangeAnnotation) object; - return target.getModifiable(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - RangeAnnotation target = (RangeAnnotation) object; - target.setModifiable( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _modifiable - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _group - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_group", "group", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - RangeAnnotation target = (RangeAnnotation) object; - return target.getGroup(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - RangeAnnotation target = (RangeAnnotation) object; - target.setGroup( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _group - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _type - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - RangeAnnotation target = (RangeAnnotation) object; - return target.getType(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - RangeAnnotation target = (RangeAnnotation) object; - target.setType( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _type - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _label - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_label", "label", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - RangeAnnotation target = (RangeAnnotation) object; - return target.getLabel(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - RangeAnnotation target = (RangeAnnotation) object; - target.setLabel( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _label - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _description - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - RangeAnnotation target = (RangeAnnotation) object; - return target.getDescription(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - RangeAnnotation target = (RangeAnnotation) object; - target.setDescription( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _description - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _status - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_status", "status", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - RangeAnnotation target = (RangeAnnotation) object; - return target.getStatus(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - RangeAnnotation target = (RangeAnnotation) object; - target.setStatus( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _status - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _annotationElementList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.AnnotationElement.class, "_annotationElementList", "annotationElement", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - RangeAnnotation target = (RangeAnnotation) object; - return target.getAnnotationElement(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - RangeAnnotation target = (RangeAnnotation) object; - target.addAnnotationElement( (org.vamsas.objects.core.AnnotationElement) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.AnnotationElement(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _annotationElementList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _scoreList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Score.class, "_scoreList", "score", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - RangeAnnotation target = (RangeAnnotation) object; - return target.getScore(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - RangeAnnotation target = (RangeAnnotation) object; - target.addScore( (org.vamsas.objects.core.Score) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Score(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _scoreList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _linkList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Link.class, "_linkList", "link", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - RangeAnnotation target = (RangeAnnotation) object; - return target.getLink(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - RangeAnnotation target = (RangeAnnotation) object; - target.addLink( (org.vamsas.objects.core.Link) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Link(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _linkList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _propertyList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Property.class, "_propertyList", "property", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - RangeAnnotation target = (RangeAnnotation) object; - return target.getProperty(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - RangeAnnotation target = (RangeAnnotation) object; - target.addProperty( (org.vamsas.objects.core.Property) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Property(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _propertyList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.objects.core.RangeAnnotationDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return super.getExtends(); - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - if (identity == null) - return super.getIdentity(); - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.RangeAnnotation.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/RangeType.java b/src/org/vamsas/objects/core/RangeType.java deleted file mode 100644 index c0d6571..0000000 --- a/src/org/vamsas/objects/core/RangeType.java +++ /dev/null @@ -1,452 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; - -/** - * 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 - * - * - * @version $Revision$ $Date$ - */ -public abstract class RangeType extends org.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Internal choice value storage - */ - private java.lang.Object _choiceValue; - - /** - * a position within the associated object's coordinate system - * - */ - private java.util.Vector _posList; - - /** - * a region from start to end, with flag for inclusivity of - * terminii - */ - private java.util.Vector _segList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public RangeType() - { - super(); - _posList = new Vector(); - _segList = new Vector(); - } //-- org.vamsas.objects.core.RangeType() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addPos - * - * - * - * @param vPos - */ - public void addPos(org.vamsas.objects.core.Pos vPos) - throws java.lang.IndexOutOfBoundsException - { - _posList.addElement(vPos); - } //-- void addPos(org.vamsas.objects.core.Pos) - - /** - * Method addPos - * - * - * - * @param index - * @param vPos - */ - public void addPos(int index, org.vamsas.objects.core.Pos vPos) - throws java.lang.IndexOutOfBoundsException - { - _posList.insertElementAt(vPos, index); - } //-- void addPos(int, org.vamsas.objects.core.Pos) - - /** - * Method addSeg - * - * - * - * @param vSeg - */ - public void addSeg(org.vamsas.objects.core.Seg vSeg) - throws java.lang.IndexOutOfBoundsException - { - _segList.addElement(vSeg); - } //-- void addSeg(org.vamsas.objects.core.Seg) - - /** - * Method addSeg - * - * - * - * @param index - * @param vSeg - */ - public void addSeg(int index, org.vamsas.objects.core.Seg vSeg) - throws java.lang.IndexOutOfBoundsException - { - _segList.insertElementAt(vSeg, index); - } //-- void addSeg(int, org.vamsas.objects.core.Seg) - - /** - * Method enumeratePos - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumeratePos() - { - return _posList.elements(); - } //-- java.util.Enumeration enumeratePos() - - /** - * Method enumerateSeg - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateSeg() - { - return _segList.elements(); - } //-- java.util.Enumeration enumerateSeg() - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof RangeType) { - - RangeType temp = (RangeType)obj; - if (this._choiceValue != null) { - if (temp._choiceValue == null) return false; - else if (!(this._choiceValue.equals(temp._choiceValue))) - return false; - } - else if (temp._choiceValue != null) - return false; - if (this._posList != null) { - if (temp._posList == null) return false; - else if (!(this._posList.equals(temp._posList))) - return false; - } - else if (temp._posList != null) - return false; - if (this._segList != null) { - if (temp._segList == null) return false; - else if (!(this._segList.equals(temp._segList))) - return false; - } - else if (temp._segList != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'choiceValue'. The field - * 'choiceValue' has the following description: Internal choice - * value storage - * - * @return Object - * @return the value of field 'choiceValue'. - */ - public java.lang.Object getChoiceValue() - { - return this._choiceValue; - } //-- java.lang.Object getChoiceValue() - - /** - * Method getPos - * - * - * - * @param index - * @return Pos - */ - public org.vamsas.objects.core.Pos getPos(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _posList.size())) { - throw new IndexOutOfBoundsException("getPos: Index value '"+index+"' not in range [0.."+_posList.size()+ "]"); - } - - return (org.vamsas.objects.core.Pos) _posList.elementAt(index); - } //-- org.vamsas.objects.core.Pos getPos(int) - - /** - * Method getPos - * - * - * - * @return Pos - */ - public org.vamsas.objects.core.Pos[] getPos() - { - int size = _posList.size(); - org.vamsas.objects.core.Pos[] mArray = new org.vamsas.objects.core.Pos[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Pos) _posList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Pos[] getPos() - - /** - * Method getPosCount - * - * - * - * @return int - */ - public int getPosCount() - { - return _posList.size(); - } //-- int getPosCount() - - /** - * Method getSeg - * - * - * - * @param index - * @return Seg - */ - public org.vamsas.objects.core.Seg getSeg(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _segList.size())) { - throw new IndexOutOfBoundsException("getSeg: Index value '"+index+"' not in range [0.."+_segList.size()+ "]"); - } - - return (org.vamsas.objects.core.Seg) _segList.elementAt(index); - } //-- org.vamsas.objects.core.Seg getSeg(int) - - /** - * Method getSeg - * - * - * - * @return Seg - */ - public org.vamsas.objects.core.Seg[] getSeg() - { - int size = _segList.size(); - org.vamsas.objects.core.Seg[] mArray = new org.vamsas.objects.core.Seg[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Seg) _segList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Seg[] getSeg() - - /** - * Method getSegCount - * - * - * - * @return int - */ - public int getSegCount() - { - return _segList.size(); - } //-- int getSegCount() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method removeAllPos - * - */ - public void removeAllPos() - { - _posList.removeAllElements(); - } //-- void removeAllPos() - - /** - * Method removeAllSeg - * - */ - public void removeAllSeg() - { - _segList.removeAllElements(); - } //-- void removeAllSeg() - - /** - * Method removePos - * - * - * - * @param index - * @return Pos - */ - public org.vamsas.objects.core.Pos removePos(int index) - { - java.lang.Object obj = _posList.elementAt(index); - _posList.removeElementAt(index); - return (org.vamsas.objects.core.Pos) obj; - } //-- org.vamsas.objects.core.Pos removePos(int) - - /** - * Method removeSeg - * - * - * - * @param index - * @return Seg - */ - public org.vamsas.objects.core.Seg removeSeg(int index) - { - java.lang.Object obj = _segList.elementAt(index); - _segList.removeElementAt(index); - return (org.vamsas.objects.core.Seg) obj; - } //-- org.vamsas.objects.core.Seg removeSeg(int) - - /** - * Method setPos - * - * - * - * @param index - * @param vPos - */ - public void setPos(int index, org.vamsas.objects.core.Pos vPos) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _posList.size())) { - throw new IndexOutOfBoundsException("setPos: Index value '"+index+"' not in range [0.."+_posList.size()+ "]"); - } - _posList.setElementAt(vPos, index); - } //-- void setPos(int, org.vamsas.objects.core.Pos) - - /** - * Method setPos - * - * - * - * @param posArray - */ - public void setPos(org.vamsas.objects.core.Pos[] posArray) - { - //-- copy array - _posList.removeAllElements(); - for (int i = 0; i < posArray.length; i++) { - _posList.addElement(posArray[i]); - } - } //-- void setPos(org.vamsas.objects.core.Pos) - - /** - * Method setSeg - * - * - * - * @param index - * @param vSeg - */ - public void setSeg(int index, org.vamsas.objects.core.Seg vSeg) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _segList.size())) { - throw new IndexOutOfBoundsException("setSeg: Index value '"+index+"' not in range [0.."+_segList.size()+ "]"); - } - _segList.setElementAt(vSeg, index); - } //-- void setSeg(int, org.vamsas.objects.core.Seg) - - /** - * Method setSeg - * - * - * - * @param segArray - */ - public void setSeg(org.vamsas.objects.core.Seg[] segArray) - { - //-- copy array - _segList.removeAllElements(); - for (int i = 0; i < segArray.length; i++) { - _segList.addElement(segArray[i]); - } - } //-- void setSeg(org.vamsas.objects.core.Seg) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/RangeTypeDescriptor.java b/src/org/vamsas/objects/core/RangeTypeDescriptor.java deleted file mode 100644 index 20f0de9..0000000 --- a/src/org/vamsas/objects/core/RangeTypeDescriptor.java +++ /dev/null @@ -1,246 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class RangeTypeDescriptor. - * - * @version $Revision$ $Date$ - */ -public class RangeTypeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public RangeTypeDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "rangeType"; - - //-- set grouping compositor - setCompositorAsChoice(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- initialize element descriptors - - //-- _posList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Pos.class, "_posList", "pos", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - RangeType target = (RangeType) object; - return target.getPos(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - RangeType target = (RangeType) object; - target.addPos( (org.vamsas.objects.core.Pos) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _posList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _segList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Seg.class, "_segList", "seg", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - RangeType target = (RangeType) object; - return target.getSeg(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - RangeType target = (RangeType) object; - target.addSeg( (org.vamsas.objects.core.Seg) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _segList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.objects.core.RangeTypeDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return null; - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.RangeType.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/Score.java b/src/org/vamsas/objects/core/Score.java deleted file mode 100644 index cb294f3..0000000 --- a/src/org/vamsas/objects/core/Score.java +++ /dev/null @@ -1,240 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Ordered set of optionally named float values for the - * whole annotation - * - * @version $Revision$ $Date$ - */ -public class Score extends org.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * internal content storage - */ - private float _content; - - /** - * keeps track of state for field: _content - */ - private boolean _has_content; - - /** - * Field _name - */ - private java.lang.String _name = "score"; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Score() - { - super(); - setName("score"); - } //-- org.vamsas.objects.core.Score() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method deleteContent - * - */ - public void deleteContent() - { - this._has_content= false; - } //-- void deleteContent() - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof Score) { - - Score temp = (Score)obj; - if (this._content != temp._content) - return false; - if (this._has_content != temp._has_content) - return false; - if (this._name != null) { - if (temp._name == null) return false; - else if (!(this._name.equals(temp._name))) - return false; - } - else if (temp._name != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'content'. The field 'content' - * has the following description: internal content storage - * - * @return float - * @return the value of field 'content'. - */ - public float getContent() - { - return this._content; - } //-- float getContent() - - /** - * Returns the value of field 'name'. - * - * @return String - * @return the value of field 'name'. - */ - public java.lang.String getName() - { - return this._name; - } //-- java.lang.String getName() - - /** - * Method hasContent - * - * - * - * @return boolean - */ - public boolean hasContent() - { - return this._has_content; - } //-- boolean hasContent() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Sets the value of field 'content'. The field 'content' has - * the following description: internal content storage - * - * @param content the value of field 'content'. - */ - public void setContent(float content) - { - this._content = content; - this._has_content = true; - } //-- void setContent(float) - - /** - * Sets the value of field 'name'. - * - * @param name the value of field 'name'. - */ - public void setName(java.lang.String name) - { - this._name = name; - } //-- void setName(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Score - */ - public static org.vamsas.objects.core.Score unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Score) Unmarshaller.unmarshal(org.vamsas.objects.core.Score.class, reader); - } //-- org.vamsas.objects.core.Score unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/ScoreDescriptor.java b/src/org/vamsas/objects/core/ScoreDescriptor.java deleted file mode 100644 index c9c1eda..0000000 --- a/src/org/vamsas/objects/core/ScoreDescriptor.java +++ /dev/null @@ -1,249 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class ScoreDescriptor. - * - * @version $Revision$ $Date$ - */ -public class ScoreDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public ScoreDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "score"; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- _content - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Score target = (Score) object; - if(!target.hasContent()) - return null; - return new java.lang.Float(target.getContent()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Score target = (Score) object; - // if null, use delete method for optional primitives - if (value == null) { - target.deleteContent(); - return; - } - target.setContent( ((java.lang.Float)value).floatValue()); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - addFieldDescriptor(desc); - - //-- validation code for: _content - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - FloatValidator typeValidator = new FloatValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize attribute descriptors - - //-- _name - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Score target = (Score) object; - return target.getName(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Score target = (Score) object; - target.setName( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _name - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } //-- org.vamsas.objects.core.ScoreDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return null; - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.Score.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/Seg.java b/src/org/vamsas/objects/core/Seg.java deleted file mode 100644 index 5e36703..0000000 --- a/src/org/vamsas/objects/core/Seg.java +++ /dev/null @@ -1,331 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * a region from start to end, with flag for inclusivity of - * terminii - * - * @version $Revision$ $Date$ - */ -public class Seg extends org.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _start - */ - private int _start; - - /** - * keeps track of state for field: _start - */ - private boolean _has_start; - - /** - * Field _end - */ - private int _end; - - /** - * keeps track of state for field: _end - */ - private boolean _has_end; - - /** - * when false, a consecutive range like 'start=1, end=2' - * means the region lying after position 1 and before position - * 2 - * - */ - private boolean _inclusive; - - /** - * keeps track of state for field: _inclusive - */ - private boolean _has_inclusive; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Seg() - { - super(); - } //-- org.vamsas.objects.core.Seg() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method deleteEnd - * - */ - public void deleteEnd() - { - this._has_end= false; - } //-- void deleteEnd() - - /** - * Method deleteInclusive - * - */ - public void deleteInclusive() - { - this._has_inclusive= false; - } //-- void deleteInclusive() - - /** - * Method deleteStart - * - */ - public void deleteStart() - { - this._has_start= false; - } //-- void deleteStart() - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof Seg) { - - Seg temp = (Seg)obj; - if (this._start != temp._start) - return false; - if (this._has_start != temp._has_start) - return false; - if (this._end != temp._end) - return false; - if (this._has_end != temp._has_end) - return false; - if (this._inclusive != temp._inclusive) - return false; - if (this._has_inclusive != temp._has_inclusive) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'end'. - * - * @return int - * @return the value of field 'end'. - */ - public int getEnd() - { - return this._end; - } //-- int getEnd() - - /** - * Returns the value of field 'inclusive'. The field - * 'inclusive' has the following description: when false, a - * consecutive range like 'start=1, end=2' - * means the region lying after position 1 and before position - * 2 - * - * - * @return boolean - * @return the value of field 'inclusive'. - */ - public boolean getInclusive() - { - return this._inclusive; - } //-- boolean getInclusive() - - /** - * Returns the value of field 'start'. - * - * @return int - * @return the value of field 'start'. - */ - public int getStart() - { - return this._start; - } //-- int getStart() - - /** - * Method hasEnd - * - * - * - * @return boolean - */ - public boolean hasEnd() - { - return this._has_end; - } //-- boolean hasEnd() - - /** - * Method hasInclusive - * - * - * - * @return boolean - */ - public boolean hasInclusive() - { - return this._has_inclusive; - } //-- boolean hasInclusive() - - /** - * Method hasStart - * - * - * - * @return boolean - */ - public boolean hasStart() - { - return this._has_start; - } //-- boolean hasStart() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Sets the value of field 'end'. - * - * @param end the value of field 'end'. - */ - public void setEnd(int end) - { - this._end = end; - this._has_end = true; - } //-- void setEnd(int) - - /** - * Sets the value of field 'inclusive'. The field 'inclusive' - * has the following description: when false, a consecutive - * range like 'start=1, end=2' - * means the region lying after position 1 and before position - * 2 - * - * - * @param inclusive the value of field 'inclusive'. - */ - public void setInclusive(boolean inclusive) - { - this._inclusive = inclusive; - this._has_inclusive = true; - } //-- void setInclusive(boolean) - - /** - * Sets the value of field 'start'. - * - * @param start the value of field 'start'. - */ - public void setStart(int start) - { - this._start = start; - this._has_start = true; - } //-- void setStart(int) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Seg - */ - public static org.vamsas.objects.core.Seg unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Seg) Unmarshaller.unmarshal(org.vamsas.objects.core.Seg.class, reader); - } //-- org.vamsas.objects.core.Seg unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/SegDescriptor.java b/src/org/vamsas/objects/core/SegDescriptor.java deleted file mode 100644 index 41a423c..0000000 --- a/src/org/vamsas/objects/core/SegDescriptor.java +++ /dev/null @@ -1,297 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class SegDescriptor. - * - * @version $Revision$ $Date$ - */ -public class SegDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public SegDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "seg"; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _start - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Seg target = (Seg) object; - if(!target.hasStart()) - return null; - return new java.lang.Integer(target.getStart()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Seg target = (Seg) object; - // ignore null values for non optional primitives - if (value == null) return; - - target.setStart( ((java.lang.Integer)value).intValue()); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _start - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - IntegerValidator typeValidator= new IntegerValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _end - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Seg target = (Seg) object; - if(!target.hasEnd()) - return null; - return new java.lang.Integer(target.getEnd()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Seg target = (Seg) object; - // ignore null values for non optional primitives - if (value == null) return; - - target.setEnd( ((java.lang.Integer)value).intValue()); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _end - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - IntegerValidator typeValidator= new IntegerValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _inclusive - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_inclusive", "inclusive", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Seg target = (Seg) object; - if(!target.hasInclusive()) - return null; - return (target.getInclusive() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Seg target = (Seg) object; - // ignore null values for non optional primitives - if (value == null) return; - - target.setInclusive( ((java.lang.Boolean)value).booleanValue()); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _inclusive - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - BooleanValidator typeValidator = new BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } //-- org.vamsas.objects.core.SegDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return null; - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.Seg.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/Sequence.java b/src/org/vamsas/objects/core/Sequence.java deleted file mode 100644 index 66dc569..0000000 --- a/src/org/vamsas/objects/core/Sequence.java +++ /dev/null @@ -1,387 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Sequence. - * - * @version $Revision$ $Date$ - */ -public class Sequence extends org.vamsas.objects.core.SequenceType -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Primary Key for vamsas object referencing - * - */ - private java.lang.String _id; - - /** - * symbol class for sequence - * - */ - private java.lang.String _dictionary; - - /** - * Store a list of database references - * for this sequence record - with optional mapping - * from database sequence to the given sequence record - */ - private java.util.Vector _dbRefList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Sequence() - { - super(); - _dbRefList = new Vector(); - } //-- org.vamsas.objects.core.Sequence() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addDbRef - * - * - * - * @param vDbRef - */ - public void addDbRef(org.vamsas.objects.core.DbRef vDbRef) - throws java.lang.IndexOutOfBoundsException - { - _dbRefList.addElement(vDbRef); - } //-- void addDbRef(org.vamsas.objects.core.DbRef) - - /** - * Method addDbRef - * - * - * - * @param index - * @param vDbRef - */ - public void addDbRef(int index, org.vamsas.objects.core.DbRef vDbRef) - throws java.lang.IndexOutOfBoundsException - { - _dbRefList.insertElementAt(vDbRef, index); - } //-- void addDbRef(int, org.vamsas.objects.core.DbRef) - - /** - * Method enumerateDbRef - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateDbRef() - { - return _dbRefList.elements(); - } //-- java.util.Enumeration enumerateDbRef() - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof Sequence) { - - Sequence temp = (Sequence)obj; - if (this._id != null) { - if (temp._id == null) return false; - else if (!(this._id.equals(temp._id))) - return false; - } - else if (temp._id != null) - return false; - if (this._dictionary != null) { - if (temp._dictionary == null) return false; - else if (!(this._dictionary.equals(temp._dictionary))) - return false; - } - else if (temp._dictionary != null) - return false; - if (this._dbRefList != null) { - if (temp._dbRefList == null) return false; - else if (!(this._dbRefList.equals(temp._dbRefList))) - return false; - } - else if (temp._dbRefList != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Method getDbRef - * - * - * - * @param index - * @return DbRef - */ - public org.vamsas.objects.core.DbRef getDbRef(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _dbRefList.size())) { - throw new IndexOutOfBoundsException("getDbRef: Index value '"+index+"' not in range [0.."+_dbRefList.size()+ "]"); - } - - return (org.vamsas.objects.core.DbRef) _dbRefList.elementAt(index); - } //-- org.vamsas.objects.core.DbRef getDbRef(int) - - /** - * Method getDbRef - * - * - * - * @return DbRef - */ - public org.vamsas.objects.core.DbRef[] getDbRef() - { - int size = _dbRefList.size(); - org.vamsas.objects.core.DbRef[] mArray = new org.vamsas.objects.core.DbRef[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.DbRef) _dbRefList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.DbRef[] getDbRef() - - /** - * Method getDbRefCount - * - * - * - * @return int - */ - public int getDbRefCount() - { - return _dbRefList.size(); - } //-- int getDbRefCount() - - /** - * Returns the value of field 'dictionary'. The field - * 'dictionary' has the following description: symbol class for - * sequence - * - * - * @return String - * @return the value of field 'dictionary'. - */ - public java.lang.String getDictionary() - { - return this._dictionary; - } //-- java.lang.String getDictionary() - - /** - * Returns the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * - * @return String - * @return the value of field 'id'. - */ - public java.lang.String getId() - { - return this._id; - } //-- java.lang.String getId() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method removeAllDbRef - * - */ - public void removeAllDbRef() - { - _dbRefList.removeAllElements(); - } //-- void removeAllDbRef() - - /** - * Method removeDbRef - * - * - * - * @param index - * @return DbRef - */ - public org.vamsas.objects.core.DbRef removeDbRef(int index) - { - java.lang.Object obj = _dbRefList.elementAt(index); - _dbRefList.removeElementAt(index); - return (org.vamsas.objects.core.DbRef) obj; - } //-- org.vamsas.objects.core.DbRef removeDbRef(int) - - /** - * Method setDbRef - * - * - * - * @param index - * @param vDbRef - */ - public void setDbRef(int index, org.vamsas.objects.core.DbRef vDbRef) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _dbRefList.size())) { - throw new IndexOutOfBoundsException("setDbRef: Index value '"+index+"' not in range [0.."+_dbRefList.size()+ "]"); - } - _dbRefList.setElementAt(vDbRef, index); - } //-- void setDbRef(int, org.vamsas.objects.core.DbRef) - - /** - * Method setDbRef - * - * - * - * @param dbRefArray - */ - public void setDbRef(org.vamsas.objects.core.DbRef[] dbRefArray) - { - //-- copy array - _dbRefList.removeAllElements(); - for (int i = 0; i < dbRefArray.length; i++) { - _dbRefList.addElement(dbRefArray[i]); - } - } //-- void setDbRef(org.vamsas.objects.core.DbRef) - - /** - * Sets the value of field 'dictionary'. The field 'dictionary' - * has the following description: symbol class for sequence - * - * - * @param dictionary the value of field 'dictionary'. - */ - public void setDictionary(java.lang.String dictionary) - { - this._dictionary = dictionary; - } //-- void setDictionary(java.lang.String) - - /** - * Sets the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * - * @param id the value of field 'id'. - */ - public void setId(java.lang.String id) - { - this._id = id; - } //-- void setId(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return SequenceType - */ - public static org.vamsas.objects.core.SequenceType unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Sequence) Unmarshaller.unmarshal(org.vamsas.objects.core.Sequence.class, reader); - } //-- org.vamsas.objects.core.SequenceType unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/SequenceDescriptor.java b/src/org/vamsas/objects/core/SequenceDescriptor.java deleted file mode 100644 index 440d8e0..0000000 --- a/src/org/vamsas/objects/core/SequenceDescriptor.java +++ /dev/null @@ -1,285 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class SequenceDescriptor. - * - * @version $Revision$ $Date$ - */ -public class SequenceDescriptor extends org.vamsas.objects.core.SequenceTypeDescriptor { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public SequenceDescriptor() - { - super(); - setExtendsWithoutFlatten(new org.vamsas.objects.core.SequenceTypeDescriptor()); - nsURI = "http://www.vamsas.org"; - xmlName = "Sequence"; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); - this.identity = desc; - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Sequence target = (Sequence) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Sequence target = (Sequence) object; - target.setId( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new java.lang.String(); - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _dictionary - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dictionary", "dictionary", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Sequence target = (Sequence) object; - return target.getDictionary(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Sequence target = (Sequence) object; - target.setDictionary( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _dictionary - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _dbRefList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.DbRef.class, "_dbRefList", "dbRef", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Sequence target = (Sequence) object; - return target.getDbRef(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Sequence target = (Sequence) object; - target.addDbRef( (org.vamsas.objects.core.DbRef) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.DbRef(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _dbRefList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.objects.core.SequenceDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return super.getExtends(); - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - if (identity == null) - return super.getIdentity(); - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.Sequence.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/SequenceType.java b/src/org/vamsas/objects/core/SequenceType.java deleted file mode 100644 index 96fba5b..0000000 --- a/src/org/vamsas/objects/core/SequenceType.java +++ /dev/null @@ -1,677 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class SequenceType. - * - * @version $Revision$ $Date$ - */ -public class SequenceType extends org.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _start - */ - private int _start; - - /** - * keeps track of state for field: _start - */ - private boolean _has_start; - - /** - * Field _end - */ - private int _end; - - /** - * keeps track of state for field: _end - */ - private boolean _has_end; - - /** - * Field _sequence - */ - private java.lang.String _sequence; - - /** - * Field _name - */ - private java.lang.String _name; - - /** - * Field _description - */ - private java.lang.String _description; - - /** - * additional typed properties - */ - private java.util.Vector _propertyList; - - /** - * Field _mappingList - */ - private java.util.Vector _mappingList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public SequenceType() - { - super(); - _propertyList = new Vector(); - _mappingList = new Vector(); - } //-- org.vamsas.objects.core.SequenceType() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addMapping - * - * - * - * @param vMapping - */ - public void addMapping(org.vamsas.objects.core.Mapping vMapping) - throws java.lang.IndexOutOfBoundsException - { - _mappingList.addElement(vMapping); - } //-- void addMapping(org.vamsas.objects.core.Mapping) - - /** - * Method addMapping - * - * - * - * @param index - * @param vMapping - */ - public void addMapping(int index, org.vamsas.objects.core.Mapping vMapping) - throws java.lang.IndexOutOfBoundsException - { - _mappingList.insertElementAt(vMapping, index); - } //-- void addMapping(int, org.vamsas.objects.core.Mapping) - - /** - * Method addProperty - * - * - * - * @param vProperty - */ - public void addProperty(org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - _propertyList.addElement(vProperty); - } //-- void addProperty(org.vamsas.objects.core.Property) - - /** - * Method addProperty - * - * - * - * @param index - * @param vProperty - */ - public void addProperty(int index, org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - _propertyList.insertElementAt(vProperty, index); - } //-- void addProperty(int, org.vamsas.objects.core.Property) - - /** - * Method deleteEnd - * - */ - public void deleteEnd() - { - this._has_end= false; - } //-- void deleteEnd() - - /** - * Method deleteStart - * - */ - public void deleteStart() - { - this._has_start= false; - } //-- void deleteStart() - - /** - * Method enumerateMapping - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateMapping() - { - return _mappingList.elements(); - } //-- java.util.Enumeration enumerateMapping() - - /** - * Method enumerateProperty - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateProperty() - { - return _propertyList.elements(); - } //-- java.util.Enumeration enumerateProperty() - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof SequenceType) { - - SequenceType temp = (SequenceType)obj; - if (this._start != temp._start) - return false; - if (this._has_start != temp._has_start) - return false; - if (this._end != temp._end) - return false; - if (this._has_end != temp._has_end) - return false; - if (this._sequence != null) { - if (temp._sequence == null) return false; - else if (!(this._sequence.equals(temp._sequence))) - return false; - } - else if (temp._sequence != null) - return false; - if (this._name != null) { - if (temp._name == null) return false; - else if (!(this._name.equals(temp._name))) - return false; - } - else if (temp._name != null) - return false; - if (this._description != null) { - if (temp._description == null) return false; - else if (!(this._description.equals(temp._description))) - return false; - } - else if (temp._description != null) - return false; - if (this._propertyList != null) { - if (temp._propertyList == null) return false; - else if (!(this._propertyList.equals(temp._propertyList))) - return false; - } - else if (temp._propertyList != null) - return false; - if (this._mappingList != null) { - if (temp._mappingList == null) return false; - else if (!(this._mappingList.equals(temp._mappingList))) - return false; - } - else if (temp._mappingList != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'description'. - * - * @return String - * @return the value of field 'description'. - */ - public java.lang.String getDescription() - { - return this._description; - } //-- java.lang.String getDescription() - - /** - * Returns the value of field 'end'. - * - * @return int - * @return the value of field 'end'. - */ - public int getEnd() - { - return this._end; - } //-- int getEnd() - - /** - * Method getMapping - * - * - * - * @param index - * @return Mapping - */ - public org.vamsas.objects.core.Mapping getMapping(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _mappingList.size())) { - throw new IndexOutOfBoundsException("getMapping: Index value '"+index+"' not in range [0.."+_mappingList.size()+ "]"); - } - - return (org.vamsas.objects.core.Mapping) _mappingList.elementAt(index); - } //-- org.vamsas.objects.core.Mapping getMapping(int) - - /** - * Method getMapping - * - * - * - * @return Mapping - */ - public org.vamsas.objects.core.Mapping[] getMapping() - { - int size = _mappingList.size(); - org.vamsas.objects.core.Mapping[] mArray = new org.vamsas.objects.core.Mapping[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Mapping) _mappingList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Mapping[] getMapping() - - /** - * Method getMappingCount - * - * - * - * @return int - */ - public int getMappingCount() - { - return _mappingList.size(); - } //-- int getMappingCount() - - /** - * Returns the value of field 'name'. - * - * @return String - * @return the value of field 'name'. - */ - public java.lang.String getName() - { - return this._name; - } //-- java.lang.String getName() - - /** - * Method getProperty - * - * - * - * @param index - * @return Property - */ - public org.vamsas.objects.core.Property getProperty(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _propertyList.size())) { - throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]"); - } - - return (org.vamsas.objects.core.Property) _propertyList.elementAt(index); - } //-- org.vamsas.objects.core.Property getProperty(int) - - /** - * Method getProperty - * - * - * - * @return Property - */ - public org.vamsas.objects.core.Property[] getProperty() - { - int size = _propertyList.size(); - org.vamsas.objects.core.Property[] mArray = new org.vamsas.objects.core.Property[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Property) _propertyList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Property[] getProperty() - - /** - * Method getPropertyCount - * - * - * - * @return int - */ - public int getPropertyCount() - { - return _propertyList.size(); - } //-- int getPropertyCount() - - /** - * Returns the value of field 'sequence'. - * - * @return String - * @return the value of field 'sequence'. - */ - public java.lang.String getSequence() - { - return this._sequence; - } //-- java.lang.String getSequence() - - /** - * Returns the value of field 'start'. - * - * @return int - * @return the value of field 'start'. - */ - public int getStart() - { - return this._start; - } //-- int getStart() - - /** - * Method hasEnd - * - * - * - * @return boolean - */ - public boolean hasEnd() - { - return this._has_end; - } //-- boolean hasEnd() - - /** - * Method hasStart - * - * - * - * @return boolean - */ - public boolean hasStart() - { - return this._has_start; - } //-- boolean hasStart() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method removeAllMapping - * - */ - public void removeAllMapping() - { - _mappingList.removeAllElements(); - } //-- void removeAllMapping() - - /** - * Method removeAllProperty - * - */ - public void removeAllProperty() - { - _propertyList.removeAllElements(); - } //-- void removeAllProperty() - - /** - * Method removeMapping - * - * - * - * @param index - * @return Mapping - */ - public org.vamsas.objects.core.Mapping removeMapping(int index) - { - java.lang.Object obj = _mappingList.elementAt(index); - _mappingList.removeElementAt(index); - return (org.vamsas.objects.core.Mapping) obj; - } //-- org.vamsas.objects.core.Mapping removeMapping(int) - - /** - * Method removeProperty - * - * - * - * @param index - * @return Property - */ - public org.vamsas.objects.core.Property removeProperty(int index) - { - java.lang.Object obj = _propertyList.elementAt(index); - _propertyList.removeElementAt(index); - return (org.vamsas.objects.core.Property) obj; - } //-- org.vamsas.objects.core.Property removeProperty(int) - - /** - * Sets the value of field 'description'. - * - * @param description the value of field 'description'. - */ - public void setDescription(java.lang.String description) - { - this._description = description; - } //-- void setDescription(java.lang.String) - - /** - * Sets the value of field 'end'. - * - * @param end the value of field 'end'. - */ - public void setEnd(int end) - { - this._end = end; - this._has_end = true; - } //-- void setEnd(int) - - /** - * Method setMapping - * - * - * - * @param index - * @param vMapping - */ - public void setMapping(int index, org.vamsas.objects.core.Mapping vMapping) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _mappingList.size())) { - throw new IndexOutOfBoundsException("setMapping: Index value '"+index+"' not in range [0.."+_mappingList.size()+ "]"); - } - _mappingList.setElementAt(vMapping, index); - } //-- void setMapping(int, org.vamsas.objects.core.Mapping) - - /** - * Method setMapping - * - * - * - * @param mappingArray - */ - public void setMapping(org.vamsas.objects.core.Mapping[] mappingArray) - { - //-- copy array - _mappingList.removeAllElements(); - for (int i = 0; i < mappingArray.length; i++) { - _mappingList.addElement(mappingArray[i]); - } - } //-- void setMapping(org.vamsas.objects.core.Mapping) - - /** - * Sets the value of field 'name'. - * - * @param name the value of field 'name'. - */ - public void setName(java.lang.String name) - { - this._name = name; - } //-- void setName(java.lang.String) - - /** - * Method setProperty - * - * - * - * @param index - * @param vProperty - */ - public void setProperty(int index, org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _propertyList.size())) { - throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]"); - } - _propertyList.setElementAt(vProperty, index); - } //-- void setProperty(int, org.vamsas.objects.core.Property) - - /** - * Method setProperty - * - * - * - * @param propertyArray - */ - public void setProperty(org.vamsas.objects.core.Property[] propertyArray) - { - //-- copy array - _propertyList.removeAllElements(); - for (int i = 0; i < propertyArray.length; i++) { - _propertyList.addElement(propertyArray[i]); - } - } //-- void setProperty(org.vamsas.objects.core.Property) - - /** - * Sets the value of field 'sequence'. - * - * @param sequence the value of field 'sequence'. - */ - public void setSequence(java.lang.String sequence) - { - this._sequence = sequence; - } //-- void setSequence(java.lang.String) - - /** - * Sets the value of field 'start'. - * - * @param start the value of field 'start'. - */ - public void setStart(int start) - { - this._start = start; - this._has_start = true; - } //-- void setStart(int) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return SequenceType - */ - public static org.vamsas.objects.core.SequenceType unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.SequenceType) Unmarshaller.unmarshal(org.vamsas.objects.core.SequenceType.class, reader); - } //-- org.vamsas.objects.core.SequenceType unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/SequenceTypeDescriptor.java b/src/org/vamsas/objects/core/SequenceTypeDescriptor.java deleted file mode 100644 index 0cb00aa..0000000 --- a/src/org/vamsas/objects/core/SequenceTypeDescriptor.java +++ /dev/null @@ -1,446 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class SequenceTypeDescriptor. - * - * @version $Revision$ $Date$ - */ -public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public SequenceTypeDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "SequenceType"; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _start - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceType target = (SequenceType) object; - if(!target.hasStart()) - return null; - return new java.lang.Integer(target.getStart()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceType target = (SequenceType) object; - // ignore null values for non optional primitives - if (value == null) return; - - target.setStart( ((java.lang.Integer)value).intValue()); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _start - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - IntegerValidator typeValidator = new IntegerValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _end - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceType target = (SequenceType) object; - if(!target.hasEnd()) - return null; - return new java.lang.Integer(target.getEnd()); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceType target = (SequenceType) object; - // ignore null values for non optional primitives - if (value == null) return; - - target.setEnd( ((java.lang.Integer)value).intValue()); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _end - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - IntegerValidator typeValidator = new IntegerValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _sequence - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequence", "sequence", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceType target = (SequenceType) object; - return target.getSequence(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceType target = (SequenceType) object; - target.setSequence( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _sequence - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _name - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceType target = (SequenceType) object; - return target.getName(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceType target = (SequenceType) object; - target.setName( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _name - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _description - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceType target = (SequenceType) object; - return target.getDescription(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceType target = (SequenceType) object; - target.setDescription( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _description - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _propertyList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Property.class, "_propertyList", "property", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceType target = (SequenceType) object; - return target.getProperty(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceType target = (SequenceType) object; - target.addProperty( (org.vamsas.objects.core.Property) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Property(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _propertyList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _mappingList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Mapping.class, "_mappingList", "mapping", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceType target = (SequenceType) object; - return target.getMapping(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceType target = (SequenceType) object; - target.addMapping( (org.vamsas.objects.core.Mapping) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Mapping(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _mappingList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.objects.core.SequenceTypeDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return null; - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.SequenceType.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/Tree.java b/src/org/vamsas/objects/core/Tree.java deleted file mode 100644 index 5b9ea99..0000000 --- a/src/org/vamsas/objects/core/Tree.java +++ /dev/null @@ -1,600 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Tree. - * - * @version $Revision$ $Date$ - */ -public class Tree extends org.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Primary Key for vamsas object referencing - */ - private java.lang.String _id; - - /** - * Field _modifiable - */ - private java.lang.String _modifiable; - - /** - * Field _title - */ - private java.lang.String _title; - - /** - * Field _newickList - */ - private java.util.Vector _newickList; - - /** - * Field _propertyList - */ - private java.util.Vector _propertyList; - - /** - * Field _provenance - */ - private org.vamsas.objects.core.Provenance _provenance; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Tree() - { - super(); - _newickList = new Vector(); - _propertyList = new Vector(); - } //-- org.vamsas.objects.core.Tree() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addNewick - * - * - * - * @param vNewick - */ - public void addNewick(org.vamsas.objects.core.Newick vNewick) - throws java.lang.IndexOutOfBoundsException - { - _newickList.addElement(vNewick); - } //-- void addNewick(org.vamsas.objects.core.Newick) - - /** - * Method addNewick - * - * - * - * @param index - * @param vNewick - */ - public void addNewick(int index, org.vamsas.objects.core.Newick vNewick) - throws java.lang.IndexOutOfBoundsException - { - _newickList.insertElementAt(vNewick, index); - } //-- void addNewick(int, org.vamsas.objects.core.Newick) - - /** - * Method addProperty - * - * - * - * @param vProperty - */ - public void addProperty(org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - _propertyList.addElement(vProperty); - } //-- void addProperty(org.vamsas.objects.core.Property) - - /** - * Method addProperty - * - * - * - * @param index - * @param vProperty - */ - public void addProperty(int index, org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - _propertyList.insertElementAt(vProperty, index); - } //-- void addProperty(int, org.vamsas.objects.core.Property) - - /** - * Method enumerateNewick - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateNewick() - { - return _newickList.elements(); - } //-- java.util.Enumeration enumerateNewick() - - /** - * Method enumerateProperty - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateProperty() - { - return _propertyList.elements(); - } //-- java.util.Enumeration enumerateProperty() - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof Tree) { - - Tree temp = (Tree)obj; - if (this._id != null) { - if (temp._id == null) return false; - else if (!(this._id.equals(temp._id))) - return false; - } - else if (temp._id != null) - return false; - if (this._modifiable != null) { - if (temp._modifiable == null) return false; - else if (!(this._modifiable.equals(temp._modifiable))) - return false; - } - else if (temp._modifiable != null) - return false; - if (this._title != null) { - if (temp._title == null) return false; - else if (!(this._title.equals(temp._title))) - return false; - } - else if (temp._title != null) - return false; - if (this._newickList != null) { - if (temp._newickList == null) return false; - else if (!(this._newickList.equals(temp._newickList))) - return false; - } - else if (temp._newickList != null) - return false; - if (this._propertyList != null) { - if (temp._propertyList == null) return false; - else if (!(this._propertyList.equals(temp._propertyList))) - return false; - } - else if (temp._propertyList != null) - return false; - if (this._provenance != null) { - if (temp._provenance == null) return false; - else if (!(this._provenance.equals(temp._provenance))) - return false; - } - else if (temp._provenance != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * @return String - * @return the value of field 'id'. - */ - public java.lang.String getId() - { - return this._id; - } //-- java.lang.String getId() - - /** - * Returns the value of field 'modifiable'. - * - * @return String - * @return the value of field 'modifiable'. - */ - public java.lang.String getModifiable() - { - return this._modifiable; - } //-- java.lang.String getModifiable() - - /** - * Method getNewick - * - * - * - * @param index - * @return Newick - */ - public org.vamsas.objects.core.Newick getNewick(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _newickList.size())) { - throw new IndexOutOfBoundsException("getNewick: Index value '"+index+"' not in range [0.."+_newickList.size()+ "]"); - } - - return (org.vamsas.objects.core.Newick) _newickList.elementAt(index); - } //-- org.vamsas.objects.core.Newick getNewick(int) - - /** - * Method getNewick - * - * - * - * @return Newick - */ - public org.vamsas.objects.core.Newick[] getNewick() - { - int size = _newickList.size(); - org.vamsas.objects.core.Newick[] mArray = new org.vamsas.objects.core.Newick[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Newick) _newickList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Newick[] getNewick() - - /** - * Method getNewickCount - * - * - * - * @return int - */ - public int getNewickCount() - { - return _newickList.size(); - } //-- int getNewickCount() - - /** - * Method getProperty - * - * - * - * @param index - * @return Property - */ - public org.vamsas.objects.core.Property getProperty(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _propertyList.size())) { - throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]"); - } - - return (org.vamsas.objects.core.Property) _propertyList.elementAt(index); - } //-- org.vamsas.objects.core.Property getProperty(int) - - /** - * Method getProperty - * - * - * - * @return Property - */ - public org.vamsas.objects.core.Property[] getProperty() - { - int size = _propertyList.size(); - org.vamsas.objects.core.Property[] mArray = new org.vamsas.objects.core.Property[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Property) _propertyList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Property[] getProperty() - - /** - * Method getPropertyCount - * - * - * - * @return int - */ - public int getPropertyCount() - { - return _propertyList.size(); - } //-- int getPropertyCount() - - /** - * Returns the value of field 'provenance'. - * - * @return Provenance - * @return the value of field 'provenance'. - */ - public org.vamsas.objects.core.Provenance getProvenance() - { - return this._provenance; - } //-- org.vamsas.objects.core.Provenance getProvenance() - - /** - * Returns the value of field 'title'. - * - * @return String - * @return the value of field 'title'. - */ - public java.lang.String getTitle() - { - return this._title; - } //-- java.lang.String getTitle() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method removeAllNewick - * - */ - public void removeAllNewick() - { - _newickList.removeAllElements(); - } //-- void removeAllNewick() - - /** - * Method removeAllProperty - * - */ - public void removeAllProperty() - { - _propertyList.removeAllElements(); - } //-- void removeAllProperty() - - /** - * Method removeNewick - * - * - * - * @param index - * @return Newick - */ - public org.vamsas.objects.core.Newick removeNewick(int index) - { - java.lang.Object obj = _newickList.elementAt(index); - _newickList.removeElementAt(index); - return (org.vamsas.objects.core.Newick) obj; - } //-- org.vamsas.objects.core.Newick removeNewick(int) - - /** - * Method removeProperty - * - * - * - * @param index - * @return Property - */ - public org.vamsas.objects.core.Property removeProperty(int index) - { - java.lang.Object obj = _propertyList.elementAt(index); - _propertyList.removeElementAt(index); - return (org.vamsas.objects.core.Property) obj; - } //-- org.vamsas.objects.core.Property removeProperty(int) - - /** - * Sets the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * @param id the value of field 'id'. - */ - public void setId(java.lang.String id) - { - this._id = id; - } //-- void setId(java.lang.String) - - /** - * Sets the value of field 'modifiable'. - * - * @param modifiable the value of field 'modifiable'. - */ - public void setModifiable(java.lang.String modifiable) - { - this._modifiable = modifiable; - } //-- void setModifiable(java.lang.String) - - /** - * Method setNewick - * - * - * - * @param index - * @param vNewick - */ - public void setNewick(int index, org.vamsas.objects.core.Newick vNewick) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _newickList.size())) { - throw new IndexOutOfBoundsException("setNewick: Index value '"+index+"' not in range [0.."+_newickList.size()+ "]"); - } - _newickList.setElementAt(vNewick, index); - } //-- void setNewick(int, org.vamsas.objects.core.Newick) - - /** - * Method setNewick - * - * - * - * @param newickArray - */ - public void setNewick(org.vamsas.objects.core.Newick[] newickArray) - { - //-- copy array - _newickList.removeAllElements(); - for (int i = 0; i < newickArray.length; i++) { - _newickList.addElement(newickArray[i]); - } - } //-- void setNewick(org.vamsas.objects.core.Newick) - - /** - * Method setProperty - * - * - * - * @param index - * @param vProperty - */ - public void setProperty(int index, org.vamsas.objects.core.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _propertyList.size())) { - throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]"); - } - _propertyList.setElementAt(vProperty, index); - } //-- void setProperty(int, org.vamsas.objects.core.Property) - - /** - * Method setProperty - * - * - * - * @param propertyArray - */ - public void setProperty(org.vamsas.objects.core.Property[] propertyArray) - { - //-- copy array - _propertyList.removeAllElements(); - for (int i = 0; i < propertyArray.length; i++) { - _propertyList.addElement(propertyArray[i]); - } - } //-- void setProperty(org.vamsas.objects.core.Property) - - /** - * Sets the value of field 'provenance'. - * - * @param provenance the value of field 'provenance'. - */ - public void setProvenance(org.vamsas.objects.core.Provenance provenance) - { - this._provenance = provenance; - } //-- void setProvenance(org.vamsas.objects.core.Provenance) - - /** - * Sets the value of field 'title'. - * - * @param title the value of field 'title'. - */ - public void setTitle(java.lang.String title) - { - this._title = title; - } //-- void setTitle(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Tree - */ - public static org.vamsas.objects.core.Tree unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.Tree) Unmarshaller.unmarshal(org.vamsas.objects.core.Tree.class, reader); - } //-- org.vamsas.objects.core.Tree unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/TreeDescriptor.java b/src/org/vamsas/objects/core/TreeDescriptor.java deleted file mode 100644 index 1ca69de..0000000 --- a/src/org/vamsas/objects/core/TreeDescriptor.java +++ /dev/null @@ -1,390 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class TreeDescriptor. - * - * @version $Revision$ $Date$ - */ -public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public TreeDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "Tree"; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); - this.identity = desc; - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Tree target = (Tree) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Tree target = (Tree) object; - target.setId( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new java.lang.String(); - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _modifiable - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_modifiable", "modifiable", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Tree target = (Tree) object; - return target.getModifiable(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Tree target = (Tree) object; - target.setModifiable( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _modifiable - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _title - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Tree target = (Tree) object; - return target.getTitle(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Tree target = (Tree) object; - target.setTitle( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _title - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _newickList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Newick.class, "_newickList", "newick", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Tree target = (Tree) object; - return target.getNewick(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Tree target = (Tree) object; - target.addNewick( (org.vamsas.objects.core.Newick) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Newick(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _newickList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _propertyList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Property.class, "_propertyList", "property", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Tree target = (Tree) object; - return target.getProperty(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Tree target = (Tree) object; - target.addProperty( (org.vamsas.objects.core.Property) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Property(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _propertyList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _provenance - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - Tree target = (Tree) object; - return target.getProvenance(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - Tree target = (Tree) object; - target.setProvenance( (org.vamsas.objects.core.Provenance) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Provenance(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _provenance - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.objects.core.TreeDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return null; - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.Tree.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/User.java b/src/org/vamsas/objects/core/User.java deleted file mode 100644 index 6efdd05..0000000 --- a/src/org/vamsas/objects/core/User.java +++ /dev/null @@ -1,212 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class User. - * - * @version $Revision$ $Date$ - */ -public class User extends org.vamsas.objects.core.AppData -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _fullname - */ - private java.lang.String _fullname; - - /** - * Field _organization - */ - private java.lang.String _organization; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public User() - { - super(); - } //-- org.vamsas.objects.core.User() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof User) { - - User temp = (User)obj; - if (this._fullname != null) { - if (temp._fullname == null) return false; - else if (!(this._fullname.equals(temp._fullname))) - return false; - } - else if (temp._fullname != null) - return false; - if (this._organization != null) { - if (temp._organization == null) return false; - else if (!(this._organization.equals(temp._organization))) - return false; - } - else if (temp._organization != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Returns the value of field 'fullname'. - * - * @return String - * @return the value of field 'fullname'. - */ - public java.lang.String getFullname() - { - return this._fullname; - } //-- java.lang.String getFullname() - - /** - * Returns the value of field 'organization'. - * - * @return String - * @return the value of field 'organization'. - */ - public java.lang.String getOrganization() - { - return this._organization; - } //-- java.lang.String getOrganization() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Sets the value of field 'fullname'. - * - * @param fullname the value of field 'fullname'. - */ - public void setFullname(java.lang.String fullname) - { - this._fullname = fullname; - } //-- void setFullname(java.lang.String) - - /** - * Sets the value of field 'organization'. - * - * @param organization the value of field 'organization'. - */ - public void setOrganization(java.lang.String organization) - { - this._organization = organization; - } //-- void setOrganization(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return AppData - */ - public static org.vamsas.objects.core.AppData unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.User) Unmarshaller.unmarshal(org.vamsas.objects.core.User.class, reader); - } //-- org.vamsas.objects.core.AppData unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/UserDescriptor.java b/src/org/vamsas/objects/core/UserDescriptor.java deleted file mode 100644 index a90dbb1..0000000 --- a/src/org/vamsas/objects/core/UserDescriptor.java +++ /dev/null @@ -1,252 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class UserDescriptor. - * - * @version $Revision$ $Date$ - */ -public class UserDescriptor extends org.vamsas.objects.core.AppDataDescriptor { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public UserDescriptor() - { - super(); - setExtendsWithoutFlatten(new org.vamsas.objects.core.AppDataDescriptor()); - nsURI = "http://www.vamsas.org"; - xmlName = "User"; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _fullname - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_fullname", "fullname", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - User target = (User) object; - return target.getFullname(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - User target = (User) object; - target.setFullname( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _fullname - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _organization - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_organization", "organization", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - User target = (User) object; - return target.getOrganization(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - User target = (User) object; - target.setOrganization( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _organization - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - } //-- org.vamsas.objects.core.UserDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return super.getExtends(); - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - if (identity == null) - return super.getIdentity(); - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.User.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/VAMSAS.java b/src/org/vamsas/objects/core/VAMSAS.java deleted file mode 100644 index c359593..0000000 --- a/src/org/vamsas/objects/core/VAMSAS.java +++ /dev/null @@ -1,535 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * contains unassociated trees and a number of analysis sets - * - * - * @version $Revision$ $Date$ - */ -public class VAMSAS extends org.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Primary Key for vamsas object referencing - */ - private java.lang.String _id; - - /** - * Field _modifiable - */ - private java.lang.String _modifiable; - - /** - * Field _treeList - */ - private java.util.Vector _treeList; - - /** - * Field _dataSetList - */ - private java.util.Vector _dataSetList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public VAMSAS() - { - super(); - _treeList = new Vector(); - _dataSetList = new Vector(); - } //-- org.vamsas.objects.core.VAMSAS() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addDataSet - * - * - * - * @param vDataSet - */ - public void addDataSet(org.vamsas.objects.core.DataSet vDataSet) - throws java.lang.IndexOutOfBoundsException - { - _dataSetList.addElement(vDataSet); - } //-- void addDataSet(org.vamsas.objects.core.DataSet) - - /** - * Method addDataSet - * - * - * - * @param index - * @param vDataSet - */ - public void addDataSet(int index, org.vamsas.objects.core.DataSet vDataSet) - throws java.lang.IndexOutOfBoundsException - { - _dataSetList.insertElementAt(vDataSet, index); - } //-- void addDataSet(int, org.vamsas.objects.core.DataSet) - - /** - * Method addTree - * - * - * - * @param vTree - */ - public void addTree(org.vamsas.objects.core.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - _treeList.addElement(vTree); - } //-- void addTree(org.vamsas.objects.core.Tree) - - /** - * Method addTree - * - * - * - * @param index - * @param vTree - */ - public void addTree(int index, org.vamsas.objects.core.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - _treeList.insertElementAt(vTree, index); - } //-- void addTree(int, org.vamsas.objects.core.Tree) - - /** - * Method enumerateDataSet - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateDataSet() - { - return _dataSetList.elements(); - } //-- java.util.Enumeration enumerateDataSet() - - /** - * Method enumerateTree - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateTree() - { - return _treeList.elements(); - } //-- java.util.Enumeration enumerateTree() - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof VAMSAS) { - - VAMSAS temp = (VAMSAS)obj; - if (this._id != null) { - if (temp._id == null) return false; - else if (!(this._id.equals(temp._id))) - return false; - } - else if (temp._id != null) - return false; - if (this._modifiable != null) { - if (temp._modifiable == null) return false; - else if (!(this._modifiable.equals(temp._modifiable))) - return false; - } - else if (temp._modifiable != null) - return false; - if (this._treeList != null) { - if (temp._treeList == null) return false; - else if (!(this._treeList.equals(temp._treeList))) - return false; - } - else if (temp._treeList != null) - return false; - if (this._dataSetList != null) { - if (temp._dataSetList == null) return false; - else if (!(this._dataSetList.equals(temp._dataSetList))) - return false; - } - else if (temp._dataSetList != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Method getDataSet - * - * - * - * @param index - * @return DataSet - */ - public org.vamsas.objects.core.DataSet getDataSet(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _dataSetList.size())) { - throw new IndexOutOfBoundsException("getDataSet: Index value '"+index+"' not in range [0.."+_dataSetList.size()+ "]"); - } - - return (org.vamsas.objects.core.DataSet) _dataSetList.elementAt(index); - } //-- org.vamsas.objects.core.DataSet getDataSet(int) - - /** - * Method getDataSet - * - * - * - * @return DataSet - */ - public org.vamsas.objects.core.DataSet[] getDataSet() - { - int size = _dataSetList.size(); - org.vamsas.objects.core.DataSet[] mArray = new org.vamsas.objects.core.DataSet[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.DataSet) _dataSetList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.DataSet[] getDataSet() - - /** - * Method getDataSetCount - * - * - * - * @return int - */ - public int getDataSetCount() - { - return _dataSetList.size(); - } //-- int getDataSetCount() - - /** - * Returns the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * @return String - * @return the value of field 'id'. - */ - public java.lang.String getId() - { - return this._id; - } //-- java.lang.String getId() - - /** - * Returns the value of field 'modifiable'. - * - * @return String - * @return the value of field 'modifiable'. - */ - public java.lang.String getModifiable() - { - return this._modifiable; - } //-- java.lang.String getModifiable() - - /** - * Method getTree - * - * - * - * @param index - * @return Tree - */ - public org.vamsas.objects.core.Tree getTree(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _treeList.size())) { - throw new IndexOutOfBoundsException("getTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]"); - } - - return (org.vamsas.objects.core.Tree) _treeList.elementAt(index); - } //-- org.vamsas.objects.core.Tree getTree(int) - - /** - * Method getTree - * - * - * - * @return Tree - */ - public org.vamsas.objects.core.Tree[] getTree() - { - int size = _treeList.size(); - org.vamsas.objects.core.Tree[] mArray = new org.vamsas.objects.core.Tree[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (org.vamsas.objects.core.Tree) _treeList.elementAt(index); - } - return mArray; - } //-- org.vamsas.objects.core.Tree[] getTree() - - /** - * Method getTreeCount - * - * - * - * @return int - */ - public int getTreeCount() - { - return _treeList.size(); - } //-- int getTreeCount() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method removeAllDataSet - * - */ - public void removeAllDataSet() - { - _dataSetList.removeAllElements(); - } //-- void removeAllDataSet() - - /** - * Method removeAllTree - * - */ - public void removeAllTree() - { - _treeList.removeAllElements(); - } //-- void removeAllTree() - - /** - * Method removeDataSet - * - * - * - * @param index - * @return DataSet - */ - public org.vamsas.objects.core.DataSet removeDataSet(int index) - { - java.lang.Object obj = _dataSetList.elementAt(index); - _dataSetList.removeElementAt(index); - return (org.vamsas.objects.core.DataSet) obj; - } //-- org.vamsas.objects.core.DataSet removeDataSet(int) - - /** - * Method removeTree - * - * - * - * @param index - * @return Tree - */ - public org.vamsas.objects.core.Tree removeTree(int index) - { - java.lang.Object obj = _treeList.elementAt(index); - _treeList.removeElementAt(index); - return (org.vamsas.objects.core.Tree) obj; - } //-- org.vamsas.objects.core.Tree removeTree(int) - - /** - * Method setDataSet - * - * - * - * @param index - * @param vDataSet - */ - public void setDataSet(int index, org.vamsas.objects.core.DataSet vDataSet) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _dataSetList.size())) { - throw new IndexOutOfBoundsException("setDataSet: Index value '"+index+"' not in range [0.."+_dataSetList.size()+ "]"); - } - _dataSetList.setElementAt(vDataSet, index); - } //-- void setDataSet(int, org.vamsas.objects.core.DataSet) - - /** - * Method setDataSet - * - * - * - * @param dataSetArray - */ - public void setDataSet(org.vamsas.objects.core.DataSet[] dataSetArray) - { - //-- copy array - _dataSetList.removeAllElements(); - for (int i = 0; i < dataSetArray.length; i++) { - _dataSetList.addElement(dataSetArray[i]); - } - } //-- void setDataSet(org.vamsas.objects.core.DataSet) - - /** - * Sets the value of field 'id'. The field 'id' has the - * following description: Primary Key for vamsas object - * referencing - * - * @param id the value of field 'id'. - */ - public void setId(java.lang.String id) - { - this._id = id; - } //-- void setId(java.lang.String) - - /** - * Sets the value of field 'modifiable'. - * - * @param modifiable the value of field 'modifiable'. - */ - public void setModifiable(java.lang.String modifiable) - { - this._modifiable = modifiable; - } //-- void setModifiable(java.lang.String) - - /** - * Method setTree - * - * - * - * @param index - * @param vTree - */ - public void setTree(int index, org.vamsas.objects.core.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _treeList.size())) { - throw new IndexOutOfBoundsException("setTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]"); - } - _treeList.setElementAt(vTree, index); - } //-- void setTree(int, org.vamsas.objects.core.Tree) - - /** - * Method setTree - * - * - * - * @param treeArray - */ - public void setTree(org.vamsas.objects.core.Tree[] treeArray) - { - //-- copy array - _treeList.removeAllElements(); - for (int i = 0; i < treeArray.length; i++) { - _treeList.addElement(treeArray[i]); - } - } //-- void setTree(org.vamsas.objects.core.Tree) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return VAMSAS - */ - public static org.vamsas.objects.core.VAMSAS unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.VAMSAS) Unmarshaller.unmarshal(org.vamsas.objects.core.VAMSAS.class, reader); - } //-- org.vamsas.objects.core.VAMSAS unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/VAMSASDescriptor.java b/src/org/vamsas/objects/core/VAMSASDescriptor.java deleted file mode 100644 index 9eb4e29..0000000 --- a/src/org/vamsas/objects/core/VAMSASDescriptor.java +++ /dev/null @@ -1,315 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class VAMSASDescriptor. - * - * @version $Revision$ $Date$ - */ -public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public VAMSASDescriptor() - { - super(); - nsURI = "http://www.vamsas.org"; - xmlName = "VAMSAS"; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); - this.identity = desc; - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - VAMSAS target = (VAMSAS) object; - return target.getId(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - VAMSAS target = (VAMSAS) object; - target.setId( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new java.lang.String(); - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _modifiable - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_modifiable", "modifiable", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - VAMSAS target = (VAMSAS) object; - return target.getModifiable(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - VAMSAS target = (VAMSAS) object; - target.setModifiable( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _modifiable - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _treeList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Tree.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - VAMSAS target = (VAMSAS) object; - return target.getTree(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - VAMSAS target = (VAMSAS) object; - target.addTree( (org.vamsas.objects.core.Tree) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.Tree(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _treeList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _dataSetList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.DataSet.class, "_dataSetList", "DataSet", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - VAMSAS target = (VAMSAS) object; - return target.getDataSet(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - VAMSAS target = (VAMSAS) object; - target.addDataSet( (org.vamsas.objects.core.DataSet) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.DataSet(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _dataSetList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.objects.core.VAMSASDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return null; - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.VAMSAS.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/core/VamsasDocument.java b/src/org/vamsas/objects/core/VamsasDocument.java deleted file mode 100644 index f8df822..0000000 --- a/src/org/vamsas/objects/core/VamsasDocument.java +++ /dev/null @@ -1,725 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class VamsasDocument. - * - * @version $Revision$ $Date$ - */ -public class VamsasDocument extends org.vamsas.client.Vobject -implements java.io.Serializable -{ - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Vamsas Document Version Number - */ - private java.lang.String _version; - - /** - * Field _lockFile - */ - private org.vamsas.objects.core.LockFile _lockFile; - - /** - * Field _provenance - */ - private Provenance _provenance; - - /** - * contains unassociated trees and a number of analysis sets - * - */ - private java.util.Vector _VAMSASList; - - /** - * Field _applicationDataList - */ - private java.util.Vector _applicationDataList; - - /** - * Field _attachmentList - */ - private java.util.Vector _attachmentList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public VamsasDocument() - { - super(); - _VAMSASList = new Vector(); - _applicationDataList = new Vector(); - _attachmentList = new Vector(); - } //-- org.vamsas.objects.core.VamsasDocument() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addApplicationData - * - * - * - * @param vApplicationData - */ - public void addApplicationData(ApplicationData vApplicationData) - throws java.lang.IndexOutOfBoundsException - { - _applicationDataList.addElement(vApplicationData); - } //-- void addApplicationData(ApplicationData) - - /** - * Method addApplicationData - * - * - * - * @param index - * @param vApplicationData - */ - public void addApplicationData(int index, ApplicationData vApplicationData) - throws java.lang.IndexOutOfBoundsException - { - _applicationDataList.insertElementAt(vApplicationData, index); - } //-- void addApplicationData(int, ApplicationData) - - /** - * Method addAttachment - * - * - * - * @param vAttachment - */ - public void addAttachment(Attachment vAttachment) - throws java.lang.IndexOutOfBoundsException - { - _attachmentList.addElement(vAttachment); - } //-- void addAttachment(Attachment) - - /** - * Method addAttachment - * - * - * - * @param index - * @param vAttachment - */ - public void addAttachment(int index, Attachment vAttachment) - throws java.lang.IndexOutOfBoundsException - { - _attachmentList.insertElementAt(vAttachment, index); - } //-- void addAttachment(int, Attachment) - - /** - * Method addVAMSAS - * - * - * - * @param vVAMSAS - */ - public void addVAMSAS(VAMSAS vVAMSAS) - throws java.lang.IndexOutOfBoundsException - { - _VAMSASList.addElement(vVAMSAS); - } //-- void addVAMSAS(VAMSAS) - - /** - * Method addVAMSAS - * - * - * - * @param index - * @param vVAMSAS - */ - public void addVAMSAS(int index, VAMSAS vVAMSAS) - throws java.lang.IndexOutOfBoundsException - { - _VAMSASList.insertElementAt(vVAMSAS, index); - } //-- void addVAMSAS(int, VAMSAS) - - /** - * Method enumerateApplicationData - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateApplicationData() - { - return _applicationDataList.elements(); - } //-- java.util.Enumeration enumerateApplicationData() - - /** - * Method enumerateAttachment - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateAttachment() - { - return _attachmentList.elements(); - } //-- java.util.Enumeration enumerateAttachment() - - /** - * Method enumerateVAMSAS - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateVAMSAS() - { - return _VAMSASList.elements(); - } //-- java.util.Enumeration enumerateVAMSAS() - - /** - * Note: hashCode() has not been overriden - * - * @param obj - * @return boolean - */ - public boolean equals(java.lang.Object obj) - { - if ( this == obj ) - return true; - - if (super.equals(obj)==false) - return false; - - if (obj instanceof VamsasDocument) { - - VamsasDocument temp = (VamsasDocument)obj; - if (this._version != null) { - if (temp._version == null) return false; - else if (!(this._version.equals(temp._version))) - return false; - } - else if (temp._version != null) - return false; - if (this._lockFile != null) { - if (temp._lockFile == null) return false; - else if (!(this._lockFile.equals(temp._lockFile))) - return false; - } - else if (temp._lockFile != null) - return false; - if (this._provenance != null) { - if (temp._provenance == null) return false; - else if (!(this._provenance.equals(temp._provenance))) - return false; - } - else if (temp._provenance != null) - return false; - if (this._VAMSASList != null) { - if (temp._VAMSASList == null) return false; - else if (!(this._VAMSASList.equals(temp._VAMSASList))) - return false; - } - else if (temp._VAMSASList != null) - return false; - if (this._applicationDataList != null) { - if (temp._applicationDataList == null) return false; - else if (!(this._applicationDataList.equals(temp._applicationDataList))) - return false; - } - else if (temp._applicationDataList != null) - return false; - if (this._attachmentList != null) { - if (temp._attachmentList == null) return false; - else if (!(this._attachmentList.equals(temp._attachmentList))) - return false; - } - else if (temp._attachmentList != null) - return false; - return true; - } - return false; - } //-- boolean equals(java.lang.Object) - - /** - * Method getApplicationData - * - * - * - * @param index - * @return ApplicationData - */ - public ApplicationData getApplicationData(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _applicationDataList.size())) { - throw new IndexOutOfBoundsException("getApplicationData: Index value '"+index+"' not in range [0.."+_applicationDataList.size()+ "]"); - } - - return (ApplicationData) _applicationDataList.elementAt(index); - } //-- ApplicationData getApplicationData(int) - - /** - * Method getApplicationData - * - * - * - * @return ApplicationData - */ - public ApplicationData[] getApplicationData() - { - int size = _applicationDataList.size(); - ApplicationData[] mArray = new ApplicationData[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (ApplicationData) _applicationDataList.elementAt(index); - } - return mArray; - } //-- ApplicationData[] getApplicationData() - - /** - * Method getApplicationDataCount - * - * - * - * @return int - */ - public int getApplicationDataCount() - { - return _applicationDataList.size(); - } //-- int getApplicationDataCount() - - /** - * Method getAttachment - * - * - * - * @param index - * @return Attachment - */ - public Attachment getAttachment(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _attachmentList.size())) { - throw new IndexOutOfBoundsException("getAttachment: Index value '"+index+"' not in range [0.."+_attachmentList.size()+ "]"); - } - - return (Attachment) _attachmentList.elementAt(index); - } //-- Attachment getAttachment(int) - - /** - * Method getAttachment - * - * - * - * @return Attachment - */ - public Attachment[] getAttachment() - { - int size = _attachmentList.size(); - Attachment[] mArray = new Attachment[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (Attachment) _attachmentList.elementAt(index); - } - return mArray; - } //-- Attachment[] getAttachment() - - /** - * Method getAttachmentCount - * - * - * - * @return int - */ - public int getAttachmentCount() - { - return _attachmentList.size(); - } //-- int getAttachmentCount() - - /** - * Returns the value of field 'lockFile'. - * - * @return LockFile - * @return the value of field 'lockFile'. - */ - public org.vamsas.objects.core.LockFile getLockFile() - { - return this._lockFile; - } //-- org.vamsas.objects.core.LockFile getLockFile() - - /** - * Returns the value of field 'provenance'. - * - * @return Provenance - * @return the value of field 'provenance'. - */ - public Provenance getProvenance() - { - return this._provenance; - } //-- Provenance getProvenance() - - /** - * Method getVAMSAS - * - * - * - * @param index - * @return VAMSAS - */ - public VAMSAS getVAMSAS(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _VAMSASList.size())) { - throw new IndexOutOfBoundsException("getVAMSAS: Index value '"+index+"' not in range [0.."+_VAMSASList.size()+ "]"); - } - - return (VAMSAS) _VAMSASList.elementAt(index); - } //-- VAMSAS getVAMSAS(int) - - /** - * Method getVAMSAS - * - * - * - * @return VAMSAS - */ - public VAMSAS[] getVAMSAS() - { - int size = _VAMSASList.size(); - VAMSAS[] mArray = new VAMSAS[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (VAMSAS) _VAMSASList.elementAt(index); - } - return mArray; - } //-- VAMSAS[] getVAMSAS() - - /** - * Method getVAMSASCount - * - * - * - * @return int - */ - public int getVAMSASCount() - { - return _VAMSASList.size(); - } //-- int getVAMSASCount() - - /** - * Returns the value of field 'version'. The field 'version' - * has the following description: Vamsas Document Version - * Number - * - * @return String - * @return the value of field 'version'. - */ - public java.lang.String getVersion() - { - return this._version; - } //-- java.lang.String getVersion() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method removeAllApplicationData - * - */ - public void removeAllApplicationData() - { - _applicationDataList.removeAllElements(); - } //-- void removeAllApplicationData() - - /** - * Method removeAllAttachment - * - */ - public void removeAllAttachment() - { - _attachmentList.removeAllElements(); - } //-- void removeAllAttachment() - - /** - * Method removeAllVAMSAS - * - */ - public void removeAllVAMSAS() - { - _VAMSASList.removeAllElements(); - } //-- void removeAllVAMSAS() - - /** - * Method removeApplicationData - * - * - * - * @param index - * @return ApplicationData - */ - public ApplicationData removeApplicationData(int index) - { - java.lang.Object obj = _applicationDataList.elementAt(index); - _applicationDataList.removeElementAt(index); - return (ApplicationData) obj; - } //-- ApplicationData removeApplicationData(int) - - /** - * Method removeAttachment - * - * - * - * @param index - * @return Attachment - */ - public Attachment removeAttachment(int index) - { - java.lang.Object obj = _attachmentList.elementAt(index); - _attachmentList.removeElementAt(index); - return (Attachment) obj; - } //-- Attachment removeAttachment(int) - - /** - * Method removeVAMSAS - * - * - * - * @param index - * @return VAMSAS - */ - public VAMSAS removeVAMSAS(int index) - { - java.lang.Object obj = _VAMSASList.elementAt(index); - _VAMSASList.removeElementAt(index); - return (VAMSAS) obj; - } //-- VAMSAS removeVAMSAS(int) - - /** - * Method setApplicationData - * - * - * - * @param index - * @param vApplicationData - */ - public void setApplicationData(int index, ApplicationData vApplicationData) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _applicationDataList.size())) { - throw new IndexOutOfBoundsException("setApplicationData: Index value '"+index+"' not in range [0.."+_applicationDataList.size()+ "]"); - } - _applicationDataList.setElementAt(vApplicationData, index); - } //-- void setApplicationData(int, ApplicationData) - - /** - * Method setApplicationData - * - * - * - * @param applicationDataArray - */ - public void setApplicationData(ApplicationData[] applicationDataArray) - { - //-- copy array - _applicationDataList.removeAllElements(); - for (int i = 0; i < applicationDataArray.length; i++) { - _applicationDataList.addElement(applicationDataArray[i]); - } - } //-- void setApplicationData(ApplicationData) - - /** - * Method setAttachment - * - * - * - * @param index - * @param vAttachment - */ - public void setAttachment(int index, Attachment vAttachment) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _attachmentList.size())) { - throw new IndexOutOfBoundsException("setAttachment: Index value '"+index+"' not in range [0.."+_attachmentList.size()+ "]"); - } - _attachmentList.setElementAt(vAttachment, index); - } //-- void setAttachment(int, Attachment) - - /** - * Method setAttachment - * - * - * - * @param attachmentArray - */ - public void setAttachment(Attachment[] attachmentArray) - { - //-- copy array - _attachmentList.removeAllElements(); - for (int i = 0; i < attachmentArray.length; i++) { - _attachmentList.addElement(attachmentArray[i]); - } - } //-- void setAttachment(Attachment) - - /** - * Sets the value of field 'lockFile'. - * - * @param lockFile the value of field 'lockFile'. - */ - public void setLockFile(org.vamsas.objects.core.LockFile lockFile) - { - this._lockFile = lockFile; - } //-- void setLockFile(org.vamsas.objects.core.LockFile) - - /** - * Sets the value of field 'provenance'. - * - * @param provenance the value of field 'provenance'. - */ - public void setProvenance(Provenance provenance) - { - this._provenance = provenance; - } //-- void setProvenance(Provenance) - - /** - * Method setVAMSAS - * - * - * - * @param index - * @param vVAMSAS - */ - public void setVAMSAS(int index, VAMSAS vVAMSAS) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _VAMSASList.size())) { - throw new IndexOutOfBoundsException("setVAMSAS: Index value '"+index+"' not in range [0.."+_VAMSASList.size()+ "]"); - } - _VAMSASList.setElementAt(vVAMSAS, index); - } //-- void setVAMSAS(int, VAMSAS) - - /** - * Method setVAMSAS - * - * - * - * @param VAMSASArray - */ - public void setVAMSAS(VAMSAS[] VAMSASArray) - { - //-- copy array - _VAMSASList.removeAllElements(); - for (int i = 0; i < VAMSASArray.length; i++) { - _VAMSASList.addElement(VAMSASArray[i]); - } - } //-- void setVAMSAS(VAMSAS) - - /** - * Sets the value of field 'version'. The field 'version' has - * the following description: Vamsas Document Version Number - * - * @param version the value of field 'version'. - */ - public void setVersion(java.lang.String version) - { - this._version = version; - } //-- void setVersion(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return VamsasDocument - */ - public static org.vamsas.objects.core.VamsasDocument unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (org.vamsas.objects.core.VamsasDocument) Unmarshaller.unmarshal(org.vamsas.objects.core.VamsasDocument.class, reader); - } //-- org.vamsas.objects.core.VamsasDocument unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} diff --git a/src/org/vamsas/objects/core/VamsasDocumentDescriptor.java b/src/org/vamsas/objects/core/VamsasDocumentDescriptor.java deleted file mode 100644 index 425e16a..0000000 --- a/src/org/vamsas/objects/core/VamsasDocumentDescriptor.java +++ /dev/null @@ -1,388 +0,0 @@ -/* - * This class was automatically generated with - * Castor 0.9.9M2, using an XML - * Schema. - * $Id$ - */ - -package org.vamsas.objects.core; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.mapping.AccessMode; -import org.exolab.castor.xml.TypeValidator; -import org.exolab.castor.xml.XMLFieldDescriptor; -import org.exolab.castor.xml.validators.*; - -/** - * Class VamsasDocumentDescriptor. - * - * @version $Revision$ $Date$ - */ -public class VamsasDocumentDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field nsPrefix - */ - private java.lang.String nsPrefix; - - /** - * Field nsURI - */ - private java.lang.String nsURI; - - /** - * Field xmlName - */ - private java.lang.String xmlName; - - /** - * Field identity - */ - private org.exolab.castor.xml.XMLFieldDescriptor identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public VamsasDocumentDescriptor() - { - super(); - nsURI = "http://www.vamsas.ac.uk/vamsasDocument"; - xmlName = "VamsasDocument"; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- initialize element descriptors - - //-- _version - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "Version", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - VamsasDocument target = (VamsasDocument) object; - return target.getVersion(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - VamsasDocument target = (VamsasDocument) object; - target.setVersion( (java.lang.String) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.ac.uk/vamsasDocument"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _version - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - StringValidator typeValidator = new StringValidator(); - typeValidator.setWhiteSpace("preserve"); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - //-- _lockFile - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.LockFile.class, "_lockFile", "LockFile", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - VamsasDocument target = (VamsasDocument) object; - return target.getLockFile(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - VamsasDocument target = (VamsasDocument) object; - target.setLockFile( (org.vamsas.objects.core.LockFile) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new org.vamsas.objects.core.LockFile(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.ac.uk/vamsasDocument"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _lockFile - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _provenance - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - VamsasDocument target = (VamsasDocument) object; - return target.getProvenance(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - VamsasDocument target = (VamsasDocument) object; - target.setProvenance( (Provenance) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new Provenance(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _provenance - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _VAMSASList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(VAMSAS.class, "_VAMSASList", "VAMSAS", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - VamsasDocument target = (VamsasDocument) object; - return target.getVAMSAS(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - VamsasDocument target = (VamsasDocument) object; - target.addVAMSAS( (VAMSAS) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new VAMSAS(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setRequired(true); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _VAMSASList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _applicationDataList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(ApplicationData.class, "_applicationDataList", "ApplicationData", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - VamsasDocument target = (VamsasDocument) object; - return target.getApplicationData(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - VamsasDocument target = (VamsasDocument) object; - target.addApplicationData( (ApplicationData) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new ApplicationData(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _applicationDataList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _attachmentList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(Attachment.class, "_attachmentList", "Attachment", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - VamsasDocument target = (VamsasDocument) object; - return target.getAttachment(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - VamsasDocument target = (VamsasDocument) object; - target.addAttachment( (Attachment) value); - } - catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance( java.lang.Object parent ) { - return new Attachment(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("http://www.vamsas.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _attachmentList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - } //-- org.vamsas.objects.core.VamsasDocumentDescriptor() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode - * - * - * - * @return AccessMode - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } //-- org.exolab.castor.mapping.AccessMode getAccessMode() - - /** - * Method getExtends - * - * - * - * @return ClassDescriptor - */ - public org.exolab.castor.mapping.ClassDescriptor getExtends() - { - return null; - } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() - - /** - * Method getIdentity - * - * - * - * @return FieldDescriptor - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return identity; - } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() - - /** - * Method getJavaClass - * - * - * - * @return Class - */ - public java.lang.Class getJavaClass() - { - return org.vamsas.objects.core.VamsasDocument.class; - } //-- java.lang.Class getJavaClass() - - /** - * Method getNameSpacePrefix - * - * - * - * @return String - */ - public java.lang.String getNameSpacePrefix() - { - return nsPrefix; - } //-- java.lang.String getNameSpacePrefix() - - /** - * Method getNameSpaceURI - * - * - * - * @return String - */ - public java.lang.String getNameSpaceURI() - { - return nsURI; - } //-- java.lang.String getNameSpaceURI() - - /** - * Method getValidator - * - * - * - * @return TypeValidator - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } //-- org.exolab.castor.xml.TypeValidator getValidator() - - /** - * Method getXMLName - * - * - * - * @return String - */ - public java.lang.String getXMLName() - { - return xmlName; - } //-- java.lang.String getXMLName() - -} diff --git a/src/org/vamsas/objects/utils/AppDataReference.java b/src/org/vamsas/objects/utils/AppDataReference.java deleted file mode 100644 index 414c8da..0000000 --- a/src/org/vamsas/objects/utils/AppDataReference.java +++ /dev/null @@ -1,160 +0,0 @@ -/** - * - */ -package org.vamsas.objects.utils; -import java.util.Vector; - -import org.vamsas.client.ClientHandle; -import org.vamsas.client.UserHandle; -import org.vamsas.client.simpleclient.VamsasArchive; -import org.vamsas.client.simpleclient.VamsasArchiveReader; -import org.vamsas.objects.core.*; -/** - * Form, accessors and validation for ApplicationData references in - * vamsas document. - * TODO: LATER:extend XML Schema to properly validate against the same forms required by this class - * TODO: VAMSAS: URNS for appDatas are supposed to be unique, aren't they ? - */ -public class AppDataReference { - /** - * search interface for collecting particular types of AppDatas in a vamsas document - * @author jimp - * - */ - interface IAppDSearch { - /** - * process the appData Vobject d - * @param d - * @return true if appData should be collected - */ - public boolean process(AppData d); - } - /** - * collect all appData reference strings in a vamsas document - * @param doc - * @return vector of String objects - */ - static public Vector getAppDataReferences(VamsasDocument doc) { - if ((doc!=null) && (doc.getApplicationDataCount()>0)) { - Vector apdrefs = new Vector(); - ApplicationData[] appdatas = doc.getApplicationData(); - for (int q=0; q0) - return apdrefs; - } - return null; - } - /** - * General search through the set of AppData objects for a particular profile of Client and User handle. - * @param doc - * @param test interface implemented by the filter selecting particular AppDatas. - * @param cascade if true only User objects for ApplicationData objects that test.process returned true will be tested. - * @return set of org.vamsas.objects.core.AppData objects for which test.process returned true - */ - static public Vector searchAppDatas(VamsasDocument doc, IAppDSearch test, boolean cascade) { - if ((doc!=null) && (doc.getApplicationDataCount()>0)) { - Vector apdrefs = new Vector(); - ApplicationData[] appdatas = doc.getApplicationData(); - for (int q=0; q0) - return apdrefs; - } - return null; - } - static public boolean equals(User p, UserHandle u) { - if (p.getFullname().equals(u.getFullName()) - && p.getOrganization().equals(u.getOrganization())) - return true; - return false; - } - /** - * 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) - * @param p - * @param c - * @return match of p on template c. - */ - static public boolean equals(ApplicationData p, ClientHandle c) { - if ( - //((c.getClientUrn()==null) || p.getUrn().equals(c.getClientUrn())) - //&& - (p.getName().equals(c.getClientName())) - && - ((c.getVersion()==null) || (p.getVersion().equals(c.getVersion()))) - ) - return true; - return false; - } - /** - * Searches document appData structure for particular combinations of client and user data - * @param doc the data - * @param user template user data to match against - * @see AppDataReference.equals(org.vamsas.objects.core.User, org.vamsas.client.UserHandle) - * @param app - * @see AppDataReference.equals(org.vamsas.objects.core.ApplicationData, org.vamsas.client.ClientHandle) - * @return set of matching client app datas for this client and user combination - */ - static public Vector getUserandApplicationsData(VamsasDocument doc, UserHandle user, ClientHandle app) { - if (doc==null) { - return null; - } - final UserHandle u = user; - final ClientHandle c = app; - - IAppDSearch match = new IAppDSearch() { - public boolean process(AppData p) { - if (p instanceof User) { - if (AppDataReference.equals((User) p, u)) - return true; - } else - if (p instanceof ApplicationData) { - if (AppDataReference.equals((ApplicationData) p, c)) - return true; - } - return false; - } - }; - - return searchAppDatas(doc, match, true); // only return AppDatas belonging to appdata app. - } - /** - * safely creates a new appData reference - * @param dest destination document Vobject - * @param entry base application reference to make unique - */ - public static String uniqueAppDataReference(VamsasDocument dest,String base) { - String urn = new String(base); - - for (int i=0, j=dest.getApplicationDataCount(); i - *
  • a % (required) - *
  • a modifier (optional) - *
    - *
    +
    forces display of + for positive numbers - *
    0
    show leading zeroes - *
    -
    align left in the field - *
    space
    prepend a space in front of positive numbers - *
    #
    use "alternate" format. Add 0 or 0x for octal or hexadecimal numbers. Don't suppress trailing zeroes in general floating point format. - *
    - *
  • an integer denoting field width (optional) - *
  • a period followed by an integer denoting precision (optional) - *
  • a format descriptor (required) - *
    - *
    f
    floating point number in fixed format - *
    e, E
    floating point number in exponential notation (scientific format). The E format results in an uppercase E for the exponent (1.14130E+003), the e format in a lowercase e. - *
    g, G
    floating point number in general format (fixed format for small numbers, exponential format for large numbers). Trailing zeroes are suppressed. The G format results in an uppercase E for the exponent (if any), the g format in a lowercase e. - *
    d, i
    integer in decimal - *
    x
    integer in hexadecimal - *
    o
    integer in octal - *
    s
    string - *
    c
    character - *
    - * - * @exception IllegalArgumentException if bad format - */ - - public Format(String s) { - width = 0; - precision = -1; - pre = ""; - post = ""; - leading_zeroes = false; - show_plus = false; - alternate = false; - show_space = false; - left_align = false; - fmt = ' '; - - int state = 0; - int length = s.length(); - int parse_state = 0; - // 0 = prefix, 1 = flags, 2 = width, 3 = precision, - // 4 = format, 5 = end - int i = 0; - - while (parse_state == 0) { - if (i >= length) - parse_state = 5; - else if (s.charAt(i) == '%') { - if (i < length - 1) { - if (s.charAt(i + 1) == '%') { - pre = pre + '%'; - i++; - } else - parse_state = 1; - } else - throw new java.lang.IllegalArgumentException(); - } else - pre = pre + s.charAt(i); - i++; - } - while (parse_state == 1) { - if (i >= length) - parse_state = 5; - else if (s.charAt(i) == ' ') - show_space = true; - else if (s.charAt(i) == '-') - left_align = true; - else if (s.charAt(i) == '+') - show_plus = true; - else if (s.charAt(i) == '0') - leading_zeroes = true; - else if (s.charAt(i) == '#') - alternate = true; - else { - parse_state = 2; - i--; - } - i++; - } - while (parse_state == 2) { - if (i >= length) - parse_state = 5; - else if ('0' <= s.charAt(i) && s.charAt(i) <= '9') { - width = width * 10 + s.charAt(i) - '0'; - i++; - } else if (s.charAt(i) == '.') { - parse_state = 3; - precision = 0; - i++; - } else - parse_state = 4; - } - while (parse_state == 3) { - if (i >= length) - parse_state = 5; - else if ('0' <= s.charAt(i) && s.charAt(i) <= '9') { - precision = precision * 10 + s.charAt(i) - '0'; - i++; - } else - parse_state = 4; - } - if (parse_state == 4) { - if (i >= length) - parse_state = 5; - else - fmt = s.charAt(i); - i++; - } - if (i < length) - post = s.substring(i, length); - } - - /** - * prints a formatted number following printf conventions - * @param s a PrintStream - * @param fmt the format string - * @param x the double to print - */ - - public static void print(java.io.PrintStream s, String fmt, double x) { - s.print(new Format(fmt).form(x)); - } - - /** - * prints a formatted number following printf conventions - * @param s a PrintStream - * @param fmt the format string - * @param x the long to print - */ - public static void print(java.io.PrintStream s, String fmt, long x) { - s.print(new Format(fmt).form(x)); - } - - /** - * prints a formatted number following printf conventions - * @param s a PrintStream - * @param fmt the format string - * @param x the character to - */ - - public static void print(java.io.PrintStream s, String fmt, char x) { - s.print(new Format(fmt).form(x)); - } - - /** - * prints a formatted number following printf conventions - * @param s a PrintStream, fmt the format string - * @param x a string that represents the digits to print - */ - - public static void print(java.io.PrintStream s, String fmt, String x) { - s.print(new Format(fmt).form(x)); - } - - /** - * Converts a string of digits (decimal, octal or hex) to an integer - * @param s a string - * @return the numeric value of the prefix of s representing a base 10 integer - */ - - public static int atoi(String s) { - return (int)atol(s); - } - - /** - * Converts a string of digits (decimal, octal or hex) to a long integer - * @param s a string - * @return the numeric value of the prefix of s representing a base 10 integer - */ - - public static long atol(String s) { - int i = 0; - - while (i < s.length() && Character.isWhitespace(s.charAt(i))) - i++; - if (i < s.length() && s.charAt(i) == '0') { - if (i + 1 < s.length() && (s.charAt(i + 1) == 'x' || s.charAt(i + 1) == 'X')) - return parseLong(s.substring(i + 2), 16); - else - return parseLong(s, 8); - } else - return parseLong(s, 10); - } - - private static long parseLong(String s, int base) { - int i = 0; - int sign = 1; - long r = 0; - - while (i < s.length() && Character.isWhitespace(s.charAt(i))) - i++; - if (i < s.length() && s.charAt(i) == '-') { - sign = -1; - i++; - } else if (i < s.length() && s.charAt(i) == '+') { - i++; - } - while (i < s.length()) { - char ch = s.charAt(i); - if ('0' <= ch && ch < '0' + base) - r = r * base + ch - '0'; - else if ('A' <= ch && ch < 'A' + base - 10) - r = r * base + ch - 'A' + 10 ; - else if ('a' <= ch && ch < 'a' + base - 10) - r = r * base + ch - 'a' + 10 ; - else - return r * sign; - i++; - } - return r * sign; - } - - /** - * Converts a string of digits to an double - * @param s a string - */ - - public static double atof(String s) { - int i = 0; - int sign = 1; - double r = 0; // integer part - double f = 0; // fractional part - double p = 1; // exponent of fractional part - int state = 0; // 0 = int part, 1 = frac part - - while (i < s.length() && Character.isWhitespace(s.charAt(i))) - i++; - if (i < s.length() && s.charAt(i) == '-') { - sign = -1; - i++; - } else if (i < s.length() && s.charAt(i) == '+') { - i++; - } - while (i < s.length()) { - char ch = s.charAt(i); - if ('0' <= ch && ch <= '9') { - if (state == 0) - r = r * 10 + ch - '0'; - else if (state == 1) { - p = p / 10; - r = r + p * (ch - '0'); - } - } else if (ch == '.') { - if (state == 0) - state = 1; - else - return sign * r; - } else if (ch == 'e' || ch == 'E') { - long e = (int)parseLong(s.substring(i + 1), 10); - return sign * r * Math.pow(10, e); - } else - return sign * r; - i++; - } - return sign * r; - } - - /** - * Formats a double into a string (like sprintf in C) - * @param x the number to format - * @return the formatted string - * @exception IllegalArgumentException if bad argument - */ - - public String form(double x) { - String r; - if (precision < 0) - precision = 6; - int s = 1; - if (x < 0) { - x = -x; - s = -1; - } - if (fmt == 'f') - r = fixed_format(x); - else if (fmt == 'e' || fmt == 'E' || fmt == 'g' || fmt == 'G') - r = exp_format(x); - else - throw new java.lang.IllegalArgumentException(); - - return pad(sign(s, r)); - } - - /** - * Formats a long integer into a string (like sprintf in C) - * @param x the number to format - * @return the formatted string - */ - - public String form(long x) { - String r; - int s = 0; - if (fmt == 'd' || fmt == 'i') { - if (x < 0) { - r = ("" + x).substring(1); - s = -1; - } else { - r = "" + x; - s = 1; - } - } else if (fmt == 'o') - r = convert(x, 3, 7, "01234567"); - else if (fmt == 'x') - r = convert(x, 4, 15, "0123456789abcdef"); - else if (fmt == 'X') - r = convert(x, 4, 15, "0123456789ABCDEF"); - else - throw new java.lang.IllegalArgumentException(); - - return pad(sign(s, r)); - } - - /** - * Formats a character into a string (like sprintf in C) - * @param x the value to format - * @return the formatted string - */ - - public String form(char c) { - if (fmt != 'c') - throw new java.lang.IllegalArgumentException(); - - String r = "" + c; - return pad(r); - } - - /** - * Formats a string into a larger string (like sprintf in C) - * @param x the value to format - * @return the formatted string - */ - - public String form(String s) { - if (fmt != 's') - throw new java.lang.IllegalArgumentException(); - if (precision >= 0) - s = s.substring(0, precision); - return pad(s); - } - - - /** - * a test stub for the format class - */ - - public static void main(String[] a) { - double x = 1.23456789012; - double y = 123; - double z = 1.2345e30; - double w = 1.02; - double u = 1.234e-5; - int d = 0xCAFE; - Format.print(System.out, "x = |%f|\n", x); - Format.print(System.out, "u = |%20f|\n", u); - Format.print(System.out, "x = |% .5f|\n", x); - Format.print(System.out, "w = |%20.5f|\n", w); - Format.print(System.out, "x = |%020.5f|\n", x); - Format.print(System.out, "x = |%+20.5f|\n", x); - Format.print(System.out, "x = |%+020.5f|\n", x); - Format.print(System.out, "x = |% 020.5f|\n", x); - Format.print(System.out, "y = |%#+20.5f|\n", y); - Format.print(System.out, "y = |%-+20.5f|\n", y); - Format.print(System.out, "z = |%20.5f|\n", z); - - Format.print(System.out, "x = |%e|\n", x); - Format.print(System.out, "u = |%20e|\n", u); - Format.print(System.out, "x = |% .5e|\n", x); - Format.print(System.out, "w = |%20.5e|\n", w); - Format.print(System.out, "x = |%020.5e|\n", x); - Format.print(System.out, "x = |%+20.5e|\n", x); - Format.print(System.out, "x = |%+020.5e|\n", x); - Format.print(System.out, "x = |% 020.5e|\n", x); - Format.print(System.out, "y = |%#+20.5e|\n", y); - Format.print(System.out, "y = |%-+20.5e|\n", y); - - Format.print(System.out, "x = |%g|\n", x); - Format.print(System.out, "z = |%g|\n", z); - Format.print(System.out, "w = |%g|\n", w); - Format.print(System.out, "u = |%g|\n", u); - Format.print(System.out, "y = |%.2g|\n", y); - Format.print(System.out, "y = |%#.2g|\n", y); - - Format.print(System.out, "d = |%d|\n", d); - Format.print(System.out, "d = |%20d|\n", d); - Format.print(System.out, "d = |%020d|\n", d); - Format.print(System.out, "d = |%+20d|\n", d); - Format.print(System.out, "d = |% 020d|\n", d); - Format.print(System.out, "d = |%-20d|\n", d); - Format.print(System.out, "d = |%20.8d|\n", d); - Format.print(System.out, "d = |%x|\n", d); - Format.print(System.out, "d = |%20X|\n", d); - Format.print(System.out, "d = |%#20x|\n", d); - Format.print(System.out, "d = |%020X|\n", d); - Format.print(System.out, "d = |%20.8x|\n", d); - Format.print(System.out, "d = |%o|\n", d); - Format.print(System.out, "d = |%020o|\n", d); - Format.print(System.out, "d = |%#20o|\n", d); - Format.print(System.out, "d = |%#020o|\n", d); - Format.print(System.out, "d = |%20.12o|\n", d); - - Format.print(System.out, "s = |%-20s|\n", "Hello"); - Format.print(System.out, "s = |%-20c|\n", '!'); - - // regression test to confirm fix of reported bugs - - Format.print(System.out, "|%i|\n", Long.MIN_VALUE); - - Format.print(System.out, "|%6.2e|\n", 0.0); - Format.print(System.out, "|%6.2g|\n", 0.0); - - Format.print(System.out, "|%6.2f|\n", 9.99); - Format.print(System.out, "|%6.2f|\n", 9.999); - - Format.print(System.out, "|%6.0f|\n", 9.999); - } - - private static String repeat(char c, int n) { - if (n <= 0) - return ""; - StringBuffer s = new StringBuffer(n); - for (int i = 0; i < n; i++) - s.append(c); - return s.toString(); - } - - private static String convert(long x, int n, int m, String d) { - if (x == 0) - return "0"; - String r = ""; - while (x != 0) { - r = d.charAt((int)(x & m)) + r; - x = x >>> n; - } - return r; - } - - private String pad(String r) { - String p = repeat(' ', width - r.length()); - if (left_align) - return pre + r + p + post; - else - return pre + p + r + post; - } - - private String sign(int s, String r) { - String p = ""; - if (s < 0) - p = "-"; - else if (s > 0) { - if (show_plus) - p = "+"; - else if (show_space) - p = " "; - } else { - if (fmt == 'o' && alternate && r.length() > 0 && r.charAt(0) != '0') - p = "0"; - else if (fmt == 'x' && alternate) - p = "0x"; - else if (fmt == 'X' && alternate) - p = "0X"; - } - int w = 0; - if (leading_zeroes) - w = width; - else if ((fmt == 'd' || fmt == 'i' || fmt == 'x' || fmt == 'X' || fmt == 'o') - && precision > 0) - w = precision; - - return p + repeat('0', w - p.length() - r.length()) + r; - } - - private String fixed_format(double d) { - boolean removeTrailing - = (fmt == 'G' || fmt == 'g') && !alternate; - // remove trailing zeroes and decimal point - - if (d > 0x7FFFFFFFFFFFFFFFL) - return exp_format(d); - if (precision == 0) - return (long)(d + 0.5) + (removeTrailing ? "" : "."); - - long whole = (long)d; - double fr = d - whole; // fractional part - if (fr >= 1 || fr < 0) - return exp_format(d); - - double factor = 1; - String leading_zeroes = ""; - for (int i = 1; i <= precision && factor <= 0x7FFFFFFFFFFFFFFFL; i++) { - factor *= 10; - leading_zeroes = leading_zeroes + "0"; - } - long l = (long) (factor * fr + 0.5); - if (l >= factor) { - l = 0; - whole++; - } // CSH 10-25-97 - - String z = leading_zeroes + l; - z = "." + z.substring(z.length() - precision, z.length()); - - if (removeTrailing) { - int t = z.length() - 1; - while (t >= 0 && z.charAt(t) == '0') - t--; - if (t >= 0 && z.charAt(t) == '.') - t--; - z = z.substring(0, t + 1); - } - - return whole + z; - } - - private String exp_format(double d) { - String f = ""; - int e = 0; - double dd = d; - double factor = 1; - if (d != 0) { - while (dd > 10) { - e++; - factor /= 10; - dd = dd / 10; - } - while (dd < 1) { - e--; - factor *= 10; - dd = dd * 10; - } - } - if ((fmt == 'g' || fmt == 'G') && e >= -4 && e < precision) - return fixed_format(d); - - d = d * factor; - f = f + fixed_format(d); - - if (fmt == 'e' || fmt == 'g') - f = f + "e"; - else - f = f + "E"; - - String p = "000"; - if (e >= 0) { - f = f + "+"; - p = p + e; - } else { - f = f + "-"; - p = p + (-e); - } - - return f + p.substring(p.length() - 3, p.length()); - } - - private int width; - private int precision; - private String pre; - private String post; - private boolean leading_zeroes; - private boolean show_plus; - private boolean alternate; - private boolean show_space; - private boolean left_align; - private char fmt; // one of cdeEfgGiosxXos -} - - - - - diff --git a/src/org/vamsas/objects/utils/GlyphDictionary.java b/src/org/vamsas/objects/utils/GlyphDictionary.java deleted file mode 100644 index 1ed7b20..0000000 --- a/src/org/vamsas/objects/utils/GlyphDictionary.java +++ /dev/null @@ -1,23 +0,0 @@ -package org.vamsas.objects.utils; - -/** - * dict attribute values for glyph symbol sets found in org.vamsas.objects.core.AnnotationElement - * TODO: add validators and multilength symbols. - * @author JimP - * - */ -public class GlyphDictionary { - /** - * standard H, E, or C three state secondary structure assignment. - */ - static final public String PROTEIN_SS_3STATE="aasecstr_3"; // HE, blank or C - /** - * default glyph type attribute indicates a UTF8 character - */ - static final public String DEFAULT="utf8"; - /** - * kyte and doolittle hydrophobicity - * TODO: specify this glyph set. - */ - static final public String PROTEIN_HD_HYDRO="kd_hydrophobicity"; -} diff --git a/src/org/vamsas/objects/utils/ProvenanceStuff.java b/src/org/vamsas/objects/utils/ProvenanceStuff.java deleted file mode 100644 index 2e813f7..0000000 --- a/src/org/vamsas/objects/utils/ProvenanceStuff.java +++ /dev/null @@ -1,45 +0,0 @@ -package org.vamsas.objects.utils; - -import java.util.Date; - -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.vamsas.objects.core.Entry; -import org.vamsas.objects.core.Provenance; - -public class ProvenanceStuff { - - /** - * stuff for making and doing things with provenance objects. - */ - static Log log = LogFactory.getLog(ProvenanceStuff.class); - - /** - * @param app TODO - * @param action - * text for action entry - * @return new Provenance entry for ArchiveWriter created docs. - * TODO: Verify and move to SimpleClient class for provenance handling - */ - public static Entry newProvenanceEntry(String app, String user, String action) { - log.debug("Adding ProvenanceEntry("+user+","+action+")"); - Entry e = new Entry(); - e.setApp(app); - e.setAction(action); - e.setUser(user); - e.setDate(new org.exolab.castor.types.Date(new Date())); - return e; - } - public static Provenance newProvenance(Entry entry) { - Provenance list = new Provenance(); - list.addEntry(entry); - return list; - } - public static Provenance newProvenance(String user, String action) { - return newProvenance(ProvenanceStuff.newProvenanceEntry("vamsasApp:ExampleVamsasClient/alpha", user, action)); - } - public static Provenance newProvenance(String app, String user, String action) { - return newProvenance(ProvenanceStuff.newProvenanceEntry(app, user, action)); - } - -} diff --git a/src/org/vamsas/objects/utils/Seq.java b/src/org/vamsas/objects/utils/Seq.java deleted file mode 100644 index b1955a1..0000000 --- a/src/org/vamsas/objects/utils/Seq.java +++ /dev/null @@ -1,131 +0,0 @@ -/* - * Created on 17-May-2005 - * - * TODO To change the template for this generated file go to - * Window - Preferences - Java - Code Style - Code Templates - */ -package org.vamsas.objects.utils; - -import java.io.BufferedWriter; -import java.io.IOException; -import java.io.OutputStream; -import java.io.OutputStreamWriter; -import java.util.regex.Pattern; - -import org.vamsas.objects.core.AlignmentSequence; -import org.vamsas.objects.core.Sequence; -import org.vamsas.objects.core.SequenceType; - -/** - * @author jimp - * - * TODO To change the template for this generated type comment go to - * Window - Preferences - Java - Code Style - Code Templates - */ -public class Seq { - - public static void write_PirSeq(OutputStream os, SequenceType seq, int wid) throws IOException { - BufferedWriter pir_out = new BufferedWriter(new OutputStreamWriter(os)); - pir_out.write(">P1;"+seq.getName()+"\n"); - int width = (wid<1) ? 80 : wid; - for (int j=0,k=seq.getSequence().length(); j"+seq.getName()+"\n"); - fasta_out.write(seq.getSequence()+"\n"); - fasta_out.flush(); - } - - public static void write_FastaSeq(OutputStream os, SequenceType seq, int wid) throws IOException { - BufferedWriter fasta_out = new BufferedWriter(new OutputStreamWriter(os)); - fasta_out.write(">"+seq.getName()+"\n"); - int width = (wid<1) ? 80 : wid; - for (int j=0,k=seq.getSequence().length(); jend on Sequence Vobject - if ((start-end)!=Sequence.length()) - seq.setEnd(end+Sequence.length()); - } - return seq; - } - public static AlignmentSequence newAlignmentSequence(String name, String alSequence, Sequence refseq, int start, int end) { - if (refseq!=null) { - AlignmentSequence asq = new AlignmentSequence(); - asq.setName(name); - asq.setSequence(alSequence); - asq.setRefid(refseq); - if (startrefseq.getEnd()) - end = refseq.getEnd(); - asq.setEnd(end); - return asq; - } - return null; - } - public static boolean is_valid_aa_seq(SequenceType s) { - Sequence q; - boolean validref=false; - if (s instanceof Sequence) { - q=(Sequence) s; - if (q.getDictionary()!=null - - && q.getDictionary().length()>0 - || !q.getDictionary().equals(SymbolDictionary.STANDARD_AA)) - return false; - return valid_aadictionary_string(q.getSequence(), SymbolDictionary.STANDARD_AA); - } - - // follow references - if (s instanceof AlignmentSequence) { - Object w = (((AlignmentSequence) s).getRefid()); - if (w!=null && w!=s && w instanceof SequenceType) - return is_valid_aa_seq((SequenceType) w) - && valid_aadictionary_string(((AlignmentSequence) s).getSequence(), SymbolDictionary.STANDARD_AA); - } - - return false; - } -} diff --git a/src/org/vamsas/objects/utils/SeqAln.java b/src/org/vamsas/objects/utils/SeqAln.java deleted file mode 100644 index 5e351f9..0000000 --- a/src/org/vamsas/objects/utils/SeqAln.java +++ /dev/null @@ -1,238 +0,0 @@ -/* - * Created on 17-May-2005 - * - * TODO To change the template for this generated file go to - * Window - Preferences - Java - Code Style - Code Templates - */ -package org.vamsas.objects.utils; - -import java.io.BufferedOutputStream; -import java.io.BufferedReader; -import java.io.BufferedWriter; -import java.io.IOException; -import java.io.InputStream; -import java.io.InputStreamReader; -import java.util.Hashtable; -import java.util.StringTokenizer; -import java.util.Vector; -import java.util.regex.Pattern; - -import org.vamsas.objects.core.*; - -/** - * @author jimp - * - * TODO To change the template for this generated type comment go to Window - - * Preferences - Java - Code Style - Code Templates - */ -public class SeqAln extends org.vamsas.objects.core.Alignment { - - public static Sequence[] ReadClustalFile(InputStream os) throws Exception { - System.err.println("NOT FULLY IMPLEMENTED!"); // TODO: Finish adapting this method - Pattern nonGap = Pattern.compile("[A-Z*0-9]", Pattern.CASE_INSENSITIVE); - String gapchars = ""; - char gapchar = '-'; - - int i = 0; - boolean flag = false; - - Vector headers = new Vector(); - Hashtable seqhash = new Hashtable(); - Sequence[] seqs = null; - int noSeqs = 0; - String line; - - try { - BufferedReader ins = new BufferedReader(new InputStreamReader(os)); - while ((line = ins.readLine()) != null) { - if (line.indexOf(" ") != 0) { - java.util.StringTokenizer str = new StringTokenizer(line, " "); - String id = ""; - - if (str.hasMoreTokens()) { - id = str.nextToken(); - if (id.equals("CLUSTAL")) { - flag = true; - } else { - if (flag) { - StringBuffer tempseq; - if (seqhash.containsKey(id)) { - tempseq = (StringBuffer) seqhash.get(id); - } else { - tempseq = new StringBuffer(); - seqhash.put(id, tempseq); - } - - if (!(headers.contains(id))) { - headers.addElement(id); - } - - tempseq.append(str.nextToken()); - } - } - } - } - } - - } catch (IOException e) { - throw (new Exception("Exception parsing clustal file ", e)); - } - - if (flag) { - noSeqs = headers.size(); - - // Add sequences to the hash - seqs = new Sequence[headers.size()]; - for (i = 0; i < headers.size(); i++) { - if (seqhash.get(headers.elementAt(i)) != null) { - // TODO: develop automatic dictionary typing for sequences - Sequence newSeq = Seq.newSequence(headers.elementAt(i).toString(), - seqhash.get(headers.elementAt(i).toString()).toString(), - SymbolDictionary.STANDARD_AA,0,0); - - seqs[i] = newSeq; - - } else { - throw (new Exception("Bizarreness! Can't find sequence for " - + headers.elementAt(i))); - } - } - } - return seqs; - } - - public static void WriteClustalWAlignment(java.io.OutputStream os, - Alignment seqAl) throws IOException { - System.err.println("NOT FULLY IMPLEMENTED!"); // TODO: Finish adapting this method - AlignmentSequence[] s = seqAl.getAlignmentSequence(); - - java.io.BufferedWriter out = new BufferedWriter( - new java.io.OutputStreamWriter(os)); - - out.write("CLUSTAL\n\n"); - - int max = 0; - int maxid = 0; - - int i = 0; - - while (i < s.length && s[i] != null) { - String tmp = s[i].getId(); - - if (s[i].getSequence().length() > max) { - max = s[i].getSequence().length(); - } - if (tmp.length() > maxid) { - maxid = tmp.length(); - } - i++; - } - - if (maxid < 15) { - maxid = 15; - } - maxid++; - int len = 60; - int nochunks = max / len + 1; - - for (i = 0; i < nochunks; i++) { - int j = 0; - while (j < s.length && s[j] != null) { - out.write(new Format("%-" + maxid + "s").form(s[j].getId() + " ")); - int start = i * len; - int end = start + len; - - if (end < s[j].getSequence().length() && start < s[j].getSequence().length()) { - out.write(s[j].getSequence().substring(start, end) + "\n"); - } else { - if (start < s[j].getSequence().length()) { - out.write(s[j].getSequence().substring(start) + "\n"); - } - } - j++; - } - out.write("\n"); - - } - } - /** - * manufacture an alignment/dataset from an array of sequences - * @param origin - * @param seqs - * @return - * @throws Exception - */ - public static Alignment make_Alignment(Entry origin, - Sequence[] seqs) throws Exception { - System.err.println("NOT FULLY IMPLEMENTED!"); // TODO: Finish adapting this method - Alignment al = new Alignment(); - al.setProvenance(ProvenanceStuff.newProvenance(origin)); - - Pattern nonGap = Pattern.compile("[A-Z*0-9]", Pattern.CASE_INSENSITIVE); - boolean gapsset = false; - char gapchar = '-'; - int seqLength = 0; - - for (int i = 0, nseq = seqs.length; i < nseq; i++) { - String seq = seqs[i].getSequence(); - String gaps = nonGap.matcher(seq).replaceAll(""); - if (seqLength == 0) { - seqLength = seq.length(); - } else if (seqLength != seq.length()) - throw (new Exception(i + "th Sequence (>" + seqs[i].getId() - + ") is not aligned.\n"));// TODO: move this to assertions part of - // Alignment - - // common check for any sequence... - if (gaps != null && gaps.length() > 0) { - if (!gapsset) - gapchar = gaps.charAt(0); - for (int c = 0, gc = gaps.length(); c < gc; c++) { - if (gapchar != gaps.charAt(c)) { - throw (new IOException("Inconsistent gap characters in sequence " - + i + ": '" + seq + "'")); - } - } - } - AlignmentSequence sq = new AlignmentSequence(); - // TODO: use as basis of default AlignSequence(Sequence) constructor. - sq.setSequence(seq); - sq.setName(seqs[i].getId()); - sq.setRefid(seqs[i].getVorbaId()); - sq.setStart(seqs[i].getStart()); - sq.setEnd(seqs[i].getEnd()); - al.addAlignmentSequence(sq); - } - al.setGapChar(String.valueOf(gapchar)); - return al; - } - - public static Alignment read_FastaAlignment(InputStream os, Entry entry) - throws Exception { - Sequence[] seqs; - System.err.println("NOT FULLY IMPLEMENTED!"); // TODO: Finish adapting this method - try { - seqs = SeqSet.read_SeqFasta(os); - if (seqs == null) - throw (new Exception("Empty alignment stream!\n")); - } catch (Exception e) { - throw new Exception("Invalid fasta alignment\n", e); - } - - return make_Alignment(entry, seqs); - } - - public static Alignment read_ClustalAlignment(InputStream os, Entry entry) - throws Exception { - Sequence[] seqs; - try { - seqs = SeqAln.ReadClustalFile(os); - if (seqs == null) - throw (new Exception("Empty alignment stream!\n")); - } catch (Exception e) { - throw new Exception("Invalid fasta alignment\n", e); - } - System.err.println("NOT FULLY IMPLEMENTED!"); // TODO: Finish adapting this method - return make_Alignment(entry, seqs); - } -} diff --git a/src/org/vamsas/objects/utils/SeqSet.java b/src/org/vamsas/objects/utils/SeqSet.java deleted file mode 100644 index 294ce43..0000000 --- a/src/org/vamsas/objects/utils/SeqSet.java +++ /dev/null @@ -1,138 +0,0 @@ -/* - * Created on 17-May-2005 - * Slurped into VamsasClient object set on 12th Jan 2006 - * - * TODO To change the template for this generated file go to - * Window - Preferences - Java - Code Style - Code Templates - */ -package org.vamsas.objects.utils; - -import java.io.BufferedReader; -import java.io.BufferedWriter; -import java.io.IOException; -import java.io.InputStream; -import java.io.InputStreamReader; -import java.io.OutputStream; -import java.io.OutputStreamWriter; -import java.util.Hashtable; -import java.util.Vector; -import java.util.regex.Pattern; - -import org.vamsas.objects.core.*; - -/** - * @author jimp - * - * TODO To change the template for this generated type comment go to - * Window - Preferences - Java - Code Style - Code Templates - */ -public class SeqSet { - - public static void write_Fasta(OutputStream os, SequenceType[] seqs) throws IOException { - write_Fasta(os, seqs, 80); - } - - public static void write_Fasta(OutputStream os, SequenceType[] seqs, boolean width80) throws IOException { - write_Fasta(os, seqs, (width80) ? 80 : 0); - } - - public static void write_Fasta(OutputStream os, SequenceType[] seqs, int width) throws IOException { - int i, nseq = seqs.length; - BufferedWriter fasta_out = new BufferedWriter(new OutputStreamWriter(os)); - System.err.println("NOT FULLY IMPLEMENTED!"); // TODO: Finish adapting this method - for (i=0; i"+seqs[i].getName()+"\n"); - if (width<=0) { - fasta_out.write(seqs[i].getSequence()+"\n"); - } else { - // TODO: adapt to SymbolDictionary labelwidths - String tempseq = seqs[i].getSequence(); - int j=0, k=tempseq.length(); - while (j=width) { - fasta_out.write(tempseq, j, width); - } else { - fasta_out.write(tempseq, j, d); - } - fasta_out.write("\n"); - j+=width; - } - } - } - fasta_out.flush(); - } - /** - * TODO: introduce a dictionary parameter for qualified sequence symbols - * Reads a sequence set from a stream - will only read prescribed amino acid - * symbols. - * @param os - * @return - * @throws IOException - */ - public static Sequence[] read_SeqFasta(InputStream os) throws IOException { - Vector seqs = new Vector(); - int nseq = 0; - BufferedReader infasta = new BufferedReader(new InputStreamReader(os)); - System.err.println("NOT FULLY IMPLEMENTED!"); // TODO: Finish adapting this method - // TODO: decide on return type - SequenceType is a partly complete vamsas Vobject - either for a dataset or alignment sequence - // so could go in either! - String line; - Sequence seq = null; - Pattern aaMatch = Pattern.compile("[ARNDCQEGHILKMFPSTUWYV]", Pattern.CASE_INSENSITIVE); - String sname = "", seqstr=null; - do { - line = infasta.readLine(); - if (line==null || line.startsWith(">")) { - if (seqstr!=null) - seqs.add((Object) Seq.newSequence(sname.substring(1), seqstr, SymbolDictionary.STANDARD_AA, 0,0)); - sname = line; // remove > - seqstr=""; - } else { - String subseq = Pattern.compile("//s+").matcher(line).replaceAll(""); - seqstr += subseq; - } - } while (line!=null); - nseq = seqs.size(); - if (nseq>0) { - // TODO:POSS: should really return a sequence if there's only one in the file. - Sequence[] seqset = new Sequence[nseq]; - for (int i=0; i is one of :\n\tsave,update,close,watch"; - - private static boolean parseArgs(String args[]) { - return true; // incorrect arguments. - } - public static void main(String[] args) { - if ((args.length<=2) || !parseArgs(args)) { - System.err.print(Usage); - } - - // get IClientFactory - try { - clientfactory = new org.vamsas.client.simpleclient.SimpleClientFactory(args[0]); - } catch (IOException e) { - System.err.println(e+"\n"+Usage); - System.exit(1); - } - - // get an Iclient with session data - app = new ClientHandle("org.vamsas.test.ExampleApplication","0.1"); - user = new UserHandle("arnolduser","deathsdoor"); - try { - vorbaclient = clientfactory.getIClient(app, user); - } catch (NoDefaultSessionException e) { - System.err.println("There appear to be several sessions to choose from :"); - String[] sessions = clientfactory.getCurrentSessions(); - for (int s=0;sSystem.currentTimeMillis())); // tuning. - if (doclock==null) - return null; - else { - return getUpdateable(vsess.getLock(doclock)); - /*VamsasArchiveReader varc = new VamsasArchiveReader(vsess.getVamsasFile()); - return _getReadonly(varc);*/ - } - } catch (Exception e) { - log.error("Whilst watching file "+vsess.getVamsasFile(), e); - } - return null; - } - - // from ClientDocument.getClientAppdata - private AppData[] getAppData(VamsasDocument doc) { - if (doc==null) { - log.debug("extractAppData called for null document object"); - return null; - } - AppData appsGlobal=null, usersData=null; - Vector apldataset = AppDataReference.getUserandApplicationsData( - doc, this.getUserHandle(), this.getClientHandle()); - if (apldataset!=null) { - if (apldataset.size()>0) { - AppData clientdat = (AppData) apldataset.get(0); - if (clientdat instanceof ApplicationData) { - appsGlobal = (ApplicationData) clientdat; - if (apldataset.size()>1) { - clientdat = (AppData) apldataset.get(1); - if (clientdat instanceof User) { - usersData = (User) clientdat; - } - if (apldataset.size()>2) - log.info("Ignoring additional ("+(apldataset.size()-2)+") AppDatas returned by document appdata query."); - } - } else { - log.warn("Unexpected entry in AppDataReference query: id="+clientdat.getVorbaId()+" type="+clientdat.getClass().getName()); - } - apldataset.removeAllElements(); // destroy references. - } - } - return new AppData[] { appsGlobal, usersData}; - } - - protected ClientDoc _getReadonly(VamsasArchiveReader vreader) throws IOException, ValidationException, MarshalException { - valid(); - if (vreader!=null) { - SimpleDocBinding docb = new SimpleDocBinding(); - docb.setVorba(this); - VamsasDocument d; - d = docb.getVamsasDocument(vreader); - - if (d!=null) { - ClientDoc creader = new ClientDoc(d, null, vreader, getClientHandle().getClientUrn(), getProvenanceUser(), getVorbaIdHash()); - return creader; - } - } - return null; - } - /** - * from SimpleClient - * @return user field for a provenance entry - */ - protected String getProvenanceUser() { - return new String(getUserHandle().getFullName()+" ["+getClientHandle().getClientUrn()+"]"); - } - - public ClientDoc getUpdateable() { - return getUpdateable(null); - } - public ClientDoc getUpdateable(org.vamsas.client.simpleclient.Lock lock) { - getVorbaIdHash().clear(); - valid(); - try { - // patiently wait for a lock on the document. - long tries=5000; - while (lock==null && ((lock=vsess.getLock())==null || !lock.isLocked()) && --tries>0) { -// Thread.sleep(1); - log.debug("Trying to get a document lock for the "+tries+"'th time."); - } - VamsasArchive varc = new VamsasArchive(vsess, true, false); // read archive, write as vamsasDocument, don't erase original contents. - varc.setVorba(this); - VamsasDocument d = varc.getVamsasDocument(getProvenanceUser(), "Created new document.", VersionEntries.latestVersion()); // VAMSAS: provenance user and client combined - - if (d==null) { - log.warn("Backing out from opening a VamsasArchive writable IO session"); - varc.cancelArchive(); - return null; - } - ClientDoc cdoc = new ClientDoc(d, varc, varc.getOriginalArchiveReader(), getClientHandle().getClientUrn(), getProvenanceUser(), getVorbaIdHash()); - return cdoc; - // do appHandle? - } catch (Exception e) { - log.error("Failed to get Updateable version of "+vsess.getVamsasFile(), e); - } - return null; - } - /** - * trust client to not do anything stupid to the document roots which will now be written to the archive. - * @param cdoc - * @return true if write was a success. - */ - public boolean doUpdate(ClientDoc cdoc) { - valid(); - if (cdoc==null) { - log.warn("Invalid ClientDoc passed to org.vamsas.test.simpleclient.doUpdate()"); - return false; - } - if (cdoc.iohandler==null) { - log.warn("Read only ClientDoc object passed to org.vamsas.test.simpleclient.doUpdate()"); - return false; - } - if (cdoc.iohandler.getVorba()!=this) { - log.error("Mismatch between ClientDoc instances and ArchiveClient instances!"); - return false; - } - try { - // do any appDatas first. - if (cdoc.iohandler.transferRemainingAppDatas()) - log.debug("Remaining appdatas were transfered."); - cdoc.updateDocumentRoots(); - cdoc.iohandler.putVamsasDocument(cdoc.doc); - cdoc.iohandler.closeArchive(); - this.extantids.clear();// we forget our ids after we close the document. - cdoc.iohandler=null; - cdoc = null; - vsess.unLock(); - } catch (Exception e) { - log.warn("While updating archive in "+vsess.getVamsasFile(),e); - return false; - } - return true; - } - /** - * @param args - */ - public static void usage() { - throw new Error("Usage: Username Organization VamsasFile [command,args]*"); - } - public static void main(String[] args) { - // really simple. - if (args.length<3) - usage(); - - ArchiveClient client = new ArchiveClient(args[0],args[1], new File(args[2])); - ClientDoc cdoc=null; - // sanity test. - try { - cdoc = client.getUpdateable(); - // ArchiveReports.reportDocument(cdoc.doc, cdoc.getReader(), true, System.out); - System.out.println("Report Roots :"); - ArchiveReports.rootReport(cdoc.getVamsasRoots(), true, System.out); - cdoc.addVamsasRoot(Core.getDemoVamsas()); - System.out.println("Doing update."); - client.doUpdate(cdoc); - cdoc.closeDoc(); - cdoc = null; - int u=5; - while (--u>0) { - System.out.println("Watch for more... ("+u+" left)"); - ClientDoc ucdoc = client.watch(0000); - if (ucdoc!=null) { - System.out.println("****\nUpdate detected at "+new Date()); - ArchiveReports.reportDocument(ucdoc.doc, ucdoc.getReader(), true, System.out); - ucdoc.closeDoc(); - ucdoc=null; - } else { - System.out.println("!!!! Null document update detected at "+new Date()); - } - } - } - catch (Exception e) { - client.log.error("Broken!", e); - } - System.out.println("Finished at "+new Date()); - } - public org.vamsas.client.Vobject getObject(VorbaId id) { - Hashtable idhash = this.getVorbaIdHash(); - if (idhash!=null && idhash.containsKey(id)) - return (Vobject) idhash.get(id); - return null; - } -} diff --git a/src/org/vamsas/test/simpleclient/ArchiveReader.java b/src/org/vamsas/test/simpleclient/ArchiveReader.java deleted file mode 100644 index d7959b4..0000000 --- a/src/org/vamsas/test/simpleclient/ArchiveReader.java +++ /dev/null @@ -1,50 +0,0 @@ -package org.vamsas.test.simpleclient; - -import java.io.BufferedInputStream; -import java.io.File; -import java.io.InputStream; -import java.io.InputStreamReader; - -import org.vamsas.client.simpleclient.VamsasArchiveReader; -import org.vamsas.objects.core.VAMSAS; -import org.vamsas.objects.core.VamsasDocument; - -public class ArchiveReader { - /** - * tests VamsasArchiveReader archive reader on a vamsas jar file - * @param args - */ - public static void main(String args[]) { - - try { - File av = new File(args[0]); - VamsasArchiveReader var = new VamsasArchiveReader(av); - VAMSAS roots[]=null; - if (var.isValid()) { - InputStreamReader vdoc = new InputStreamReader(var.getVamsasDocumentStream()); - VamsasDocument doc = VamsasDocument.unmarshal(vdoc); - if (ArchiveReports.reportDocument(doc, var, true, System.out)) { - roots = doc.getVAMSAS(); - } - } else { - InputStream vxmlis = var.getVamsasXmlStream(); - - if (vxmlis!=null) { // Might be an old vamsas file. - BufferedInputStream ixml = new BufferedInputStream(var.getVamsasXmlStream()); - InputStreamReader vxml = new InputStreamReader(ixml); - VAMSAS root; - // unmarshal seems to always close the stream (should check this) - if ((root = VAMSAS.unmarshal(vxml))!=null) { - System.out.println("Read a root."); - roots = new VAMSAS[1]; - roots[0] = root; - } - } - } - if (!ArchiveReports.rootReport(roots, true, System.out)) - System.err.print(args[0]+" is not a valid vamsas archive."); - } catch (Exception e) { - e.printStackTrace(System.err); - } - } -} diff --git a/src/org/vamsas/test/simpleclient/ArchiveReports.java b/src/org/vamsas/test/simpleclient/ArchiveReports.java deleted file mode 100644 index 4a3a284..0000000 --- a/src/org/vamsas/test/simpleclient/ArchiveReports.java +++ /dev/null @@ -1,186 +0,0 @@ -package org.vamsas.test.simpleclient; - -import java.io.InputStream; -import java.io.PrintStream; -import java.io.PrintWriter; - -import org.vamsas.client.ClientDocument; -import org.vamsas.client.Vobject; -import org.vamsas.client.simpleclient.VamsasArchiveReader; -import org.vamsas.objects.core.Alignment; -import org.vamsas.objects.core.AppData; -import org.vamsas.objects.core.ApplicationData; -import org.vamsas.objects.core.DataSet; -import org.vamsas.objects.core.Entry; -import org.vamsas.objects.core.Instance; -import org.vamsas.objects.core.Provenance; -import org.vamsas.objects.core.Tree; -import org.vamsas.objects.core.User; -import org.vamsas.objects.core.VAMSAS; -import org.vamsas.objects.core.VamsasDocument; -/** - * 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. - * Methods return true or false - indicating if the Vobject was valid or not - * TODO: LATER: propagate true/false return so that an invalid vamsas Vobject invalidates the whole document - * @author jimp - * - */ -public class ArchiveReports { - /** - * print an informative summary on a VamsasDocument - * @param outstr TODO - * @param document - the document itself - * @param archive - document source archive for resolving any appData refs - * @return - */ - public static boolean reportProvenance(Provenance p, PrintStream outstr) { - if (p==null) { - outstr.println("No Provenance"); - return false; - } - Entry[] pe = p.getEntry(); - for (int i=0; i1) { - outstr.print("a reference ("+appData+")"); - InputStream jstrm; - if ((jstrm=archive.getAppdataStream(appData))!=null) - outstr.println(" which resolves to a JarEntry."); - else { - outstr.println(" which does not resolve to a JarEntry."); - outstr.println("Unresolved appdata reference '"+appData+"'"); - } - } else { - nulldata=true; - } - } else { - if (appD.getData()==null) - nulldata &= true; - else - outstr.println("an embedded chunk of "+appD.getData().length+" bytes."); - } - if (nulldata) - outstr.println("Null AppData reference/data chunk."); - } - return true; - } - - public static boolean appDataReport(ApplicationData appD, VamsasArchiveReader archive, boolean cascade, PrintStream outstr) { - if (appD!=null) { - // Report on root appData - appDataEntryReport(appD, archive, cascade, outstr); - if (appD.getInstanceCount()>0) { - Instance inst[] = appD.getInstance(); - for (int i=0,j=inst.hashCode(); i0) { - User users[] = appD.getUser(); - for (int i=0,j=users.length; i0 && cascade) - rootReport(document.getVAMSAS(), true, outstr); - if (document.getApplicationDataCount()>0) { - outstr.print("There are "+document.getApplicationDataCount()+" ApplicationData references.\n"); - ApplicationData appd[] = document.getApplicationData(); - for (int i=0,j=appd.length; i") - +") contains "+(ds=r.getDataSetCount())+" DataSets, " - + (tr=r.getTreeCount())+" Global trees\n"); - if (cascade) { - for (int j=0; j0) { - for (int i=0; i0) { - File archive = new File(args[0]); - log.info("Watching file "+args[0]); - int argc=1; - while (argc < args.length) { - // vars needed for operations - ClientHandle ch; - int com = cproc.getCommand(args, argc); - argc++; - switch (com) { - case 0: - // new - log.info("Doing locked deletion and new-file creation."); - { - if (!archive.exists()) - archive.createNewFile(); - VamsasFile sf = new VamsasFile(archive); - Lock l = sf.getLock(); - archive.delete(); - archive.createNewFile(); - sf.unLock(); - } - break; - case 1: - // delete - log.info("Deleting "+archive+" without locking it first."); - archive.delete(); - break; - case 2: - // watch - log.info("Endlessly Watching file "+archive); - /* if (!archive.exists()) - archive.createNewFile(); - */ // watch the new file... - taken straight from ClientsFileTest - FileWatcher w = new FileWatcher(archive); - while (true) { - // get watcher's lock to ensure state change is fixed for retrieval - Lock chlock = w.getChangedState(); - if (chlock != null) { - log.info("Got lock on "+archive+(archive.exists() ? " exists l="+archive.length() : "(non existant)")); - if (archive.length()>0) { - VamsasArchiveReader vreader = new VamsasArchiveReader(archive); - SimpleDocument sdoc = new SimpleDocument("testing vamsas watcher"); - try { - VamsasDocument d = sdoc.getVamsasDocument(vreader); - if (d!=null) { - ArchiveReports.reportDocument(d, vreader, false, System.out); - } - System.out.println("Update at "+System.currentTimeMillis()+"\n\n********************************************************\n"); - } catch (Exception e) { - log.error("Unmarshalling failed.",e); - } - vreader.close(); - w.setState(); - } - } - } - // break; - case 3: // set file - archive = new File(args[argc++]); - break; - case 4: - break; - default: - log.warn("Unknown command + "+args[argc++]); - } - } - } - } catch (Exception e) { - log.error(e); - } - - } -} diff --git a/src/org/vamsas/test/simpleclient/ArchiveWriter.java b/src/org/vamsas/test/simpleclient/ArchiveWriter.java deleted file mode 100644 index d6f8ee9..0000000 --- a/src/org/vamsas/test/simpleclient/ArchiveWriter.java +++ /dev/null @@ -1,180 +0,0 @@ -package org.vamsas.test.simpleclient; - -import java.io.File; -import java.io.InputStream; -import java.io.InputStreamReader; -import java.io.PrintWriter; -import java.text.DateFormat; -import java.util.Date; -import java.util.Hashtable; -import java.util.Vector; - -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.vamsas.client.simpleclient.VamsasArchive; -import org.vamsas.client.simpleclient.VamsasArchiveReader; -import org.vamsas.objects.core.Alignment; -import org.vamsas.objects.core.ApplicationData; -import org.vamsas.objects.core.Entry; -import org.vamsas.objects.core.Instance; -import org.vamsas.objects.core.Provenance; -import org.vamsas.objects.core.VAMSAS; -import org.vamsas.objects.core.VamsasDocument; -import org.vamsas.objects.utils.ProvenanceStuff; - -public class ArchiveWriter { - - /** - * Test program for writing archive files. - * form is ArchiveWriter new/modified argive command list - */ - - static Log log = LogFactory.getLog(ArchiveWriter.class); - - private static void mergeVecs(Object[] destvec, Object[] svec1, Object[] svec2) { - int i; - for (i=0; i0) { - ApplicationData[] newdat = new ApplicationData[source.getApplicationDataCount()+dest.getApplicationDataCount()]; - ApplicationData[] sappd = source.getApplicationData(); - // check refs and update/modify if necessary - for (int i=0; i [(commands)]"); - return; - } - File newarch = new File(argv[0]); - int argpos = 0; - try { - // test fully fledged doc construction - VamsasArchive varc = new VamsasArchive(newarch, true); - VamsasDocument docroot; - docroot = new VamsasDocument(); - docroot.setProvenance(ProvenanceStuff.newProvenance("ArchiveWriter", "user", "Created new Vamsas Document")); - while (++argpos-1) { - if (isValidUpdate(newr[k], original[i])) { - modified=true; - rts.add(newr[k]); - newr[k]=null; - } else { - // LATER: try harder to merge ducument roots. - log.warn("Couldn't merge new VAMSAS root "+newr[k].getId()); - newr[k] = null; // LATER: this means we ignore mangled roots. NOT GOOD - } - } else { - // add in order. - rts.add(original[i]); - } - } - // add remaining (new) roots - for (int i=0,j=newr.length; i2) - complainArgs(args.length, argc+1, comnext); - return com; - } - } - return -1; - - } -} diff --git a/src/org/vamsas/test/simpleclient/VamsasArchive.java b/src/org/vamsas/test/simpleclient/VamsasArchive.java deleted file mode 100644 index 09ddf34..0000000 --- a/src/org/vamsas/test/simpleclient/VamsasArchive.java +++ /dev/null @@ -1,205 +0,0 @@ -package org.vamsas.test.simpleclient; - -import java.io.File; -import java.io.ObjectOutputStream; - -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.vamsas.client.simpleclient.Lock; -import org.vamsas.client.simpleclient.SessionFile; -import org.vamsas.client.simpleclient.SimpleDocument; -import org.vamsas.client.simpleclient.VamsasArchiveReader; -import org.vamsas.client.simpleclient.VamsasFile; -import org.vamsas.objects.core.ApplicationData; -import org.vamsas.objects.core.User; -import org.vamsas.objects.core.VAMSAS; -import org.vamsas.objects.core.VamsasDocument; -import org.vamsas.test.objects.Core; - -public class VamsasArchive { - /** - * test the org.vamsas.simpleclient.vamsasArchive class - */ - static Log log = LogFactory.getLog(VamsasArchive.class); - public static ApplicationData makeDemoAppdata(org.vamsas.client.simpleclient.VamsasArchive va, String apname, String userName, String userOrg) { - if (va==null) - return null; - VamsasArchiveReader vread=null; - try { - vread = va.getOriginalArchiveReader(); - } - catch (Exception e) { - log.error("Failed to get original archive reader!",e); - return null; - } - ApplicationData appdata = new ApplicationData(); - appdata.setName("org.vamsas.test.simpleclient.VamsasArchive"); - appdata.setData(new String("this is some test data.").getBytes()); - User apuser = new User(); - apuser.setFullname(userName); - apuser.setOrganization(userOrg); - String appdata_ref = "vamsas:"+apname+"/"+apuser.getOrganization()+"/"+apuser.getFullname(); - SimpleDocument sdoc = new SimpleDocument("test.simpleclient.VamsasArchive"); - if (vread!=null) { - VamsasDocument orignalnew; - try { - orignalnew = sdoc.getVamsasDocument(vread); - log.info("*** Dump follows ***"); - - ArchiveReports.reportDocument(orignalnew, vread, false, System.out); - log.info("*** Dump precedes ***"); - } catch (Exception e) { - log.info("makeDemoAppdata: Problems accessing original document"); - } - - log.info("Reading (and avoiding references to) original data"); - if (vread.getAppdataStream(appdata_ref)!=null) { - // transfer over - try { - va.transferAppDataEntry(appdata_ref); - } catch (Exception e) { - log.warn("Exception when transferring appdata reference : "+appdata_ref, e); - } - int i=0; - while (vread.getAppdataStream(appdata_ref+"/"+Integer.toString(++i))!=null) { - try { - // copy over another duplicate. - va.transferAppDataEntry(appdata_ref+"/"+Integer.toString(i)); - } catch (Exception e) { - log.warn("Exception when transferring appdata reference : "+appdata_ref, e); - } - } - // this one must be unique! - appdata_ref+="/"+Integer.toString(i); - } - } - - log.info("Adding new data stuff."); - log.info("Writing an apdata reference using AppDataStream interface."); - apuser.setDataReference(appdata_ref); - appdata.addUser(apuser); - appdata.setVersion("noggin"); - //TODO: write instance appdata appdata.setUrn("program:/the.nog/"); - try { - ObjectOutputStream ost = new ObjectOutputStream(va.getAppDataStream(appdata_ref)); - ost.writeObject(appdata); - ost.close(); - } catch (Exception e) { - log.warn("Couldn't write appdata reference "+appdata_ref); - } - return appdata; - } - public static void main(String args[]) { - - try { - File av; - if (args.length>0) - av = new File(args[0]); - else - av = new File("test/vamsas.zip"); - log.info("Opening archive "+av); - org.vamsas.client.simpleclient.VamsasArchive varchive = new org.vamsas.client.simpleclient.VamsasArchive(av, true); - - VAMSAS[] roots = (VAMSAS[]) varchive.getOriginalRoots(); - - if (roots!=null) { - log.info("Report on Original roots in archive:"); - ArchiveReports.rootReport(roots, true, System.out); - } - log.info("Getting current vamsas document."); - VamsasDocument doc = varchive.getVamsasDocument(); - ArchiveReports.reportDocument(doc, varchive.getOriginalArchiveReader(), true, System.out); // not modified document so references will still be valid - // do some stuff - log.info("Retrieving backup"); - File backup = varchive.backupFile(); - if (backup==null) - log.info(av+" is a New Archive."); - else - log.info(av+" has been backed up as "+backup); - File newf=new File(av.getAbsolutePath()+"_new.zip"); - VamsasFile sfile = new VamsasFile(newf); - /* if (newf.exists()) { - int q=1; - do { - newf=new File(av.getAbsolutePath()+"_"+q+++"_new.zip"); - } - while (newf.exists()); - } */ - if (newf.exists()) { - log.info("Removing existing "+newf); - newf.delete(); - } - - log.info("Now writing new Archive into "+newf.getAbsolutePath()); - org.vamsas.client.simpleclient.VamsasArchive va=null; - { // hold lock over deletion and write of new archive. - //Lock wlock = sfile.getLock(); - //newf.delete(); // clear out old file. - sfile.getLock(); - va = new org.vamsas.client.simpleclient.VamsasArchive(newf, true, true, sfile); - // open another and... - ApplicationData appdata = makeDemoAppdata(va, - "org.vamsas.test.simpleclient.VamsasArchive", "arnold Bugger esq", "disOrganised"); - log.info("Preparing to write new document."); - doc.addApplicationData(appdata); - doc.addVAMSAS(Core.getDemoVamsas()); - va.putVamsasDocument(doc); // gets stream and puts it. - va.closeArchive(); - sfile.unLock(); - } - log.info("Dump of new vamsas document :"); - log.info("Testing update: "); - { - Lock lock=sfile.getLock(); - if (lock==null) - while ((lock=sfile.getLock())==null) { - log.info("Waiting for lock."); - Thread.sleep(100); - } - VamsasArchiveReader vreader = new VamsasArchiveReader(sfile.getVamsasFile());// lock); // cannot do new JarFile on a locked file. // newf); - SimpleDocument sdoc = new SimpleDocument("testing new vamsas write"); - ArchiveReports.reportDocument(sdoc.getVamsasDocument(vreader), vreader, true, System.out); - sfile.unLock(); - } - // backup.delete(); // tidy up - - log.info("Now Cancelling write to original archive "+av); - if (varchive.cancelArchive()) - log.info("Successfully cancelled."); - else - log.info("Didn't cancel."); - long t=System.currentTimeMillis()+200; while (t>System.currentTimeMillis()); - log.info("Now testing archive update."); - va = new org.vamsas.client.simpleclient.VamsasArchive(newf, false, true, sfile); - doc = va.getVamsasDocument(); - doc.addVAMSAS(Core.getDemoVamsas()); - doc.addApplicationData(makeDemoAppdata(va, - "org.vamsas.test.simpleclient.VamsasArchive", "another old Bugger esq", "rescinded")); - if (va.transferRemainingAppDatas()) - log.info("Remain appdatas were transferred."); - else - log.warn("No appdatas were transferred. This is wrong."); - va.putVamsasDocument(doc); - va.closeArchive(); - sfile.unLock(); - log.info("Testing update: "); - { - Lock lock=sfile.getLock(); - if (lock==null) - while ((lock=sfile.getLock())==null) - log.info("Waiting for lock."); - // VamsasArchiveReader vreader = new VamsasArchiveReader(lock); - VamsasArchiveReader vreader = new VamsasArchiveReader(newf); - - SimpleDocument sdoc = new SimpleDocument("testing vamsas update"); - VamsasDocument finaldoc = sdoc.getVamsasDocument(vreader); - if (finaldoc!=null) - ArchiveReports.reportDocument(finaldoc, vreader, true, System.out); - else - log.error("Null Document Read from "+newf); - } - } catch (Exception e) { - e.printStackTrace(System.err); - } - } -} diff --git a/src/org/vamsas/test/simpleclient/simpleapp/VamsasClient.java b/src/org/vamsas/test/simpleclient/simpleapp/VamsasClient.java deleted file mode 100644 index 2b70a0a..0000000 --- a/src/org/vamsas/test/simpleclient/simpleapp/VamsasClient.java +++ /dev/null @@ -1,186 +0,0 @@ -/** - * - */ -package org.vamsas.test.simpleclient.simpleapp; - -import java.io.File; -import java.io.FileOutputStream; -import java.io.OutputStreamWriter; -import java.io.PrintWriter; -import java.util.Hashtable; -import java.util.IdentityHashMap; -import java.util.Vector; -import java.util.jar.JarOutputStream; - -import javax.swing.JInternalFrame; - -import org.vamsas.client.UserHandle; -import org.vamsas.client.simpleclient.FileWatcher; -import org.vamsas.client.simpleclient.VamsasArchive; -import org.vamsas.client.simpleclient.VamsasFile; -import org.vamsas.objects.core.Entry; -import org.vamsas.objects.core.VamsasDocument; -import org.vamsas.test.simpleclient.ArchiveClient; -import org.vamsas.test.simpleclient.ClientDoc; - -/** - * @author jimp - * - */ -public class VamsasClient extends ArchiveClient { - org.apache.commons.logging.Log log=org.apache.commons.logging.LogFactory.getLog(VamsasClient.class); - /** - * create a new vamsas client session from the archive at sessionPath. - * @param sessionPath - */ - public VamsasClient(File sessionPath) { - super(System.getProperty("user.name"),System.getProperty("host.name"), "SimpleVamsasClientApp","0.1", - sessionPath); - } - /** - * Called by gui to read anything from the vamsas session into the apps datamodel - * after it has started up. - * - */ - public void initial_update() { - log.info("Jalview loading the Vamsas Session."); - // load in the vamsas archive for the first time - ClientDoc cdoc = this.getUpdateable(); - updateJalview(cdoc); - // TODO: flush any new VorbaIds to the document : updateVamsasClient may actually generate new Vamsas Document data in the form of vamsas element ids - these should be written back to the document. - //doUpdate(cdoc); // JBPNote: this should flush new VorbaIds but I've not tested it yet. - cdoc.closeDoc(); - // then tell app to update its display based on the datamodel changes. - } - VamsasClientWatcher watcher=null; - /** - * Called by app when internal datamodel should exported (syncrhonised outwards) to vamsas document - * - */ - public void push_update() { - - watchForChange=false; // this makes any watch(long) loops return. - // we should also wait arount for this.WATCH_SLEEP to really make sure the watcher thread has stopped. - try { - Thread.sleep(WATCH_SLEEP); - } catch (Exception e) { - - }; - - ClientDoc cdoc = getUpdateable(); - updateVamsasDocument(cdoc); - doUpdate(cdoc); - cdoc.closeDoc(); - cdoc=null; - watchForChange=true; - startWatcher(); - } - public void end_session() { - watchForChange=false; // this makes any watch(long) loops return. - // we should also wait arount for this.WATCH_SLEEP to really make sure the watcher thread has stopped. - try { - Thread.sleep(WATCH_SLEEP); - } catch (Exception e) { - - }; - - // stop any update/watcher thread. - log.info("VamsasClientApplication disconnecting from the Vamsas Session."); - } - public void updateJalview(ClientDoc cdoc) { - ensureVamsasBindings(); - VamsasDatastore vds = new VamsasDatastore(cdoc, vobj2jv, jv2vobj, baseProvEntry()); - vds.updateToJalview(); - } - private void ensureVamsasBindings() { - if (jv2vobj==null) { - jv2vobj = new IdentityHashMap(); - vobj2jv = new Hashtable(); - } - } - /** - * App's object binding to VorbaIds - */ - IdentityHashMap jv2vobj = null; - Hashtable vobj2jv = null; - /** - * called with a vamsas document which will be updated with new data from the app - * @param doc - */ - public void updateVamsasDocument(ClientDoc doc) { - ensureVamsasBindings(); - VamsasDatastore vds = new VamsasDatastore(doc, vobj2jv, jv2vobj, baseProvEntry()); - // wander through frames - vds.storeVAMSAS(new Object()); // Object is the apps datamodel ;) - } - /** - * - * @return a base provenance entry used by the VamsasDatastore object to get attributes from. this isn't particularly elegant either. - */ - private Entry baseProvEntry() { - org.vamsas.objects.core.Entry pentry = new org.vamsas.objects.core.Entry(); - pentry.setUser(this.getProvenanceUser()); - pentry.setApp(this.getClientHandle().getClientName()); - pentry.setDate(new org.exolab.castor.types.Date(new java.util.Date())); - pentry.setAction("created"); - return pentry; - } - protected class VamsasClientWatcher extends Thread implements Runnable { - /* (non-Javadoc) - * @see java.lang.Thread#run() - */ - VamsasClient client=null; - VamsasClientWatcher(VamsasClient client) { - this.client = client; - } - boolean running=false; - public void run() { - running=true; - while (client.watchForChange) { - ClientDoc docio = client.watch(0); - if (docio!=null) { - // VamsasClient GUI bits should be disabled whilst an update is in progress so the user doesn't screw anything up. - client.disableGui(true); - log.debug("Updating VamsasClient app from changed vamsas document."); - client.updateJalview(docio); - log.debug("Finished updating from document change."); - docio.closeDoc(); - docio=null; - client.disableGui(false); - } - } - running=false; - - } - - } - /** - * @param args - */ - public static void main(String[] args) { - // TODO Auto-generated method stub - - } - /** - * 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. - * @param b - */ - public void disableGui(boolean b) { - // in jalview, we turn off the VAMSAS Session menu : Desktop.instance.setVamsasUpdate(b); - } - /** - * spawn a new thread to start the VamsasClientWatcher. - * - */ - public void startWatcher() { - if (watcher==null) - watcher=new VamsasClientWatcher(this); - Thread thr = new Thread() { - public void run() { - watcher.start(); - } - }; - thr.start(); - } - -} diff --git a/src/org/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java b/src/org/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java deleted file mode 100644 index 9114e88..0000000 --- a/src/org/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java +++ /dev/null @@ -1,333 +0,0 @@ -/* - * VamsasClientSimpleApp - A framework for interoparable Sequence analysis - * Copyright (C) 2006 VAMSAS - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ - -package org.vamsas.test.simpleclient.simpleapp; - -import org.vamsas.client.Vobject; -import org.vamsas.client.VorbaId; -import org.vamsas.objects.core.*; -import org.vamsas.objects.utils.DocumentStuff; -import org.vamsas.test.simpleclient.ClientDoc; - - -import java.io.*; -import java.util.HashMap; -import java.util.HashSet; -import java.util.Hashtable; -import java.util.IdentityHashMap; -import java.util.Vector; -import java.util.jar.*; -import org.exolab.castor.xml.*; -import org.exolab.castor.mapping.Mapping; - -/* - * - * static { - * org.exolab.castor.util.LocalConfiguration.getInstance().getProperties().setProperty( - * "org.exolab.castor.serializer", "org.apache.xml.serialize.XMLSerilazizer"); } - * - */ - -public class VamsasDatastore { - org.apache.commons.logging.Log log=org.apache.commons.logging.LogFactory.getLog(VamsasDatastore.class); - Entry provEntry = null; - - - org.exolab.castor.types.Date date = new org.exolab.castor.types.Date( - new java.util.Date()); - - ClientDoc cdoc; - - Hashtable vobj2jv; - - IdentityHashMap jv2vobj; - - public VamsasDatastore(ClientDoc cdoc, Hashtable vobj2jv, - IdentityHashMap jv2vobj, Entry provEntry) { - this.cdoc = cdoc; - this.vobj2jv = vobj2jv; - this.jv2vobj = jv2vobj; - this.provEntry = provEntry; - } - - /* - * public void storeJalview(String file, AlignFrame af) { try { // 1. Load the - * mapping information from the file Mapping map = new - * Mapping(getClass().getClassLoader()); java.net.URL url = - * getClass().getResource("/jalview_mapping.xml"); map.loadMapping(url); // 2. - * Unmarshal the data // Unmarshaller unmar = new Unmarshaller(); - * //unmar.setIgnoreExtraElements(true); //unmar.setMapping(map); // uni = - * (UniprotFile) unmar.unmarshal(new FileReader(file)); // 3. marshal the data - * with the total price back and print the XML in the console Marshaller - * marshaller = new Marshaller( new FileWriter(file) ); - * - * marshaller.setMapping(map); marshaller.marshal(af); } catch (Exception e) { - * e.printStackTrace(); } } - * - * - */ - /** - * @return the Vobject bound to Jalview datamodel object - */ - protected Vobject getjv2vObj(Object jvobj) { - if (jv2vobj.containsKey(jvobj)) - return cdoc.getObject((VorbaId) jv2vobj.get(jvobj)); - return null; - } - - /** - * - * @param vobj - * @return Jalview datamodel object bound to the vamsas document object - */ - protected Object getvObj2jv(org.vamsas.client.Vobject vobj) { - VorbaId id = vobj.getVorbaId(); - if (id == null) - { - id = cdoc.registerObject(vobj); - log - .debug("Registering new object and returning null for getvObj2jv"); - return null; - } - if (vobj2jv.containsKey(vobj.getVorbaId())) - return vobj2jv.get(vobj.getVorbaId()); - return null; - } - - protected void bindjvvobj(Object jvobj, org.vamsas.client.Vobject vobj) { - VorbaId id = vobj.getVorbaId(); - if (id == null) - { - id = cdoc.registerObject(vobj); - if (id==null || vobj.getVorbaId()==null) - log.error("Failed to get id for "+(vobj.isRegisterable() ? "registerable" : "unregisterable") +" object "+vobj); - } - if (vobj2jv.containsKey(vobj.getVorbaId()) || jv2vobj.containsKey(jvobj)) - { - log.error("Duplicate object binding! "+vobj+" id " +vobj.getVorbaId().getId()+" to "+jvobj); - } - else - { - vobj2jv.put(vobj.getVorbaId(), jvobj);// JBPNote - better implementing a - // hybrid invertible hash. - jv2vobj.put(jvobj, vobj.getVorbaId()); - } - } - - /** - * put the alignment viewed by AlignViewport into cdoc. - * - * @param av - */ - public void storeVAMSAS(Object fromAppsDatamodel) { - boolean nw = false; - VAMSAS root = null; // will be resolved based on Dataset Parent. - DataSet dataset = (DataSet) getjv2vObj(fromAppsDatamodel); - if (dataset == null) - { - root = cdoc.getVamsasRoots()[0]; // default vamsas root for modifying. - dataset = new DataSet(); - root.addDataSet(dataset); - bindjvvobj(fromAppsDatamodel, dataset); - dataset.setProvenance(dummyProvenance()); - dataset.getProvenance().addEntry(provEntry); - nw = true; - } else { - root = (VAMSAS) dataset.getV_parent(); - } - // etc... - } - - private Property newProperty(String name, String type, String content) { - Property vProperty=new Property(); - vProperty.setName(name); - if (type!=null) - vProperty.setType(type); - vProperty.setContent(content); - return vProperty; - } - - /** - * get start0 && dseta.getPosCount()>0) - throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!"); - if (dseta.getSegCount() > 0) - { - se = getSegRange(dseta.getSeg(0),true); - for (int s = 1, sSize = dseta.getSegCount(); s < sSize; s++) - { - int nse[] = getSegRange(dseta.getSeg(s), true); - if (se[0] > nse[0]) - se[0] = nse[0]; - if (se[1] < nse[1]) - se[1] = nse[1]; - } - } - if (dseta.getPosCount() > 0) - { - // could do a polarity for pos range too. and pass back indication of discontinuities. - int pos = dseta.getPos(0).getI(); - se = new int[] { pos, pos }; - for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++) - { - pos = dseta.getPos(p).getI(); - if (se[0] > pos) - se[0] = pos; - if (se[1] < pos) - se[1] = pos; - } - } - return se; - } - return null; - } - /** - * map from a rangeType's internal frame to the referenced object's coordinate frame. - * @param dseta - * @return int [] { ref(pos)...} for all pos in rangeType's frame. - */ - private int[] getMapping(RangeType dseta) { - Vector posList=new Vector(); - if (dseta != null) - { - int[] se = null; - if (dseta.getSegCount()>0 && dseta.getPosCount()>0) - throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!"); - if (dseta.getSegCount() > 0) - { - for (int s = 0, sSize = dseta.getSegCount(); s < sSize; s++) - { - se = getSegRange(dseta.getSeg(s), false); - int se_end=se[1-se[2]]+(se[2]==0 ? 1 : -1); - for (int p=se[se[2]]; p!=se_end; p+=se[2]==0 ? 1 : -1 ) { - posList.add(Integer.valueOf(p)); - } - } - } - else if (dseta.getPosCount() > 0) - { - int pos = dseta.getPos(0).getI(); - - for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++) - { - pos = dseta.getPos(p).getI(); - posList.add(Integer.valueOf(pos)); - } - } - } - if (posList!=null && posList.size()>0) { - int[] range=new int[posList.size()]; - for (int i=0; i