+++ /dev/null
-/*
- *
- */
-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();
- }
-}
+++ /dev/null
-/*
- */
-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));
- }
-}
+++ /dev/null
-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: <Vamsas-session URN>
- */
- 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: <Vamsas-session URN>
- * 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;
- }
-}
+++ /dev/null
-/**
- * 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;
-}
+++ /dev/null
-/**
- *
- */
-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();
-}
+++ /dev/null
-/*
- * 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
+++ /dev/null
-/*
- * 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();
-
-}
+++ /dev/null
-package org.vamsas.client;\r
-\r
-/**\r
- * Methods implemented by a Vamsas Application's Object Update handler\r
- * @author vamsas\r
- * Introduced November 2006 Vamsas Meeting\r
- * TODO: verify this is sufficient for the per-object update event mechanism\r
- */\r
-public interface IObjectUpdate {\r
- /**\r
- * Called by the library to find out which vamsas document object this update handler is interested in\r
- * @return class that extends org.vamsas.Vobject\r
- */\r
- Class getRootVobject();\r
- /**\r
- * Called to test if this handler is to be called for updates to any Vobjects below the Root Vobject in the vamsas document.\r
- * @return false means IObjectUpdate.update(updated, cdoc) will only be called with instances of type getRootVobject(). \r
- */\r
- boolean handlesSubtreeUpdates();\r
- /**\r
- * Method called by Vamsas Client Library for all updated objects that the handler is registered for.\r
- * @param updated\r
- * @param cdoc\r
- */\r
- void update(org.vamsas.client.Vobject updated, org.vamsas.client.IClientDocument cdoc);\r
-}\r
+++ /dev/null
-/*
- * 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
+++ /dev/null
-/**
- * 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
- */
-
-};
+++ /dev/null
-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
- }
-
-}
+++ /dev/null
-/**
- *
- */
-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
- }
-
-}
+++ /dev/null
-/*
- * 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;
-
-}
+++ /dev/null
-/**
- *
- */
-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();
- }
-}
+++ /dev/null
-/*
- * 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;
- }
-}
+++ /dev/null
-/**
- *
- */
-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<j; i++) {
- Class type= fields[i].getFieldType();
- if (type.isArray()) {
- if (Vobject[].class.isAssignableFrom(type)) {
- try {
- Object val = fields[i].getHandler().getValue(this);
- if (val!=null) {
- Vobject vals[] = (Vobject[]) val;
- for (int k=0, l=vals.length; k<l; k++) {
- if (vals[k].__vorba==null)
- vals[k].__vorba = __vorba; // propagate IVorbaIdFactory
- if (vals[k].V_parent==null)
- vals[k].V_parent=this; // propagate parent reference to this element.
- vals[k].__ensure_instance_ids(visited);
- }
- }
- }
- catch (Exception e) {
- log.error("Client error - could not access array "+type.getName()+" in "+this.getClass().getName(), e);
- }
- }
- } else
- if (Vobject.class.isAssignableFrom(type)) {
- try {
- FieldHandler fh = fields[i].getHandler();
- Vobject rf = null;
- if (fh != null) {
- Object fval = fh.getValue(this);
- if (fval!=null) {
- if (fval.getClass().isArray()) {
- //if (Vobject[].class.isAssignableFrom(type)) {
- try {
- Vobject vals[] = (Vobject[]) fval;
- for (int k=0, l=vals.length; k<l; k++) {
- if (vals[k].__vorba==null)
- vals[k].__vorba = __vorba; // propagate IVorbaIdFactory
- if (vals[k].V_parent==null)
- vals[k].V_parent=this; // propagate parent reference to this field object
- vals[k].__ensure_instance_ids(visited);
- }
- }
- catch (Exception e) {
- log.error("Client error - could not access (fhval)array "+type.getName()+" in "+this.getClass().getName(), e);
- }
- //}
- } else {
- rf = (Vobject) fval;
- log.debug("Got value for "+fields[i].getFieldName());
- }
- }
- } else {
- // castor's mechanism doesn't work for this object... so...*/
- // fuck around, fuck around, jump up jump up and get down! */
- Object o = fields[i].getClassDescriptor();
- if (o!=null) {
- // XMLClassDescriptorImpl fclasdes = (XMLClassDescriptorImpl) o;
- String methname = "get"+fields[i].getFieldName();
- Method fgetmeth = this.getClass().getMethod(methname,(Class[])null);
- if (fgetmeth!=null) {
- Object fval = fgetmeth.invoke(this,(Object[])null);
- if (fval!=null)
- rf = (Vobject) fval;
- } else {
- log.warn("Couldn't find "+this.getClass().getName()+"."+methname);
- }
- }
- }
- if (rf!=null) {
- if (rf.__vorba==null)
- rf.__vorba = __vorba; // propagate IVorbaIdFactory
- if (rf.V_parent==null)
- rf.V_parent=this; // propagate parent reference
- rf.__ensure_instance_ids(visited);
- }
- }
- catch (Exception e) {
- log.error("Client error - could not access "+type.getName()+" in "+this.getClass().getName(), e);
- }
- }
- }
-
- }
-
- /**
- * @return the __parent
- */
- public Vobject getV_parent() {
- return V_parent;
- }
-
- /**
- * @param __parent the __parent to set
- */
- protected void setV_parent(Vobject V_parent) {
- this.V_parent = V_parent;
- }
-}
+++ /dev/null
-package org.vamsas.client;\r
-\r
-/**\r
- * Holds information about Vobj instances that is held over between different writes to the document.\r
- * @author JimP\r
- *\r
- */\r
-public class Vobjhash {\r
- int hashvalue;\r
- /**\r
- * creates a record of the hash value for a vamsas document object\r
- * @param tobemarshalled\r
- */\r
- public Vobjhash(Vobject tobemarshalled) {\r
- hashvalue = tobemarshalled.get__last_hash();\r
- }\r
- /**\r
- * compares the old hash value with the unmarshalled object's most recently computed hash value.\r
- * @param unmarshalled\r
- * @return true if the hash values differ\r
- */\r
- public boolean isUpdated(Vobject unmarshalled) {\r
- return hashvalue==unmarshalled.get__last_hash();\r
- }\r
-}\r
+++ /dev/null
-/*
- * 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;
-
-/**
- * The unique reference id for a Vamsas document Vobject,
- * used by applications to refer to the vamsas Vobject
- * within their own data space in the vamsas document.
- * TODO: decide if VorbaId should contain a reference
- * to either the IVorbaIdFactory that made it or the
- * IClient that defines the session (it might be
- * convenient).
- * @author jimp
- */
-public class VorbaId {
- protected String id;
- protected VorbaId() {
- super();
- }
- private VorbaId(String Id) {
- super();
- id = Id;
- }
- /**
- *
- * @param vorbaObject the source of vorba Ids
- * @param vobject the Vobject to be registered with a new vorba id
- * @return
- */
- protected static VorbaId newId(IVorbaIdFactory vorbaObject, Vobject vobject) {
- // Make unique id from appSpace info in vorbaObject
- synchronized (vorbaObject) {
- vobject.vorbaId=vorbaObject.makeVorbaId(vobject);
- return vobject.vorbaId;
- }
- }
- protected static VorbaId newId(String id) {
- return new VorbaId(id);
- }
- /**
- * @return Returns the id.
- */
- public String getId() {
- return id;
- }
- /* (non-Javadoc)
- * @see java.lang.Object#equals(java.lang.Object)
- */
- public boolean equals(Object obj) {
- if (obj instanceof String)
- return id.equals(obj);
- else if (obj instanceof VorbaId)
- return id.equals(((VorbaId)obj).id);
- return false;
- }
- /* (non-Javadoc)
- * @see java.lang.Object#hashCode()
- */
- public int hashCode() {
- return id.hashCode();
- }
- /* (non-Javadoc)
- * @see java.lang.Object#toString()
- */
- public String toString() {
- return id;
- }
-
-}
+++ /dev/null
-/*
- * 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;
-
-import java.util.Hashtable;
-import java.util.Vector;
-
-/**
- * A VorbaIdFactory is constructed by an IClient instance.
- * It guarantees that any new VorbaId objects are unique
- * within the VAMSAS session.
- *
- * @author jimp
- */
-public abstract class VorbaIdFactory implements IVorbaIdFactory {
- /**
- * hash of VorbaIds to Vobject.
- */
- protected Hashtable extantids=null;
- /**
- * hash of VorbaIds to persisted hash values
- */
- protected Hashtable extanthashv=null;
- /**
- * list of Vobjects added since last Document read.
- */
- protected Vector newobj=null;
-
- /**
- * construct a new id appropriate for this client in the vamsas session.
- *
- * @return valid VorbaId for session, or null if VorbaIdFactory not configured
- * correctly.
- */
- public abstract VorbaId makeVorbaId(Vobject vobject);
-
- /**
- * internal method to access the protected VorbaId object constructor
- * This shennanigan is to prevent casual generation of VorbaIds
- * (which may destroy the integrity of a Vamsas Document!)
- * @param id
- * @return new VorbaId object
- */
- protected VorbaId newId(String id) {
- return VorbaId.newId(id);
- }
- /**
- * Called by VorbaXmlBinder so the record of newly unmarshalled Vobject Ids
- * is accessible to the Document's VorbaIdFactory instance.
- * @param idtable
- */
- protected void setNewIdHash(Hashtable idtable) {
- extantids = idtable;
- }
-
- /* (non-Javadoc)
- * @see org.vamsas.client.IVorbaIdFactory#updateHashValue(org.vamsas.client.Vobject)
- */
- public void updateHashValue(Vobject vobject) {
- if (vobject.isRegisterable())
- extanthashv.put(vobject.getVorbaId(), new Vobjhash(vobject));
- }
-
- /**
- * TODO: decide if these are needed.
- *
- * @param sessionHandle
- */
- protected abstract void setSession(SessionHandle sessionhandle);
-
- public abstract SessionHandle getSessionHandle();
-
- protected abstract void setClient(ClientHandle appHandle);
-
- public abstract ClientHandle getClientHandle();
-
- protected abstract void setUser(UserHandle userHandle);
-
- public abstract UserHandle getUserHandle();
-}
+++ /dev/null
-/**
- *
- */
-package org.vamsas.client;
-
-import java.io.IOException;
-import java.io.PrintWriter;
-import java.io.Reader;
-import java.io.Writer;
-import java.lang.reflect.Field;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.Vector;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.exolab.castor.mapping.FieldHandler;
-import org.exolab.castor.mapping.GeneralizedFieldHandler;
-import org.exolab.castor.mapping.ValidityException;
-import org.exolab.castor.xml.IDResolver;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.MarshalListener;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.UnmarshalListener;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.vamsas.objects.core.VamsasDocument;
-/**
- * Implements the Vamsas Vobject ID machinery for translating
- * between non-volatile XML IDs and Vobject references. Use the
- * marshalling and unmarshalling methods in this class in order
- * to add automatically computed values for required fields in objects,
- * so as to avoid validation exceptions when marshalling new objects
- * into the vamsas document.
- */
-public class VorbaXmlBinder implements UnmarshalListener {
- private static Log log = LogFactory.getLog(VorbaXmlBinder.class);
- private final IVorbaIdFactory vorbafactory;
-
- private final Vector obj;
- private final Hashtable oldobjhashes;
- private final Hashtable objrefs;
- private final Vector updatedobjs;
-
- public VorbaXmlBinder(IVorbaIdFactory vorbafactory, Vector obj, Hashtable objrefs, Hashtable oldobjhashes, Vector updatedobjs) {
- this.vorbafactory = vorbafactory;
- this.obj = obj;
- this.objrefs = objrefs;
- this.oldobjhashes = oldobjhashes;
- this.updatedobjs = updatedobjs;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.exolab.castor.xml.UnmarshalListener#attributesProcessed(java.lang.Object)
- */
- public void attributesProcessed(Object object) {
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.exolab.castor.xml.UnmarshalListener#fieldAdded(java.lang.String,
- * java.lang.Object, java.lang.Object)
- */
- public void fieldAdded(String fieldName, Object parent, Object child) {
- if (parent instanceof Vobject && child instanceof Vobject) {
- if (((Vobject) child).V_parent==null) {
- // System.err.println("Setting parent of "+fieldName);
- ((Vobject) child).setV_parent((Vobject) parent);
- }
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.exolab.castor.xml.UnmarshalListener#initialized(java.lang.Object)
- */
- public void initialized(Object object) {
- }
-
- /*
- * Check if the object has an 'id' field - if it does, copy the value into
- * the VorbaId field of Vobject, and add the Vobject to the VorbaId hash.
- *
- * @see org.exolab.castor.xml.UnmarshalListener#unmarshalled(java.lang.Object)
- */
- public void unmarshalled(Object newobj) {
- if (newobj instanceof Vobject) {
- Vobject nobj = (Vobject) newobj;
- nobj.set__stored_in_document(true);
- try {
- if (nobj.isRegisterable() && nobj.___id_field!=null) {
- VorbaId nobj_id=null;
- // look for the id field (should be an NCName string)
- nobj.__vorba = vorbafactory;
- // use the Vobject accessor method to avoid unpleasant security exceptions.
- String idstring = nobj.__getInstanceIdField();
- if (idstring!=null) {
- if (idstring.length() > 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 <return>sync</return> 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
+++ /dev/null
-package org.vamsas.client.picking;\r
-\r
-import java.io.*;\r
-import java.net.*;\r
-\r
-class PickEndPoint extends Thread\r
-{\r
- private Socket socket;\r
- private int rPort;\r
- private BufferedWriter os;\r
- private BufferedReader in;\r
-\r
- private PickManager manager; \r
- \r
- PickEndPoint(PickManager manager, Socket s)\r
- {\r
- this.manager = manager;\r
- socket = s;\r
- }\r
- \r
- boolean openConnection()\r
- {\r
- try\r
- {\r
- // Create the socket if it doesn't already exist\r
- if (socket == null)\r
- socket = new Socket(InetAddress.getLocalHost(), PickServer.PORT);\r
- \r
- rPort = socket.getPort();\r
- socket.setKeepAlive(true);\r
- \r
- // Open the streams for reading/writing\r
- os = new BufferedWriter(new OutputStreamWriter(socket.getOutputStream()));\r
- in = new BufferedReader(new InputStreamReader(socket.getInputStream()));\r
- \r
- // Start the thread to listen for incoming messages\r
- System.out.println("CLIENT: connection successful to port "\r
- + socket.getPort() + " via port " + socket.getLocalPort());\r
- start();\r
- \r
- return true;\r
- }\r
- catch (Exception e)\r
- {\r
- System.out.println("CLIENT: connection failed: " + e);\r
- return false;\r
- }\r
- }\r
- \r
- void send(String str)\r
- {\r
- try\r
- {\r
- System.out.println("CLIENT: send " + str + " to " + rPort);\r
- os.write(str);\r
- \r
- // We use a newline to terminate the message\r
- os.newLine();\r
- os.flush();\r
- }\r
- catch (Exception e)\r
- {\r
- System.out.println("CLIENT: failed to send");\r
- \r
- // TODO: terminate the connection on a failed send or retry?\r
- terminate();\r
- }\r
- }\r
- \r
- // void receive() (threaded)\r
- public void run()\r
- {\r
- try\r
- {\r
- while (true)\r
- {\r
- String str = in.readLine(); \r
- System.out.println("CLIENT: recv " + str + " from " + rPort);\r
- \r
- manager.handleMessage(this, str);\r
- }\r
- }\r
- catch (Exception e)\r
- {\r
- // Means the other end of the connection has (probably died) so we need\r
- // terminate this endpoint (if this is server side)\r
- System.out.println("CLIENT: read failed: " + e);\r
- \r
- terminate();\r
- }\r
- }\r
- \r
- private void terminate()\r
- {\r
- try { socket.close(); }\r
- catch (IOException e) {}\r
- \r
- System.out.println("CLIENT: closing connection to port " + socket.getPort());\r
- manager.removeEndPoint(this);\r
- }\r
-}
\ No newline at end of file
+++ /dev/null
-package org.vamsas.client.picking;\r
-\r
-import java.net.*;\r
-import java.util.*;\r
-import java.util.logging.*;\r
-\r
-/**\r
- * Manager class that maintains a list of connected clients in addition to\r
- * attempting to run a server to listen for client connections. If the server\r
- * initialization fails, then an attempt to connect (as a client) to another JVM\r
- * that is already a server happens instead.\r
- */\r
-public class PickManager\r
-{\r
- private static Logger logger = Logger.getLogger("org.vamsas.client.picking");\r
- \r
- // Maintains a list of client communication objects - each object represents\r
- // a way of talking to either:\r
- // the server - if this is client side (and in which case, the list will only contain one element\r
- // the other clients - if this is server side\r
- private LinkedList clients;\r
- \r
- private PickServer server;\r
- \r
- /**\r
- * Constructs a new PickManager. This method will return immediately, while\r
- * a looping thread runs that attempts to run the server or connect to an\r
- * existing server.\r
- */\r
- public PickManager()\r
- {\r
- server = new PickServer(this);\r
- clients = new LinkedList();\r
- \r
- new InitializeThread().start();\r
- }\r
- \r
- /**\r
- * Attempts to establish a connection between two client endpoints. This\r
- * method is called in two ways: 1) by the server when it receives a remote\r
- * request (in which case the socket will already be established) and 2) by\r
- * a client that is attempting to connect *to* the server.\r
- * @param socket a socket endpoint for the connection\r
- * @return true if the connection is successfully, false otherwise\r
- */\r
- boolean addEndPoint(Socket socket)\r
- {\r
- PickEndPoint client = new PickEndPoint(this, socket);\r
- \r
- if (client.openConnection())\r
- {\r
- clients.add(client);\r
- logger.fine("List now contains " + clients.size() + " client(s)");\r
- return true;\r
- }\r
- \r
- return false;\r
- }\r
- \r
- /**\r
- * Sends a message to other clients.\r
- * @param str the message to send\r
- */\r
- public void sendMessage(String str)\r
- {\r
- forwardMessage(null, str);\r
- }\r
- \r
- /**\r
- * Forwards (or sends) a message. When the server (client A) receives a\r
- * message from client B, it must also forward it to clients C and D (etc),\r
- * but mustn't forward it *back* to client B.\r
- * @param origin the client endpoint that received the message (will be null\r
- * if the message originates from this instance\r
- * @param str the message to send\r
- */\r
- private void forwardMessage(PickEndPoint origin, String str)\r
- {\r
- ListIterator itor = clients.listIterator();\r
- while (itor.hasNext())\r
- {\r
- PickEndPoint client = (PickEndPoint) itor.next();\r
- \r
- if (client != origin)\r
- client.send(str);\r
- }\r
- }\r
- \r
- /**\r
- * Handles a received message. If the manager is running in server mode,\r
- * then it must ensure the message is also forwarded to the other clients.\r
- * @param origin the client endpoint that received the message\r
- * @str the message that was received\r
- */\r
- void handleMessage(PickEndPoint origin, String str)\r
- {\r
- if (server.isServer())\r
- forwardMessage(origin, str);\r
- \r
- // TODO: pass message to VAMSAS API\r
- }\r
- \r
- /**\r
- * Removes a client connection from the list when its connection is no\r
- * longer valid.\r
- * @param client the client endpoint to remove\r
- */\r
- void removeEndPoint(PickEndPoint client)\r
- {\r
- clients.remove(client);\r
- logger.fine("List now contains " + clients.size() + " client(s)");\r
- \r
- // If there's no endpoints left, then we've lost all connections and\r
- // need to reinitialize\r
- if (clients.size() == 0)\r
- new InitializeThread().start();\r
- }\r
- \r
- /**\r
- * Thread extension class to handle the actual initialization\r
- */\r
- private class InitializeThread extends Thread\r
- {\r
- public void run()\r
- {\r
- logger.fine("Initializing connection...");\r
- boolean connected = false;\r
- \r
- // Loop until we can get a connection (one way or the other)\r
- while (!connected)\r
- {\r
- // Sleep for a rnd time so we don't end up with all the VAMSAS\r
- // apps trying to initialize servers at the same time\r
- try { Thread.sleep((int)Math.random()); }\r
- catch (InterruptedException e) {}\r
- \r
- // Attempt to open the server port...\r
- if (server.isServer() || server.createServer())\r
- connected = true;\r
-\r
- // If it fails, then attempt to make a client connection...\r
- else if (addEndPoint(null))\r
- connected = true;\r
- }\r
- }\r
- }\r
-}
\ No newline at end of file
+++ /dev/null
-package org.vamsas.client.picking;\r
-\r
-import java.io.*;\r
-import java.net.*;\r
-import java.util.logging.*;\r
-\r
-/**\r
- * Server class that listens for incoming connections on a predefined port.\r
- */\r
-class PickServer extends Thread\r
-{\r
- private static Logger logger = Logger.getLogger("org.vamsas.client.picking");\r
- \r
- // The port number we'll listen on\r
- static final int PORT = 53782;\r
- \r
- private ServerSocket serverSocket;\r
- // Set to true once the server is established\r
- private boolean isServer = false;\r
- \r
- private PickManager manager;\r
- \r
- /**\r
- * Constructs a new instance of the server (but doesn't start it).\r
- * @param manager a reference to the pick manager that owns this server\r
- */\r
- PickServer(PickManager manager)\r
- {\r
- this.manager = manager;\r
- }\r
- \r
- /**\r
- * Returns true if this server instance is running.\r
- * Return true if this server instance is running\r
- */\r
- boolean isServer()\r
- { return isServer; }\r
- \r
- /**\r
- * Attempts to create the server by opening a server socket on the port.\r
- * @return true if the server was created; false otherwise\r
- */\r
- boolean createServer()\r
- {\r
- try\r
- {\r
- serverSocket = new ServerSocket(PORT);\r
- start(); \r
- \r
- return isServer = true;\r
- }\r
- catch (IOException e)\r
- {\r
- logger.info("SERVER: " + e);\r
- return false;\r
- }\r
- }\r
- \r
- /**\r
- * Thread listening method - loops indefinitely listening for connections.\r
- * When one is received, the socket object is passed to the manager so it\r
- * can make a full client connection for further comms.\r
- */\r
- public void run()\r
- {\r
- logger.fine("SERVER: listening on " + PORT + " - SERVER");\r
- \r
- // Loop forever, accepting connectons from other clients\r
- // TODO: add in the ability to terminate the server if a VAMSAS session\r
- // is ended\r
- while (true)\r
- {\r
- try\r
- {\r
- Socket socket = serverSocket.accept(); \r
- logger.fine("SERVER: connection detected");\r
- \r
- manager.addEndPoint(socket);\r
- }\r
- catch (IOException e) {}\r
- }\r
- }\r
-}
\ No newline at end of file
+++ /dev/null
-package org.vamsas.client.picking;\r
-\r
-import java.util.logging.*;\r
-\r
-public class TestApp\r
-{\r
- private static Logger logger = Logger.getLogger("org.vamsas.client.picking");\r
- \r
- public static void main(String[] args)\r
- throws Exception\r
- {\r
-// logger.setLevel(Level.INFO);\r
- \r
- TestApp app = new TestApp();\r
- \r
- PickManager manager = new PickManager();\r
- \r
- // Send 5 test messages...\r
-// for (int i = 0; i < 5; i++)\r
- while (true)\r
- { \r
- try { Thread.sleep((int) (Math.random()*20000)); }\r
- catch (InterruptedException e) {}\r
- \r
- int rnd = (int) (Math.random()*100);\r
- manager.sendMessage("" + rnd);\r
- }\r
- }\r
- \r
- public TestApp()\r
- {\r
- }\r
-}
\ No newline at end of file
+++ /dev/null
-/**
- *
- */
-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;
- }
-
-}
+++ /dev/null
-/**
- *
- */
-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;
- }
-
-}
+++ /dev/null
-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
-}
+++ /dev/null
-/*
- *
- */
-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<j;i++)
- if (vamsasObjects.containsKey(ids[i]))
- vo[i] = (Vobject) vamsasObjects.get(ids[i]);
- else
- log.debug("Returning null Vobject reference for id "+ids[i].getId());
- return vo;
- }
- /**
- * internal reference to single copy of Document Roots array
- */
- private VAMSAS[] _VamsasRoots=null;
- /*
- * (non-Javadoc)
- * LATER: currently there is only one Vector of roots ever passed to client - decide if this is correct (means this is not thread safe and may behave unexpectedly)
- * @see org.vamsas.client.IClientDocument#getVamsasRoots()
- */
- public VAMSAS[] getVamsasRoots() {
- if (doc==null) {
- log.debug("Null document for getVamsasRoots(), returning null");
- return null;
- }
- if (archive==null) {
- // LATER: decide on read-only status of ClientDocument object
- log.warn("getVamsasRoots() called on possibly read-only document.");
- }
- if (_VamsasRoots!=null)
- return _VamsasRoots;
- VAMSAS[] roots = doc.getVAMSAS();
- if (roots == null) {
- // Make a new one to return to client to get filled.
- _VamsasRoots = new VAMSAS[] { new VAMSAS() };
- // Do provenance now. just in case.
- doc.getProvenance().addEntry(sclient.getProvenanceEntry("Created new document root [id="+_VamsasRoots[0].getId()+"]"));
- doc.addVAMSAS(_VamsasRoots[0]);
- } else {
- _VamsasRoots = new VAMSAS[roots.length];
- for (int r=0;r<roots.length; r++)
- _VamsasRoots[r] = roots[r];
- }
- return _VamsasRoots;
- }
-
- private int _contains(VAMSAS root, VAMSAS[] docRoots) {
- if (root==null)
- return -1;
- if (docRoots==null || docRoots.length==0)
- return -1;
- String r_id = root.getId();
- for (int i=0,j=docRoots.length; i<j; i++)
- if (docRoots[i]==root || (docRoots[i]!=null && docRoots[i].getId().equals(r_id)))
- return i;
- return -1;
- }
-/**
- * verify that newr version is really an intact version of the
- * @param newVersion (may be modified)
- * @param oldVersion
- * @return true if newVersion is a valid root that preserves original references
- */
- private boolean isValidUpdate(VAMSAS newVersion, final VAMSAS oldVersion) {
- // ideal - this cascades down the two structures, ensuring that all ID'd objects in one are present in the other.
- if (oldVersion==newVersion) {
- // may be a virgin root element.
- if (!newVersion.isRegistered())
- _registerObject(newVersion);
- // Should retrieve original version and compare - unless local hashes can be used to determine if resultSet has been truncated.
- // just do internal validation for moment.
- if (newVersion.isValid())
- return true;
- return false;
- } else {
- // redundant ? if (oldVersion.is__stored_in_document())
- if (!newVersion.isRegistered())
- _registerObject(newVersion);
- if (newVersion.isValid())
- return true;
- }
- return false;
- /**
- * LATER isValidUpdate : Ideally. we efficiently walk down, comparing hashes, to deal with merging and verifying provenance for objects
-
- // extract root objects
- if (newroots != null) {
- // check newroots for objects that were present in the old document
- // check to see if the 'old' objects have been modified
- // if they have ? we overwrite them with their new version, ensuring that
- // provenance is updated.
- // if they haven't ? do nothing ?
-
- for (int i = 0, k = newroots.length; i < k; i++) {
- if (newroots[i].isRegistered()) {
- // easy - just check if anything has changed and do provenance
- Vobject oldversion = getObject(newroots[i].getVorbaId());
- if (oldversion instanceof VAMSAS) {
- // LATER: appropriate merging behaviour when two clients have improperly modified the same Vobject independently.
- if (newroots[i].get__last_hash() != newroots[i].hashCode()) {
- // client has modified this Vobject since last retrieval.
- if (newroots[i].get__last_hash() != oldversion.get__last_hash()) {
- // Vobject has been modified by another client since this
- // client's
- // last access to document.
- }
- }
- } else {
- throw new Error(
- "SimpleClient error when using setVamsasRoots : The vorbaId for Vobject "
- + i
- + " does not refer to an Vobject of type VAMSAS in the current document!");
- }
- } else {
- if (!newroots[i].is__stored_in_document()) {
- // check if Vobject is modified
- if (newroots[i].get__last_hash() != newroots[i].hashCode()) {
- // it is - so we add newroots[i] as a new Vobject, with updated
- // provenance.
- } else {
- // do nothing
- newroots[i] = null;
- }
- } else {
- // just add newroots[i] as a new Vobject in the document
- // - with appropriate provenance.
- }
- }
- }*/
- }
- /**
- * merge old and new root vectors
- * @param newr This array may be written to
- * @param original
- * @param the client document (usually this) which this root set belongs to.
- * @return merged vector of vamsas roots
- */
- private VAMSAS[] _combineRoots(VAMSAS[] newr, final VAMSAS[] original, ClientDocument modflag) {
- Vector rts = new Vector();
- boolean modified=false;
- for (int i=0,j=original.length; i<j; i++) {
- int k = _contains(original[i], newr);
- if (k>-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; i<j; i++) {
- if (newr[i]!=null) {
- rts.add(newr[i]);
- modified=true;
- }
- }
- newr = new VAMSAS[rts.size()];
- for (int i=0,j=rts.size(); i<j; i++)
- newr[i] = (VAMSAS) rts.get(i);
- if (modflag!=null)
- modflag.isModified = modified;
- return newr;
- }
-
- /**
- * update the document with new roots.
- * LATER: decide: this affects the next call to getVamsasRoots()
- * @see org.vamsas.IClientDocument.setVamsasRoots
- */
- public void setVamsasRoots(VAMSAS[] newroots) {
- if (doc==null) {
- log.debug("setVamsasRoots called on null document.");
- return;
- }
- VAMSAS[] newr;
- if (newroots==null) {
- log.debug("setVamsasRoots(null) - do nothing.");
- return;
- }
- // are we dealing with same array ?
- if (_VamsasRoots!=newroots) {
- // merge roots into local version.
- newr = new VAMSAS[newroots.length];
- for (int i=0;i<newr.length;i++)
- newr[i] = newroots[i];
- newr=_combineRoots(newr,_VamsasRoots,this);
- } else {
- newr = new VAMSAS[_VamsasRoots.length];
- for (int i=0;i<newr.length;i++)
- newr[i]=_VamsasRoots[i];
- }
- // actually compare with document root set for final combination (to ensure nothing is lost)
- _VamsasRoots = _combineRoots(newr, doc.getVAMSAS(), this);
- }
-
-
- /* (non-Javadoc)
- * LATER: decide: this affects the next call to getVamsasRoots()
- * @see org.vamsas.client.IClientDocument#addVamsasRoot(org.vamsas.objects.core.VAMSAS)
- */
- public void addVamsasRoot(VAMSAS newroot) {
- if (doc==null) {
- log.debug("addVamsasRoots called on null document.");
- return;
- }
- VAMSAS[] newroots = _combineRoots(new VAMSAS[] {newroot}, _VamsasRoots, this);
- _VamsasRoots = newroots;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.vamsas.client.IClientDocument#registerObjects(org.vamsas.client.Vobject[])
- */
- public VorbaId[] registerObjects(Vobject[] unregistered) {
- if (doc==null) {
- log.warn("registerObjects[] called on null document.");
- return null;
- }
- if (vamsasObjects==null) {
- log.warn("registerObjects[] called for null vamsasObjects hasharray.");
- return null;
- }
- if (unregistered!=null) {
- VorbaId ids[] = new VorbaId[unregistered.length];
- for (int i=0,k=unregistered.length; i<k; i++)
- if (unregistered[i]!=null) {
- log.warn("Null Vobject passed to registerObject[] at position "+i);
- return null;
- } else {
- ids[i]=registerObject(unregistered[i]);
- }
- log.debug("Registered "+unregistered.length+" objects - total of "+vamsasObjects.size()+" ids.");
- return ids;
- }
- return null;
- }
- /* (non-Javadoc)
- * @see org.vamsas.client.IClientDocument#registerObject(org.vamsas.client.Vobject)
- */
- public VorbaId registerObject(Vobject unregistered) {
- if (doc==null) {
- log.warn("registerObjects called on null document.");
- return null;
- }
- if (vamsasObjects==null) {
- log.warn("registerObjects called for null vamsasObjects hasharray.");
- return null;
- }
- if (unregistered!=null) {
- VorbaId id = _registerObject(unregistered);
- log.debug("Registered object - total of "+vamsasObjects.size()+" ids.");
- return id;
- }
- log.warn("Null Vobject passed to registerObject.");
- return null;
- }
- /**
- * IClientAppdata instance - if it exists.
- */
- SimpleClientAppdata scappd = null;
- /* (non-Javadoc)
- * @see org.vamsas.client.IClientDocument#getClientAppdata()
- */
- public IClientAppdata getClientAppdata() {
- if (doc==null) {
- log.warn("getClientAppdata called on null document.");
- return null;
- }
- if (scappd==null) {
- log.debug("Creating new SimpleClientAppdata instance for "+sclient.getSessionHandle());
- scappd = new SimpleClientAppdata(this);
- if (scappd==null) {
- // LATER: may not need this as a warning message.
- log.warn("Null appdata object for "+sclient.getSessionHandle());
- } else {
- log.debug("Created SimpleClientAppdata successfully.");
- }
- } else {
- log.debug("Returning existing SimpleClientAppdata reference.");
- }
- return scappd;
- }
- /**
- * access the vamsas document
- * @return the session's vamsas document
- */
- protected VamsasDocument getVamsasDocument() {
- return doc;
- }
- /**
- * returns the read-only IO interface for the vamsas document Jar file
- * @return
- */
- protected VamsasArchiveReader getVamsasArchiveReader() {
- try {
- return archive.getOriginalArchiveReader();
- } catch (Exception e) {
- log.warn("Unable to create OriginalArchiveReader!", e);
- }
- return null;
- }
- protected boolean updateSessionDocument() throws java.io.IOException {
- boolean docupdate = true; // 'non-serious' problems below set this false
- if (doc==null) {
- log.warn("updateSessionDocument called on null document.");
- throw new java.io.IOException("Document is closed.");
- }
- if (archive==null) {
- log.warn("updateSessionDocument called document archive handler.");
- throw new java.io.IOException("Document is closed.");
- }
-
- if (!isModified() && !scappd.isModified()) {
- log.debug("Document update not necessary. returning false.");
- return false;
- }
- VamsasSession session = sclient._session;
- log.debug("updating Session Document in "+session.sessionDir);
- // update the VamsasDocument structure with any new appData's.
- // try to update the sessionFile
- log.debug("Attempting to update session "+sclient.session.getSessionUrn());
- if (scappd.isModified()) {
- ClientHandle client = sclient.client;
- UserHandle user = sclient.user;
- scappd.closeForWriting();
- if (scappd.appsGlobal==null) {
- log.debug("Creating new appData entry for this application...");
- // first write for this application - add a new section in document
- ApplicationData appd = scappd.appsGlobal = new ApplicationData();
- appd.setName(client.getClientName());
- // appd.setUrn(client.getClientUrn());
- appd.setVersion(client.getVersion());
- doc.addApplicationData(appd);
- // embed or jarEntry ? - for now only jarEntry's are dealt with.
- appd.setDataReference(AppDataReference.uniqueAppDataReference(doc, sclient.client.getClientUrn()));
- log.debug("... created.");
- }
- if (scappd.newAppData!=null && scappd.newAppData.sessionFile.exists()) {
- log.debug("Beginning update for new Global Appdata...");
- // new global appdata to write.
- if (scappd.appsGlobal.getData()!=null) {
- scappd.appsGlobal.setData(null);
- scappd.appsGlobal.setDataReference(AppDataReference.uniqueAppDataReference(doc, sclient.client.getClientUrn()));
- }
- // LATER: use a switch to decide if the data should be written as a reference or as an embedded data chunk
- scappd.updateAnAppdataEntry(archive, scappd.appsGlobal, scappd.newAppData);
- log.debug("...Successfully updated Global Appdata Entry.");
- }
- if (scappd.newUserData!=null && scappd.newUserData.sessionFile.exists()) {
- log.debug("Beginning to update Users Appdata entry....");
- if (scappd.usersData==null) {
- // create new user appdata
- scappd.usersData = new User();
- scappd.usersData.setFullname(user.getFullName());
- scappd.usersData.setOrganization(user.getOrganization());
- scappd.appsGlobal.addUser(scappd.usersData);
- }
- User appd = scappd.usersData;
- if (appd.getData()!=null || appd.getDataReference()==null) {
- // LATER make standard appDataReference constructor for client+user
- appd.setData(null);
- String safe_username = user.getFullName();
- int t = safe_username.indexOf(" ");
- if (t!=-1) {
- safe_username = safe_username.substring(t);
- }
- appd.setDataReference(AppDataReference.uniqueAppDataReference(doc, sclient.client.getClientUrn()+safe_username));
- }
- scappd.updateAnAppdataEntry(archive, scappd.usersData, scappd.newUserData);
- log.debug("...Successfully updated user AppData entry.");
- }
- }
- log.debug("Updating Document...");
- // now update the document.
- try {
- archive.putVamsasDocument(doc);
- log.debug("Successfully written document entry.");
- }
- catch (Exception e) {
- log.error("Marshalling error for vamsas document.",e);
- docupdate = false; // pass on the (probable) object validation error
- }
- if (archive.transferRemainingAppDatas())
- log.debug("Remaining appdatas were transferred.");
- else
- log.debug("No remaining appdatas were transferred. (Correct?)");
- archive.closeArchive();
- log.debug("...successully finished and closed.");
- return docupdate; // no errors ?
- }
- /* (non-Javadoc)
- * @see java.lang.Object#finalize()
- */
- protected void finalize() throws Throwable {
- log.debug("Garbage collecting on ClientDocument instance.");
- if (scappd!=null) {
- scappd.finalize();
- scappd = null;
- }
- if (doc!=null) {
- doc = null;
- }
- // disengage from client
- if (sclient!=null)
- sclient.cdocument = null;
- sclient=null;
-
- super.finalize();
- }
- public Vector getUpdatedObjects() {
- return updatedObjects;
- }
-}
+++ /dev/null
-package org.vamsas.client.simpleclient;
-
-import org.vamsas.client.*;
-
-import java.io.BufferedInputStream;
-import java.io.BufferedOutputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.io.ObjectInputStream;
-import java.io.ObjectOutput;
-import java.io.ObjectOutputStream;
-import java.io.OutputStream;
-import java.util.Vector;
-
-/**
- * Handler for the clientsFile within a vamsas session thread.
- * @author jim
- */
-public class ClientsFile extends ListFile {
- private static org.apache.commons.logging.Log log = org.apache.commons.logging.LogFactory.getLog(ClientsFile.class);
- /**
- * number of my client in list - passed back when a client
- * is added to list, and used (if valid) for quickly
- * looking up presence of client handle in the list.
- */
- private int syncnum = 1;
-
- public ClientsFile(File filelist) throws IOException {
- super(filelist);
- }
-
- /**
- * internal method for getting clientList - ensures a lock has been made but
- * does not release it.
- *
- * @return list of clients
- */
- private ClientHandle[] retrieveClientHandles() {
- if (lockFile()) {
- try {
- ClientHandle[] clients=null;
- if (fileLock.length()>0) {
-
- 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);
-
- }
- }
-
- }
-}
+++ /dev/null
-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: <Vamsas-session URN>
- * 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()<l)
- ;
- }
-
-
- private boolean block_document_updates=false;
- int STORE_WAIT=5; // how many units before we decide all clients have finalized their appdatas
-
- /**
- * client App requests offline storage of vamsas data.
- * Call blocks whilst other apps do any appData finalizing
- * and then returns (after locking the vamsasDocument in the session)
- * Note - the calling app may also receive events through the EventGeneratorThread for document updates.
- *
- * @return Lock for session.vamArchive
- * @param STORE_WAIT indicates how lock the call will block for when nothing appears to be happening to the session.
- */
- protected Lock want_to_store() {
- log.debug("Setting flag for document_update requests to be ignored");
- block_document_updates=true;
- log.debug("Waiting for other apps to do FinalizeApp handling.");
- try {
- session.addStoreDocumentRequest(client.getClientHandle(), client.getUserHandle());
- } catch (Exception e) {
- log.warn("Whilst writing StoreDocumentRequest for "+client.getClientHandle().getClientUrn()+" "+client.getUserHandle(),
- e);
- log.info("trying to continue.");
- }
- // LATER: refine this semaphore process
- // to make a robust signalling mechanism:
- // app1 requests, app1..n do something (or don't - they may be dead),
- // app1 realises all apps have done their thing, it then continues with synchronized data.
- // this probably needs two files - a request file,
- // and a response file which is acknowledged by the app1 requestor for each app.
- // eventually, no more responses are received for the request, and the app can then only continue with its store.
- int units = 0;
- while (units<STORE_WAIT) {
- wait(1);
- if (storeFile.hasChanged() || vamsasfile.hasChanged())
- units=0;
- else
- units++;
- }
-
- block_document_updates=false;
- log.debug("Cleared flag for ignoring document_update requests");
- // wait around again (until our own watcher has woken up and synchronized).
- while (units<STORE_WAIT) {
- wait(1);
- if (storeFile.hasChanged() || vamsasfile.hasChanged())
- units=0;
- else
- units++;
- }
-
-
- log.debug("finished waiting.");
- return session.vamArchive.getLock();
- }
- /**
- * count handlers for a particular vamsas event
- * @param event string enumeration from org.vamsas.client.Events
- * @return -1 for an invalid event, otherwise the number of handlers
- */
- protected int countHandlersFor(String event) {
- if (handlers.containsKey(event)) {
- PropertyChangeSupport handler = (PropertyChangeSupport) handlers.get(event);
- PropertyChangeListener[] listeners;
- if (handler!=null)
- return ((listeners=handler.getPropertyChangeListeners())==null)
- ? -1 : listeners.length;
- }
- return -1;
- }
- /**
- * probably don't need any of these below.
- */
- /* (non-Javadoc)
- * @see java.lang.Thread#destroy()
- */
- public void destroy() {
- super.destroy();
- }
- /* (non-Javadoc)
- * @see java.lang.Thread#interrupt()
- */
- public void interrupt() {
- // TODO Auto-generated method stub
- super.interrupt();
- }
- /* (non-Javadoc)
- * @see java.lang.Thread#isInterrupted()
- */
- public boolean isInterrupted() {
- // TODO Auto-generated method stub
- return super.isInterrupted();
- }
- /* (non-Javadoc)
- * @see java.lang.Thread#run()
- */
- public void run() {
- // TODO Auto-generated method stub
- super.run();
- }
-
-
-}
+++ /dev/null
-package org.vamsas.client.simpleclient;
-
-import java.io.BufferedOutputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.RandomAccessFile;
-import java.nio.channels.FileChannel;
-import java.nio.channels.ReadableByteChannel;
-/**
- * File based Locking mechanism to get around some bizarre limitations of JarEntry seeking.
- * Abstract locks have a target file, to which access is controlled when a lock is held. Native locks on WindowsXP seem to conflict with Jar seek operations, so a file lock creates an advisory lock.
- * Method:
- * A lock file is created, if it doesn't already exist - the naming convention is TargetFile+suffixSeparator+_LockSuffix.
- * A lock is obtained by locking the lock file with a native lock. The NativeLock is used for this.
- * @author JimP
- *
- */
-public class FileLock extends Lock {
- private File _lock = null;
- protected static String _LockSuffix="lck";
- private NativeLock advisory=null;
- /**
- * ensure that the _lock file exists
- * and create a lock
- */
- private boolean ensureLockFile(boolean block) {
- if (_lock==null)
- return false;
- if (advisory!=null && advisory.isLocked())
- return true;
- try {
- advisory=new NativeLock(_lock, block);
- } catch (Exception e) {
- log.fatal("Failed to create advisory lock file "+_lock,e);
- throw new Error("Failed to create advisory lock file "+_lock);
- }
- return advisory.isLocked();
- }
- /**
- * call to clear up a filelock file after its been made
- *
- */
- private void tidy() {
- if (_lock!=null) {
- if ( advisory!=null)
- advisory.release(true);
- advisory.target.deleteOnExit();
- advisory=null;
- _lock=null;
- }
- }
- /**
- * @param lockfile
- * @param block true means thread blocks until FileLock is obtained.
- */
- public FileLock(File lockfile, boolean block) {
- super(lockfile);
- // try and get a lock.
- try {
- _lock = new File(lockfile.getParentFile(), lockfile.getName()+"."+_LockSuffix);
- if (!ensureLockFile(block)) {
- log.debug("Couldn't get lock on "+_lock);
- tidy();
- return;
- }
- // create target file ready to be written to if necessary.
- if (!lockfile.exists())
- if (!lockfile.createNewFile()) {
- log.warn("Failed to create locked file "+lockfile);
- return;
- }
- //openRaFile();
- } catch (FileNotFoundException e) {
- //
- log.debug("FileLock failed with target="+lockfile+" and lockfile suffix of "+_LockSuffix);
- //log.error("Error! Couldn't create a lockfile at "
- // + lockfile.getAbsolutePath(), e);
- } catch (IOException e) {
- log.error("Error! Problems with IO when creating a lock on "
- + lockfile.getAbsolutePath(),e);
- }
- }
-
- private boolean openRaFile() throws IOException {
- if (target==null)
- return false;
- if (advisory==null || !advisory.isLocked())
- return false;
- if (rafile==null || rafile.getFD()==null || !rafile.getFD().valid()) {
- rafile=new RandomAccessFile(target,"rw");
- } else {
- if (log.isDebugEnabled())
- log.debug("Reusing existing RandomAccessFile on "+target);
- }
- return (rafile.getChannel()!=null) && rafile.getChannel().isOpen();
- }
-
- public boolean isLocked() {
- if (advisory != null) {
- if (advisory.isLocked())
- return true;
- advisory=null;
- if (log.isDebugEnabled())
- log.debug("Lockfile "+_lock+" unexpectedly deleted ?");
- }
- return false;
- }
-
- public void release() {
- release(true);
- }
-
- public void release(boolean closeChannel) {
- if (!isLocked())
- return;
- if (log.isDebugEnabled())
- log.debug("Releasing advisory lock on "+target);
- if (closeChannel) {
- if (rafile!=null)
- try {
- rafile.close();
- } catch (Exception e) {
- log.debug("Unexpected exception whilst closing RandomAccessFile on "+target, e);
- }
- rafile=null;
- }
- tidy();
- }
-
- public FileInputStream getFileInputStream(boolean atStart) throws IOException {
- if (!isLocked()) {
- log.debug("Don't hold lock on "+target+" to get locked FileInputStream.");
- return null;
- }
- openRaFile();
- if (atStart)
- rafile.seek(0);
- return new FileInputStream(rafile.getFD());
- }
-
-
- public FileOutputStream getFileOutputStream(boolean clear) throws IOException {
- if (!isLocked()) {
- log.debug("Don't hold lock on "+target+" to get locked FileOutputStream.");
- return null;
- }
- openRaFile();
- if (clear) {
- rafile.seek(0);
- rafile.setLength(0);
- } else
- rafile.seek(rafile.length());
- return new LockedFileOutputStream(rafile.getFD());
- }
-
-
- public BufferedOutputStream getBufferedOutputStream(boolean clear) throws IOException {
- log.debug("Getting BufferedOutputStream (clear="+clear+")");
- FileOutputStream fos = getFileOutputStream(clear);
- if (fos!=null)
- return new BufferedOutputStream(fos);
- return null;
- }
-
- /* (non-Javadoc)
- * @see org.vamsas.client.simpleclient.Lock#getLength()
- */
- public long length() {
- if (isLocked()) {
- if (!target.exists()) {
- try {
- target.createNewFile();
- } catch (Exception e) {
- log.error("Invalid lock:Failed to create target file "+target);
- tidy();
- return -1;
- }
- return 0;
- }
- return target.length();
- }
- return -1;
- }
- protected void finalize() throws Throwable {
- release(true); // we explicitly lose the lock here.
- super.finalize();
- }
- public RandomAccessFile getRaFile() throws IOException {
- if (isLocked() && openRaFile()) {
- return rafile;
- }
- log.debug("Failed to getRaFile on target "+target);
- return null;
- }
- public FileChannel getRaChannel() throws IOException {
- if (isLocked() && openRaFile()) {
- return rafile.getChannel();
- }
- log.debug("Failed to getRaChannel on target "+target);
- return null;
- }
-}
+++ /dev/null
-/**
- *
- */
-package org.vamsas.client.simpleclient;
-
-import java.io.File;
-
-
-/**
- * Watches a particular file for its creation, deletion, or
- * modification. The watcher is thread safe and different
- * instances watching the state of a particular file carry
- * their own state record for the file.
- */
-public class FileWatcher {
-
- private File subject = null;
-
- private long lastStat[];
- boolean waslocked=false;
- boolean exists = false;
- /**
- * transient lock on subject - can be passed back to calling class
- * to preserve new state of file for immediate reading.
- */
- private Lock subjectLock = null;
- /**
- * clear local locks on subject.
- *
- */
- private void clearLock() {
- if (subjectLock!=null)
- subjectLock.release();
- subjectLock=null;
- }
- /**
- *
- * @return true if subject exists and is locked by another process.
- */
- private boolean checkLock() {
- if (subject!=null && subject.exists()) {
- if (subjectLock!=null) {
- subjectLock.release();
- }
- subjectLock = LockFactory.tryLock(subject);
- if (subjectLock.isLocked()) {
- return false;
- }
- clearLock();
- return true;
- }
- return false;
- }
-
- private long[] getStat(File subject) {
- return new long[] { subject.lastModified(), subject.length() };
- }
- private boolean compStat(long[] stat, long[] newstat) {
- if (stat[0]!=newstat[0] || stat[1]!=newstat[1])
- return false;
- return true;
- }
- /**
- * Detect changes in file state and release of any
- * lock in place during change.
- * @return true if file state has changed. Leaves lock in subjectLock (ready to be passed to caller)
- */
- private boolean check() {
- if (subject != null) {
- if (!subject.exists()) {
- if (exists) {
- if (!waslocked) {
- // !checkLock()) {
-
- exists = false;
- // waslocked=false;
- return true;
- }
- }
- // locked - state change registered after lock is released
- return false;
- } else {
- long[] newStat = getStat(subject); // subject.lastModified();
- if (!checkLock()) {
- // file is free to access, return state change
- if (!exists || !compStat(lastStat, newStat)) {
- waslocked=false;
- exists=true;
- lastStat=newStat;
- return true;
- }
- // no change
- return false;
- } else {
- waslocked=true;
- return false;
- }
- }
- }
- return false;
- }
- /**
- * updates internal record of file state when caller has intentionally
- * modified subject. (ignores locked-state of subject)
- */
- public void setState() {
- if (subject!=null) {
- if (exists = subject.exists()) {
- lastStat = getStat(subject);
- waslocked = false;
- }
- }
- }
-
- /**
- * Make a watcher for a particular file. If the file doesn't exist, the
- * watcher will watch for its creation (and indicate a change of state)
- * For locked files, the removal of a lock constitutes a change of
- * state if the file was modified.
- *
- * @param subject
- */
-
- public FileWatcher(File subject) {
- this.subject = subject;
- setState();
- }
- /**
- * Test for change in file state. Only indicates a change
- * after any lock on a file has been released.
- * @return true if file has been modified.
- */
- public boolean hasChanged() {
- boolean res = check();
- clearLock();
- return res;
- }
- /**
- * passes lock back to caller if hasChanged returned true.
- * @return
- */
- public Lock getChangedState() {
- boolean res = check();
- if (res)
- return subjectLock;
- else {
- clearLock();
- return null;
- }
- }
- /**
- * safely? getting current state of the watched file
- * @return
- */
- public long[] getCurrentState() {
- return getStat(subject);
- }
- /**
- * safely compare an externally recorded state with the current state
- * for significant modifications.
- * @param a
- * @param b
- * @return
- */
- public boolean diffState(long[] a, long[] b) {
- return compStat(a,b);
- }
-}
+++ /dev/null
-/**
- *
- */
-package org.vamsas.client.simpleclient;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.vamsas.client.ClientHandle;
-import org.vamsas.client.SessionHandle;
-import org.vamsas.client.UserHandle;
-import org.vamsas.client.VorbaId;
-import org.vamsas.client.VorbaIdFactory;
-import org.vamsas.client.Vobject;
-import org.vamsas.objects.utils.document.VersionEntries;
-
-import java.util.Hashtable;
-import java.util.zip.CRC32;
-/**
- * Simplest VorbaId constructor
- * @author jimp
- *
- */
-public class IdFactory extends VorbaIdFactory {
- static Log log = LogFactory.getLog(IdFactory.class);
- private SessionHandle session=null;
- private ClientHandle client;
- private UserHandle user;
- private CRC32 unique=new CRC32(); // used to attempt a unique but predictable stream for IDs
- private String idstring;
- int sequence=1; // incrementing value for next new ID
- /**
- *
- */
- public IdFactory() {
- super();
- // TODO Auto-generated constructor stub
- }
-
- /**
- * @param session
- * @param client
- * @param user
- */
- protected IdFactory(SessionHandle session, ClientHandle client, UserHandle user) {
- super();
- this.session = session;
- this.client = client;
- this.user = user;
- unique.reset();
- unique.update(new Object[] { session, client, user}.toString().getBytes());
- // TODO: Ensure format of URNs and use standard composition methods.
- idstring = client.getClientName()+":"+unique.getValue()+".";
- extantids=new Hashtable();
- this.extanthashv=new Hashtable();
- }
- /**
- * values for keys in this hash can be used to reference the org.vamsas.client.Vobject instance for the VorbaId string.
- * @return the hash of all VorbaIds
- */
- protected Hashtable getVorbaIdHash() {
- return extantids;
- }
- /**
- * values for keys in this hash are Vobjhash objects created for each Vobj with a VorbaId
- * after this factory has been used to write a vamsas archive.
- * @return the hash of all VorbaIds and their hash values.
- */
- protected Hashtable getVobjhashVals() {
- return extanthashv;
- }
- /* (non-Javadoc)
- * @see org.vamsas.client.VorbaIdFactory#makeVorbaId()
- */
- public VorbaId makeVorbaId(Vobject vobject) {
- if (session==null)
- throw new Error("makeVorbaId called on improperly initialised IdFactory Vobject!");
- if (!vobject.isRegisterable())
- throw new Error("makeVorbaId called on unregisterable object.");
- if (vobject.isRegistered())
- throw new Error("makeVorbaId called on already registered object.");
- String newidstring;
- do {
- if (sequence>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."));
- }
-}
+++ /dev/null
-/**
- *
- */
-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();
- }
-
-}
+++ /dev/null
-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 <method>isLocked</method>)
- * if a lock could be obtained for <param>lockfile</param>
- * @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;
-}
+++ /dev/null
-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 && locktypes[i].equalsIgnoreCase(lockt); i++)
- ;
- if (i>=j) {
- String lt = "'"+locktypes[0]+"'";
- for (i=1; i<j; i++)
- lt += ",'"+locktypes[i]+"'";
- log.warn("System property vamsas.locktype takes one of "+lt);
- log.warn("Defaulting to Locktype of "+locktypes[locktype]);
- }
- } else
- log.debug("Defaulting to Locktype of "+locktypes[locktype]);
- }
- /**
- * lock target (blocks until lock is obtained)
- * @param target
- * @return lock
- */
- public static Lock getLock(java.io.File target) {
- return getLock(target, true);
- }
- public static Lock getLock(java.io.File target, boolean block) {
- if (locktype==0)
- return new FileLock(target, block);
- if (locktype==1)
- return new NativeLock(target, block);
- log.fatal("Implementation Error! No valid Locktype value");
- return null;
- }
- /**
- * try to lock target
- * @param target
- * @return null if lock was not possible
- */
- public static Lock tryLock(File target) {
- return getLock(target, false);
- }
-}
+++ /dev/null
-/**
- *
- */
-package org.vamsas.client.simpleclient;
-
-/**
- * @author jimp
- *
- */
-public class LockTimeoutException extends Exception {
- static final long serialVersionUID=1;
- static final String defaultMessage = "Timeout whilst waiting for lock on VamsasDocument";
- public LockTimeoutException() {
- super(defaultMessage);
- }
- public LockTimeoutException(String arg0, Throwable arg1) {
- super(arg0+" (timeout whilst waiting for lock)", arg1);
- // TODO Auto-generated constructor stub
- }
- public LockTimeoutException(String arg0) {
- super(arg0+" (timeout whilst waiting for lock)");
- // TODO Auto-generated constructor stub
- }
- public LockTimeoutException(Throwable arg0) {
- super(defaultMessage, arg0);
- // TODO Auto-generated constructor stub
- }
-
-}
+++ /dev/null
-/**\r
- * \r
- */\r
-package org.vamsas.client.simpleclient;\r
-\r
-import java.io.File;\r
-import java.io.FileDescriptor;\r
-import java.io.FileNotFoundException;\r
-import java.io.FileOutputStream;\r
-import java.io.IOException;\r
-import java.io.OutputStream;\r
-import java.nio.channels.FileChannel;\r
-\r
-import org.apache.commons.logging.LogFactory;\r
-\r
-/**\r
- * @author Jim\r
- *\r
- */\r
-public class LockedFileOutputStream extends FileOutputStream {\r
- private static org.apache.commons.logging.Log log = LogFactory.getLog(LockedFileOutputStream.class);\r
- //FileOutputStream ostream=null;\r
- boolean closed=true;\r
- private void init() {\r
- FileChannel ch = super.getChannel();\r
- if (ch!=null) {\r
- try { closed = !ch.isOpen();\r
- } catch (Exception e) {\r
- closed=true;\r
- log.debug("Invalid LockedOutputStream marked closed.",e);\r
- }\r
- }\r
- }\r
- /**\r
- * @param file\r
- * @throws FileNotFoundException\r
- */\r
- public LockedFileOutputStream(File file) throws FileNotFoundException {\r
- super(file); // super(file);\r
- init();\r
- }\r
-\r
- /**\r
- * @param file\r
- * @param append\r
- * @throws FileNotFoundException\r
- */\r
- public LockedFileOutputStream(File file, boolean append)\r
- throws FileNotFoundException {\r
- super(file, append);\r
- init();\r
- }\r
-\r
- /**\r
- * @param fdObj\r
- */\r
- public LockedFileOutputStream(FileDescriptor fdObj) {\r
- super(fdObj);\r
- init();\r
- if (fdObj.valid())\r
- closed=false;\r
- }\r
-\r
- /**\r
- * @param name\r
- * @throws FileNotFoundException\r
- */\r
- public LockedFileOutputStream(String name) throws FileNotFoundException {\r
- super(name);\r
- init();\r
- }\r
-\r
- /**\r
- * @param name\r
- * @param append\r
- * @throws FileNotFoundException\r
- */\r
- public LockedFileOutputStream(String name, boolean append)\r
- throws FileNotFoundException {\r
- super(name, append);\r
- init();\r
- }\r
- /**\r
- * closes - actually just flushes the stream instead.\r
- */\r
- public void close() throws IOException {\r
- if (!closed) {\r
- super.flush();\r
- super.getChannel().force(true);\r
- log.debug("Marking Lockedoutputstream closed.");\r
- } else\r
- throw new IOException("Close on already closed FileOutputStream.");\r
- closed=true;\r
- }\r
-\r
-\r
- /**\r
- * @throws IOException\r
- * @see java.io.OutputStream#flush()\r
- */\r
- public void flush() throws IOException {\r
- if (!closed)\r
- super.flush();\r
- else\r
- throw new IOException("flush on closed FileOutputStream");\r
- }\r
-\r
- /**\r
- * @return\r
- * @see java.io.FileOutputStream#getChannel()\r
- */\r
- public FileChannel getChannel() {\r
- if (!closed)\r
- return super.getChannel();\r
- else\r
- return null;\r
- }\r
-\r
-\r
-\r
- /**\r
- * @param b\r
- * @param off\r
- * @param len\r
- * @throws IOException\r
- * @see java.io.FileOutputStream#write(byte[], int, int)\r
- */\r
- public void write(byte[] b, int off, int len) throws IOException {\r
- if (!closed)\r
- super.write(b, off, len);\r
- else\r
- throw new IOException("write on Closed FileOutputStream");\r
- }\r
-\r
- /**\r
- * @param b\r
- * @throws IOException\r
- * @see java.io.FileOutputStream#write(byte[])\r
- */\r
- public void write(byte[] b) throws IOException {\r
- if (!closed)\r
- super.write(b);\r
- else\r
- throw new IOException("write on Closed FileOutputStream");\r
- }\r
-\r
- /**\r
- * @param b\r
- * @throws IOException\r
- * @see java.io.FileOutputStream#write(int)\r
- */\r
- public void write(int b) throws IOException {\r
- if (!closed)\r
- super.write(b);\r
- else\r
- throw new IOException("write on Closed FileOutputStream");\r
- }\r
- \r
-}\r
+++ /dev/null
-package org.vamsas.client.simpleclient;
-
-import java.io.BufferedInputStream;
-import java.io.BufferedOutputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.OutputStream;
-import java.io.RandomAccessFile;
-import java.nio.channels.FileChannel;
-import java.nio.channels.FileLock;
-import java.nio.channels.ReadableByteChannel;
-
-/**
- * @author JimP
- *
- */
-public class NativeLock extends Lock {
-
- protected FileLock lock = null;
-
- /**
- * @param lockfile
- * @param block true means thread will block until a lock is obtained.
- */
- public NativeLock(File lockfile, boolean block) {
- super(lockfile);
- // try and get a lock.
- lock = null;
-
- try {
- if (!lockfile.exists())
- if (!lockfile.createNewFile()) {
- log.warn("Failed to create locked file "+lockfile);
- return;
- }
-
- rafile=new RandomAccessFile(lockfile,"rw");
- if (block)
- lock = rafile.getChannel().lock();
- else
- lock = rafile.getChannel().tryLock();
- if (lock==null || !lock.isValid()) {
- // failed to get lock. Close the file channel
- log.debug("failed to get lock for "+lockfile);
- rafile.getChannel().close();
- lock=null;
- }
- } catch (FileNotFoundException e) {
- //
- log.debug("Lock failed - normal behaviour for windows locking.");
- //log.error("Error! Couldn't create a lockfile at "
- // + lockfile.getAbsolutePath(), e);
- } catch (IOException e) {
- log.error("Error! Problems with IO when creating a lock on "
- + lockfile.getAbsolutePath(),e);
- }
- }
-
- public boolean isLocked() {
- if (lock != null && lock.isValid()) {
- return true;
- }
- return false;
- }
-
- public void release() {
- release(true);
- }
-
- public void release(boolean closeChannel) {
- try {
- // channel.close should be called before release() for rigourous locking.
- if (rafile!=null && rafile.getFD().valid() && rafile.getChannel()!=null && lock.isValid()) {
- if (closeChannel && rafile.getChannel().isOpen()) {
- rafile.close();
- rafile=null;
- }
- if (lock!=null && lock.isValid())
- lock.release();
-
- }
- } catch (IOException e) {
- log.warn("Whilst releasing lock",e);
- }
- lock=null;
- }
-
- /**
- * 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 FileInputStream getFileInputStream(boolean atStart) throws IOException {
- if (!isLocked())
- return null;
- if (atStart)
- rafile.seek(0);
- return new FileInputStream(rafile.getFD());
- }
-
- /**
- * 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 FileOutputStream getFileOutputStream(boolean clear) throws IOException {
- if (!isLocked())
- return null;
- if (clear) {
- rafile.seek(0);
- rafile.setLength(0);
- } else
- rafile.seek(rafile.length());
- return new LockedFileOutputStream(rafile.getFD());
- }
-
- /**
- * return buffered output stream to locked file.
- * @param clear - true means file is truncated to 0 length before writing
- * @return
- */
- public BufferedOutputStream getBufferedOutputStream(boolean clear) throws IOException {
- OutputStream fos = getFileOutputStream(clear);
- if (fos!=null)
- return new BufferedOutputStream(fos);
- return null;
- }
- /**
- * @see org.vamsas.client.simpleclient.Lock#finalize()
- */
- protected void finalize() throws Throwable {
- release(true); // we explicitly lose the lock here.
- // log.debug("lock closing through garbage collection ?");
- super.finalize();
- }
-
- /* (non-Javadoc)
- * @see org.vamsas.client.simpleclient.Lock#getLength()
- */
- public long length() {
- if (isLocked()){
- try {
- return rafile.length();
- } catch (Exception e) {
- log.debug("getLength exception:",e);
- }
- }
- return -1;
- }
-
- public RandomAccessFile getRaFile() throws IOException {
- if (isLocked())
- return rafile;
- else
- log.debug("Failed to getRaFile on "+target);
- return null;
- }
-
- public FileChannel getRaChannel() throws IOException {
- if (isLocked())
- return rafile.getChannel();
- else
- log.debug("Failed to getRaChannel on "+target);
- return null;
- }
-
-}
+++ /dev/null
-package org.vamsas.client.simpleclient;
-
-import java.io.BufferedInputStream;
-import java.io.BufferedOutputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.RandomAccessFile;
-import java.nio.channels.ReadableByteChannel;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-/**
- * Basic methods for classes handling locked IO on files
- * monitored by all (simpleclient) clients in a vamsas session.
- * @author jimp
- *TODO: support non nio file locking capable systems
- */
-public class SessionFile {
- private static Log log = LogFactory.getLog(SessionFile.class);
- protected File sessionFile;
- protected Lock fileLock = null;
-
- protected SessionFile(File file) {
- super();
- sessionFile = file;
- }
-
- protected boolean lockFile(Lock extantlock) {
- if (fileLock!=null && !fileLock.isLocked()) {
- fileLock.release();// tidy up invalid lock
- fileLock=null;
- }
- if (extantlock!=null && extantlock.isLocked())
- fileLock=extantlock; // THIS IS BROKEN - lockFile then nulls the lock.
- return lockFile();
- }
- private boolean ensureSessionFile() {
- if (sessionFile != null) {
- if (!sessionFile.exists()) {
- // create new file
- try {
- if (!sessionFile.createNewFile()) {
- log.error("Failed to create file prior to locking: "+sessionFile);
- return false;
- }
- } catch (IOException e) {
- log.error("Exception when trying to create file "+sessionFile, e);
- return false;
- }
- }
- return true;
- }
- log.error("ensureSessionFile called for non-initialised SessionFile!");
- return false;
- }
- /**
- * Get a lock for the SessionFile
- *
- * @return true if lock was made
- */
- protected boolean lockFile() {
- if (fileLock != null) {
- if (fileLock.isLocked()) {
- if (!ensureSessionFile())
- return false;
- return true;
- } else {
- // lock failed for some reason.
- fileLock.release();
- log.info("Unexpected session file lock failure. Trying to get it again.");
- fileLock=null;
- }
- }
- if (!ensureSessionFile())
- return false;
- // TODO: see if we need to loop-wait for locks or they just block until
- // lock is made...
- long tries=5000;
- do {
- tries--;
- if (fileLock==null || !fileLock.isLocked()) {
- //try { Thread.sleep(1); } catch (Exception e) {};
- fileLock = LockFactory.getLock(sessionFile,true); // TODO: wait around if we can't get the lock.
- }
- } while (tries>0 && !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);
- }
-
-}
+++ /dev/null
-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;
- };
-}
+++ /dev/null
-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
-}
+++ /dev/null
-/* 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 <a href="mailto:pierre@ebi.ac.uk">Pierre MARGUERITE</a>
-*
-* 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 <a href="mailto:pierre@ebi.ac.uk">Pierre MARGUERITE</a>
- *
- *
- */
-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);
-
- }
- }
-
- }
-}
+++ /dev/null
-/*
- * 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
-
- }
-}
+++ /dev/null
-/**
- *
- */
-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();
- }
-
-}
+++ /dev/null
-/*
-* 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;
- }
-
-
-
-}
+++ /dev/null
-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 (i<j);
- }
- return entries;
- }
-}
+++ /dev/null
-package org.vamsas.client.simpleclient;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.vamsas.client.VorbaIdFactory;
-
-/**
- * @see SimpleDocBinding
- * Additional constructors for 'headless' Vamsas Document access
- * @author jimp
- */
-public class SimpleDocument extends SimpleDocBinding {
- private static Log log = LogFactory.getLog(SimpleDocument.class);
-
- private VorbaIdFactory makeDefaultFactory(String name) {
- return IdFactory.getDummyFactory(name);
- }
-
- public SimpleDocument(String name) {
- vorba = makeDefaultFactory(name);
- }
- public SimpleDocument(VorbaIdFactory Vorba) {
- if (Vorba!=null)
- vorba = Vorba;
- else
- log.error("Invalid SimpleDocument construction - no VorbaIdFactory defined!");
- }
-}
+++ /dev/null
-package org.vamsas.client.simpleclient;
-
-import java.io.BufferedInputStream;
-import java.io.BufferedOutputStream;
-import java.io.DataOutputStream;
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.OutputStream;
-import java.io.OutputStreamWriter;
-import java.io.PrintWriter;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.Vector;
-import java.util.jar.JarEntry;
-import java.util.jar.JarOutputStream;
-import java.util.jar.Manifest;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.vamsas.client.ClientHandle;
-import org.vamsas.client.IVorbaIdFactory;
-import org.vamsas.client.SessionHandle;
-import org.vamsas.client.UserHandle;
-import org.vamsas.client.VorbaIdFactory;
-import org.vamsas.client.VorbaXmlBinder;
-import org.vamsas.client.Vobject;
-import org.vamsas.objects.core.ApplicationData;
-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;
-
-/**
- * Class for high-level io and Jar manipulation involved in creating
- * or updating a vamsas archive (with backups).
- * Writes to a temporary file and then swaps new file for backup.
- * uses the sessionFile locking mechanism for safe I/O
- * @author jimp
- *
- */
-public class VamsasArchive {
- private static Log log = LogFactory.getLog(VamsasArchive.class);
- /**
- * Access original document if it exists, and get VAMSAS root objects.
- * @return vector of vamsas roots from original document
- * @throws IOException
- */
- public static Vobject[] getOriginalRoots(VamsasArchive ths) throws IOException,
- org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- VamsasArchiveReader oReader = ths.getOriginalArchiveReader();
- if (oReader!=null) {
-
- if (oReader.isValid()) {
- InputStreamReader vdoc = new InputStreamReader(oReader.getVamsasDocumentStream());
- VamsasDocument doc = VamsasDocument.unmarshal(vdoc);
- if (doc!=null)
- return doc.getVAMSAS();
- // TODO ensure embedded appDatas are garbage collected to save memory
- } else {
- InputStream vxmlis = oReader.getVamsasXmlStream();
- if (vxmlis!=null) { // Might be an old vamsas file.
- BufferedInputStream ixml = new BufferedInputStream(oReader.getVamsasXmlStream());
- InputStreamReader vxml = new InputStreamReader(ixml);
- VAMSAS root[] = new VAMSAS[1];
- root[0] = VAMSAS.unmarshal(vxml);
- if (root[0]!=null)
- return root;
- }
- }
- }
- return null;
- }
- /**
- * Access the original vamsas document for a VamsasArchive class, and return it.
- * Users of the VamsasArchive class should use the getVamsasDocument method to retrieve
- * the current document - only use this one if you want the 'backup' version.
- * TODO: catch OutOfMemoryError - they are likely to occur here.
- * NOTE: vamsas.xml datastreams are constructed as 'ALPHA_VERSION' vamsas documents.
- * @param ths
- * @return null if no document exists.
- * @throws IOException
- * @throws org.exolab.castor.xml.MarshalException
- * @throws org.exolab.castor.xml.ValidationException
- */
- public static VamsasDocument getOriginalVamsasDocument(VamsasArchive ths) throws IOException,
- org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return VamsasArchive.getOriginalVamsasDocument(ths, null);
- }
- /**
- * Uses VorbaXmlBinder to retrieve the VamsasDocument from the original archive referred to by ths
- * @param ths
- * @param vorba
- * @return
- * @throws IOException
- * @throws org.exolab.castor.xml.MarshalException
- * @throws org.exolab.castor.xml.ValidationException
- */
- public static VamsasDocument getOriginalVamsasDocument(VamsasArchive ths, VorbaIdFactory vorba) throws IOException,
- org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- VamsasArchiveReader oReader = ths.getOriginalArchiveReader();
- if (oReader!=null) {
- ths.setVorba(vorba);
- return ths.vorba.getVamsasDocument(oReader);
- }
- // otherwise - there was no valid original document to read.
- return null;
- }
- /**
- * destination of new archive data (tempfile if virginarchive=true, original archive location otherwise)
- */
- java.io.File archive=null;
- /**
- * locked IO handler for new archive file
- */
- SessionFile rchive=null;
- /**
- * original archive file to be updated (or null if virgin) where new data will finally reside
- */
- java.io.File original=null;
- /**
- * original archive IO handler
- */
- SessionFile odoclock = null;
- Lock destinationLock = null;
- /**
- * Original archive reader class
- */
- VamsasArchiveReader odoc = null;
- /**
- * true if a real vamsas document is being written.
- */
- boolean vamsasdocument=true;
- /**
- * Output stream for archived data
- */
- JarOutputStream newarchive=null;
- /**
- * JarEntries written to archive
- */
- Hashtable entries = null;
-
- /**
- * true if we aren't just updating an archive
- */
- private boolean virginArchive=false;
-
- /**
- * name of backup of existing archive that has been updated/overwritten.
- * only one backup will be made - and this is it.
- */
- File originalBackup = null;
-
- boolean donotdeletebackup=false;
- private final int _TRANSFER_BUFFER=4096*4;
- protected SimpleDocument vorba = null;
- /**
- * LATER: ? CUT'n'Paste error ?
- * Access and return current vamsas Document, if it exists, or create a new one
- * (without affecting VamsasArchive object state - so is NOT THREAD SAFE)
- * _TODO: possibly modify internal state to lock low-level files
- * (like the IClientDocument interface instance constructer would do)
- * @see org.vamsas.simpleclient.VamsasArchive.getOriginalVamsasDocument for additional caveats
- *
- * @return
- * @throws IOException
- * @throws org.exolab.castor.xml.MarshalException
- * @throws org.exolab.castor.xml.ValidationException
- * ????? where does this live JBPNote ?
- */
- private VamsasDocument _doc=null;
-
- /**
- * Create a new vamsas archive
- * File locks are made immediately to avoid contention
- *
- * @param archive - file spec for new vamsas archive
- * @param vamsasdocument true if archive is to be a fully fledged vamsas document archive
- * @throws IOException if call to accessOriginal failed for updates, or openArchive failed.
- */
- public VamsasArchive(File archive, boolean vamsasdocument) throws IOException {
- this(archive, false, vamsasdocument, null);
- }
- public VamsasArchive(File archive, boolean vamsasdocument, boolean overwrite) throws IOException {
- this(archive, overwrite, vamsasdocument, null);
- }
- /**
- * Constructor for accessing Files under file-lock management (ie a session file)
- * @param archive
- * @param vamsasdocument
- * @param overwrite
- * @throws IOException
- */
- public VamsasArchive(VamsasFile archive, boolean vamsasdocument, boolean overwrite) throws IOException {
- this(archive.sessionFile, overwrite, vamsasdocument, archive);
- // log.debug("using non-functional lock-IO stream jar access constructor");
- }
- /**
- * read and write to archive - will not overwrite original contents, and will always write an up to date vamsas document structure.
- * @param archive
- * @throws IOException
- */
- public VamsasArchive(VamsasFile archive) throws IOException {
- this(archive, true, false);
- }
- /**
- *
- * @param archive file to write
- * @param overwrite true if original contents should be deleted
- * @param vamsasdocument true if a proper VamsasDocument archive is to be written.
- * @param extantLock SessionFile object holding a lock for the <object>archive</object>
- * @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 {
-
-
- }
- }
-}
+++ /dev/null
-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;
- }
- }
+++ /dev/null
-
-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();
- }
-
-}
+++ /dev/null
-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:
- * - <applicationname>.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;
- }
-}
-
-
+++ /dev/null
--- listing properties --\r
-org.vamsas.objects.core.LockFile=org.vamsas.objects.core.LockFileDescr...\r
-org.vamsas.objects.core.VamsasDocument=org.vamsas.objects.core.VamsasDocumen...\r
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * This is annotation over the coordinate frame\r
- * defined by all the columns in the alignment.\r
- * \r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class AlignmentAnnotation extends org.vamsas.objects.core.RangeAnnotation \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * TODO: decide if this flag is\r
- * redundant - when true it would suggest that\r
- * the annotationElement values together form a\r
- * graph \r
- */\r
- private boolean _graph;\r
-\r
- /**\r
- * keeps track of state for field: _graph\r
- */\r
- private boolean _has_graph;\r
-\r
- /**\r
- * Field _provenance\r
- */\r
- private org.vamsas.objects.core.Provenance _provenance;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public AlignmentAnnotation() \r
- {\r
- super();\r
- } //-- org.vamsas.objects.core.AlignmentAnnotation()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method deleteGraph\r
- * \r
- */\r
- public void deleteGraph()\r
- {\r
- this._has_graph= false;\r
- } //-- void deleteGraph() \r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof AlignmentAnnotation) {\r
- \r
- AlignmentAnnotation temp = (AlignmentAnnotation)obj;\r
- if (this._graph != temp._graph)\r
- return false;\r
- if (this._has_graph != temp._has_graph)\r
- return false;\r
- if (this._provenance != null) {\r
- if (temp._provenance == null) return false;\r
- else if (!(this._provenance.equals(temp._provenance))) \r
- return false;\r
- }\r
- else if (temp._provenance != null)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Returns the value of field 'graph'. The field 'graph' has\r
- * the following description: TODO: decide if this flag is\r
- * redundant - when true it would suggest that\r
- * the annotationElement values together form a\r
- * graph \r
- * \r
- * @return boolean\r
- * @return the value of field 'graph'.\r
- */\r
- public boolean getGraph()\r
- {\r
- return this._graph;\r
- } //-- boolean getGraph() \r
-\r
- /**\r
- * Returns the value of field 'provenance'.\r
- * \r
- * @return Provenance\r
- * @return the value of field 'provenance'.\r
- */\r
- public org.vamsas.objects.core.Provenance getProvenance()\r
- {\r
- return this._provenance;\r
- } //-- org.vamsas.objects.core.Provenance getProvenance() \r
-\r
- /**\r
- * Method hasGraph\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasGraph()\r
- {\r
- return this._has_graph;\r
- } //-- boolean hasGraph() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'graph'. The field 'graph' has the\r
- * following description: TODO: decide if this flag is\r
- * redundant - when true it would suggest that\r
- * the annotationElement values together form a\r
- * graph \r
- * \r
- * @param graph the value of field 'graph'.\r
- */\r
- public void setGraph(boolean graph)\r
- {\r
- this._graph = graph;\r
- this._has_graph = true;\r
- } //-- void setGraph(boolean) \r
-\r
- /**\r
- * Sets the value of field 'provenance'.\r
- * \r
- * @param provenance the value of field 'provenance'.\r
- */\r
- public void setProvenance(org.vamsas.objects.core.Provenance provenance)\r
- {\r
- this._provenance = provenance;\r
- } //-- void setProvenance(org.vamsas.objects.core.Provenance) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return RangeType\r
- */\r
- public static org.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.AlignmentAnnotation) Unmarshaller.unmarshal(org.vamsas.objects.core.AlignmentAnnotation.class, reader);\r
- } //-- org.vamsas.objects.core.RangeType unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class AlignmentAnnotationDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class AlignmentAnnotationDescriptor extends org.vamsas.objects.core.RangeAnnotationDescriptor {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public AlignmentAnnotationDescriptor() \r
- {\r
- super();\r
- setExtendsWithoutFlatten(new org.vamsas.objects.core.RangeAnnotationDescriptor());\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "AlignmentAnnotation";\r
- \r
- //-- set grouping compositor\r
- setCompositorAsSequence();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- initialize attribute descriptors\r
- \r
- //-- _graph\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_graph", "graph", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- AlignmentAnnotation target = (AlignmentAnnotation) object;\r
- if(!target.hasGraph())\r
- return null;\r
- return (target.getGraph() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- AlignmentAnnotation target = (AlignmentAnnotation) object;\r
- // ignore null values for non optional primitives\r
- if (value == null) return;\r
- \r
- target.setGraph( ((java.lang.Boolean)value).booleanValue());\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _graph\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- BooleanValidator typeValidator = new BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize element descriptors\r
- \r
- //-- _provenance\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- AlignmentAnnotation target = (AlignmentAnnotation) object;\r
- return target.getProvenance();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- AlignmentAnnotation target = (AlignmentAnnotation) object;\r
- target.setProvenance( (org.vamsas.objects.core.Provenance) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return new org.vamsas.objects.core.Provenance();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("http://www.vamsas.org");\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _provenance\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- } //-- org.vamsas.objects.core.AlignmentAnnotationDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return super.getExtends();\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- if (identity == null)\r
- return super.getIdentity();\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.AlignmentAnnotation.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class AlignmentSequenceAnnotation.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class AlignmentSequenceAnnotation extends org.vamsas.objects.core.RangeAnnotation \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * TODO:\r
- * decide if this flag is\r
- * redundant - when true it\r
- * would suggest that the\r
- * annotationElement values\r
- * together form a graph\r
- * \r
- */\r
- private boolean _graph;\r
-\r
- /**\r
- * keeps track of state for field: _graph\r
- */\r
- private boolean _has_graph;\r
-\r
- /**\r
- * Field _provenance\r
- */\r
- private org.vamsas.objects.core.Provenance _provenance;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public AlignmentSequenceAnnotation() \r
- {\r
- super();\r
- } //-- org.vamsas.objects.core.AlignmentSequenceAnnotation()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method deleteGraph\r
- * \r
- */\r
- public void deleteGraph()\r
- {\r
- this._has_graph= false;\r
- } //-- void deleteGraph() \r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof AlignmentSequenceAnnotation) {\r
- \r
- AlignmentSequenceAnnotation temp = (AlignmentSequenceAnnotation)obj;\r
- if (this._graph != temp._graph)\r
- return false;\r
- if (this._has_graph != temp._has_graph)\r
- return false;\r
- if (this._provenance != null) {\r
- if (temp._provenance == null) return false;\r
- else if (!(this._provenance.equals(temp._provenance))) \r
- return false;\r
- }\r
- else if (temp._provenance != null)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Returns the value of field 'graph'. The field 'graph' has\r
- * the following description: TODO:\r
- * decide if this flag is\r
- * redundant - when true it\r
- * would suggest that the\r
- * annotationElement values\r
- * together form a graph\r
- * \r
- * \r
- * @return boolean\r
- * @return the value of field 'graph'.\r
- */\r
- public boolean getGraph()\r
- {\r
- return this._graph;\r
- } //-- boolean getGraph() \r
-\r
- /**\r
- * Returns the value of field 'provenance'.\r
- * \r
- * @return Provenance\r
- * @return the value of field 'provenance'.\r
- */\r
- public org.vamsas.objects.core.Provenance getProvenance()\r
- {\r
- return this._provenance;\r
- } //-- org.vamsas.objects.core.Provenance getProvenance() \r
-\r
- /**\r
- * Method hasGraph\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasGraph()\r
- {\r
- return this._has_graph;\r
- } //-- boolean hasGraph() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'graph'. The field 'graph' has the\r
- * following description: TODO:\r
- * decide if this flag is\r
- * redundant - when true it\r
- * would suggest that the\r
- * annotationElement values\r
- * together form a graph\r
- * \r
- * \r
- * @param graph the value of field 'graph'.\r
- */\r
- public void setGraph(boolean graph)\r
- {\r
- this._graph = graph;\r
- this._has_graph = true;\r
- } //-- void setGraph(boolean) \r
-\r
- /**\r
- * Sets the value of field 'provenance'.\r
- * \r
- * @param provenance the value of field 'provenance'.\r
- */\r
- public void setProvenance(org.vamsas.objects.core.Provenance provenance)\r
- {\r
- this._provenance = provenance;\r
- } //-- void setProvenance(org.vamsas.objects.core.Provenance) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return RangeType\r
- */\r
- public static org.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.AlignmentSequenceAnnotation) Unmarshaller.unmarshal(org.vamsas.objects.core.AlignmentSequenceAnnotation.class, reader);\r
- } //-- org.vamsas.objects.core.RangeType unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class AlignmentSequenceAnnotationDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class AlignmentSequenceAnnotationDescriptor extends org.vamsas.objects.core.RangeAnnotationDescriptor {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public AlignmentSequenceAnnotationDescriptor() \r
- {\r
- super();\r
- setExtendsWithoutFlatten(new org.vamsas.objects.core.RangeAnnotationDescriptor());\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "AlignmentSequenceAnnotation";\r
- \r
- //-- set grouping compositor\r
- setCompositorAsSequence();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- initialize attribute descriptors\r
- \r
- //-- _graph\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_graph", "graph", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- AlignmentSequenceAnnotation target = (AlignmentSequenceAnnotation) object;\r
- if(!target.hasGraph())\r
- return null;\r
- return (target.getGraph() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- AlignmentSequenceAnnotation target = (AlignmentSequenceAnnotation) object;\r
- // ignore null values for non optional primitives\r
- if (value == null) return;\r
- \r
- target.setGraph( ((java.lang.Boolean)value).booleanValue());\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _graph\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- BooleanValidator typeValidator = new BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize element descriptors\r
- \r
- //-- _provenance\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- AlignmentSequenceAnnotation target = (AlignmentSequenceAnnotation) object;\r
- return target.getProvenance();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- AlignmentSequenceAnnotation target = (AlignmentSequenceAnnotation) object;\r
- target.setProvenance( (org.vamsas.objects.core.Provenance) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return new org.vamsas.objects.core.Provenance();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("http://www.vamsas.org");\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _provenance\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- } //-- org.vamsas.objects.core.AlignmentSequenceAnnotationDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return super.getExtends();\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- if (identity == null)\r
- return super.getIdentity();\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.AlignmentSequenceAnnotation.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class AppData.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class AppData extends org.vamsas.client.Vobject \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Internal choice value storage\r
- */\r
- private java.lang.Object _choiceValue;\r
-\r
- /**\r
- * Field _data\r
- */\r
- private byte[] _data;\r
-\r
- /**\r
- * Field _dataReference\r
- */\r
- private java.lang.String _dataReference;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public AppData() \r
- {\r
- super();\r
- } //-- org.vamsas.objects.core.AppData()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof AppData) {\r
- \r
- AppData temp = (AppData)obj;\r
- if (this._choiceValue != null) {\r
- if (temp._choiceValue == null) return false;\r
- else if (!(this._choiceValue.equals(temp._choiceValue))) \r
- return false;\r
- }\r
- else if (temp._choiceValue != null)\r
- return false;\r
- if (this._data != null) {\r
- if (temp._data == null) return false;\r
- else if (!(this._data.equals(temp._data))) \r
- return false;\r
- }\r
- else if (temp._data != null)\r
- return false;\r
- if (this._dataReference != null) {\r
- if (temp._dataReference == null) return false;\r
- else if (!(this._dataReference.equals(temp._dataReference))) \r
- return false;\r
- }\r
- else if (temp._dataReference != null)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Returns the value of field 'choiceValue'. The field\r
- * 'choiceValue' has the following description: Internal choice\r
- * value storage\r
- * \r
- * @return Object\r
- * @return the value of field 'choiceValue'.\r
- */\r
- public java.lang.Object getChoiceValue()\r
- {\r
- return this._choiceValue;\r
- } //-- java.lang.Object getChoiceValue() \r
-\r
- /**\r
- * Returns the value of field 'data'.\r
- * \r
- * @return byte\r
- * @return the value of field 'data'.\r
- */\r
- public byte[] getData()\r
- {\r
- return this._data;\r
- } //-- byte[] getData() \r
-\r
- /**\r
- * Returns the value of field 'dataReference'.\r
- * \r
- * @return String\r
- * @return the value of field 'dataReference'.\r
- */\r
- public java.lang.String getDataReference()\r
- {\r
- return this._dataReference;\r
- } //-- java.lang.String getDataReference() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'data'.\r
- * \r
- * @param data the value of field 'data'.\r
- */\r
- public void setData(byte[] data)\r
- {\r
- this._data = data;\r
- this._choiceValue = data;\r
- } //-- void setData(byte) \r
-\r
- /**\r
- * Sets the value of field 'dataReference'.\r
- * \r
- * @param dataReference the value of field 'dataReference'.\r
- */\r
- public void setDataReference(java.lang.String dataReference)\r
- {\r
- this._dataReference = dataReference;\r
- this._choiceValue = dataReference;\r
- } //-- void setDataReference(java.lang.String) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return AppData\r
- */\r
- public static org.vamsas.objects.core.AppData unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.AppData) Unmarshaller.unmarshal(org.vamsas.objects.core.AppData.class, reader);\r
- } //-- org.vamsas.objects.core.AppData unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class AppDataDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class AppDataDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public AppDataDescriptor() \r
- {\r
- super();\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "appData";\r
- \r
- //-- set grouping compositor\r
- setCompositorAsChoice();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- initialize attribute descriptors\r
- \r
- //-- initialize element descriptors\r
- \r
- //-- _data\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(byte[].class, "_data", "data", org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- AppData target = (AppData) object;\r
- return target.getData();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- AppData target = (AppData) object;\r
- target.setData( (byte[]) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("http://www.vamsas.org");\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _data\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _dataReference\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dataReference", "dataReference", org.exolab.castor.xml.NodeType.Element);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- AppData target = (AppData) object;\r
- return target.getDataReference();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- AppData target = (AppData) object;\r
- target.setDataReference( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("http://www.vamsas.org");\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _dataReference\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- } //-- org.vamsas.objects.core.AppDataDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.AppData.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class Attachment.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Attachment extends org.vamsas.objects.core.AppData \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * true implies data will be decompresses with Zip\r
- * before presenting to application \r
- */\r
- private boolean _compressed = false;\r
-\r
- /**\r
- * keeps track of state for field: _compressed\r
- */\r
- private boolean _has_compressed;\r
-\r
- /**\r
- * Type of arbitrary data - TODO: decide format - use\r
- * (extended) MIME types ? \r
- */\r
- private java.lang.String _type;\r
-\r
- /**\r
- * Object the arbitrary data is associated with\r
- * \r
- */\r
- private java.lang.Object _objectref;\r
-\r
- /**\r
- * Primary Key for vamsas object referencing\r
- * \r
- */\r
- private java.lang.String _id;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Attachment() \r
- {\r
- super();\r
- } //-- org.vamsas.objects.core.Attachment()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method deleteCompressed\r
- * \r
- */\r
- public void deleteCompressed()\r
- {\r
- this._has_compressed= false;\r
- } //-- void deleteCompressed() \r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof Attachment) {\r
- \r
- Attachment temp = (Attachment)obj;\r
- if (this._compressed != temp._compressed)\r
- return false;\r
- if (this._has_compressed != temp._has_compressed)\r
- return false;\r
- if (this._type != null) {\r
- if (temp._type == null) return false;\r
- else if (!(this._type.equals(temp._type))) \r
- return false;\r
- }\r
- else if (temp._type != null)\r
- return false;\r
- if (this._objectref != null) {\r
- if (temp._objectref == null) return false;\r
- else if (!(this._objectref.equals(temp._objectref))) \r
- return false;\r
- }\r
- else if (temp._objectref != null)\r
- return false;\r
- if (this._id != null) {\r
- if (temp._id == null) return false;\r
- else if (!(this._id.equals(temp._id))) \r
- return false;\r
- }\r
- else if (temp._id != null)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Returns the value of field 'compressed'. The field\r
- * 'compressed' has the following description: true implies\r
- * data will be decompresses with Zip\r
- * before presenting to application \r
- * \r
- * @return boolean\r
- * @return the value of field 'compressed'.\r
- */\r
- public boolean getCompressed()\r
- {\r
- return this._compressed;\r
- } //-- boolean getCompressed() \r
-\r
- /**\r
- * Returns the value of field 'id'. The field 'id' has the\r
- * following description: Primary Key for vamsas object\r
- * referencing\r
- * \r
- * \r
- * @return String\r
- * @return the value of field 'id'.\r
- */\r
- public java.lang.String getId()\r
- {\r
- return this._id;\r
- } //-- java.lang.String getId() \r
-\r
- /**\r
- * Returns the value of field 'objectref'. The field\r
- * 'objectref' has the following description: Object the\r
- * arbitrary data is associated with\r
- * \r
- * \r
- * @return Object\r
- * @return the value of field 'objectref'.\r
- */\r
- public java.lang.Object getObjectref()\r
- {\r
- return this._objectref;\r
- } //-- java.lang.Object getObjectref() \r
-\r
- /**\r
- * Returns the value of field 'type'. The field 'type' has the\r
- * following description: Type of arbitrary data - TODO: decide\r
- * format - use\r
- * (extended) MIME types ? \r
- * \r
- * @return String\r
- * @return the value of field 'type'.\r
- */\r
- public java.lang.String getType()\r
- {\r
- return this._type;\r
- } //-- java.lang.String getType() \r
-\r
- /**\r
- * Method hasCompressed\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasCompressed()\r
- {\r
- return this._has_compressed;\r
- } //-- boolean hasCompressed() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'compressed'. The field 'compressed'\r
- * has the following description: true implies data will be\r
- * decompresses with Zip\r
- * before presenting to application \r
- * \r
- * @param compressed the value of field 'compressed'.\r
- */\r
- public void setCompressed(boolean compressed)\r
- {\r
- this._compressed = compressed;\r
- this._has_compressed = true;\r
- } //-- void setCompressed(boolean) \r
-\r
- /**\r
- * Sets the value of field 'id'. The field 'id' has the\r
- * following description: Primary Key for vamsas object\r
- * referencing\r
- * \r
- * \r
- * @param id the value of field 'id'.\r
- */\r
- public void setId(java.lang.String id)\r
- {\r
- this._id = id;\r
- } //-- void setId(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'objectref'. The field 'objectref'\r
- * has the following description: Object the arbitrary data is\r
- * associated with\r
- * \r
- * \r
- * @param objectref the value of field 'objectref'.\r
- */\r
- public void setObjectref(java.lang.Object objectref)\r
- {\r
- this._objectref = objectref;\r
- } //-- void setObjectref(java.lang.Object) \r
-\r
- /**\r
- * Sets the value of field 'type'. The field 'type' has the\r
- * following description: Type of arbitrary data - TODO: decide\r
- * format - use\r
- * (extended) MIME types ? \r
- * \r
- * @param type the value of field 'type'.\r
- */\r
- public void setType(java.lang.String type)\r
- {\r
- this._type = type;\r
- } //-- void setType(java.lang.String) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return AppData\r
- */\r
- public static org.vamsas.objects.core.AppData unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.Attachment) Unmarshaller.unmarshal(org.vamsas.objects.core.Attachment.class, reader);\r
- } //-- org.vamsas.objects.core.AppData unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class AttachmentDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class AttachmentDescriptor extends org.vamsas.objects.core.AppDataDescriptor {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public AttachmentDescriptor() \r
- {\r
- super();\r
- setExtendsWithoutFlatten(new org.vamsas.objects.core.AppDataDescriptor());\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "Attachment";\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- initialize attribute descriptors\r
- \r
- //-- _compressed\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_compressed", "compressed", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Attachment target = (Attachment) object;\r
- if(!target.hasCompressed())\r
- return null;\r
- return (target.getCompressed() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Attachment target = (Attachment) object;\r
- // if null, use delete method for optional primitives \r
- if (value == null) {\r
- target.deleteCompressed();\r
- return;\r
- }\r
- target.setCompressed( ((java.lang.Boolean)value).booleanValue());\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _compressed\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- BooleanValidator typeValidator = new BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _type\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Attachment target = (Attachment) object;\r
- return target.getType();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Attachment target = (Attachment) object;\r
- target.setType( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _type\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _objectref\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_objectref", "objectref", org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setReference(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Attachment target = (Attachment) object;\r
- return target.getObjectref();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Attachment target = (Attachment) object;\r
- target.setObjectref( (java.lang.Object) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return new java.lang.Object();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _objectref\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _id\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
- this.identity = desc;\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Attachment target = (Attachment) object;\r
- return target.getId();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Attachment target = (Attachment) object;\r
- target.setId( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return new java.lang.String();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _id\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize element descriptors\r
- \r
- } //-- org.vamsas.objects.core.AttachmentDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return super.getExtends();\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- if (identity == null)\r
- return super.getIdentity();\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.Attachment.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class Common.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Common extends org.vamsas.objects.core.AppData \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Common() \r
- {\r
- super();\r
- } //-- org.vamsas.objects.core.Common()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof Common) {\r
- \r
- Common temp = (Common)obj;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return AppData\r
- */\r
- public static org.vamsas.objects.core.AppData unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.Common) Unmarshaller.unmarshal(org.vamsas.objects.core.Common.class, reader);\r
- } //-- org.vamsas.objects.core.AppData unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class CommonDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class CommonDescriptor extends org.vamsas.objects.core.AppDataDescriptor {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public CommonDescriptor() \r
- {\r
- super();\r
- setExtendsWithoutFlatten(new org.vamsas.objects.core.AppDataDescriptor());\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "Common";\r
- } //-- org.vamsas.objects.core.CommonDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return super.getExtends();\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- if (identity == null)\r
- return super.getIdentity();\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.Common.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Discrete symbol - possibly graphically represented\r
- * \r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Glyph extends org.vamsas.client.Vobject \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * internal content storage\r
- */\r
- private java.lang.String _content = "";\r
-\r
- /**\r
- * specifies the symbol dictionary for this\r
- * glyph - eg utf8 (the default), aasecstr_3 or\r
- * kd_hydrophobicity - the content is not validated so\r
- * applications must ensure they gracefully deal with\r
- * invalid entries here \r
- */\r
- private java.lang.String _dict = "utf8";\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Glyph() \r
- {\r
- super();\r
- setContent("");\r
- setDict("utf8");\r
- } //-- org.vamsas.objects.core.Glyph()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof Glyph) {\r
- \r
- Glyph temp = (Glyph)obj;\r
- if (this._content != null) {\r
- if (temp._content == null) return false;\r
- else if (!(this._content.equals(temp._content))) \r
- return false;\r
- }\r
- else if (temp._content != null)\r
- return false;\r
- if (this._dict != null) {\r
- if (temp._dict == null) return false;\r
- else if (!(this._dict.equals(temp._dict))) \r
- return false;\r
- }\r
- else if (temp._dict != null)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Returns the value of field 'content'. The field 'content'\r
- * has the following description: internal content storage\r
- * \r
- * @return String\r
- * @return the value of field 'content'.\r
- */\r
- public java.lang.String getContent()\r
- {\r
- return this._content;\r
- } //-- java.lang.String getContent() \r
-\r
- /**\r
- * Returns the value of field 'dict'. The field 'dict' has the\r
- * following description: specifies the symbol dictionary for\r
- * this\r
- * glyph - eg utf8 (the default), aasecstr_3 or\r
- * kd_hydrophobicity - the content is not validated so\r
- * applications must ensure they gracefully deal with\r
- * invalid entries here \r
- * \r
- * @return String\r
- * @return the value of field 'dict'.\r
- */\r
- public java.lang.String getDict()\r
- {\r
- return this._dict;\r
- } //-- java.lang.String getDict() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'content'. The field 'content' has\r
- * the following description: internal content storage\r
- * \r
- * @param content the value of field 'content'.\r
- */\r
- public void setContent(java.lang.String content)\r
- {\r
- this._content = content;\r
- } //-- void setContent(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'dict'. The field 'dict' has the\r
- * following description: specifies the symbol dictionary for\r
- * this\r
- * glyph - eg utf8 (the default), aasecstr_3 or\r
- * kd_hydrophobicity - the content is not validated so\r
- * applications must ensure they gracefully deal with\r
- * invalid entries here \r
- * \r
- * @param dict the value of field 'dict'.\r
- */\r
- public void setDict(java.lang.String dict)\r
- {\r
- this._dict = dict;\r
- } //-- void setDict(java.lang.String) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return Glyph\r
- */\r
- public static org.vamsas.objects.core.Glyph unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.Glyph) Unmarshaller.unmarshal(org.vamsas.objects.core.Glyph.class, reader);\r
- } //-- org.vamsas.objects.core.Glyph unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class GlyphDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class GlyphDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public GlyphDescriptor() \r
- {\r
- super();\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "glyph";\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- _content\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Glyph target = (Glyph) object;\r
- return target.getContent();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Glyph target = (Glyph) object;\r
- target.setContent( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _content\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize attribute descriptors\r
- \r
- //-- _dict\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dict", "dict", org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Glyph target = (Glyph) object;\r
- return target.getDict();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Glyph target = (Glyph) object;\r
- target.setDict( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _dict\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize element descriptors\r
- \r
- } //-- org.vamsas.objects.core.GlyphDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.Glyph.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class Input.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Input extends org.vamsas.objects.core.RangeType \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _name\r
- */\r
- private java.lang.String _name;\r
-\r
- /**\r
- * Reference Frame for rangeType specfication\r
- * \r
- */\r
- private java.lang.Object _objRef;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Input() \r
- {\r
- super();\r
- } //-- org.vamsas.objects.core.Input()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof Input) {\r
- \r
- Input temp = (Input)obj;\r
- if (this._name != null) {\r
- if (temp._name == null) return false;\r
- else if (!(this._name.equals(temp._name))) \r
- return false;\r
- }\r
- else if (temp._name != null)\r
- return false;\r
- if (this._objRef != null) {\r
- if (temp._objRef == null) return false;\r
- else if (!(this._objRef.equals(temp._objRef))) \r
- return false;\r
- }\r
- else if (temp._objRef != null)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Returns the value of field 'name'.\r
- * \r
- * @return String\r
- * @return the value of field 'name'.\r
- */\r
- public java.lang.String getName()\r
- {\r
- return this._name;\r
- } //-- java.lang.String getName() \r
-\r
- /**\r
- * Returns the value of field 'objRef'. The field 'objRef' has\r
- * the following description: Reference Frame for rangeType\r
- * specfication\r
- * \r
- * \r
- * @return Object\r
- * @return the value of field 'objRef'.\r
- */\r
- public java.lang.Object getObjRef()\r
- {\r
- return this._objRef;\r
- } //-- java.lang.Object getObjRef() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'name'.\r
- * \r
- * @param name the value of field 'name'.\r
- */\r
- public void setName(java.lang.String name)\r
- {\r
- this._name = name;\r
- } //-- void setName(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'objRef'. The field 'objRef' has the\r
- * following description: Reference Frame for rangeType\r
- * specfication\r
- * \r
- * \r
- * @param objRef the value of field 'objRef'.\r
- */\r
- public void setObjRef(java.lang.Object objRef)\r
- {\r
- this._objRef = objRef;\r
- } //-- void setObjRef(java.lang.Object) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return RangeType\r
- */\r
- public static org.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.Input) Unmarshaller.unmarshal(org.vamsas.objects.core.Input.class, reader);\r
- } //-- org.vamsas.objects.core.RangeType unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class InputDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class InputDescriptor extends org.vamsas.objects.core.RangeTypeDescriptor {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public InputDescriptor() \r
- {\r
- super();\r
- setExtendsWithoutFlatten(new org.vamsas.objects.core.RangeTypeDescriptor());\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "input";\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- initialize attribute descriptors\r
- \r
- //-- _name\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Input target = (Input) object;\r
- return target.getName();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Input target = (Input) object;\r
- target.setName( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _name\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _objRef\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_objRef", "objRef", org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setReference(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Input target = (Input) object;\r
- return target.getObjRef();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Input target = (Input) object;\r
- target.setObjRef( (java.lang.Object) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return new java.lang.Object();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _objRef\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize element descriptors\r
- \r
- } //-- org.vamsas.objects.core.InputDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return super.getExtends();\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- if (identity == null)\r
- return super.getIdentity();\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.Input.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class Instance.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Instance extends org.vamsas.objects.core.AppData \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _urn\r
- */\r
- private java.lang.String _urn;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Instance() \r
- {\r
- super();\r
- } //-- org.vamsas.objects.core.Instance()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof Instance) {\r
- \r
- Instance temp = (Instance)obj;\r
- if (this._urn != null) {\r
- if (temp._urn == null) return false;\r
- else if (!(this._urn.equals(temp._urn))) \r
- return false;\r
- }\r
- else if (temp._urn != null)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Returns the value of field 'urn'.\r
- * \r
- * @return String\r
- * @return the value of field 'urn'.\r
- */\r
- public java.lang.String getUrn()\r
- {\r
- return this._urn;\r
- } //-- java.lang.String getUrn() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'urn'.\r
- * \r
- * @param urn the value of field 'urn'.\r
- */\r
- public void setUrn(java.lang.String urn)\r
- {\r
- this._urn = urn;\r
- } //-- void setUrn(java.lang.String) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return AppData\r
- */\r
- public static org.vamsas.objects.core.AppData unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.Instance) Unmarshaller.unmarshal(org.vamsas.objects.core.Instance.class, reader);\r
- } //-- org.vamsas.objects.core.AppData unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class InstanceDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class InstanceDescriptor extends org.vamsas.objects.core.AppDataDescriptor {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public InstanceDescriptor() \r
- {\r
- super();\r
- setExtendsWithoutFlatten(new org.vamsas.objects.core.AppDataDescriptor());\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "Instance";\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- initialize attribute descriptors\r
- \r
- //-- _urn\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_urn", "urn", org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Instance target = (Instance) object;\r
- return target.getUrn();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Instance target = (Instance) object;\r
- target.setUrn( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _urn\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize element descriptors\r
- \r
- } //-- org.vamsas.objects.core.InstanceDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return super.getExtends();\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- if (identity == null)\r
- return super.getIdentity();\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.Instance.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class Link.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Link extends org.vamsas.client.Vobject \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * internal content storage\r
- */\r
- private java.lang.String _content = "";\r
-\r
- /**\r
- * The URI\r
- */\r
- private java.lang.String _href;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Link() \r
- {\r
- super();\r
- setContent("");\r
- } //-- org.vamsas.objects.core.Link()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof Link) {\r
- \r
- Link temp = (Link)obj;\r
- if (this._content != null) {\r
- if (temp._content == null) return false;\r
- else if (!(this._content.equals(temp._content))) \r
- return false;\r
- }\r
- else if (temp._content != null)\r
- return false;\r
- if (this._href != null) {\r
- if (temp._href == null) return false;\r
- else if (!(this._href.equals(temp._href))) \r
- return false;\r
- }\r
- else if (temp._href != null)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Returns the value of field 'content'. The field 'content'\r
- * has the following description: internal content storage\r
- * \r
- * @return String\r
- * @return the value of field 'content'.\r
- */\r
- public java.lang.String getContent()\r
- {\r
- return this._content;\r
- } //-- java.lang.String getContent() \r
-\r
- /**\r
- * Returns the value of field 'href'. The field 'href' has the\r
- * following description: The URI\r
- * \r
- * @return String\r
- * @return the value of field 'href'.\r
- */\r
- public java.lang.String getHref()\r
- {\r
- return this._href;\r
- } //-- java.lang.String getHref() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'content'. The field 'content' has\r
- * the following description: internal content storage\r
- * \r
- * @param content the value of field 'content'.\r
- */\r
- public void setContent(java.lang.String content)\r
- {\r
- this._content = content;\r
- } //-- void setContent(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'href'. The field 'href' has the\r
- * following description: The URI\r
- * \r
- * @param href the value of field 'href'.\r
- */\r
- public void setHref(java.lang.String href)\r
- {\r
- this._href = href;\r
- } //-- void setHref(java.lang.String) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return Link\r
- */\r
- public static org.vamsas.objects.core.Link unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.Link) Unmarshaller.unmarshal(org.vamsas.objects.core.Link.class, reader);\r
- } //-- org.vamsas.objects.core.Link unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class LinkDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class LinkDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public LinkDescriptor() \r
- {\r
- super();\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "link";\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- _content\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Link target = (Link) object;\r
- return target.getContent();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Link target = (Link) object;\r
- target.setContent( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _content\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize attribute descriptors\r
- \r
- //-- _href\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_href", "href", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Link target = (Link) object;\r
- return target.getHref();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Link target = (Link) object;\r
- target.setHref( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return new java.lang.String();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _href\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize element descriptors\r
- \r
- } //-- org.vamsas.objects.core.LinkDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.Link.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * From: Offset to first\r
- * position in dataset sequence record that\r
- * this database entry maps to To: Offset\r
- * to last position in dataset sequence\r
- * record that this database entry maps to\r
- * Start: Offset to first last position in\r
- * database entry that first (or offset)\r
- * position in sequence maps to End: Offset\r
- * to last position in database entry that\r
- * last (offset) position in sequence maps\r
- * to \r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Map extends org.vamsas.objects.core.MapList \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Map() \r
- {\r
- super();\r
- } //-- org.vamsas.objects.core.Map()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof Map) {\r
- \r
- Map temp = (Map)obj;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return MapList\r
- */\r
- public static org.vamsas.objects.core.MapList unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.Map) Unmarshaller.unmarshal(org.vamsas.objects.core.Map.class, reader);\r
- } //-- org.vamsas.objects.core.MapList unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class MapDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class MapDescriptor extends org.vamsas.objects.core.MapListDescriptor {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public MapDescriptor() \r
- {\r
- super();\r
- setExtendsWithoutFlatten(new org.vamsas.objects.core.MapListDescriptor());\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "map";\r
- } //-- org.vamsas.objects.core.MapDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return super.getExtends();\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- if (identity == null)\r
- return super.getIdentity();\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.Map.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class MapList.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class MapList extends org.vamsas.client.Vobject \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Offset to first position in dataset sequence record that\r
- * start\r
- * position on 'onto' maps to \r
- */\r
- private int _from = 0;\r
-\r
- /**\r
- * keeps track of state for field: _from\r
- */\r
- private boolean _has_from;\r
-\r
- /**\r
- * Offset to last position in dataset sequence record that end\r
- * position on 'onto' maps to \r
- */\r
- private int _to = 0;\r
-\r
- /**\r
- * keeps track of state for field: _to\r
- */\r
- private boolean _has_to;\r
-\r
- /**\r
- * Offset to first position in database entry that first (or\r
- * offset)\r
- * position in sequence maps to \r
- */\r
- private int _start;\r
-\r
- /**\r
- * keeps track of state for field: _start\r
- */\r
- private boolean _has_start;\r
-\r
- /**\r
- * Offset to last position in database entry that last (offset)\r
- * position in sequence maps to \r
- */\r
- private int _end;\r
-\r
- /**\r
- * keeps track of state for field: _end\r
- */\r
- private boolean _has_end;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public MapList() \r
- {\r
- super();\r
- } //-- org.vamsas.objects.core.MapList()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method deleteEnd\r
- * \r
- */\r
- public void deleteEnd()\r
- {\r
- this._has_end= false;\r
- } //-- void deleteEnd() \r
-\r
- /**\r
- * Method deleteFrom\r
- * \r
- */\r
- public void deleteFrom()\r
- {\r
- this._has_from= false;\r
- } //-- void deleteFrom() \r
-\r
- /**\r
- * Method deleteStart\r
- * \r
- */\r
- public void deleteStart()\r
- {\r
- this._has_start= false;\r
- } //-- void deleteStart() \r
-\r
- /**\r
- * Method deleteTo\r
- * \r
- */\r
- public void deleteTo()\r
- {\r
- this._has_to= false;\r
- } //-- void deleteTo() \r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof MapList) {\r
- \r
- MapList temp = (MapList)obj;\r
- if (this._from != temp._from)\r
- return false;\r
- if (this._has_from != temp._has_from)\r
- return false;\r
- if (this._to != temp._to)\r
- return false;\r
- if (this._has_to != temp._has_to)\r
- return false;\r
- if (this._start != temp._start)\r
- return false;\r
- if (this._has_start != temp._has_start)\r
- return false;\r
- if (this._end != temp._end)\r
- return false;\r
- if (this._has_end != temp._has_end)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Returns the value of field 'end'. The field 'end' has the\r
- * following description: Offset to last position in database\r
- * entry that last (offset)\r
- * position in sequence maps to \r
- * \r
- * @return int\r
- * @return the value of field 'end'.\r
- */\r
- public int getEnd()\r
- {\r
- return this._end;\r
- } //-- int getEnd() \r
-\r
- /**\r
- * Returns the value of field 'from'. The field 'from' has the\r
- * following description: Offset to first position in dataset\r
- * sequence record that start\r
- * position on 'onto' maps to \r
- * \r
- * @return int\r
- * @return the value of field 'from'.\r
- */\r
- public int getFrom()\r
- {\r
- return this._from;\r
- } //-- int getFrom() \r
-\r
- /**\r
- * Returns the value of field 'start'. The field 'start' has\r
- * the following description: Offset to first position in\r
- * database entry that first (or offset)\r
- * position in sequence maps to \r
- * \r
- * @return int\r
- * @return the value of field 'start'.\r
- */\r
- public int getStart()\r
- {\r
- return this._start;\r
- } //-- int getStart() \r
-\r
- /**\r
- * Returns the value of field 'to'. The field 'to' has the\r
- * following description: Offset to last position in dataset\r
- * sequence record that end\r
- * position on 'onto' maps to \r
- * \r
- * @return int\r
- * @return the value of field 'to'.\r
- */\r
- public int getTo()\r
- {\r
- return this._to;\r
- } //-- int getTo() \r
-\r
- /**\r
- * Method hasEnd\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasEnd()\r
- {\r
- return this._has_end;\r
- } //-- boolean hasEnd() \r
-\r
- /**\r
- * Method hasFrom\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasFrom()\r
- {\r
- return this._has_from;\r
- } //-- boolean hasFrom() \r
-\r
- /**\r
- * Method hasStart\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasStart()\r
- {\r
- return this._has_start;\r
- } //-- boolean hasStart() \r
-\r
- /**\r
- * Method hasTo\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasTo()\r
- {\r
- return this._has_to;\r
- } //-- boolean hasTo() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'end'. The field 'end' has the\r
- * following description: Offset to last position in database\r
- * entry that last (offset)\r
- * position in sequence maps to \r
- * \r
- * @param end the value of field 'end'.\r
- */\r
- public void setEnd(int end)\r
- {\r
- this._end = end;\r
- this._has_end = true;\r
- } //-- void setEnd(int) \r
-\r
- /**\r
- * Sets the value of field 'from'. The field 'from' has the\r
- * following description: Offset to first position in dataset\r
- * sequence record that start\r
- * position on 'onto' maps to \r
- * \r
- * @param from the value of field 'from'.\r
- */\r
- public void setFrom(int from)\r
- {\r
- this._from = from;\r
- this._has_from = true;\r
- } //-- void setFrom(int) \r
-\r
- /**\r
- * Sets the value of field 'start'. The field 'start' has the\r
- * following description: Offset to first position in database\r
- * entry that first (or offset)\r
- * position in sequence maps to \r
- * \r
- * @param start the value of field 'start'.\r
- */\r
- public void setStart(int start)\r
- {\r
- this._start = start;\r
- this._has_start = true;\r
- } //-- void setStart(int) \r
-\r
- /**\r
- * Sets the value of field 'to'. The field 'to' has the\r
- * following description: Offset to last position in dataset\r
- * sequence record that end\r
- * position on 'onto' maps to \r
- * \r
- * @param to the value of field 'to'.\r
- */\r
- public void setTo(int to)\r
- {\r
- this._to = to;\r
- this._has_to = true;\r
- } //-- void setTo(int) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return MapList\r
- */\r
- public static org.vamsas.objects.core.MapList unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.MapList) Unmarshaller.unmarshal(org.vamsas.objects.core.MapList.class, reader);\r
- } //-- org.vamsas.objects.core.MapList unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class MapListDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class MapListDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public MapListDescriptor() \r
- {\r
- super();\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "mapList";\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- initialize attribute descriptors\r
- \r
- //-- _from\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_from", "from", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- MapList target = (MapList) object;\r
- if(!target.hasFrom())\r
- return null;\r
- return new java.lang.Integer(target.getFrom());\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- MapList target = (MapList) object;\r
- // if null, use delete method for optional primitives \r
- if (value == null) {\r
- target.deleteFrom();\r
- return;\r
- }\r
- target.setFrom( ((java.lang.Integer)value).intValue());\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _from\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- IntegerValidator typeValidator = new IntegerValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _to\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_to", "to", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- MapList target = (MapList) object;\r
- if(!target.hasTo())\r
- return null;\r
- return new java.lang.Integer(target.getTo());\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- MapList target = (MapList) object;\r
- // if null, use delete method for optional primitives \r
- if (value == null) {\r
- target.deleteTo();\r
- return;\r
- }\r
- target.setTo( ((java.lang.Integer)value).intValue());\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _to\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- IntegerValidator typeValidator = new IntegerValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _start\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- MapList target = (MapList) object;\r
- if(!target.hasStart())\r
- return null;\r
- return new java.lang.Integer(target.getStart());\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- MapList target = (MapList) object;\r
- // ignore null values for non optional primitives\r
- if (value == null) return;\r
- \r
- target.setStart( ((java.lang.Integer)value).intValue());\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _start\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- IntegerValidator typeValidator = new IntegerValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _end\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- MapList target = (MapList) object;\r
- if(!target.hasEnd())\r
- return null;\r
- return new java.lang.Integer(target.getEnd());\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- MapList target = (MapList) object;\r
- // ignore null values for non optional primitives\r
- if (value == null) return;\r
- \r
- target.setEnd( ((java.lang.Integer)value).intValue());\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _end\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- IntegerValidator typeValidator = new IntegerValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize element descriptors\r
- \r
- } //-- org.vamsas.objects.core.MapListDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.MapList.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class Mapping.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Mapping extends org.vamsas.objects.core.MapList \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * object to which the mapping is being mapped\r
- * \r
- */\r
- private java.lang.Object _onto;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Mapping() \r
- {\r
- super();\r
- } //-- org.vamsas.objects.core.Mapping()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof Mapping) {\r
- \r
- Mapping temp = (Mapping)obj;\r
- if (this._onto != null) {\r
- if (temp._onto == null) return false;\r
- else if (!(this._onto.equals(temp._onto))) \r
- return false;\r
- }\r
- else if (temp._onto != null)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Returns the value of field 'onto'. The field 'onto' has the\r
- * following description: object to which the mapping is being\r
- * mapped\r
- * \r
- * \r
- * @return Object\r
- * @return the value of field 'onto'.\r
- */\r
- public java.lang.Object getOnto()\r
- {\r
- return this._onto;\r
- } //-- java.lang.Object getOnto() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'onto'. The field 'onto' has the\r
- * following description: object to which the mapping is being\r
- * mapped\r
- * \r
- * \r
- * @param onto the value of field 'onto'.\r
- */\r
- public void setOnto(java.lang.Object onto)\r
- {\r
- this._onto = onto;\r
- } //-- void setOnto(java.lang.Object) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return MapList\r
- */\r
- public static org.vamsas.objects.core.MapList unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.Mapping) Unmarshaller.unmarshal(org.vamsas.objects.core.Mapping.class, reader);\r
- } //-- org.vamsas.objects.core.MapList unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class MappingDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class MappingDescriptor extends org.vamsas.objects.core.MapListDescriptor {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public MappingDescriptor() \r
- {\r
- super();\r
- setExtendsWithoutFlatten(new org.vamsas.objects.core.MapListDescriptor());\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "mapping";\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- initialize attribute descriptors\r
- \r
- //-- _onto\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_onto", "onto", org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setReference(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Mapping target = (Mapping) object;\r
- return target.getOnto();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Mapping target = (Mapping) object;\r
- target.setOnto( (java.lang.Object) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return new java.lang.Object();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _onto\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize element descriptors\r
- \r
- } //-- org.vamsas.objects.core.MappingDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return super.getExtends();\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- if (identity == null)\r
- return super.getIdentity();\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.Mapping.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class Param.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Param extends org.vamsas.client.Vobject \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * internal content storage\r
- */\r
- private java.lang.String _content = "";\r
-\r
- /**\r
- * Field _name\r
- */\r
- private java.lang.String _name;\r
-\r
- /**\r
- * The type specifies how the property will be parsed.\r
- * Empty property strings are allowed, and can be used to\r
- * prototype the\r
- * input to a document. TODO: specify allowed types \r
- */\r
- private java.lang.String _type;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Param() \r
- {\r
- super();\r
- setContent("");\r
- } //-- org.vamsas.objects.core.Param()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof Param) {\r
- \r
- Param temp = (Param)obj;\r
- if (this._content != null) {\r
- if (temp._content == null) return false;\r
- else if (!(this._content.equals(temp._content))) \r
- return false;\r
- }\r
- else if (temp._content != null)\r
- return false;\r
- if (this._name != null) {\r
- if (temp._name == null) return false;\r
- else if (!(this._name.equals(temp._name))) \r
- return false;\r
- }\r
- else if (temp._name != null)\r
- return false;\r
- if (this._type != null) {\r
- if (temp._type == null) return false;\r
- else if (!(this._type.equals(temp._type))) \r
- return false;\r
- }\r
- else if (temp._type != null)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Returns the value of field 'content'. The field 'content'\r
- * has the following description: internal content storage\r
- * \r
- * @return String\r
- * @return the value of field 'content'.\r
- */\r
- public java.lang.String getContent()\r
- {\r
- return this._content;\r
- } //-- java.lang.String getContent() \r
-\r
- /**\r
- * Returns the value of field 'name'.\r
- * \r
- * @return String\r
- * @return the value of field 'name'.\r
- */\r
- public java.lang.String getName()\r
- {\r
- return this._name;\r
- } //-- java.lang.String getName() \r
-\r
- /**\r
- * Returns the value of field 'type'. The field 'type' has the\r
- * following description: The type specifies how the property\r
- * will be parsed.\r
- * Empty property strings are allowed, and can be used to\r
- * prototype the\r
- * input to a document. TODO: specify allowed types \r
- * \r
- * @return String\r
- * @return the value of field 'type'.\r
- */\r
- public java.lang.String getType()\r
- {\r
- return this._type;\r
- } //-- java.lang.String getType() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'content'. The field 'content' has\r
- * the following description: internal content storage\r
- * \r
- * @param content the value of field 'content'.\r
- */\r
- public void setContent(java.lang.String content)\r
- {\r
- this._content = content;\r
- } //-- void setContent(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'name'.\r
- * \r
- * @param name the value of field 'name'.\r
- */\r
- public void setName(java.lang.String name)\r
- {\r
- this._name = name;\r
- } //-- void setName(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'type'. The field 'type' has the\r
- * following description: The type specifies how the property\r
- * will be parsed.\r
- * Empty property strings are allowed, and can be used to\r
- * prototype the\r
- * input to a document. TODO: specify allowed types \r
- * \r
- * @param type the value of field 'type'.\r
- */\r
- public void setType(java.lang.String type)\r
- {\r
- this._type = type;\r
- } //-- void setType(java.lang.String) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return Param\r
- */\r
- public static org.vamsas.objects.core.Param unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.Param) Unmarshaller.unmarshal(org.vamsas.objects.core.Param.class, reader);\r
- } //-- org.vamsas.objects.core.Param unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class ParamDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class ParamDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public ParamDescriptor() \r
- {\r
- super();\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "param";\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- _content\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Param target = (Param) object;\r
- return target.getContent();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Param target = (Param) object;\r
- target.setContent( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _content\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize attribute descriptors\r
- \r
- //-- _name\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Param target = (Param) object;\r
- return target.getName();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Param target = (Param) object;\r
- target.setName( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _name\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _type\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Param target = (Param) object;\r
- return target.getType();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Param target = (Param) object;\r
- target.setType( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _type\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize element descriptors\r
- \r
- } //-- org.vamsas.objects.core.ParamDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.Param.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * a position within the associated object's coordinate system\r
- * \r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Pos extends org.vamsas.client.Vobject \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _i\r
- */\r
- private int _i;\r
-\r
- /**\r
- * keeps track of state for field: _i\r
- */\r
- private boolean _has_i;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Pos() \r
- {\r
- super();\r
- } //-- org.vamsas.objects.core.Pos()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method deleteI\r
- * \r
- */\r
- public void deleteI()\r
- {\r
- this._has_i= false;\r
- } //-- void deleteI() \r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof Pos) {\r
- \r
- Pos temp = (Pos)obj;\r
- if (this._i != temp._i)\r
- return false;\r
- if (this._has_i != temp._has_i)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Returns the value of field 'i'.\r
- * \r
- * @return int\r
- * @return the value of field 'i'.\r
- */\r
- public int getI()\r
- {\r
- return this._i;\r
- } //-- int getI() \r
-\r
- /**\r
- * Method hasI\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasI()\r
- {\r
- return this._has_i;\r
- } //-- boolean hasI() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'i'.\r
- * \r
- * @param i the value of field 'i'.\r
- */\r
- public void setI(int i)\r
- {\r
- this._i = i;\r
- this._has_i = true;\r
- } //-- void setI(int) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return Pos\r
- */\r
- public static org.vamsas.objects.core.Pos unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.Pos) Unmarshaller.unmarshal(org.vamsas.objects.core.Pos.class, reader);\r
- } //-- org.vamsas.objects.core.Pos unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class PosDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class PosDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public PosDescriptor() \r
- {\r
- super();\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "pos";\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- initialize attribute descriptors\r
- \r
- //-- _i\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_i", "i", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Pos target = (Pos) object;\r
- if(!target.hasI())\r
- return null;\r
- return new java.lang.Integer(target.getI());\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Pos target = (Pos) object;\r
- // ignore null values for non optional primitives\r
- if (value == null) return;\r
- \r
- target.setI( ((java.lang.Integer)value).intValue());\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _i\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- IntegerValidator typeValidator= new IntegerValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize element descriptors\r
- \r
- } //-- org.vamsas.objects.core.PosDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.Pos.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class Property.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Property extends org.vamsas.client.Vobject \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * internal content storage\r
- */\r
- private java.lang.String _content = "";\r
-\r
- /**\r
- * Field _name\r
- */\r
- private java.lang.String _name;\r
-\r
- /**\r
- * The type specifies how the property will be parsed.\r
- * Empty property strings are allowed, and can be used to\r
- * prototype the\r
- * input to a document. TODO: specify allowed types \r
- */\r
- private java.lang.String _type;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Property() \r
- {\r
- super();\r
- setContent("");\r
- } //-- org.vamsas.objects.core.Property()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof Property) {\r
- \r
- Property temp = (Property)obj;\r
- if (this._content != null) {\r
- if (temp._content == null) return false;\r
- else if (!(this._content.equals(temp._content))) \r
- return false;\r
- }\r
- else if (temp._content != null)\r
- return false;\r
- if (this._name != null) {\r
- if (temp._name == null) return false;\r
- else if (!(this._name.equals(temp._name))) \r
- return false;\r
- }\r
- else if (temp._name != null)\r
- return false;\r
- if (this._type != null) {\r
- if (temp._type == null) return false;\r
- else if (!(this._type.equals(temp._type))) \r
- return false;\r
- }\r
- else if (temp._type != null)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Returns the value of field 'content'. The field 'content'\r
- * has the following description: internal content storage\r
- * \r
- * @return String\r
- * @return the value of field 'content'.\r
- */\r
- public java.lang.String getContent()\r
- {\r
- return this._content;\r
- } //-- java.lang.String getContent() \r
-\r
- /**\r
- * Returns the value of field 'name'.\r
- * \r
- * @return String\r
- * @return the value of field 'name'.\r
- */\r
- public java.lang.String getName()\r
- {\r
- return this._name;\r
- } //-- java.lang.String getName() \r
-\r
- /**\r
- * Returns the value of field 'type'. The field 'type' has the\r
- * following description: The type specifies how the property\r
- * will be parsed.\r
- * Empty property strings are allowed, and can be used to\r
- * prototype the\r
- * input to a document. TODO: specify allowed types \r
- * \r
- * @return String\r
- * @return the value of field 'type'.\r
- */\r
- public java.lang.String getType()\r
- {\r
- return this._type;\r
- } //-- java.lang.String getType() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'content'. The field 'content' has\r
- * the following description: internal content storage\r
- * \r
- * @param content the value of field 'content'.\r
- */\r
- public void setContent(java.lang.String content)\r
- {\r
- this._content = content;\r
- } //-- void setContent(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'name'.\r
- * \r
- * @param name the value of field 'name'.\r
- */\r
- public void setName(java.lang.String name)\r
- {\r
- this._name = name;\r
- } //-- void setName(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'type'. The field 'type' has the\r
- * following description: The type specifies how the property\r
- * will be parsed.\r
- * Empty property strings are allowed, and can be used to\r
- * prototype the\r
- * input to a document. TODO: specify allowed types \r
- * \r
- * @param type the value of field 'type'.\r
- */\r
- public void setType(java.lang.String type)\r
- {\r
- this._type = type;\r
- } //-- void setType(java.lang.String) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return Property\r
- */\r
- public static org.vamsas.objects.core.Property unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.Property) Unmarshaller.unmarshal(org.vamsas.objects.core.Property.class, reader);\r
- } //-- org.vamsas.objects.core.Property unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class PropertyDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class PropertyDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public PropertyDescriptor() \r
- {\r
- super();\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "property";\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- _content\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Property target = (Property) object;\r
- return target.getContent();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Property target = (Property) object;\r
- target.setContent( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _content\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize attribute descriptors\r
- \r
- //-- _name\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Property target = (Property) object;\r
- return target.getName();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Property target = (Property) object;\r
- target.setName( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _name\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _type\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Property target = (Property) object;\r
- return target.getType();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Property target = (Property) object;\r
- target.setType( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _type\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize element descriptors\r
- \r
- } //-- org.vamsas.objects.core.PropertyDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.Property.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import java.util.Enumeration;\r
-import java.util.Vector;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Annotation for a rangeSpec - values can be attached for the\r
- * whole\r
- * specification, and to each position within the spec. following\r
- * the orientation\r
- * specified by the ordered set of rangeSpec (pos, seg) elements. \r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class RangeAnnotation extends org.vamsas.objects.core.RangeType \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Primary Key for vamsas object referencing\r
- * \r
- */\r
- private java.lang.String _id;\r
-\r
- /**\r
- * Field _modifiable\r
- */\r
- private java.lang.String _modifiable;\r
-\r
- /**\r
- * Annotation with the same non-empty group name are grouped\r
- * together \r
- */\r
- private java.lang.String _group = "";\r
-\r
- /**\r
- * A Das Feature has both a type and a Type ID. We go the\r
- * route of requiring the type string to be taken from a\r
- * controlled\r
- * vocabulary if an application expects others to make sense\r
- * of it. The\r
- * type may qualified - so uniprot:CHAIN is a valid type name,\r
- * and\r
- * considered distinct from someotherDB:CHAIN \r
- */\r
- private java.lang.String _type;\r
-\r
- /**\r
- * Short, meaningful name for the annotation - if this\r
- * is absent, then the type string should be used in its\r
- * place.\r
- * \r
- */\r
- private java.lang.String _label;\r
-\r
- /**\r
- * Human readable description of the annotation\r
- * \r
- */\r
- private java.lang.String _description;\r
-\r
- /**\r
- * TODO: specify this - we have considered taking the GO\r
- * evidence codes as a model for assessing a measure of\r
- * quality to an\r
- * annotation. \r
- */\r
- private java.lang.String _status;\r
-\r
- /**\r
- * Annotation Element position maps to ordered positions\r
- * defined by the sequence of rangeType pos positions or\r
- * concatenated\r
- * seg start/end segments. \r
- */\r
- private java.util.Vector _annotationElementList;\r
-\r
- /**\r
- * Ordered set of optionally named float values for the\r
- * whole annotation \r
- */\r
- private java.util.Vector _scoreList;\r
-\r
- /**\r
- * Field _linkList\r
- */\r
- private java.util.Vector _linkList;\r
-\r
- /**\r
- * Note:These are mutable so an application should check\r
- * them each time. \r
- */\r
- private java.util.Vector _propertyList;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public RangeAnnotation() \r
- {\r
- super();\r
- setGroup("");\r
- _annotationElementList = new Vector();\r
- _scoreList = new Vector();\r
- _linkList = new Vector();\r
- _propertyList = new Vector();\r
- } //-- org.vamsas.objects.core.RangeAnnotation()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addAnnotationElement\r
- * \r
- * \r
- * \r
- * @param vAnnotationElement\r
- */\r
- public void addAnnotationElement(org.vamsas.objects.core.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _annotationElementList.addElement(vAnnotationElement);\r
- } //-- void addAnnotationElement(org.vamsas.objects.core.AnnotationElement) \r
-\r
- /**\r
- * Method addAnnotationElement\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vAnnotationElement\r
- */\r
- public void addAnnotationElement(int index, org.vamsas.objects.core.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _annotationElementList.insertElementAt(vAnnotationElement, index);\r
- } //-- void addAnnotationElement(int, org.vamsas.objects.core.AnnotationElement) \r
-\r
- /**\r
- * Method addLink\r
- * \r
- * \r
- * \r
- * @param vLink\r
- */\r
- public void addLink(org.vamsas.objects.core.Link vLink)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _linkList.addElement(vLink);\r
- } //-- void addLink(org.vamsas.objects.core.Link) \r
-\r
- /**\r
- * Method addLink\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vLink\r
- */\r
- public void addLink(int index, org.vamsas.objects.core.Link vLink)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _linkList.insertElementAt(vLink, index);\r
- } //-- void addLink(int, org.vamsas.objects.core.Link) \r
-\r
- /**\r
- * Method addProperty\r
- * \r
- * \r
- * \r
- * @param vProperty\r
- */\r
- public void addProperty(org.vamsas.objects.core.Property vProperty)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _propertyList.addElement(vProperty);\r
- } //-- void addProperty(org.vamsas.objects.core.Property) \r
-\r
- /**\r
- * Method addProperty\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vProperty\r
- */\r
- public void addProperty(int index, org.vamsas.objects.core.Property vProperty)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _propertyList.insertElementAt(vProperty, index);\r
- } //-- void addProperty(int, org.vamsas.objects.core.Property) \r
-\r
- /**\r
- * Method addScore\r
- * \r
- * \r
- * \r
- * @param vScore\r
- */\r
- public void addScore(org.vamsas.objects.core.Score vScore)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _scoreList.addElement(vScore);\r
- } //-- void addScore(org.vamsas.objects.core.Score) \r
-\r
- /**\r
- * Method addScore\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vScore\r
- */\r
- public void addScore(int index, org.vamsas.objects.core.Score vScore)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _scoreList.insertElementAt(vScore, index);\r
- } //-- void addScore(int, org.vamsas.objects.core.Score) \r
-\r
- /**\r
- * Method enumerateAnnotationElement\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateAnnotationElement()\r
- {\r
- return _annotationElementList.elements();\r
- } //-- java.util.Enumeration enumerateAnnotationElement() \r
-\r
- /**\r
- * Method enumerateLink\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateLink()\r
- {\r
- return _linkList.elements();\r
- } //-- java.util.Enumeration enumerateLink() \r
-\r
- /**\r
- * Method enumerateProperty\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateProperty()\r
- {\r
- return _propertyList.elements();\r
- } //-- java.util.Enumeration enumerateProperty() \r
-\r
- /**\r
- * Method enumerateScore\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateScore()\r
- {\r
- return _scoreList.elements();\r
- } //-- java.util.Enumeration enumerateScore() \r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof RangeAnnotation) {\r
- \r
- RangeAnnotation temp = (RangeAnnotation)obj;\r
- if (this._id != null) {\r
- if (temp._id == null) return false;\r
- else if (!(this._id.equals(temp._id))) \r
- return false;\r
- }\r
- else if (temp._id != null)\r
- return false;\r
- if (this._modifiable != null) {\r
- if (temp._modifiable == null) return false;\r
- else if (!(this._modifiable.equals(temp._modifiable))) \r
- return false;\r
- }\r
- else if (temp._modifiable != null)\r
- return false;\r
- if (this._group != null) {\r
- if (temp._group == null) return false;\r
- else if (!(this._group.equals(temp._group))) \r
- return false;\r
- }\r
- else if (temp._group != null)\r
- return false;\r
- if (this._type != null) {\r
- if (temp._type == null) return false;\r
- else if (!(this._type.equals(temp._type))) \r
- return false;\r
- }\r
- else if (temp._type != null)\r
- return false;\r
- if (this._label != null) {\r
- if (temp._label == null) return false;\r
- else if (!(this._label.equals(temp._label))) \r
- return false;\r
- }\r
- else if (temp._label != null)\r
- return false;\r
- if (this._description != null) {\r
- if (temp._description == null) return false;\r
- else if (!(this._description.equals(temp._description))) \r
- return false;\r
- }\r
- else if (temp._description != null)\r
- return false;\r
- if (this._status != null) {\r
- if (temp._status == null) return false;\r
- else if (!(this._status.equals(temp._status))) \r
- return false;\r
- }\r
- else if (temp._status != null)\r
- return false;\r
- if (this._annotationElementList != null) {\r
- if (temp._annotationElementList == null) return false;\r
- else if (!(this._annotationElementList.equals(temp._annotationElementList))) \r
- return false;\r
- }\r
- else if (temp._annotationElementList != null)\r
- return false;\r
- if (this._scoreList != null) {\r
- if (temp._scoreList == null) return false;\r
- else if (!(this._scoreList.equals(temp._scoreList))) \r
- return false;\r
- }\r
- else if (temp._scoreList != null)\r
- return false;\r
- if (this._linkList != null) {\r
- if (temp._linkList == null) return false;\r
- else if (!(this._linkList.equals(temp._linkList))) \r
- return false;\r
- }\r
- else if (temp._linkList != null)\r
- return false;\r
- if (this._propertyList != null) {\r
- if (temp._propertyList == null) return false;\r
- else if (!(this._propertyList.equals(temp._propertyList))) \r
- return false;\r
- }\r
- else if (temp._propertyList != null)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Method getAnnotationElement\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return AnnotationElement\r
- */\r
- public org.vamsas.objects.core.AnnotationElement getAnnotationElement(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _annotationElementList.size())) {\r
- throw new IndexOutOfBoundsException("getAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]");\r
- }\r
- \r
- return (org.vamsas.objects.core.AnnotationElement) _annotationElementList.elementAt(index);\r
- } //-- org.vamsas.objects.core.AnnotationElement getAnnotationElement(int) \r
-\r
- /**\r
- * Method getAnnotationElement\r
- * \r
- * \r
- * \r
- * @return AnnotationElement\r
- */\r
- public org.vamsas.objects.core.AnnotationElement[] getAnnotationElement()\r
- {\r
- int size = _annotationElementList.size();\r
- org.vamsas.objects.core.AnnotationElement[] mArray = new org.vamsas.objects.core.AnnotationElement[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (org.vamsas.objects.core.AnnotationElement) _annotationElementList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- org.vamsas.objects.core.AnnotationElement[] getAnnotationElement() \r
-\r
- /**\r
- * Method getAnnotationElementCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getAnnotationElementCount()\r
- {\r
- return _annotationElementList.size();\r
- } //-- int getAnnotationElementCount() \r
-\r
- /**\r
- * Returns the value of field 'description'. The field\r
- * 'description' has the following description: Human readable\r
- * description of the annotation\r
- * \r
- * \r
- * @return String\r
- * @return the value of field 'description'.\r
- */\r
- public java.lang.String getDescription()\r
- {\r
- return this._description;\r
- } //-- java.lang.String getDescription() \r
-\r
- /**\r
- * Returns the value of field 'group'. The field 'group' has\r
- * the following description: Annotation with the same\r
- * non-empty group name are grouped\r
- * together \r
- * \r
- * @return String\r
- * @return the value of field 'group'.\r
- */\r
- public java.lang.String getGroup()\r
- {\r
- return this._group;\r
- } //-- java.lang.String getGroup() \r
-\r
- /**\r
- * Returns the value of field 'id'. The field 'id' has the\r
- * following description: Primary Key for vamsas object\r
- * referencing\r
- * \r
- * \r
- * @return String\r
- * @return the value of field 'id'.\r
- */\r
- public java.lang.String getId()\r
- {\r
- return this._id;\r
- } //-- java.lang.String getId() \r
-\r
- /**\r
- * Returns the value of field 'label'. The field 'label' has\r
- * the following description: Short, meaningful name for the\r
- * annotation - if this\r
- * is absent, then the type string should be used in its\r
- * place.\r
- * \r
- * \r
- * @return String\r
- * @return the value of field 'label'.\r
- */\r
- public java.lang.String getLabel()\r
- {\r
- return this._label;\r
- } //-- java.lang.String getLabel() \r
-\r
- /**\r
- * Method getLink\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Link\r
- */\r
- public org.vamsas.objects.core.Link getLink(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _linkList.size())) {\r
- throw new IndexOutOfBoundsException("getLink: Index value '"+index+"' not in range [0.."+_linkList.size()+ "]");\r
- }\r
- \r
- return (org.vamsas.objects.core.Link) _linkList.elementAt(index);\r
- } //-- org.vamsas.objects.core.Link getLink(int) \r
-\r
- /**\r
- * Method getLink\r
- * \r
- * \r
- * \r
- * @return Link\r
- */\r
- public org.vamsas.objects.core.Link[] getLink()\r
- {\r
- int size = _linkList.size();\r
- org.vamsas.objects.core.Link[] mArray = new org.vamsas.objects.core.Link[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (org.vamsas.objects.core.Link) _linkList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- org.vamsas.objects.core.Link[] getLink() \r
-\r
- /**\r
- * Method getLinkCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getLinkCount()\r
- {\r
- return _linkList.size();\r
- } //-- int getLinkCount() \r
-\r
- /**\r
- * Returns the value of field 'modifiable'.\r
- * \r
- * @return String\r
- * @return the value of field 'modifiable'.\r
- */\r
- public java.lang.String getModifiable()\r
- {\r
- return this._modifiable;\r
- } //-- java.lang.String getModifiable() \r
-\r
- /**\r
- * Method getProperty\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Property\r
- */\r
- public org.vamsas.objects.core.Property getProperty(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _propertyList.size())) {\r
- throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");\r
- }\r
- \r
- return (org.vamsas.objects.core.Property) _propertyList.elementAt(index);\r
- } //-- org.vamsas.objects.core.Property getProperty(int) \r
-\r
- /**\r
- * Method getProperty\r
- * \r
- * \r
- * \r
- * @return Property\r
- */\r
- public org.vamsas.objects.core.Property[] getProperty()\r
- {\r
- int size = _propertyList.size();\r
- org.vamsas.objects.core.Property[] mArray = new org.vamsas.objects.core.Property[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (org.vamsas.objects.core.Property) _propertyList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- org.vamsas.objects.core.Property[] getProperty() \r
-\r
- /**\r
- * Method getPropertyCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getPropertyCount()\r
- {\r
- return _propertyList.size();\r
- } //-- int getPropertyCount() \r
-\r
- /**\r
- * Method getScore\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Score\r
- */\r
- public org.vamsas.objects.core.Score getScore(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _scoreList.size())) {\r
- throw new IndexOutOfBoundsException("getScore: Index value '"+index+"' not in range [0.."+_scoreList.size()+ "]");\r
- }\r
- \r
- return (org.vamsas.objects.core.Score) _scoreList.elementAt(index);\r
- } //-- org.vamsas.objects.core.Score getScore(int) \r
-\r
- /**\r
- * Method getScore\r
- * \r
- * \r
- * \r
- * @return Score\r
- */\r
- public org.vamsas.objects.core.Score[] getScore()\r
- {\r
- int size = _scoreList.size();\r
- org.vamsas.objects.core.Score[] mArray = new org.vamsas.objects.core.Score[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (org.vamsas.objects.core.Score) _scoreList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- org.vamsas.objects.core.Score[] getScore() \r
-\r
- /**\r
- * Method getScoreCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getScoreCount()\r
- {\r
- return _scoreList.size();\r
- } //-- int getScoreCount() \r
-\r
- /**\r
- * Returns the value of field 'status'. The field 'status' has\r
- * the following description: TODO: specify this - we have\r
- * considered taking the GO\r
- * evidence codes as a model for assessing a measure of\r
- * quality to an\r
- * annotation. \r
- * \r
- * @return String\r
- * @return the value of field 'status'.\r
- */\r
- public java.lang.String getStatus()\r
- {\r
- return this._status;\r
- } //-- java.lang.String getStatus() \r
-\r
- /**\r
- * Returns the value of field 'type'. The field 'type' has the\r
- * following description: A Das Feature has both a type and a\r
- * Type ID. We go the\r
- * route of requiring the type string to be taken from a\r
- * controlled\r
- * vocabulary if an application expects others to make sense\r
- * of it. The\r
- * type may qualified - so uniprot:CHAIN is a valid type name,\r
- * and\r
- * considered distinct from someotherDB:CHAIN \r
- * \r
- * @return String\r
- * @return the value of field 'type'.\r
- */\r
- public java.lang.String getType()\r
- {\r
- return this._type;\r
- } //-- java.lang.String getType() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Method removeAllAnnotationElement\r
- * \r
- */\r
- public void removeAllAnnotationElement()\r
- {\r
- _annotationElementList.removeAllElements();\r
- } //-- void removeAllAnnotationElement() \r
-\r
- /**\r
- * Method removeAllLink\r
- * \r
- */\r
- public void removeAllLink()\r
- {\r
- _linkList.removeAllElements();\r
- } //-- void removeAllLink() \r
-\r
- /**\r
- * Method removeAllProperty\r
- * \r
- */\r
- public void removeAllProperty()\r
- {\r
- _propertyList.removeAllElements();\r
- } //-- void removeAllProperty() \r
-\r
- /**\r
- * Method removeAllScore\r
- * \r
- */\r
- public void removeAllScore()\r
- {\r
- _scoreList.removeAllElements();\r
- } //-- void removeAllScore() \r
-\r
- /**\r
- * Method removeAnnotationElement\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return AnnotationElement\r
- */\r
- public org.vamsas.objects.core.AnnotationElement removeAnnotationElement(int index)\r
- {\r
- java.lang.Object obj = _annotationElementList.elementAt(index);\r
- _annotationElementList.removeElementAt(index);\r
- return (org.vamsas.objects.core.AnnotationElement) obj;\r
- } //-- org.vamsas.objects.core.AnnotationElement removeAnnotationElement(int) \r
-\r
- /**\r
- * Method removeLink\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Link\r
- */\r
- public org.vamsas.objects.core.Link removeLink(int index)\r
- {\r
- java.lang.Object obj = _linkList.elementAt(index);\r
- _linkList.removeElementAt(index);\r
- return (org.vamsas.objects.core.Link) obj;\r
- } //-- org.vamsas.objects.core.Link removeLink(int) \r
-\r
- /**\r
- * Method removeProperty\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Property\r
- */\r
- public org.vamsas.objects.core.Property removeProperty(int index)\r
- {\r
- java.lang.Object obj = _propertyList.elementAt(index);\r
- _propertyList.removeElementAt(index);\r
- return (org.vamsas.objects.core.Property) obj;\r
- } //-- org.vamsas.objects.core.Property removeProperty(int) \r
-\r
- /**\r
- * Method removeScore\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Score\r
- */\r
- public org.vamsas.objects.core.Score removeScore(int index)\r
- {\r
- java.lang.Object obj = _scoreList.elementAt(index);\r
- _scoreList.removeElementAt(index);\r
- return (org.vamsas.objects.core.Score) obj;\r
- } //-- org.vamsas.objects.core.Score removeScore(int) \r
-\r
- /**\r
- * Method setAnnotationElement\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vAnnotationElement\r
- */\r
- public void setAnnotationElement(int index, org.vamsas.objects.core.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _annotationElementList.size())) {\r
- throw new IndexOutOfBoundsException("setAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]");\r
- }\r
- _annotationElementList.setElementAt(vAnnotationElement, index);\r
- } //-- void setAnnotationElement(int, org.vamsas.objects.core.AnnotationElement) \r
-\r
- /**\r
- * Method setAnnotationElement\r
- * \r
- * \r
- * \r
- * @param annotationElementArray\r
- */\r
- public void setAnnotationElement(org.vamsas.objects.core.AnnotationElement[] annotationElementArray)\r
- {\r
- //-- copy array\r
- _annotationElementList.removeAllElements();\r
- for (int i = 0; i < annotationElementArray.length; i++) {\r
- _annotationElementList.addElement(annotationElementArray[i]);\r
- }\r
- } //-- void setAnnotationElement(org.vamsas.objects.core.AnnotationElement) \r
-\r
- /**\r
- * Sets the value of field 'description'. The field\r
- * 'description' has the following description: Human readable\r
- * description of the annotation\r
- * \r
- * \r
- * @param description the value of field 'description'.\r
- */\r
- public void setDescription(java.lang.String description)\r
- {\r
- this._description = description;\r
- } //-- void setDescription(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'group'. The field 'group' has the\r
- * following description: Annotation with the same non-empty\r
- * group name are grouped\r
- * together \r
- * \r
- * @param group the value of field 'group'.\r
- */\r
- public void setGroup(java.lang.String group)\r
- {\r
- this._group = group;\r
- } //-- void setGroup(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'id'. The field 'id' has the\r
- * following description: Primary Key for vamsas object\r
- * referencing\r
- * \r
- * \r
- * @param id the value of field 'id'.\r
- */\r
- public void setId(java.lang.String id)\r
- {\r
- this._id = id;\r
- } //-- void setId(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'label'. The field 'label' has the\r
- * following description: Short, meaningful name for the\r
- * annotation - if this\r
- * is absent, then the type string should be used in its\r
- * place.\r
- * \r
- * \r
- * @param label the value of field 'label'.\r
- */\r
- public void setLabel(java.lang.String label)\r
- {\r
- this._label = label;\r
- } //-- void setLabel(java.lang.String) \r
-\r
- /**\r
- * Method setLink\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vLink\r
- */\r
- public void setLink(int index, org.vamsas.objects.core.Link vLink)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _linkList.size())) {\r
- throw new IndexOutOfBoundsException("setLink: Index value '"+index+"' not in range [0.."+_linkList.size()+ "]");\r
- }\r
- _linkList.setElementAt(vLink, index);\r
- } //-- void setLink(int, org.vamsas.objects.core.Link) \r
-\r
- /**\r
- * Method setLink\r
- * \r
- * \r
- * \r
- * @param linkArray\r
- */\r
- public void setLink(org.vamsas.objects.core.Link[] linkArray)\r
- {\r
- //-- copy array\r
- _linkList.removeAllElements();\r
- for (int i = 0; i < linkArray.length; i++) {\r
- _linkList.addElement(linkArray[i]);\r
- }\r
- } //-- void setLink(org.vamsas.objects.core.Link) \r
-\r
- /**\r
- * Sets the value of field 'modifiable'.\r
- * \r
- * @param modifiable the value of field 'modifiable'.\r
- */\r
- public void setModifiable(java.lang.String modifiable)\r
- {\r
- this._modifiable = modifiable;\r
- } //-- void setModifiable(java.lang.String) \r
-\r
- /**\r
- * Method setProperty\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vProperty\r
- */\r
- public void setProperty(int index, org.vamsas.objects.core.Property vProperty)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _propertyList.size())) {\r
- throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");\r
- }\r
- _propertyList.setElementAt(vProperty, index);\r
- } //-- void setProperty(int, org.vamsas.objects.core.Property) \r
-\r
- /**\r
- * Method setProperty\r
- * \r
- * \r
- * \r
- * @param propertyArray\r
- */\r
- public void setProperty(org.vamsas.objects.core.Property[] propertyArray)\r
- {\r
- //-- copy array\r
- _propertyList.removeAllElements();\r
- for (int i = 0; i < propertyArray.length; i++) {\r
- _propertyList.addElement(propertyArray[i]);\r
- }\r
- } //-- void setProperty(org.vamsas.objects.core.Property) \r
-\r
- /**\r
- * Method setScore\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vScore\r
- */\r
- public void setScore(int index, org.vamsas.objects.core.Score vScore)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _scoreList.size())) {\r
- throw new IndexOutOfBoundsException("setScore: Index value '"+index+"' not in range [0.."+_scoreList.size()+ "]");\r
- }\r
- _scoreList.setElementAt(vScore, index);\r
- } //-- void setScore(int, org.vamsas.objects.core.Score) \r
-\r
- /**\r
- * Method setScore\r
- * \r
- * \r
- * \r
- * @param scoreArray\r
- */\r
- public void setScore(org.vamsas.objects.core.Score[] scoreArray)\r
- {\r
- //-- copy array\r
- _scoreList.removeAllElements();\r
- for (int i = 0; i < scoreArray.length; i++) {\r
- _scoreList.addElement(scoreArray[i]);\r
- }\r
- } //-- void setScore(org.vamsas.objects.core.Score) \r
-\r
- /**\r
- * Sets the value of field 'status'. The field 'status' has the\r
- * following description: TODO: specify this - we have\r
- * considered taking the GO\r
- * evidence codes as a model for assessing a measure of\r
- * quality to an\r
- * annotation. \r
- * \r
- * @param status the value of field 'status'.\r
- */\r
- public void setStatus(java.lang.String status)\r
- {\r
- this._status = status;\r
- } //-- void setStatus(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'type'. The field 'type' has the\r
- * following description: A Das Feature has both a type and a\r
- * Type ID. We go the\r
- * route of requiring the type string to be taken from a\r
- * controlled\r
- * vocabulary if an application expects others to make sense\r
- * of it. The\r
- * type may qualified - so uniprot:CHAIN is a valid type name,\r
- * and\r
- * considered distinct from someotherDB:CHAIN \r
- * \r
- * @param type the value of field 'type'.\r
- */\r
- public void setType(java.lang.String type)\r
- {\r
- this._type = type;\r
- } //-- void setType(java.lang.String) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return RangeType\r
- */\r
- public static org.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.RangeAnnotation) Unmarshaller.unmarshal(org.vamsas.objects.core.RangeAnnotation.class, reader);\r
- } //-- org.vamsas.objects.core.RangeType unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class RangeAnnotationDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class RangeAnnotationDescriptor extends org.vamsas.objects.core.RangeTypeDescriptor {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public RangeAnnotationDescriptor() \r
- {\r
- super();\r
- setExtendsWithoutFlatten(new org.vamsas.objects.core.RangeTypeDescriptor());\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "rangeAnnotation";\r
- \r
- //-- set grouping compositor\r
- setCompositorAsSequence();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- initialize attribute descriptors\r
- \r
- //-- _id\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
- this.identity = desc;\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- return target.getId();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- target.setId( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return new java.lang.String();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _id\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _modifiable\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_modifiable", "modifiable", org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- return target.getModifiable();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- target.setModifiable( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _modifiable\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _group\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_group", "group", org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- return target.getGroup();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- target.setGroup( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _group\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _type\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- return target.getType();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- target.setType( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _type\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize element descriptors\r
- \r
- //-- _label\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_label", "label", org.exolab.castor.xml.NodeType.Element);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- return target.getLabel();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- target.setLabel( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("http://www.vamsas.org");\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _label\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _description\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- return target.getDescription();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- target.setDescription( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("http://www.vamsas.org");\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _description\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _status\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_status", "status", org.exolab.castor.xml.NodeType.Element);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- return target.getStatus();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- target.setStatus( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("http://www.vamsas.org");\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _status\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _annotationElementList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.AnnotationElement.class, "_annotationElementList", "annotationElement", org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- return target.getAnnotationElement();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- target.addAnnotationElement( (org.vamsas.objects.core.AnnotationElement) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return new org.vamsas.objects.core.AnnotationElement();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("http://www.vamsas.org");\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _annotationElementList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { //-- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _scoreList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Score.class, "_scoreList", "score", org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- return target.getScore();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- target.addScore( (org.vamsas.objects.core.Score) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return new org.vamsas.objects.core.Score();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("http://www.vamsas.org");\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _scoreList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { //-- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _linkList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Link.class, "_linkList", "link", org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- return target.getLink();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- target.addLink( (org.vamsas.objects.core.Link) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return new org.vamsas.objects.core.Link();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("http://www.vamsas.org");\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _linkList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { //-- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _propertyList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Property.class, "_propertyList", "property", org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- return target.getProperty();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- RangeAnnotation target = (RangeAnnotation) object;\r
- target.addProperty( (org.vamsas.objects.core.Property) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return new org.vamsas.objects.core.Property();\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("http://www.vamsas.org");\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _propertyList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(0);\r
- { //-- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- } //-- org.vamsas.objects.core.RangeAnnotationDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return super.getExtends();\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- if (identity == null)\r
- return super.getIdentity();\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.RangeAnnotation.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import java.util.Enumeration;\r
-import java.util.Vector;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-\r
-/**\r
- * Specify an ordered set of positions and/or regions on the\r
- * principle\r
- * dimension of some associated vamsas object Keeping to jaxb-1.0\r
- * specification for the moment - this choice should\r
- * become a substitution group when we use jaxb-2.0 capable\r
- * bindings\r
- * \r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public abstract class RangeType extends org.vamsas.client.Vobject \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Internal choice value storage\r
- */\r
- private java.lang.Object _choiceValue;\r
-\r
- /**\r
- * a position within the associated object's coordinate system\r
- * \r
- */\r
- private java.util.Vector _posList;\r
-\r
- /**\r
- * a region from start to end, with flag for inclusivity of\r
- * terminii \r
- */\r
- private java.util.Vector _segList;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public RangeType() \r
- {\r
- super();\r
- _posList = new Vector();\r
- _segList = new Vector();\r
- } //-- org.vamsas.objects.core.RangeType()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addPos\r
- * \r
- * \r
- * \r
- * @param vPos\r
- */\r
- public void addPos(org.vamsas.objects.core.Pos vPos)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _posList.addElement(vPos);\r
- } //-- void addPos(org.vamsas.objects.core.Pos) \r
-\r
- /**\r
- * Method addPos\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vPos\r
- */\r
- public void addPos(int index, org.vamsas.objects.core.Pos vPos)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _posList.insertElementAt(vPos, index);\r
- } //-- void addPos(int, org.vamsas.objects.core.Pos) \r
-\r
- /**\r
- * Method addSeg\r
- * \r
- * \r
- * \r
- * @param vSeg\r
- */\r
- public void addSeg(org.vamsas.objects.core.Seg vSeg)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _segList.addElement(vSeg);\r
- } //-- void addSeg(org.vamsas.objects.core.Seg) \r
-\r
- /**\r
- * Method addSeg\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vSeg\r
- */\r
- public void addSeg(int index, org.vamsas.objects.core.Seg vSeg)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _segList.insertElementAt(vSeg, index);\r
- } //-- void addSeg(int, org.vamsas.objects.core.Seg) \r
-\r
- /**\r
- * Method enumeratePos\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumeratePos()\r
- {\r
- return _posList.elements();\r
- } //-- java.util.Enumeration enumeratePos() \r
-\r
- /**\r
- * Method enumerateSeg\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateSeg()\r
- {\r
- return _segList.elements();\r
- } //-- java.util.Enumeration enumerateSeg() \r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof RangeType) {\r
- \r
- RangeType temp = (RangeType)obj;\r
- if (this._choiceValue != null) {\r
- if (temp._choiceValue == null) return false;\r
- else if (!(this._choiceValue.equals(temp._choiceValue))) \r
- return false;\r
- }\r
- else if (temp._choiceValue != null)\r
- return false;\r
- if (this._posList != null) {\r
- if (temp._posList == null) return false;\r
- else if (!(this._posList.equals(temp._posList))) \r
- return false;\r
- }\r
- else if (temp._posList != null)\r
- return false;\r
- if (this._segList != null) {\r
- if (temp._segList == null) return false;\r
- else if (!(this._segList.equals(temp._segList))) \r
- return false;\r
- }\r
- else if (temp._segList != null)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Returns the value of field 'choiceValue'. The field\r
- * 'choiceValue' has the following description: Internal choice\r
- * value storage\r
- * \r
- * @return Object\r
- * @return the value of field 'choiceValue'.\r
- */\r
- public java.lang.Object getChoiceValue()\r
- {\r
- return this._choiceValue;\r
- } //-- java.lang.Object getChoiceValue() \r
-\r
- /**\r
- * Method getPos\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Pos\r
- */\r
- public org.vamsas.objects.core.Pos getPos(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _posList.size())) {\r
- throw new IndexOutOfBoundsException("getPos: Index value '"+index+"' not in range [0.."+_posList.size()+ "]");\r
- }\r
- \r
- return (org.vamsas.objects.core.Pos) _posList.elementAt(index);\r
- } //-- org.vamsas.objects.core.Pos getPos(int) \r
-\r
- /**\r
- * Method getPos\r
- * \r
- * \r
- * \r
- * @return Pos\r
- */\r
- public org.vamsas.objects.core.Pos[] getPos()\r
- {\r
- int size = _posList.size();\r
- org.vamsas.objects.core.Pos[] mArray = new org.vamsas.objects.core.Pos[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (org.vamsas.objects.core.Pos) _posList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- org.vamsas.objects.core.Pos[] getPos() \r
-\r
- /**\r
- * Method getPosCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getPosCount()\r
- {\r
- return _posList.size();\r
- } //-- int getPosCount() \r
-\r
- /**\r
- * Method getSeg\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Seg\r
- */\r
- public org.vamsas.objects.core.Seg getSeg(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _segList.size())) {\r
- throw new IndexOutOfBoundsException("getSeg: Index value '"+index+"' not in range [0.."+_segList.size()+ "]");\r
- }\r
- \r
- return (org.vamsas.objects.core.Seg) _segList.elementAt(index);\r
- } //-- org.vamsas.objects.core.Seg getSeg(int) \r
-\r
- /**\r
- * Method getSeg\r
- * \r
- * \r
- * \r
- * @return Seg\r
- */\r
- public org.vamsas.objects.core.Seg[] getSeg()\r
- {\r
- int size = _segList.size();\r
- org.vamsas.objects.core.Seg[] mArray = new org.vamsas.objects.core.Seg[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (org.vamsas.objects.core.Seg) _segList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- org.vamsas.objects.core.Seg[] getSeg() \r
-\r
- /**\r
- * Method getSegCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getSegCount()\r
- {\r
- return _segList.size();\r
- } //-- int getSegCount() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method removeAllPos\r
- * \r
- */\r
- public void removeAllPos()\r
- {\r
- _posList.removeAllElements();\r
- } //-- void removeAllPos() \r
-\r
- /**\r
- * Method removeAllSeg\r
- * \r
- */\r
- public void removeAllSeg()\r
- {\r
- _segList.removeAllElements();\r
- } //-- void removeAllSeg() \r
-\r
- /**\r
- * Method removePos\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Pos\r
- */\r
- public org.vamsas.objects.core.Pos removePos(int index)\r
- {\r
- java.lang.Object obj = _posList.elementAt(index);\r
- _posList.removeElementAt(index);\r
- return (org.vamsas.objects.core.Pos) obj;\r
- } //-- org.vamsas.objects.core.Pos removePos(int) \r
-\r
- /**\r
- * Method removeSeg\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Seg\r
- */\r
- public org.vamsas.objects.core.Seg removeSeg(int index)\r
- {\r
- java.lang.Object obj = _segList.elementAt(index);\r
- _segList.removeElementAt(index);\r
- return (org.vamsas.objects.core.Seg) obj;\r
- } //-- org.vamsas.objects.core.Seg removeSeg(int) \r
-\r
- /**\r
- * Method setPos\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vPos\r
- */\r
- public void setPos(int index, org.vamsas.objects.core.Pos vPos)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _posList.size())) {\r
- throw new IndexOutOfBoundsException("setPos: Index value '"+index+"' not in range [0.."+_posList.size()+ "]");\r
- }\r
- _posList.setElementAt(vPos, index);\r
- } //-- void setPos(int, org.vamsas.objects.core.Pos) \r
-\r
- /**\r
- * Method setPos\r
- * \r
- * \r
- * \r
- * @param posArray\r
- */\r
- public void setPos(org.vamsas.objects.core.Pos[] posArray)\r
- {\r
- //-- copy array\r
- _posList.removeAllElements();\r
- for (int i = 0; i < posArray.length; i++) {\r
- _posList.addElement(posArray[i]);\r
- }\r
- } //-- void setPos(org.vamsas.objects.core.Pos) \r
-\r
- /**\r
- * Method setSeg\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vSeg\r
- */\r
- public void setSeg(int index, org.vamsas.objects.core.Seg vSeg)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _segList.size())) {\r
- throw new IndexOutOfBoundsException("setSeg: Index value '"+index+"' not in range [0.."+_segList.size()+ "]");\r
- }\r
- _segList.setElementAt(vSeg, index);\r
- } //-- void setSeg(int, org.vamsas.objects.core.Seg) \r
-\r
- /**\r
- * Method setSeg\r
- * \r
- * \r
- * \r
- * @param segArray\r
- */\r
- public void setSeg(org.vamsas.objects.core.Seg[] segArray)\r
- {\r
- //-- copy array\r
- _segList.removeAllElements();\r
- for (int i = 0; i < segArray.length; i++) {\r
- _segList.addElement(segArray[i]);\r
- }\r
- } //-- void setSeg(org.vamsas.objects.core.Seg) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class RangeTypeDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class RangeTypeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public RangeTypeDescriptor() \r
- {\r
- super();\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "rangeType";\r
- \r
- //-- set grouping compositor\r
- setCompositorAsChoice();\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- initialize attribute descriptors\r
- \r
- //-- initialize element descriptors\r
- \r
- //-- _posList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Pos.class, "_posList", "pos", org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- RangeType target = (RangeType) object;\r
- return target.getPos();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- RangeType target = (RangeType) object;\r
- target.addPos( (org.vamsas.objects.core.Pos) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("http://www.vamsas.org");\r
- desc.setRequired(true);\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _posList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _segList\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Seg.class, "_segList", "seg", org.exolab.castor.xml.NodeType.Element);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- RangeType target = (RangeType) object;\r
- return target.getSeg();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- RangeType target = (RangeType) object;\r
- target.addSeg( (org.vamsas.objects.core.Seg) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setNameSpaceURI("http://www.vamsas.org");\r
- desc.setRequired(true);\r
- desc.setMultivalued(true);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _segList\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- }\r
- desc.setValidator(fieldValidator);\r
- } //-- org.vamsas.objects.core.RangeTypeDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.RangeType.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Ordered set of optionally named float values for the\r
- * whole annotation \r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Score extends org.vamsas.client.Vobject \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * internal content storage\r
- */\r
- private float _content;\r
-\r
- /**\r
- * keeps track of state for field: _content\r
- */\r
- private boolean _has_content;\r
-\r
- /**\r
- * Field _name\r
- */\r
- private java.lang.String _name = "score";\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Score() \r
- {\r
- super();\r
- setName("score");\r
- } //-- org.vamsas.objects.core.Score()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method deleteContent\r
- * \r
- */\r
- public void deleteContent()\r
- {\r
- this._has_content= false;\r
- } //-- void deleteContent() \r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof Score) {\r
- \r
- Score temp = (Score)obj;\r
- if (this._content != temp._content)\r
- return false;\r
- if (this._has_content != temp._has_content)\r
- return false;\r
- if (this._name != null) {\r
- if (temp._name == null) return false;\r
- else if (!(this._name.equals(temp._name))) \r
- return false;\r
- }\r
- else if (temp._name != null)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Returns the value of field 'content'. The field 'content'\r
- * has the following description: internal content storage\r
- * \r
- * @return float\r
- * @return the value of field 'content'.\r
- */\r
- public float getContent()\r
- {\r
- return this._content;\r
- } //-- float getContent() \r
-\r
- /**\r
- * Returns the value of field 'name'.\r
- * \r
- * @return String\r
- * @return the value of field 'name'.\r
- */\r
- public java.lang.String getName()\r
- {\r
- return this._name;\r
- } //-- java.lang.String getName() \r
-\r
- /**\r
- * Method hasContent\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasContent()\r
- {\r
- return this._has_content;\r
- } //-- boolean hasContent() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'content'. The field 'content' has\r
- * the following description: internal content storage\r
- * \r
- * @param content the value of field 'content'.\r
- */\r
- public void setContent(float content)\r
- {\r
- this._content = content;\r
- this._has_content = true;\r
- } //-- void setContent(float) \r
-\r
- /**\r
- * Sets the value of field 'name'.\r
- * \r
- * @param name the value of field 'name'.\r
- */\r
- public void setName(java.lang.String name)\r
- {\r
- this._name = name;\r
- } //-- void setName(java.lang.String) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return Score\r
- */\r
- public static org.vamsas.objects.core.Score unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.Score) Unmarshaller.unmarshal(org.vamsas.objects.core.Score.class, reader);\r
- } //-- org.vamsas.objects.core.Score unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class ScoreDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class ScoreDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public ScoreDescriptor() \r
- {\r
- super();\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "score";\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- _content\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Score target = (Score) object;\r
- if(!target.hasContent())\r
- return null;\r
- return new java.lang.Float(target.getContent());\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Score target = (Score) object;\r
- // if null, use delete method for optional primitives \r
- if (value == null) {\r
- target.deleteContent();\r
- return;\r
- }\r
- target.setContent( ((java.lang.Float)value).floatValue());\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _content\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- FloatValidator typeValidator = new FloatValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize attribute descriptors\r
- \r
- //-- _name\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);\r
- desc.setImmutable(true);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Score target = (Score) object;\r
- return target.getName();\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Score target = (Score) object;\r
- target.setName( (java.lang.String) value);\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _name\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- { //-- local scope\r
- StringValidator typeValidator = new StringValidator();\r
- typeValidator.setWhiteSpace("preserve");\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize element descriptors\r
- \r
- } //-- org.vamsas.objects.core.ScoreDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.Score.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * a region from start to end, with flag for inclusivity of\r
- * terminii \r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Seg extends org.vamsas.client.Vobject \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _start\r
- */\r
- private int _start;\r
-\r
- /**\r
- * keeps track of state for field: _start\r
- */\r
- private boolean _has_start;\r
-\r
- /**\r
- * Field _end\r
- */\r
- private int _end;\r
-\r
- /**\r
- * keeps track of state for field: _end\r
- */\r
- private boolean _has_end;\r
-\r
- /**\r
- * when false, a consecutive range like 'start=1, end=2'\r
- * means the region lying after position 1 and before position\r
- * 2\r
- * \r
- */\r
- private boolean _inclusive;\r
-\r
- /**\r
- * keeps track of state for field: _inclusive\r
- */\r
- private boolean _has_inclusive;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Seg() \r
- {\r
- super();\r
- } //-- org.vamsas.objects.core.Seg()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method deleteEnd\r
- * \r
- */\r
- public void deleteEnd()\r
- {\r
- this._has_end= false;\r
- } //-- void deleteEnd() \r
-\r
- /**\r
- * Method deleteInclusive\r
- * \r
- */\r
- public void deleteInclusive()\r
- {\r
- this._has_inclusive= false;\r
- } //-- void deleteInclusive() \r
-\r
- /**\r
- * Method deleteStart\r
- * \r
- */\r
- public void deleteStart()\r
- {\r
- this._has_start= false;\r
- } //-- void deleteStart() \r
-\r
- /**\r
- * Note: hashCode() has not been overriden\r
- * \r
- * @param obj\r
- * @return boolean\r
- */\r
- public boolean equals(java.lang.Object obj)\r
- {\r
- if ( this == obj )\r
- return true;\r
- \r
- if (super.equals(obj)==false)\r
- return false;\r
- \r
- if (obj instanceof Seg) {\r
- \r
- Seg temp = (Seg)obj;\r
- if (this._start != temp._start)\r
- return false;\r
- if (this._has_start != temp._has_start)\r
- return false;\r
- if (this._end != temp._end)\r
- return false;\r
- if (this._has_end != temp._has_end)\r
- return false;\r
- if (this._inclusive != temp._inclusive)\r
- return false;\r
- if (this._has_inclusive != temp._has_inclusive)\r
- return false;\r
- return true;\r
- }\r
- return false;\r
- } //-- boolean equals(java.lang.Object) \r
-\r
- /**\r
- * Returns the value of field 'end'.\r
- * \r
- * @return int\r
- * @return the value of field 'end'.\r
- */\r
- public int getEnd()\r
- {\r
- return this._end;\r
- } //-- int getEnd() \r
-\r
- /**\r
- * Returns the value of field 'inclusive'. The field\r
- * 'inclusive' has the following description: when false, a\r
- * consecutive range like 'start=1, end=2'\r
- * means the region lying after position 1 and before position\r
- * 2\r
- * \r
- * \r
- * @return boolean\r
- * @return the value of field 'inclusive'.\r
- */\r
- public boolean getInclusive()\r
- {\r
- return this._inclusive;\r
- } //-- boolean getInclusive() \r
-\r
- /**\r
- * Returns the value of field 'start'.\r
- * \r
- * @return int\r
- * @return the value of field 'start'.\r
- */\r
- public int getStart()\r
- {\r
- return this._start;\r
- } //-- int getStart() \r
-\r
- /**\r
- * Method hasEnd\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasEnd()\r
- {\r
- return this._has_end;\r
- } //-- boolean hasEnd() \r
-\r
- /**\r
- * Method hasInclusive\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasInclusive()\r
- {\r
- return this._has_inclusive;\r
- } //-- boolean hasInclusive() \r
-\r
- /**\r
- * Method hasStart\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasStart()\r
- {\r
- return this._has_start;\r
- } //-- boolean hasStart() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'end'.\r
- * \r
- * @param end the value of field 'end'.\r
- */\r
- public void setEnd(int end)\r
- {\r
- this._end = end;\r
- this._has_end = true;\r
- } //-- void setEnd(int) \r
-\r
- /**\r
- * Sets the value of field 'inclusive'. The field 'inclusive'\r
- * has the following description: when false, a consecutive\r
- * range like 'start=1, end=2'\r
- * means the region lying after position 1 and before position\r
- * 2\r
- * \r
- * \r
- * @param inclusive the value of field 'inclusive'.\r
- */\r
- public void setInclusive(boolean inclusive)\r
- {\r
- this._inclusive = inclusive;\r
- this._has_inclusive = true;\r
- } //-- void setInclusive(boolean) \r
-\r
- /**\r
- * Sets the value of field 'start'.\r
- * \r
- * @param start the value of field 'start'.\r
- */\r
- public void setStart(int start)\r
- {\r
- this._start = start;\r
- this._has_start = true;\r
- } //-- void setStart(int) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return Seg\r
- */\r
- public static org.vamsas.objects.core.Seg unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (org.vamsas.objects.core.Seg) Unmarshaller.unmarshal(org.vamsas.objects.core.Seg.class, reader);\r
- } //-- org.vamsas.objects.core.Seg unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package org.vamsas.objects.core;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class SegDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class SegDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field nsPrefix\r
- */\r
- private java.lang.String nsPrefix;\r
-\r
- /**\r
- * Field nsURI\r
- */\r
- private java.lang.String nsURI;\r
-\r
- /**\r
- * Field xmlName\r
- */\r
- private java.lang.String xmlName;\r
-\r
- /**\r
- * Field identity\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public SegDescriptor() \r
- {\r
- super();\r
- nsURI = "http://www.vamsas.org";\r
- xmlName = "seg";\r
- org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
- org.exolab.castor.mapping.FieldHandler handler = null;\r
- org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
- //-- initialize attribute descriptors\r
- \r
- //-- _start\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Seg target = (Seg) object;\r
- if(!target.hasStart())\r
- return null;\r
- return new java.lang.Integer(target.getStart());\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Seg target = (Seg) object;\r
- // ignore null values for non optional primitives\r
- if (value == null) return;\r
- \r
- target.setStart( ((java.lang.Integer)value).intValue());\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _start\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- IntegerValidator typeValidator= new IntegerValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _end\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Seg target = (Seg) object;\r
- if(!target.hasEnd())\r
- return null;\r
- return new java.lang.Integer(target.getEnd());\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Seg target = (Seg) object;\r
- // ignore null values for non optional primitives\r
- if (value == null) return;\r
- \r
- target.setEnd( ((java.lang.Integer)value).intValue());\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _end\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- IntegerValidator typeValidator= new IntegerValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- _inclusive\r
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_inclusive", "inclusive", org.exolab.castor.xml.NodeType.Attribute);\r
- handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
- public java.lang.Object getValue( java.lang.Object object ) \r
- throws IllegalStateException\r
- {\r
- Seg target = (Seg) object;\r
- if(!target.hasInclusive())\r
- return null;\r
- return (target.getInclusive() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
- }\r
- public void setValue( java.lang.Object object, java.lang.Object value) \r
- throws IllegalStateException, IllegalArgumentException\r
- {\r
- try {\r
- Seg target = (Seg) object;\r
- // ignore null values for non optional primitives\r
- if (value == null) return;\r
- \r
- target.setInclusive( ((java.lang.Boolean)value).booleanValue());\r
- }\r
- catch (java.lang.Exception ex) {\r
- throw new IllegalStateException(ex.toString());\r
- }\r
- }\r
- public java.lang.Object newInstance( java.lang.Object parent ) {\r
- return null;\r
- }\r
- };\r
- desc.setHandler(handler);\r
- desc.setRequired(true);\r
- desc.setMultivalued(false);\r
- addFieldDescriptor(desc);\r
- \r
- //-- validation code for: _inclusive\r
- fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
- fieldValidator.setMinOccurs(1);\r
- { //-- local scope\r
- BooleanValidator typeValidator = new BooleanValidator();\r
- fieldValidator.setValidator(typeValidator);\r
- }\r
- desc.setValidator(fieldValidator);\r
- //-- initialize element descriptors\r
- \r
- } //-- org.vamsas.objects.core.SegDescriptor()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method getAccessMode\r
- * \r
- * \r
- * \r
- * @return AccessMode\r
- */\r
- public org.exolab.castor.mapping.AccessMode getAccessMode()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
- /**\r
- * Method getExtends\r
- * \r
- * \r
- * \r
- * @return ClassDescriptor\r
- */\r
- public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
- {\r
- return null;\r
- } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
- /**\r
- * Method getIdentity\r
- * \r
- * \r
- * \r
- * @return FieldDescriptor\r
- */\r
- public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
- {\r
- return identity;\r
- } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
- /**\r
- * Method getJavaClass\r
- * \r
- * \r
- * \r
- * @return Class\r
- */\r
- public java.lang.Class getJavaClass()\r
- {\r
- return org.vamsas.objects.core.Seg.class;\r
- } //-- java.lang.Class getJavaClass() \r
-\r
- /**\r
- * Method getNameSpacePrefix\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpacePrefix()\r
- {\r
- return nsPrefix;\r
- } //-- java.lang.String getNameSpacePrefix() \r
-\r
- /**\r
- * Method getNameSpaceURI\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getNameSpaceURI()\r
- {\r
- return nsURI;\r
- } //-- java.lang.String getNameSpaceURI() \r
-\r
- /**\r
- * Method getValidator\r
- * \r
- * \r
- * \r
- * @return TypeValidator\r
- */\r
- public org.exolab.castor.xml.TypeValidator getValidator()\r
- {\r
- return this;\r
- } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
- /**\r
- * Method getXMLName\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String getXMLName()\r
- {\r
- return xmlName;\r
- } //-- java.lang.String getXMLName() \r
-\r
-}\r
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, 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()
-
-}
+++ /dev/null
-/**
- *
- */
-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; q<appdatas.length; q++) {
- String refstring=appdatas[q].getDataReference();
- if (refstring!=null)
- apdrefs.add(refstring);
- User users[] = appdatas[q].getUser();
-
- if (users!=null)
- for (int u=0; u<users.length; u++) {
- refstring=users[u].getDataReference();
- if (refstring!=null)
- apdrefs.add(new String(refstring)); // avoid referencing.
- }
- }
- if (apdrefs.size()>0)
- 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; q<appdatas.length; q++) {
- boolean t;
- if (t=test.process(appdatas[q]))
- apdrefs.add(appdatas[q]);
- if (t || cascade) {
- User users[] = appdatas[q].getUser();
- if (users!=null)
- for (int u=0; u<users.length; u++)
- if (test.process(users[u]))
- apdrefs.add(users[u]);
- }
- }
- if (apdrefs.size()>0)
- 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<j; i++) {
- ApplicationData o = dest.getApplicationData()[i];
- // ensure new urn is really unique
- int v = 1;
- // TODO: while (o.getUrn().equals(urn)) {
- urn = base+"/"+v++;
- //}
- }
- return urn;
- }
-}
+++ /dev/null
-package org.vamsas.objects.utils;
-
-import org.vamsas.objects.core.*;
-import org.vamsas.objects.utils.document.VersionEntries;
-
-/**
- * various vamsas-client independent helpers
- * for creating and manipulating the vamsasDocument Vobject
- * @author jimp
- *
- */
-public class DocumentStuff {
- public static VamsasDocument newVamsasDocument(VAMSAS root[], String version) {
- return newVamsasDocument(root, ProvenanceStuff.newProvenance(
- "AUTO:org.vamsas.DocumentStuff.newVamsasDocument",
- "Vamsas Document created"),
- version);
- }
- public static VamsasDocument newVamsasDocument(VAMSAS root[]) {
- return newVamsasDocument(root, ProvenanceStuff.newProvenance(
- "AUTO:org.vamsas.DocumentStuff.newVamsasDocument",
- "Vamsas Document created"),
- VersionEntries.latestVersion());
- }
- public static VamsasDocument newVamsasDocument(VAMSAS root[], Provenance p, String version) {
- VamsasDocument doc = new VamsasDocument();
- for (int r=0; r<root.length; r++) {
- doc.addVAMSAS(root[r]);
- }
- doc.setProvenance(p);
- doc.setVersion(version);
- return doc;
- }
-}
+++ /dev/null
-/*\r
- * Cay S. Horstmann & Gary Cornell, Core Java\r
- * Published By Sun Microsystems Press/Prentice-Hall\r
- * Copyright (C) 1997 Sun Microsystems Inc.\r
- * All Rights Reserved.\r
- *\r
- * Permission to use, copy, modify, and distribute this \r
- * software and its documentation for NON-COMMERCIAL purposes\r
- * and without fee is hereby granted provided that this \r
- * copyright notice appears in all copies. \r
- * \r
- * THE AUTHORS AND PUBLISHER MAKE NO REPRESENTATIONS OR \r
- * WARRANTIES ABOUT THE SUITABILITY OF THE SOFTWARE, EITHER \r
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE \r
- * IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A \r
- * PARTICULAR PURPOSE, OR NON-INFRINGEMENT. THE AUTHORS\r
- * AND PUBLISHER SHALL NOT BE LIABLE FOR ANY DAMAGES SUFFERED \r
- * BY LICENSEE AS A RESULT OF USING, MODIFYING OR DISTRIBUTING \r
- * THIS SOFTWARE OR ITS DERIVATIVES.\r
- */\r
-\r
-/**\r
- * A class for formatting numbers that follows printf conventions.\r
- * Also implements C-like atoi and atof functions\r
- * @version 1.03 25 Oct 1997\r
- * @author Cay Horstmann\r
- */\r
-\r
-package org.vamsas.objects.utils;\r
-\r
-import java.io.*;\r
-\r
-public class Format { /**\r
- * Formats the number following printf conventions.\r
- * Main limitation: Can only handle one format parameter at a time\r
- * Use multiple Format objects to format more than one number\r
- * @param s the format string following printf conventions\r
- * The string has a prefix, a format code and a suffix. The prefix and suffix\r
- * become part of the formatted output. The format code directs the\r
- * formatting of the (single) parameter to be formatted. The code has the\r
- * following structure\r
- * <ul>\r
- * <li> a % (required)\r
- * <li> a modifier (optional)\r
- * <dl>\r
- * <dt> + <dd> forces display of + for positive numbers\r
- * <dt> 0 <dd> show leading zeroes\r
- * <dt> - <dd> align left in the field\r
- * <dt> space <dd> prepend a space in front of positive numbers\r
- * <dt> # <dd> use "alternate" format. Add 0 or 0x for octal or hexadecimal numbers. Don't suppress trailing zeroes in general floating point format.\r
- * </dl>\r
- * <li> an integer denoting field width (optional)\r
- * <li> a period followed by an integer denoting precision (optional)\r
- * <li> a format descriptor (required)\r
- * <dl>\r
- * <dt>f <dd> floating point number in fixed format\r
- * <dt>e, E <dd> 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.\r
- * <dt>g, G <dd> 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.\r
- * <dt>d, i <dd> integer in decimal\r
- * <dt>x <dd> integer in hexadecimal\r
- * <dt>o <dd> integer in octal\r
- * <dt>s <dd> string\r
- * <dt>c <dd> character\r
- * </dl>\r
- * </ul>\r
- * @exception IllegalArgumentException if bad format\r
- */\r
-\r
- public Format(String s) {\r
- width = 0;\r
- precision = -1;\r
- pre = "";\r
- post = "";\r
- leading_zeroes = false;\r
- show_plus = false;\r
- alternate = false;\r
- show_space = false;\r
- left_align = false;\r
- fmt = ' ';\r
-\r
- int state = 0;\r
- int length = s.length();\r
- int parse_state = 0;\r
- // 0 = prefix, 1 = flags, 2 = width, 3 = precision,\r
- // 4 = format, 5 = end\r
- int i = 0;\r
-\r
- while (parse_state == 0) {\r
- if (i >= length)\r
- parse_state = 5;\r
- else if (s.charAt(i) == '%') {\r
- if (i < length - 1) {\r
- if (s.charAt(i + 1) == '%') {\r
- pre = pre + '%';\r
- i++;\r
- } else\r
- parse_state = 1;\r
- } else\r
- throw new java.lang.IllegalArgumentException();\r
- } else\r
- pre = pre + s.charAt(i);\r
- i++;\r
- }\r
- while (parse_state == 1) {\r
- if (i >= length)\r
- parse_state = 5;\r
- else if (s.charAt(i) == ' ')\r
- show_space = true;\r
- else if (s.charAt(i) == '-')\r
- left_align = true;\r
- else if (s.charAt(i) == '+')\r
- show_plus = true;\r
- else if (s.charAt(i) == '0')\r
- leading_zeroes = true;\r
- else if (s.charAt(i) == '#')\r
- alternate = true;\r
- else {\r
- parse_state = 2;\r
- i--;\r
- }\r
- i++;\r
- }\r
- while (parse_state == 2) {\r
- if (i >= length)\r
- parse_state = 5;\r
- else if ('0' <= s.charAt(i) && s.charAt(i) <= '9') {\r
- width = width * 10 + s.charAt(i) - '0';\r
- i++;\r
- } else if (s.charAt(i) == '.') {\r
- parse_state = 3;\r
- precision = 0;\r
- i++;\r
- } else\r
- parse_state = 4;\r
- }\r
- while (parse_state == 3) {\r
- if (i >= length)\r
- parse_state = 5;\r
- else if ('0' <= s.charAt(i) && s.charAt(i) <= '9') {\r
- precision = precision * 10 + s.charAt(i) - '0';\r
- i++;\r
- } else\r
- parse_state = 4;\r
- }\r
- if (parse_state == 4) {\r
- if (i >= length)\r
- parse_state = 5;\r
- else\r
- fmt = s.charAt(i);\r
- i++;\r
- }\r
- if (i < length)\r
- post = s.substring(i, length);\r
- }\r
-\r
- /**\r
- * prints a formatted number following printf conventions\r
- * @param s a PrintStream\r
- * @param fmt the format string\r
- * @param x the double to print\r
- */\r
-\r
- public static void print(java.io.PrintStream s, String fmt, double x) {\r
- s.print(new Format(fmt).form(x));\r
- }\r
-\r
- /**\r
- * prints a formatted number following printf conventions\r
- * @param s a PrintStream\r
- * @param fmt the format string\r
- * @param x the long to print\r
- */\r
- public static void print(java.io.PrintStream s, String fmt, long x) {\r
- s.print(new Format(fmt).form(x));\r
- }\r
-\r
- /**\r
- * prints a formatted number following printf conventions\r
- * @param s a PrintStream\r
- * @param fmt the format string\r
- * @param x the character to \r
- */\r
-\r
- public static void print(java.io.PrintStream s, String fmt, char x) {\r
- s.print(new Format(fmt).form(x));\r
- }\r
-\r
- /**\r
- * prints a formatted number following printf conventions\r
- * @param s a PrintStream, fmt the format string\r
- * @param x a string that represents the digits to print\r
- */\r
-\r
- public static void print(java.io.PrintStream s, String fmt, String x) {\r
- s.print(new Format(fmt).form(x));\r
- }\r
-\r
- /**\r
- * Converts a string of digits (decimal, octal or hex) to an integer\r
- * @param s a string\r
- * @return the numeric value of the prefix of s representing a base 10 integer\r
- */\r
-\r
- public static int atoi(String s) {\r
- return (int)atol(s);\r
- }\r
-\r
- /**\r
- * Converts a string of digits (decimal, octal or hex) to a long integer\r
- * @param s a string\r
- * @return the numeric value of the prefix of s representing a base 10 integer\r
- */\r
-\r
- public static long atol(String s) {\r
- int i = 0;\r
-\r
- while (i < s.length() && Character.isWhitespace(s.charAt(i)))\r
- i++;\r
- if (i < s.length() && s.charAt(i) == '0') {\r
- if (i + 1 < s.length() && (s.charAt(i + 1) == 'x' || s.charAt(i + 1) == 'X'))\r
- return parseLong(s.substring(i + 2), 16);\r
- else\r
- return parseLong(s, 8);\r
- } else\r
- return parseLong(s, 10);\r
- }\r
-\r
- private static long parseLong(String s, int base) {\r
- int i = 0;\r
- int sign = 1;\r
- long r = 0;\r
-\r
- while (i < s.length() && Character.isWhitespace(s.charAt(i)))\r
- i++;\r
- if (i < s.length() && s.charAt(i) == '-') {\r
- sign = -1;\r
- i++;\r
- } else if (i < s.length() && s.charAt(i) == '+') {\r
- i++;\r
- }\r
- while (i < s.length()) {\r
- char ch = s.charAt(i);\r
- if ('0' <= ch && ch < '0' + base)\r
- r = r * base + ch - '0';\r
- else if ('A' <= ch && ch < 'A' + base - 10)\r
- r = r * base + ch - 'A' + 10 ;\r
- else if ('a' <= ch && ch < 'a' + base - 10)\r
- r = r * base + ch - 'a' + 10 ;\r
- else\r
- return r * sign;\r
- i++;\r
- }\r
- return r * sign;\r
- }\r
-\r
- /**\r
- * Converts a string of digits to an double\r
- * @param s a string\r
- */\r
-\r
- public static double atof(String s) {\r
- int i = 0;\r
- int sign = 1;\r
- double r = 0; // integer part\r
- double f = 0; // fractional part\r
- double p = 1; // exponent of fractional part\r
- int state = 0; // 0 = int part, 1 = frac part\r
-\r
- while (i < s.length() && Character.isWhitespace(s.charAt(i)))\r
- i++;\r
- if (i < s.length() && s.charAt(i) == '-') {\r
- sign = -1;\r
- i++;\r
- } else if (i < s.length() && s.charAt(i) == '+') {\r
- i++;\r
- }\r
- while (i < s.length()) {\r
- char ch = s.charAt(i);\r
- if ('0' <= ch && ch <= '9') {\r
- if (state == 0)\r
- r = r * 10 + ch - '0';\r
- else if (state == 1) {\r
- p = p / 10;\r
- r = r + p * (ch - '0');\r
- }\r
- } else if (ch == '.') {\r
- if (state == 0)\r
- state = 1;\r
- else\r
- return sign * r;\r
- } else if (ch == 'e' || ch == 'E') {\r
- long e = (int)parseLong(s.substring(i + 1), 10);\r
- return sign * r * Math.pow(10, e);\r
- } else\r
- return sign * r;\r
- i++;\r
- }\r
- return sign * r;\r
- }\r
-\r
- /**\r
- * Formats a double into a string (like sprintf in C)\r
- * @param x the number to format\r
- * @return the formatted string \r
- * @exception IllegalArgumentException if bad argument\r
- */\r
-\r
- public String form(double x) {\r
- String r;\r
- if (precision < 0)\r
- precision = 6;\r
- int s = 1;\r
- if (x < 0) {\r
- x = -x;\r
- s = -1;\r
- }\r
- if (fmt == 'f')\r
- r = fixed_format(x);\r
- else if (fmt == 'e' || fmt == 'E' || fmt == 'g' || fmt == 'G')\r
- r = exp_format(x);\r
- else\r
- throw new java.lang.IllegalArgumentException();\r
-\r
- return pad(sign(s, r));\r
- }\r
-\r
- /**\r
- * Formats a long integer into a string (like sprintf in C)\r
- * @param x the number to format\r
- * @return the formatted string \r
- */\r
-\r
- public String form(long x) {\r
- String r;\r
- int s = 0;\r
- if (fmt == 'd' || fmt == 'i') {\r
- if (x < 0) {\r
- r = ("" + x).substring(1);\r
- s = -1;\r
- } else {\r
- r = "" + x;\r
- s = 1;\r
- }\r
- } else if (fmt == 'o')\r
- r = convert(x, 3, 7, "01234567");\r
- else if (fmt == 'x')\r
- r = convert(x, 4, 15, "0123456789abcdef");\r
- else if (fmt == 'X')\r
- r = convert(x, 4, 15, "0123456789ABCDEF");\r
- else\r
- throw new java.lang.IllegalArgumentException();\r
-\r
- return pad(sign(s, r));\r
- }\r
-\r
- /**\r
- * Formats a character into a string (like sprintf in C)\r
- * @param x the value to format\r
- * @return the formatted string \r
- */\r
-\r
- public String form(char c) {\r
- if (fmt != 'c')\r
- throw new java.lang.IllegalArgumentException();\r
-\r
- String r = "" + c;\r
- return pad(r);\r
- }\r
-\r
- /**\r
- * Formats a string into a larger string (like sprintf in C)\r
- * @param x the value to format\r
- * @return the formatted string \r
- */\r
-\r
- public String form(String s) {\r
- if (fmt != 's')\r
- throw new java.lang.IllegalArgumentException();\r
- if (precision >= 0)\r
- s = s.substring(0, precision);\r
- return pad(s);\r
- }\r
-\r
-\r
- /**\r
- * a test stub for the format class\r
- */\r
-\r
- public static void main(String[] a) {\r
- double x = 1.23456789012;\r
- double y = 123;\r
- double z = 1.2345e30;\r
- double w = 1.02;\r
- double u = 1.234e-5;\r
- int d = 0xCAFE;\r
- Format.print(System.out, "x = |%f|\n", x);\r
- Format.print(System.out, "u = |%20f|\n", u);\r
- Format.print(System.out, "x = |% .5f|\n", x);\r
- Format.print(System.out, "w = |%20.5f|\n", w);\r
- Format.print(System.out, "x = |%020.5f|\n", x);\r
- Format.print(System.out, "x = |%+20.5f|\n", x);\r
- Format.print(System.out, "x = |%+020.5f|\n", x);\r
- Format.print(System.out, "x = |% 020.5f|\n", x);\r
- Format.print(System.out, "y = |%#+20.5f|\n", y);\r
- Format.print(System.out, "y = |%-+20.5f|\n", y);\r
- Format.print(System.out, "z = |%20.5f|\n", z);\r
-\r
- Format.print(System.out, "x = |%e|\n", x);\r
- Format.print(System.out, "u = |%20e|\n", u);\r
- Format.print(System.out, "x = |% .5e|\n", x);\r
- Format.print(System.out, "w = |%20.5e|\n", w);\r
- Format.print(System.out, "x = |%020.5e|\n", x);\r
- Format.print(System.out, "x = |%+20.5e|\n", x);\r
- Format.print(System.out, "x = |%+020.5e|\n", x);\r
- Format.print(System.out, "x = |% 020.5e|\n", x);\r
- Format.print(System.out, "y = |%#+20.5e|\n", y);\r
- Format.print(System.out, "y = |%-+20.5e|\n", y);\r
-\r
- Format.print(System.out, "x = |%g|\n", x);\r
- Format.print(System.out, "z = |%g|\n", z);\r
- Format.print(System.out, "w = |%g|\n", w);\r
- Format.print(System.out, "u = |%g|\n", u);\r
- Format.print(System.out, "y = |%.2g|\n", y);\r
- Format.print(System.out, "y = |%#.2g|\n", y);\r
-\r
- Format.print(System.out, "d = |%d|\n", d);\r
- Format.print(System.out, "d = |%20d|\n", d);\r
- Format.print(System.out, "d = |%020d|\n", d);\r
- Format.print(System.out, "d = |%+20d|\n", d);\r
- Format.print(System.out, "d = |% 020d|\n", d);\r
- Format.print(System.out, "d = |%-20d|\n", d);\r
- Format.print(System.out, "d = |%20.8d|\n", d);\r
- Format.print(System.out, "d = |%x|\n", d);\r
- Format.print(System.out, "d = |%20X|\n", d);\r
- Format.print(System.out, "d = |%#20x|\n", d);\r
- Format.print(System.out, "d = |%020X|\n", d);\r
- Format.print(System.out, "d = |%20.8x|\n", d);\r
- Format.print(System.out, "d = |%o|\n", d);\r
- Format.print(System.out, "d = |%020o|\n", d);\r
- Format.print(System.out, "d = |%#20o|\n", d);\r
- Format.print(System.out, "d = |%#020o|\n", d);\r
- Format.print(System.out, "d = |%20.12o|\n", d);\r
-\r
- Format.print(System.out, "s = |%-20s|\n", "Hello");\r
- Format.print(System.out, "s = |%-20c|\n", '!');\r
-\r
- // regression test to confirm fix of reported bugs\r
-\r
- Format.print(System.out, "|%i|\n", Long.MIN_VALUE);\r
-\r
- Format.print(System.out, "|%6.2e|\n", 0.0);\r
- Format.print(System.out, "|%6.2g|\n", 0.0);\r
-\r
- Format.print(System.out, "|%6.2f|\n", 9.99);\r
- Format.print(System.out, "|%6.2f|\n", 9.999);\r
-\r
- Format.print(System.out, "|%6.0f|\n", 9.999);\r
- }\r
-\r
- private static String repeat(char c, int n) {\r
- if (n <= 0)\r
- return "";\r
- StringBuffer s = new StringBuffer(n);\r
- for (int i = 0; i < n; i++)\r
- s.append(c);\r
- return s.toString();\r
- }\r
-\r
- private static String convert(long x, int n, int m, String d) {\r
- if (x == 0)\r
- return "0";\r
- String r = "";\r
- while (x != 0) {\r
- r = d.charAt((int)(x & m)) + r;\r
- x = x >>> n;\r
- }\r
- return r;\r
- }\r
-\r
- private String pad(String r) {\r
- String p = repeat(' ', width - r.length());\r
- if (left_align)\r
- return pre + r + p + post;\r
- else\r
- return pre + p + r + post;\r
- }\r
-\r
- private String sign(int s, String r) {\r
- String p = "";\r
- if (s < 0)\r
- p = "-";\r
- else if (s > 0) {\r
- if (show_plus)\r
- p = "+";\r
- else if (show_space)\r
- p = " ";\r
- } else {\r
- if (fmt == 'o' && alternate && r.length() > 0 && r.charAt(0) != '0')\r
- p = "0";\r
- else if (fmt == 'x' && alternate)\r
- p = "0x";\r
- else if (fmt == 'X' && alternate)\r
- p = "0X";\r
- }\r
- int w = 0;\r
- if (leading_zeroes)\r
- w = width;\r
- else if ((fmt == 'd' || fmt == 'i' || fmt == 'x' || fmt == 'X' || fmt == 'o')\r
- && precision > 0)\r
- w = precision;\r
-\r
- return p + repeat('0', w - p.length() - r.length()) + r;\r
- }\r
-\r
- private String fixed_format(double d) {\r
- boolean removeTrailing\r
- = (fmt == 'G' || fmt == 'g') && !alternate;\r
- // remove trailing zeroes and decimal point\r
-\r
- if (d > 0x7FFFFFFFFFFFFFFFL)\r
- return exp_format(d);\r
- if (precision == 0)\r
- return (long)(d + 0.5) + (removeTrailing ? "" : ".");\r
-\r
- long whole = (long)d;\r
- double fr = d - whole; // fractional part\r
- if (fr >= 1 || fr < 0)\r
- return exp_format(d);\r
-\r
- double factor = 1;\r
- String leading_zeroes = "";\r
- for (int i = 1; i <= precision && factor <= 0x7FFFFFFFFFFFFFFFL; i++) {\r
- factor *= 10;\r
- leading_zeroes = leading_zeroes + "0";\r
- }\r
- long l = (long) (factor * fr + 0.5);\r
- if (l >= factor) {\r
- l = 0;\r
- whole++;\r
- } // CSH 10-25-97\r
-\r
- String z = leading_zeroes + l;\r
- z = "." + z.substring(z.length() - precision, z.length());\r
-\r
- if (removeTrailing) {\r
- int t = z.length() - 1;\r
- while (t >= 0 && z.charAt(t) == '0')\r
- t--;\r
- if (t >= 0 && z.charAt(t) == '.')\r
- t--;\r
- z = z.substring(0, t + 1);\r
- }\r
-\r
- return whole + z;\r
- }\r
-\r
- private String exp_format(double d) {\r
- String f = "";\r
- int e = 0;\r
- double dd = d;\r
- double factor = 1;\r
- if (d != 0) {\r
- while (dd > 10) {\r
- e++;\r
- factor /= 10;\r
- dd = dd / 10;\r
- }\r
- while (dd < 1) {\r
- e--;\r
- factor *= 10;\r
- dd = dd * 10;\r
- }\r
- }\r
- if ((fmt == 'g' || fmt == 'G') && e >= -4 && e < precision)\r
- return fixed_format(d);\r
-\r
- d = d * factor;\r
- f = f + fixed_format(d);\r
-\r
- if (fmt == 'e' || fmt == 'g')\r
- f = f + "e";\r
- else\r
- f = f + "E";\r
-\r
- String p = "000";\r
- if (e >= 0) {\r
- f = f + "+";\r
- p = p + e;\r
- } else {\r
- f = f + "-";\r
- p = p + (-e);\r
- }\r
-\r
- return f + p.substring(p.length() - 3, p.length());\r
- }\r
-\r
- private int width;\r
- private int precision;\r
- private String pre;\r
- private String post;\r
- private boolean leading_zeroes;\r
- private boolean show_plus;\r
- private boolean alternate;\r
- private boolean show_space;\r
- private boolean left_align;\r
- private char fmt; // one of cdeEfgGiosxXos\r
-}\r
-\r
-\r
-\r
-\r
-\r
+++ /dev/null
-package org.vamsas.objects.utils;\r
-\r
-/**\r
- * dict attribute values for glyph symbol sets found in org.vamsas.objects.core.AnnotationElement\r
- * TODO: add validators and multilength symbols.\r
- * @author JimP\r
- *\r
- */\r
-public class GlyphDictionary {\r
- /**\r
- * standard H, E, or C three state secondary structure assignment.\r
- */\r
- static final public String PROTEIN_SS_3STATE="aasecstr_3"; // HE, blank or C\r
- /**\r
- * default glyph type attribute indicates a UTF8 character\r
- */\r
- static final public String DEFAULT="utf8";\r
- /**\r
- * kyte and doolittle hydrophobicity\r
- * TODO: specify this glyph set.\r
- */\r
- static final public String PROTEIN_HD_HYDRO="kd_hydrophobicity";\r
-}\r
+++ /dev/null
-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));
- }
-
-}
+++ /dev/null
-/*
- * 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<k; j+=width)
- if (j+width<k)
- pir_out.write(seq.getSequence().substring(j,j+width)+"\n");
- else
- pir_out.write(seq.getSequence().substring(j)+"\n");
- pir_out.flush();
- }
-
- public static void write_FastaSeq(OutputStream os, SequenceType seq) throws IOException {
- BufferedWriter fasta_out = new BufferedWriter(new OutputStreamWriter(os));
- fasta_out.write(">"+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(); j<k; j+=width)
- if (j+width<k)
- fasta_out.write(seq.getSequence().substring(j,j+width)+"\n");
- else
- fasta_out.write(seq.getSequence().substring(j)+"\n");
- fasta_out.flush();
- }
- /**
- *validate a SequenceType Vobject as an info:iubmb.org/aminoacid SequenceType
- *This version resolves references to Sequence objects from AlignmentSequence
- *TODO: Define info: urn for dictionary string (could also be regex of valid characters!)
- * @param s
- * @param dict TODO
- * @return true if a valid amino acid sequence Vobject
- */
- private static boolean valid_aadictionary_string(String s, String dict) {
- if (s==null)
- return false;
- // validate against dictionary
- // TODO generalise to resolve dictionary against info: urn for dictionary type
- Pattern aa_repl = Pattern.compile("[ARNDCQEGHILKMFPSTWYVUX]+", Pattern.CASE_INSENSITIVE);
- String remnants = aa_repl.matcher(s).replaceAll("");
- return !remnants.matches("//S+");
- }
-
- public static Sequence newSequence(String Name, String Sequence, String Dictionary, int start, int end) {
- //TODO: make hierarchy reflecting the SeqType Vobject.
- Sequence seq= new Sequence();
- seq.setDictionary(Dictionary);
- seq.setName(Name);
- seq.setSequence(Sequence);
- seq.setStart(start);
- if (start<=end) {
- if ((end-start)!=Sequence.length())
- seq.setEnd(start+Sequence.length());
- } else {
- // reverse topology mapping. TODO: VAMSAS: decide if allowed to do start>end 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 (start<refseq.getStart())
- start = refseq.getStart();
- asq.setStart(start);
- if (end>refseq.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;
- }
-}
+++ /dev/null
-/*
- * 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);
- }
-}
+++ /dev/null
-/*
- * 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<nseq; i++) {
- fasta_out.write(">"+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<k) {
- int d = k-j;
- if (d>=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<nseq; i++) {
- seqset[i] = (Sequence) seqs.elementAt(i);
- }
- return seqset;
- }
-
- return null;
- }
-
- public static Hashtable uniquify(SequenceType[] sequences) {
- System.err.println("NOT FULLY IMPLEMENTED!"); // TODO: Finish adapting this method
- // TODO: do we need this with vamsas sequences ?
- // Generate a safely named sequence set and a hash to recover the sequence names
- Hashtable map = new Hashtable();
- for (int i = 0; i < sequences.length; i++) {
- String safename = new String("Sequence" + i);
- map.put(safename, sequences[i].getName());
- sequences[i].setName(safename);
- }
- return map;
- }
-
- public static boolean deuniquify(Hashtable map, SequenceType[] sequences) {
- System.err.println("NOT FULLY IMPLEMENTED!"); // TODO: Finish adapting this method
- // TODO: do we need this with vamsas sequences ?
- // recover unsafe sequence names for a sequence set
- boolean allfound = true;
- for (int i = 0; i < sequences.length; i++) {
- if (map.containsKey(sequences[i].getName())) {
- String unsafename = (String) map.get(sequences[i].getName());
- sequences[i].setName(unsafename);
- } else {
- allfound = false;
- }
- }
- return allfound;
- }
-
-}
+++ /dev/null
-package org.vamsas.objects.utils;
-
-public class SymbolDictionary {
- /**
- * defines standard names and properties for vamsas sequence dictionaries
- */
- static final public String STANDARD_AA="info:iubmb.org/aminoacids"; // strict 1 letter code
- static final public String STANDARD_NA="info:iubmb.org/nucleosides";// strict 1 letter code (do not allow arbitrary rare nucleosides)
- /**
- * TODO: Vamsas Dictionary properties interface
- * an interface for dictionary provides :
- * validation for a string
- * symbolwidth (or symbol next/previous)
- * mappings to certain other dictionaries (one2three, etc)
- * gap-character test
- *
- */
-
-}
+++ /dev/null
-/**
- *
- */
-package org.vamsas.objects.utils.document;
-
-import java.util.Hashtable;
-
-/**
- * enumerates versions for the VamsasDocument.Version string
- * provides version comparison methods
- * TODO: LATER: associate schema versions with these strings
- */
-public class VersionEntries {
- public static final String ALPHA_VERSION="alpha";
- public static final String BETA_VERSION="beta";
- protected static Hashtable versions;
- static {
- versions = new Hashtable();
- // integers represent version hierarchy - 0 precedes 1
- versions.put(ALPHA_VERSION, new Integer(0));
- versions.put(BETA_VERSION, new Integer(1));
- }
- // TODO: LATER: decide on best pattern for enumeration classes (ie - need an ordered list of versions, and validator, plus explicit enum-strings)
- public static boolean isVersion(String vstring) {
- return versions.containsKey(vstring);
- }
- /**
- * returns 0 if levels are equivalent,
- * 1 if higher is valid and higher,
- * 2 if lower is valid and higher
- * -1 if both levels are invalid
- * @param higher
- * @param lower
- * @return
- */
- public static int compare(String higher, String lower) {
- int v_1 = versions.containsKey(higher) ? ((Integer) versions.get(higher)).intValue() : -1;
- int v_2 = versions.containsKey(lower) ? ((Integer) versions.get(lower)).intValue() : -1;
- int comp = v_1<v_2 ? 2 : v_1 == v_2 ? 0 : 1;
- return (comp==0) ? (v_1!=-1 ? 0 : -1) : comp;
- }
- /**
- * @return the latest version that this vamsas library supports
- */
- public static String latestVersion() {
- return BETA_VERSION;
- }
-
-}
+++ /dev/null
-/**
- * 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.test;
-
-import org.vamsas.client.*;
-
-import java.awt.Event;
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
-import java.io.IOException;
-import java.util.Vector;
-/**
- * Toy vamsas command line client application demonstrating the API.
- *
- * @author jimp
- */
-
-public class ExampleApplication {
- private static ClientHandle app;
- private static UserHandle user; // TODO: make this something defined by the api
- private static IClientFactory clientfactory;
- private static IClient vorbaclient;
- private static byte[] mydata;
- private static Vector vamsasObjects;
- private static boolean isUpdated = false;
- private static boolean isShuttingdown = false;
- private static boolean isFinalizing = false;
- private static void processVamsasDocument(IClientDocument doc) {
- // merge vamsasObjects with vamsas objects in document
- // get this apps 'mydata' if it hasn't got it already.
- // .. access this application's 'public' mydata' if there is any.
- }
- private static void addHandlers(IClient avorbaclient) {
- // make a non-volatile reference to the client instance.
- final IClient vorbaclient = avorbaclient;
- // register update handler
- vorbaclient.addDocumentUpdateHandler(new PropertyChangeListener() {
- public void propertyChange(PropertyChangeEvent evt) {
- System.out.println("Vamsas document update for "+evt.getPropertyName()
- +": "+evt.getOldValue()+" to "+evt.getNewValue());
- // merge new data into ours.
- isUpdated=true; // tell main thread to reflect change...
- }
- });
- // register close handler
- vorbaclient.addVorbaEventHandler(Events.DOCUMENT_REQUESTTOCLOSE,
- new PropertyChangeListener() {
- public void propertyChange(PropertyChangeEvent evt) {
- System.out.println("Received request to close vamsas document.");
- // ask user for a filename to save it to.
- // Then pass it to the vorba object...
- vorbaclient.storeDocument(new java.io.File("UserLocation"));
- }
- });
-
- // register some more handlers to monitor the session :
-
- vorbaclient.addVorbaEventHandler(Events.CLIENT_CREATION,
- new PropertyChangeListener() {
- public void propertyChange(PropertyChangeEvent evt) {
- System.out.println("New Vamsas client for "+evt.getPropertyName()
- +": "+evt.getOldValue()+" to "+evt.getNewValue());
- // tell app add new client to its list of clients.
- }
- });
- vorbaclient.addVorbaEventHandler(Events.CLIENT_FINALIZATION,
- new PropertyChangeListener() {
- public void propertyChange(PropertyChangeEvent evt) {
- System.out.println("Vamsas client finalizing for "+evt.getPropertyName()
- +": "+evt.getOldValue()+" to "+evt.getNewValue());
- // tell app to update its list of clients to communicate with.
- }
- });
- vorbaclient.addVorbaEventHandler(Events.SESSION_SHUTDOWN,
- new PropertyChangeListener() {
- public void propertyChange(PropertyChangeEvent evt) {
- System.out.println("Session "+evt.getPropertyName()+" is shutting down.");
- // tell app to finalize its session data before shutdown.
- }
- });
- vorbaclient.addVorbaEventHandler(Events.DOCUMENT_FINALIZEAPPDATA,
- new PropertyChangeListener() {
- public void propertyChange(PropertyChangeEvent evt) {
- System.out.println("Application received a DOCUMENT_FINALIZEAPPDATA event.");
- // tell app to finalize its session data prior to the storage of the current session as an archive.
- }
- });
-
- }
- public static String
- Usage="ExampleApplication <vamsasFileDirectory> <vamsasSessionURN> <action> [+<arguments>]\n"
- +"<action> 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;s<sessions.length; s++)
- System.err.println(sessions[s]);
- System.exit(2);
- }
- addHandlers(vorbaclient);
- try {
- vorbaclient.joinSession();
- }
- catch (Exception se) {
- se.printStackTrace();
- System.err.println(se+" when joining session.\n"+Usage);
- System.exit(1);
- }
- // register an update listener and a close listener.
- // get document data
- try {
- IClientDocument cdoc = vorbaclient.getClientDocument();
- processVamsasDocument(cdoc);
- } catch (Exception e) {
- System.err.println("Unexpected exception when retrieving the client document for the first time!");
- e.printStackTrace(System.err);
- System.exit(1);
- }
-
- // Main application event loop - wait around and do stuff...
- while (!isShuttingdown) {
- // do something with data
- // , update document, or something.
- // ..
-
- }
- // call finalizeClient
- vorbaclient.finalizeClient();
- // { meanwhile, eventHandlers are called to do any saves if need be }
- // and all registered listeners will be deregistered to avoid deadlock.
-
- // finish
- }
-}
+++ /dev/null
-/**
- *
- */
-package org.vamsas.test.objects;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.vamsas.objects.core.*;
-import org.vamsas.objects.utils.*;
-import org.vamsas.objects.utils.document.*;
-import org.vamsas.test.simpleclient.ArchiveReports;
-
-/**
- * @author jim
- * test XSD-Java binding classes in org.vamsas.objects.core
- */
-public class Core {
- static Log log = LogFactory.getLog(Core.class);
-
- /**
- *
- * complete any automatically completable entries in the dataset
- * @param ds
- */
- public static String user = "org.vamsas.test.objects.Core";
-
- public static void complete(DataSet ds) {
- Sequence[] q = ds.getSequence();
- for (int i=0,j=q.length; i<j; i++) {
- q[i].setStart(i+1);
- q[i].setEnd(q[i].getSequence().length()+i+1);
- }
- }
-
- public static VAMSAS getDemoVamsas() {
- VAMSAS v=new VAMSAS();
- DataSet ds = new DataSet();
- ds.addSequence(Seq.newSequence("Dummy1","ASDFLEQ",SymbolDictionary.STANDARD_AA, 5, 11));
- ds.addSequence(Seq.newSequence("Dummy2","ASFLEQ",SymbolDictionary.STANDARD_AA, 5, 10));
- ds.addSequence(Seq.newSequence("Dummy3","ADFEQ",SymbolDictionary.STANDARD_AA, 3, 7));
- ds.setProvenance(ProvenanceStuff.newProvenance(user, "constructed some dummy sequences"));
- complete(ds);
- v.addDataSet(ds);
- Alignment al = new Alignment();
- al.setProvenance(ProvenanceStuff.newProvenance(user, "Created dummy alignment"));
- // rely on newAlignmentSequence to set start/end correctly
- al.addAlignmentSequence(Seq.newAlignmentSequence("Aligned1", "ASDFLEQ", ds.getSequence(0), -1, -1));
- al.addAlignmentSequence(Seq.newAlignmentSequence("Aligned2", "AS-FLEQ", ds.getSequence(1), -1, -1));
- al.addAlignmentSequence(Seq.newAlignmentSequence("Aligned3", "A-DF-EQ", ds.getSequence(2), -1, -1));
- al.setGapChar("-");
- ds.addAlignment(al);
- // TODO: create annotations
- // TODO: create tree
- return v;
- }
- /**
- * @param args
- */
- public static void main(String[] args) {
-
- /**
- * test constants and controlled vocab utils
- */
- System.out.println("VersionEntries.compare(invalid, ALPHA) returned "+VersionEntries.compare("invalid", VersionEntries.ALPHA_VERSION));
- System.out.println("VersionEntries.compare(ALPHA, invalid) returned "+VersionEntries.compare(VersionEntries.ALPHA_VERSION, "invalid"));
- System.out.println("VersionEntries.compare(BETA, ALPHA) returned "+VersionEntries.compare(VersionEntries.BETA_VERSION,VersionEntries.ALPHA_VERSION));
- System.out.println("VersionEntries.compare(ALPHA, BETA) returned "+VersionEntries.compare(VersionEntries.ALPHA_VERSION,VersionEntries.BETA_VERSION));
- System.out.println("VersionEntries.compare(ALPHA, ALPHA) returned "+VersionEntries.compare(VersionEntries.ALPHA_VERSION,VersionEntries.ALPHA_VERSION));
- System.out.println("VersionEntries.compare(invalid, invalid) returned "+VersionEntries.compare("invalid", "invalid"));
- System.out.println("VersionEntries.latestVersion()="+VersionEntries.latestVersion()+
- ", dict_aa="+SymbolDictionary.STANDARD_AA+", dict_na="+SymbolDictionary.STANDARD_NA);
- /**
- * Test utils and autogenerated Vobject interfaces
- */
-
- VamsasDocument doc = DocumentStuff.newVamsasDocument(new VAMSAS[] { getDemoVamsas() },
- ProvenanceStuff.newProvenance("org.vamsas.objects.test.Core", "Created demo vamsasDocument"),
- VersionEntries.latestVersion());
- ArchiveReports.reportDocument(doc, null, true, System.out);
- }
-}
+++ /dev/null
-/**
- *
- */
-package org.vamsas.test.simpleclient;
-
-import java.io.File;
-import java.io.IOException;
-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.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.ValidationException;
-import org.vamsas.client.ClientHandle;
-import org.vamsas.client.IVorbaIdFactory;
-import org.vamsas.client.SessionHandle;
-import org.vamsas.client.UserHandle;
-import org.vamsas.client.Vobject;
-import org.vamsas.client.VorbaId;
-import org.vamsas.client.simpleclient.AppDataOutputStream;
-import org.vamsas.client.simpleclient.FileWatcher;
-import org.vamsas.client.simpleclient.IdFactory;
-import org.vamsas.client.simpleclient.SessionFile;
-import org.vamsas.client.simpleclient.SimpleDocBinding;
-import org.vamsas.client.simpleclient.SimpleDocument;
-import org.vamsas.client.simpleclient.VamsasArchive;
-import org.vamsas.client.simpleclient.VamsasArchiveReader;
-import org.vamsas.client.simpleclient.VamsasFile;
-import org.vamsas.objects.core.AppData;
-import org.vamsas.objects.core.ApplicationData;
-import org.vamsas.objects.core.User;
-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.SeqSet;
-import org.vamsas.objects.utils.document.VersionEntries;
-import org.vamsas.test.objects.Core;
-
-/**
- * @author jimp
- * test the VamsasFile routines for watching, reading and updating a vamsas document jar file.
- * simple document access base class.
- */
-public class ArchiveClient extends IdFactory {
-
- private Log log = LogFactory.getLog(ArchiveClient.class);
- // protected UserHandle user=null;
- // protected ClientHandle me = new ClientHandle("ArchiveClient","0.01");
- VamsasFile vsess;
-
- /**
- * @param user
- * @param vsess
- */
- public ArchiveClient(UserHandle user, VamsasFile vsess) {
- super(new SessionHandle("vamsasfile://"+vsess.getVamsasFile()), new ClientHandle("ArchiveClient","0.01"), user);
- this.vsess = vsess;
- valid();
- }
- private void _openVsess(File vsess) {
- try {
- this.vsess = new VamsasFile(vsess);
- }
- catch (Exception e) {
- log.error("Couldn't open session for file "+vsess,e);
- this.vsess = null;
- }
- }
- public ArchiveClient(String username, String organization, File vsess) {
- super(new SessionHandle("vamsasfile://"+vsess), new ClientHandle("ArchiveClient","0.01"), new UserHandle(username, organization));
- _openVsess(vsess);
- valid();
- }
- public ArchiveClient(String username, String organization, String clientName, String clientVersion, File vsess) {
- super(new SessionHandle("vamsasfile://"+vsess), new ClientHandle(clientName, clientVersion), new UserHandle(username, organization));
- _openVsess(vsess);
- valid();
- }
- public void valid() {
- if (vsess==null)
- throw new Error("ArchiveClient instance is invalid!.");
- }
- /**
- * set this to false if watch loop should end immediately
- */
- protected boolean watchForChange=true;
- public static int WATCH_SLEEP=300;
- /**
- * watch the document file for updates.
- * @param time - length of time to watch for.
- * @return read only IO interface for session document.
- */
- public ClientDoc watch(long time) {
- valid();
- vsess.unLock(); // doh.
- FileWatcher watcher = new FileWatcher(vsess.getVamsasFile());
- // watcher.setState();
- watchForChange=true;
- long endtime=System.currentTimeMillis()+time;
- try {
- org.vamsas.client.simpleclient.Lock doclock;
- do {
- doclock=watcher.getChangedState();
- if (doclock==null)
- Thread.sleep(WATCH_SLEEP);
- } while (watchForChange && doclock==null && (time==0 || endtime>System.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;
- }
-}
+++ /dev/null
-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);
- }
- }
-}
+++ /dev/null
-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; i<pe.length; i++)
- outstr.println(pe[i].getDate()+"\t'"+pe[i].getUser()+"'\t"+pe[i].getApp()+"\t'"+pe[i].getAction()+"'");
- return true;
- }
- public static boolean appDataEntryReport(AppData appD, VamsasArchiveReader archive, boolean cascade, PrintStream outstr) {
- if (appD!=null) {
- boolean nulldata=false;
- if (appD.getDataReference()!=null) {
- String appData=appD.getDataReference();
- if (appData==null) { outstr.println("Empty DataReference - not valid ?"); }
- else
- if (appData.length()>1) {
- 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(); i<j; i++) {
- outstr.println("Data for App Instance URN: '"+inst[i].getUrn());
- appDataEntryReport(inst[i],archive,cascade,outstr);
- }
- }
- if (appD.getUserCount()>0) {
- User users[] = appD.getUser();
- for (int i=0,j=users.length; i<j; i++) {
- outstr.println("Data for User '"+users[i].getFullname()+"' of '"+users[i].getOrganization()+"'");
- appDataEntryReport(users[i], archive, cascade, outstr);
- }
- }
- }
-
- return true;
- }
- public static boolean reportDocument(VamsasDocument document, VamsasArchiveReader archive, boolean cascade, PrintStream outstr) {
- if (document!=null) {
- outstr.println("Vamsas Document version '"+document.getVersion()+"'");
- reportProvenance(document.getProvenance(), outstr);
- outstr.print("Document contains "+document.getVAMSASCount()+" VAMSAS Elements and "+document.getApplicationDataCount()+" Application data elements.\n");
- if (document.getVAMSASCount()>0 && 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<j; i++) {
- outstr.print("Application "+i+": '"+appd[i].getName()+"'\nVersion '"+appd[i].getVersion()+"'\n");
- outstr.print("AppData is :");
- appDataReport(appd[i], archive, cascade, outstr);
- }
-
- }
- return true;
- } else {
- outstr.println("Document Object is null");
- }
- return false;
- }
-
- /**
- * summarises all the datasets in a vamsas document.
- * @param roots
- * @param cascade TODO
- * @param outstr TODO
- * @return
- */
- public static boolean rootReport(VAMSAS[] roots, boolean cascade, PrintStream outstr) {
- if (roots!=null) {
- for (int i=0; i<roots.length; i++) {
- VAMSAS r = roots[i];
- int ds, tr;
- outstr.print("Vamsas Root "+i+" (id="
- +((r.getId()!=null) ? r.getId():"<none>")
- +") contains "+(ds=r.getDataSetCount())+" DataSets, "
- + (tr=r.getTreeCount())+" Global trees\n");
- if (cascade) {
- for (int j=0; j<ds; j++) {
- outstr.println("Dataset "+j);
- cascade = datasetReport(r.getDataSet(j), true, outstr) && cascade ;
- }
- for (int j=0; j<tr; j++) {
- outstr.println("Global tree "+j);
- cascade = treeReport(r.getTree(j), true, outstr) && cascade;
- }
- }
- }
- return true;
- }
- return false;
- }
- public static boolean datasetReport(DataSet ds, boolean cascade, PrintStream outstr) {
- if (cascade)
- reportProvenance(ds.getProvenance(), outstr);
- outstr.println("Dataset contains : "+ds.getSequenceCount()
- +" sequences, "+ds.getAlignmentCount()+" alignments and "+ds.getTreeCount()+" trees.");
- if (cascade)
- alignmentReport(ds.getAlignment(), true, outstr);
- return true;
- }
- public static boolean alignmentReport(Alignment[] al, boolean cascade, PrintStream outstr) {
- boolean val=true;
- if (al!=null && al.length>0) {
- for (int i=0; i<al.length; i++) {
- outstr.println("Alignment "+i+(al[i].isRegistered() ? " ("+al[i].getVorbaId()+")" : " (unregistered)"));
- if (cascade)
- reportProvenance(al[i].getProvenance(), outstr);
- outstr.println("Involves "+al[i].getAlignmentSequenceCount()+" sequences, has "
- +al[i].getAlignmentAnnotationCount()+" annotations and "+al[i].getTreeCount()+" trees.");
- if (cascade) {
- for (int t=0; t<al[i].getTreeCount(); t++)
- treeReport(al[i].getTree(t), true, outstr);
- }
- }
- }
- return val;
- }
- public static boolean treeReport(Tree t, boolean cascade, PrintStream outstr) {
- outstr.println("Tree: '"+t.getTitle()+"'");
- return !cascade || reportProvenance(t.getProvenance(), outstr);
- }
-
-}
+++ /dev/null
-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.SessionFile;
-import org.vamsas.client.simpleclient.VamsasArchiveReader;
-import org.vamsas.client.simpleclient.VamsasFile;
-import org.vamsas.objects.core.VAMSAS;
-import org.vamsas.objects.core.VamsasDocument;
-
-public class ArchiveStreamReader {
- /**
- * tests VamsasArchiveReader archive reader on a vamsas jar file opened as a stream
- * @param args
- */
- public static void main(String args[]) {
-
- try {
- VamsasFile av = new VamsasFile(new File(args[0]));
- VamsasArchiveReader var = new VamsasArchiveReader(av.getLock());
- 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);
- }
- }
-}
+++ /dev/null
-package org.vamsas.test.simpleclient;
-
-import java.io.File;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.vamsas.client.ClientHandle;
-import org.vamsas.client.simpleclient.FileWatcher;
-import org.vamsas.client.simpleclient.Lock;
-import org.vamsas.client.simpleclient.SimpleDocument;
-import org.vamsas.client.simpleclient.VamsasArchiveReader;
-import org.vamsas.client.simpleclient.VamsasFile;
-import org.vamsas.objects.core.VamsasDocument;
-/**
- * demo of archive watching process - should mimic the clientsfileTest watcher/monitor process.
- * @author jimp
- *
- */
-public class ArchiveWatcher {
- private static Log log = LogFactory.getLog(ArchiveWatcher.class);
- private static CommandProcessor cproc=new CommandProcessor();
- static {
- cproc.addCommand("new", 0, "no args");
- cproc.addCommand("delete", 0, "no args");
- cproc.addCommand("watch", 0, "no args");
- cproc.addCommand("file", 1, "Need vamsas archive as argument.");
- }
-
- public static void main(String[] args) {
- try {
-
- if (args!=null && args.length>0) {
- 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);
- }
-
- }
-}
+++ /dev/null
-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; i<svec1.length; i++)
- destvec[i] = svec1[i];
- for (int j=0; j<svec2.length; i++, j++)
- destvec[i] = svec2[j];
- }
- // Merge appDataReferences require transfer of jar entries, perhaps with a renaming of the entry.
- // Merge appDatas require eventually unique URNS
- // TODO: merging global appdata from different documents where same app has written them causes conflict
-
- public static Hashtable hashOfAppDatas(Hashtable ht, Instance[] appdatas) {
- if (ht==null)
- ht = new Hashtable();
- for (int i=0, j=appdatas.length; i<j; i++) {
- if (!ht.containsKey(appdatas[i].getUrn())) {
- Hashtable aphash = new Hashtable();
- ht.put(appdatas[i].getUrn(), aphash);
- aphash.put(appdatas[i], appdatas[i].getDataReference());
- } else {
- // ensure urns and references are unique
-
-
- }
-
- }
- return ht;
- }
- /**
- * safely copies an appData from one archive to another.
- * @param darc destination archive
- * @param dest destination document Vobject
- * @param sarc source archive reader
- * @param entry application data to be copied from source archive
- */
- public static void addAppDataEntry(VamsasArchive darc, VamsasDocument dest, VamsasArchiveReader sarc, ApplicationData entry) {
- // TODO: fix instances
- // check uniqueness of instance's[] entry.urn amongst dest.ApplicationData[].getInstances[].urn
- // check uniqueness of entry.user[].urn amongst dest.ApplicationData[].user[].urn
- // check uniqueness of entry.user
- // entry.getAppDataChoice().getData() or getDataReference is unique
- ApplicationData newo = new ApplicationData();
- for (int i=0, j=dest.getApplicationDataCount(); i<j; i++) {
- ApplicationData o = dest.getApplicationData()[i];
- // ensure new urn is really unique
- //String urn = entry.getUrn();
- int v = 1;
- //while (o.getUrn().equals(urn)) {
- // urn = entry.getUrn()+v++;
- // }
- // uniqueness of urn
- // check each user ApplicationData
- // uniqueness (again)
- // copy over valid objects
- //
- }
- }
- /**
- * Copy new datasets and appdatas from one vamsas document to another.
- * @param darc
- * @param dest
- * @param sarc
- * @param source
- * @return true if merge was successful.
- */
- public static boolean mergeDocs(VamsasArchive darc, VamsasDocument dest, VamsasArchiveReader sarc, VamsasDocument source) {
- log.debug("mergeDocs entered.");
- // search for appDatas in cdoc
- VAMSAS[] newr = new VAMSAS[dest.getVAMSASCount()+source.getVAMSASCount()];
- mergeVecs(newr, dest.getVAMSAS(), source.getVAMSAS());
- dest.setVAMSAS(newr);
- /** TODO: LATER: should verify that all ids really are unique in newly merged document. If not then what ?
- * investigate possibility of having an id translation between appDatas and the core document -
- * the mapping is stored when an external application performs a merge, but when the owning
- * Application accesses the Vobject, the vorba_id is updated to the new one when it writes its
- * references in to its appdata again
- */
- if (source.getApplicationDataCount()>0) {
- ApplicationData[] newdat = new ApplicationData[source.getApplicationDataCount()+dest.getApplicationDataCount()];
- ApplicationData[] sappd = source.getApplicationData();
- // check refs and update/modify if necessary
- for (int i=0; i<sappd.length; i++) {
- addAppDataEntry(darc, dest, sarc, sappd[i]);
- }
-
- }
-
- return true; // success
- }
-
- private static CommandProcessor cproc;
- static {
- cproc.addCommand("new", 0, "no args");
- cproc.addCommand("add", 1, "Need another vamsas document archive filename as argument.");
- cproc.addCommand("repair", 0, "no args");
- cproc.addCommand("list", 0, "no args");
- cproc.addCommand("monitor", 0, "no args");
- }
-
- public static void main(String argv[]) {
- /**
- * TODO: switches for setting user identities for writing to vamsas document
- */
- if (argv.length<1) {
- log.fatal("Usage : <archive to create> [(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<argv.length) {
- File archive = new File(argv[argpos]);
- InputStream istream;
- if (archive.exists()) {
- VamsasArchiveReader vdoc = new VamsasArchiveReader(archive);
- if (vdoc.isValid()) {
- istream = vdoc.getVamsasDocumentStream();
- if (istream!=null) {
- VamsasDocument cdocroot = VamsasDocument.unmarshal(new InputStreamReader(istream));
- if (cdocroot!=null)
- mergeDocs(varc, docroot, vdoc, cdocroot);
- } else
- log.warn("Unexpectedly null document stream from existing document "+archive);
- } else {
- // updating an oldformat stream ?
- if ((istream = vdoc.getVamsasXmlStream())!=null) {
- // make a new vamsas document from the vamsas.xml entry
- VAMSAS root = VAMSAS.unmarshal(new InputStreamReader(istream)); // TODO: verify only one VAMSAS element per vamsas.xml entry.
- docroot.getProvenance().addEntry(ProvenanceStuff.newProvenanceEntry("ArchiveWriter", "user", "added vamsas.xml from "+argv[argpos-1]));
- docroot.addVAMSAS(root);
- }
- }
- } else {
- // Begin a new vamsas document
- PrintWriter docwriter = varc.getDocumentOutputStream();
- }
- }
- } catch (Exception e) {
- log.error("Whilst manipulating "+argv[0], e);
- }
- }
-}
+++ /dev/null
-package org.vamsas.test.simpleclient;
-
-import java.util.Hashtable;
-import java.util.Vector;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.vamsas.client.IClientAppdata;
-import org.vamsas.client.Vobject;
-import org.vamsas.client.VorbaId;
-import org.vamsas.client.simpleclient.ClientDocument;
-import org.vamsas.client.simpleclient.VamsasArchive;
-import org.vamsas.client.simpleclient.VamsasArchiveReader;
-import org.vamsas.objects.core.Entry;
-import org.vamsas.objects.core.VAMSAS;
-import org.vamsas.objects.core.VamsasDocument;
-import org.vamsas.objects.utils.ProvenanceStuff;
-
-// simple holder to pass to client.
-public class ClientDoc extends org.vamsas.client.ClientDocument {
- /* (non-Javadoc)
- * @see org.vamsas.client.IClientDocument#getClientAppdata()
- */
- public IClientAppdata getClientAppdata() {
- throw new Error("Appdata access is not implemented in the test.simpleclient.ClientDoc instance."); // TODO Auto-generated method stub
- }
- protected boolean isModified=false;
- private Log log = LogFactory.getLog(ClientDoc.class);
- protected VamsasDocument doc;
- public org.vamsas.objects.core.VAMSAS[] _VamsasRoots;
- protected VamsasArchive iohandler=null;
- protected VamsasArchiveReader reader=null;
- private String user=null;
- private String app=null;
-
- /**
- * @param doc
- * @param iohandler
- * @param reader
- * @param app
- * @param user
- */
- public ClientDoc(VamsasDocument doc, VamsasArchive iohandler, VamsasArchiveReader reader, String app, String user, Hashtable objrefs) {
- super(objrefs, (iohandler!=null) ? iohandler.getVorba() : null);
- this.doc = doc;
- this.iohandler = iohandler;
- this.reader = reader;
- this.app = app;
- this.user = user;
- this.objrefs = objrefs;
- _VamsasRoots = doc.getVAMSAS();
- }
- // AppDataOutputStream appd;
- //AppDataOutputStream userd;
- /* (non-Javadoc)
- * @see java.lang.Object#finalize()
- */
- protected Entry getProvenanceEntry(String action) {
- // VAMSAS: modify schema to allow referencing of user field (plus other issues, ClientUrn field, machine readable action, input parameters, additional data generated notes
- Entry prov = ProvenanceStuff.newProvenanceEntry(app, user, action);
- return prov;
- }
- public VAMSAS[] getVamsasRoots() {
- if (doc==null) {
- log.debug("Null document for getVamsasRoots(), returning null");
- return null;
- }
- if (iohandler==null) {
- // LATER: decide on read-only status of ClientDocument object
- log.warn("getVamsasRoots() called on possibly read-only document.");
- }
- if (_VamsasRoots!=null)
- return _VamsasRoots;
- VAMSAS[] roots = doc.getVAMSAS();
- if (roots == null) {
- // Make a new one to return to client to get filled.
- _VamsasRoots = new VAMSAS[] { new VAMSAS() };
- // Do provenance now. just in case.
- doc.getProvenance().addEntry(getProvenanceEntry("Created new document root [id="+_VamsasRoots[0].getId()+"]"));
- doc.addVAMSAS(_VamsasRoots[0]);
- } else {
- _VamsasRoots = new VAMSAS[roots.length];
- for (int r=0;r<roots.length; r++)
- _VamsasRoots[r] = roots[r];
- }
- return _VamsasRoots;
- }
-
- private int _contains(VAMSAS root, VAMSAS[] docRoots) {
- if (root==null)
- return -1;
- if (docRoots==null || docRoots.length==0)
- return -1;
- VorbaId r_id = root.getVorbaId();
- for (int i=0,j=docRoots.length; i<j; i++) {
- VorbaId n_id=null;
- if (docRoots[i]==root || (docRoots[i]!=null && (n_id=docRoots[i].getVorbaId())!=null && n_id.equals(r_id)))
- return i;
- }
- return -1;
- }
-/**
- * verify that newr version is really an intact version of the
- * @param newVersion (may be modified)
- * @param oldVersion
- * @return true if newVersion is a valid root that preserves original references
- */
- private boolean isValidUpdate(VAMSAS newVersion, final VAMSAS oldVersion) {
- // ideal - this cascades down the two structures, ensuring that all ID'd objects in one are present in the other.
- if (oldVersion==newVersion) {
- // may be a virgin root element.
- if (!newVersion.isRegistered())
- iohandler.getVorba().makeVorbaId(newVersion);
- // Should retrieve original version and compare - unless local hashes can be used to determine if resultSet has been truncated.
- // just do internal validation for moment.
- if (newVersion.isValid())
- return true;
- return false;
- } else {
- // redundant ? if (oldVersion.is__stored_in_document())
- if (!newVersion.isRegistered())
- iohandler.getVorba().makeVorbaId(newVersion);
- if (newVersion.isValid())
- return true;
- }
- return false;
- }
- /**
- /**
- * merge old and new root vectors
- * @param newr This array may be written to
- * @param original
- * @param the client document (usually this) which this root set belongs to.
- * @return merged vector of vamsas roots
- */
- private VAMSAS[] _combineRoots(VAMSAS[] newr, final VAMSAS[] original, ClientDoc modflag) {
- Vector rts = new Vector();
- boolean modified=false;
- for (int i=0,j=original.length; i<j; i++) {
- int k = _contains(original[i], newr);
- if (k>-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; i<j; i++) {
- if (newr[i]!=null) {
- rts.add(newr[i]);
- modified=true;
- }
- }
- newr = new VAMSAS[rts.size()];
- for (int i=0,j=rts.size(); i<j; i++)
- newr[i] = (VAMSAS) rts.get(i);
- if (modflag!=null)
- modflag.isModified = modified;
- return newr;
- }
-
- /**
- * update the document with new roots.
- * LATER: decide: this affects the next call to getVamsasRoots()
- * @see org.vamsas.IClientDocument.setVamsasRoots
- */
- public void setVamsasRoots(VAMSAS[] newroots) {
- if (doc==null) {
- log.debug("setVamsasRoots called on null document.");
- return;
- }
- VAMSAS[] newr;
- if (newroots==null) {
- log.debug("setVamsasRoots(null) - do nothing.");
- return;
- }
- // are we dealing with same array ?
- if (_VamsasRoots!=newroots) {
- // merge roots into local version.
- newr = new VAMSAS[newroots.length];
- for (int i=0;i<newr.length;i++)
- newr[i] = newroots[i];
- newr=_combineRoots(newr,_VamsasRoots,this);
- } else {
- newr = new VAMSAS[_VamsasRoots.length];
- for (int i=0;i<newr.length;i++)
- newr[i]=_VamsasRoots[i];
- }
- // actually compare with document root set for final combination (to ensure nothing is lost)
- _VamsasRoots = _combineRoots(newr, doc.getVAMSAS(), this);
- }
-
-
- /* (non-Javadoc)
- * LATER: decide: this affects the next call to getVamsasRoots()
- * @see org.vamsas.client.IClientDocument#addVamsasRoot(org.vamsas.objects.core.VAMSAS)
- */
- public void addVamsasRoot(VAMSAS newroot) {
- if (doc==null) {
- log.debug("addVamsasRoots called on null document.");
- return;
- }
- VAMSAS[] newroots = _combineRoots(new VAMSAS[] {newroot}, _VamsasRoots, this);
- _VamsasRoots = newroots;
- }
-
- public VamsasArchiveReader getReader() {
- return reader;
- }
- private void _finalize() {
- log.debug("finalizing clientDoc");
- if (doc!=null) {
- doc = null;
- }
- if (_VamsasRoots!=null) {
- for (int i=0; i<_VamsasRoots.length; i++)
- _VamsasRoots[i]=null;
- _VamsasRoots=null;
-
- }
-
- if (reader!=null) {
- log.debug("Closing and removing reader reference");
- reader.close();
- reader=null;
- }
- if (iohandler!=null) {
- log.debug("Removing ioHandler reference.");
- iohandler.cancelArchive();
- iohandler=null;
- }
- }
- protected void finalize() throws Throwable {
- _finalize();
- super.finalize();
- }
- private java.util.Hashtable objrefs=null;
-
- public VorbaId[] registerObjects(Vobject[] unregistered) {
- if (doc==null) {
- log.warn("registerObjects[] called on null document.");
- return null;
- }
- if (objrefs==null) {
- log.warn("registerObjects[] called for null objrefs hasharray.");
- return null;
- }
- if (unregistered!=null) {
- VorbaId ids[] = new VorbaId[unregistered.length];
- for (int i=0,k=unregistered.length; i<k; i++)
- if (unregistered[i]!=null) {
- log.warn("Null Vobject passed to registerObject[] at position "+i);
- return null;
- } else {
- ids[i]=registerObject(unregistered[i]);
- }
- log.debug("Registered "+unregistered.length+" objects - total of "+objrefs.size()+" ids.");
- return ids;
- }
- return null;
- }
- /* (non-Javadoc)
- * @see org.vamsas.client.IClientDocument#registerObject(org.vamsas.client.Vobject)
- */
- public VorbaId registerObject(Vobject unregistered) {
- if (doc==null) {
- log.warn("registerObjects called on null document.");
- return null;
- }
- if (objrefs==null) {
- log.warn("registerObjects called for null objrefs hasharray.");
- return null;
- }
- if (iohandler==null) {
- log.warn("registerObjects called for read only document.");
- return null;
- }
-
- if (unregistered!=null) {
- VorbaId id = this._registerObject(unregistered);
- log.debug("Registered object - total of "+objrefs.size()+" ids.");
- return id;
- }
- log.warn("Null Vobject passed to registerObject.");
- return null;
- }
- /*
- * (non-Javadoc)
- *
- * @see org.vamsas.client.IClientDocument#getObject(org.vamsas.client.VorbaId)
- */
- public Vobject getObject(VorbaId id) {
- if (objrefs==null) {
- log.debug("getObject called on null objrefs list.");
- return null;
- }
- if (objrefs.containsKey(id.getId()))
- return (Vobject) objrefs.get(id.getId());
- 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 (objrefs==null) {
- log.debug("getObject[] called on null objrefs list.");
- return null;
- }
- Vobject[] vo = new Vobject[ids.length];
- for (int i=0,j=ids.length; i<j;i++)
- if (objrefs.containsKey(ids[i]))
- vo[i] = (Vobject) objrefs.get(ids[i]);
- else
- log.debug("Returning null Vobject reference for id "+ids[i].getId());
- return vo;
- }
- protected void updateDocumentRoots() {
- if (doc==null) {
- log.error("updateDocumentRoots called on null document. Probably an implementation error.");
- return;
- }
- if (isModified) {
- if (_VamsasRoots!=null) {
- doc.setVAMSAS(_VamsasRoots);
- _VamsasRoots=null;
- }
- }
- }
- /**
- * tell vamsas client to close the document and reset the object. Once closed, nothing can be done with the object.
- *
- */
- public void closeDoc() {
- if (doc!=null) {
- log.debug("Closing open document.");
- _finalize();
- } else {
- log.warn("Ignoring closeDoc on invalid document.");
- }
- }
-
-}
\ No newline at end of file
+++ /dev/null
-package org.vamsas.test.simpleclient;
-
-import java.io.File;
-import java.util.Iterator;
-import java.util.Vector;
-
-import org.vamsas.client.ClientHandle;
-import org.vamsas.client.simpleclient.ClientsFile;
-import org.vamsas.client.simpleclient.FileWatcher;
-import org.vamsas.client.simpleclient.Lock;
-
-public class ClientsFileTest {
- private static CommandProcessor cproc;
-
- private static Vector commands;
- static {
- cproc = new CommandProcessor();
- ClientsFileTest.commands = new Vector();
- ClientsFileTest.commands.add(new String("add"));
- cproc.addCommand("add", 2, "for the Client's 'Name' and 'Version'");
- ClientsFileTest.commands.add(new String("remove"));
- cproc.addCommand("remove", 3, "for the Client's 'Name', Version and URN");
- ClientsFileTest.commands.add(new String("list"));
- cproc.addCommand("list", 0, "no args needed");
- ClientsFileTest.commands.add(new String("clear"));
- cproc.addCommand("clear", 0, "no args needed");
- ClientsFileTest.commands.add(new String("watch"));
- cproc.addCommand("watch", 0, "no args needed");
- ClientsFileTest.commands.add(new String("monitor"));
- cproc.addCommand("monitor", 2, "for the Client's 'Name' and 'Version'");
- }
-
- private static void complainArgs(int argl, int argpos, String cmd,
- int argneed, String msg) {
- if (argl - argpos < argneed)
- throw new Error(cmd + " needs " + argneed + " arguments : " + msg);
- }
-
- public static void main(String[] args) {
- java.io.File cf = new java.io.File(args[0]);
- System.out.println("Connecting to clientFile " + args[0]);
- ClientsFile cfhand;
- try {
- cfhand = new ClientsFile(cf);
- } catch (Exception e) {
- e.printStackTrace(System.err);
- return;
- }
- int argc = 1;
- while (argc < args.length) {
- // vars needed for operations
- ClientHandle ch;
- int com = cproc.getCommand(args, argc);
- argc++;
- switch (com) {
- case 0:
- // Add
- int pos = cfhand.addClient(ch = new ClientHandle(args[argc],
- args[argc + 1]));
- argc += 2;
- if (pos != 0)
- System.out.println("Client added at " + pos + " as urn:"
- + ch.getClientUrn());
- else
- System.out.println("Client was not added.");
- break;
- case 1:
- // remove
- ch = new ClientHandle(args[argc], args[argc + 1]);
- ch.setClientUrn(args[argc + 2]);
- argc += 3;
- cfhand.removeClient(ch, null);
- System.out.println("Client removed (apparently)");
- break;
- case 2:
- // list
- ClientHandle[] chlist = cfhand.retrieveClientList();
- if (chlist != null) {
- for (int chi = 0, che = chlist.length; chi < che; chi++) {
- System.out.println("Client " + chi + " ("
- + chlist[chi].getClientName() + " " + chlist[chi].getVersion()
- + " " + chlist[chi].getClientUrn() + ")");
- }
- } else {
- System.out.println("Client list is empty.");
- }
- break;
- case 3:
- // clear
- //cfhand.get = null;
- //cf.delete();
- try {
-
- cfhand.clearList();
-
- } catch (Exception e) {
- System.err.println("Failed on new empty clientfile creation!");
- e.printStackTrace(System.err);
- }
- break;
- case 4:
- // watch
- FileWatcher w = new FileWatcher(cf);
- while (cf.exists()) {
- // get watcher's lock to ensure state change is fixed for retrieval
- Lock chlock = w.getChangedState();
- if (chlock != null) {
- ClientHandle[] cl = cfhand.retrieveClientList(chlock);
- System.out.println("-- Watching " + cf.getName());
- //while (w.hasChanged())
- // ;
- if (cl != null) {
- for (int chi = 0, che = cl.length; chi < che; chi++) {
- System.out.println("Client " + chi + " ("
- + cl[chi].getClientName() + " " + cl[chi].getVersion()
- + " " + cl[chi].getClientUrn() + ")");
- }
- } else {
- System.out.println("Client list is empty.");
- }
- }
-
- }
- break;
- case 5:
- // monitor
- int clpos = cfhand.addClient(ch = new ClientHandle(args[argc],
- args[argc + 1]));
- argc += 2;
- if (clpos != 0)
- System.out.println("Monitor Client added at " + clpos + " as urn:"
- + ch.getClientUrn());
- else {
- System.err.println("Monitor Client was not added.");
- break;
- }
- FileWatcher mon = new FileWatcher(cf);
- while (cf.exists()) {
- // get watcher's lock to ensure state change is fixed for retrieval
- Lock chlock = mon.getChangedState();
- if (chlock != null) {
- ClientHandle[] cl = cfhand.retrieveClientList(chlock);
- System.out.println("-- Monitor " + cf.getName());
- //while (w.hasChanged())
- // ;
- int newpos = -1;
- if (cl != null) {
- for (int chi = 0, che = cl.length; chi < che; chi++) {
- if (ch.equals(cl[chi]))
- newpos = chi + 1;
- }
- }
- if (newpos == -1) {
- // add self again to cleared list.
- newpos = cfhand.addClient(ch);
- mon.setState();
- if (newpos == 0) {
- System.err
- .println("Monitor client could not be re-added to list.");
- break;
- }
- }
- if (newpos != clpos) {
- System.out.println("Monitor client moved from " + clpos + " to "
- + newpos);
- clpos = newpos;
- }
- }
- }
- break;
- default:
- if (com == -1) {
- System.err
- .println("Unknown command : " + args[argc++] + "*Ignored!*");
- } else
- System.err.println("Command " + args[argc++]
- + " *Ignored!* - its not implemented.");
- }
-
- for (int j = 0; j < 900000; j++) {
- Integer i = Integer.getInteger("1");
- Integer q = i;
- }
- }
-
- }
-
- /* Iterator coms = commands.iterator();
- int com=-1;
- while ((coms!=null) && coms.hasNext()) {
- com++;
- if (args[argc].toLowerCase().equals((String) coms.next())) {
- System.out.println("Doing "+args[argc]);
- ClientHandle ch;
- argc++;
- switch (com) {
- case 0:
- // Add
- ClientsFileTest.complainArgs(args.length, argc, "add", 2, "for the Client's 'Name' and 'Version'");
- int pos = cfhand.addClient(ch=new ClientHandle(args[argc],args[argc+1]));
- argc+=2;
- if (pos!=0)
- System.out.println("Client added at "+pos+" as urn:"+ch.getClientUrn());
- else
- System.out.println("Client was not added.");
- break;
- case 1:
- // remove
- ClientsFileTest.complainArgs(args.length, argc, "remove", 3, "for the Client's 'Name', Version and URN");
- ch=new ClientHandle(args[argc], args[argc+1]);
- ch.setClientUrn(args[argc+2]);
- argc+=3;
- cfhand.removeClient(ch, null);
- System.out.println("Client removed (apparently)");
- break;
- case 2:
- // list
- ClientHandle[] chlist = cfhand.retrieveClientList();
- if (chlist!=null) {
- for (int chi=0,che=chlist.length; chi<che; chi++) {
- System.out.println("Client "+chi+" ("+chlist[chi].getClientName()+" "+chlist[chi].getVersion()+" "+chlist[chi].getClientUrn()+")");
- }
- } else {
- System.out.println("Client list is empty.");
- }
- break;
- case 3:
- // clear
- cfhand = null;
- cf.delete();
- try {
- cf.createNewFile();
- cfhand = new ClientsFile(cf);
- }
- catch (Exception e) {
- System.err.println("Failed on new empty clientfile creation!");
- e.printStackTrace(System.err);
- }
- break;
- case 4:
- // watch
- FileWatcher w=new FileWatcher(cf);
- while (cf.exists()) {
- // get watcher's lock to ensure state change is fixed for retrieval
- Lock chlock=w.getChangedState();
- if (chlock!=null) {
- ClientHandle[] cl = cfhand.retrieveClientList(chlock);
- System.out.println("-- Watching "+cf.getName());
- //while (w.hasChanged())
- // ;
- if (cl!=null) {
- for (int chi=0,che=cl.length; chi<che; chi++) {
- System.out.println("Client "+chi+" ("+cl[chi].getClientName()+" "+cl[chi].getVersion()+" "+cl[chi].getClientUrn()+")");
- }
- } else {
- System.out.println("Client list is empty.");
- }
- }
-
- }
- break;
- case 5:
- // monitor
- ClientsFileTest.complainArgs(args.length, argc, "monitor", 2, "for the Client's 'Name' and 'Version'");
- int clpos = cfhand.addClient(ch=new ClientHandle(args[argc],args[argc+1]));
- argc+=2;
- if (clpos!=0)
- System.out.println("Monitor Client added at "+clpos+" as urn:"+ch.getClientUrn());
- else {
- System.err.println("Monitor Client was not added.");
- break;
- }
- FileWatcher mon=new FileWatcher(cf);
- while (cf.exists()) {
- // get watcher's lock to ensure state change is fixed for retrieval
- Lock chlock=mon.getChangedState();
- if (chlock!=null) {
- ClientHandle[] cl = cfhand.retrieveClientList(chlock);
- System.out.println("-- Monitor "+cf.getName());
- //while (w.hasChanged())
- // ;
- int newpos=-1;
- if (cl!=null) {
- for (int chi=0,che=cl.length; chi<che; chi++) {
- if (ch.equals(cl[chi]))
- newpos=chi+1;
- }
- }
- if (newpos==-1) {
- // add self again to cleared list.
- newpos=cfhand.addClient(ch);
- mon.setState();
- if (newpos==0) {
- System.err.println("Monitor client could not be re-added to list.");
- break;
- }
- }
- if (newpos!=clpos) {
- System.out.println("Monitor client moved from "+clpos+" to "+newpos);
- clpos=newpos;
- }
- }
- }
-
- }
- coms = null;
- }
- } */
-
-}
+++ /dev/null
-package org.vamsas.test.simpleclient;
-
-import java.util.Iterator;
-import java.util.Vector;
-
-public class CommandProcessor {
- /**
- * this is not getOPT!!!! - processes a *series* of space separated commands - some of which take arguments.
- */
- private Vector commands;
- /* static {
- ClientsFileTest.commands=new Vector();
- ClientsFileTest.commands.add(new String("add"));
- ClientsFileTest.commands.add(new String("remove"));
- ClientsFileTest.commands.add(new String("list"));
- ClientsFileTest.commands.add(new String("clear"));
- ClientsFileTest.commands.add(new String("watch"));
- ClientsFileTest.commands.add(new String("monitor"));
- } */
-
- public int addCommand(String cmd, int argneed, String complainString) {
- int cnum=0;
- if (commands==null)
- commands = new Vector();
- else
- cnum = commands.size();
- Vector cv = new Vector();
- cv.add(new String(cmd));
- cv.add(new Integer(argneed));
- cv.add(new String(complainString));
- commands.add(cv);
- return cnum;
- }
-
- /**
- * Integer argl, Integer argpos, String cmd, Integer argneed, String msg in vector
- */
- public void complainArgs(int argl, int argpos, Vector ca) {
- int argneed = ((Integer) ca.get(1)).intValue();
- if (argl-argpos<argneed)
- throw new Error(((String) ca.get(0))+" at position "+argpos+" needs "+argneed+" arguments : "+(String) ca.get(2));
- }
- /**
- * find and verify a command
- * @param args argstring
- * @param argpos position to check for command
- * @return matching command or -1
- */
- public int getCommand(String[]args, int argpos) {
- Iterator coms = commands.iterator();
- int com=-1, argc;
- argc=argpos;
- while ((coms!=null) && coms.hasNext()) {
- com++;
- Vector comnext = (Vector) coms.next();
- if (args[argc].toLowerCase().equals((String) comnext.get(0))) {
- if (comnext.size()>2)
- complainArgs(args.length, argc+1, comnext);
- return com;
- }
- }
- return -1;
-
- }
-}
+++ /dev/null
-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);
- }
- }
-}
+++ /dev/null
-/**
- *
- */
-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();
- }
-
-}
+++ /dev/null
-/*\r
- * VamsasClientSimpleApp - A framework for interoparable Sequence analysis\r
- * Copyright (C) 2006 VAMSAS\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-\r
-package org.vamsas.test.simpleclient.simpleapp;\r
-\r
-import org.vamsas.client.Vobject;\r
-import org.vamsas.client.VorbaId;\r
-import org.vamsas.objects.core.*;\r
-import org.vamsas.objects.utils.DocumentStuff;\r
-import org.vamsas.test.simpleclient.ClientDoc;\r
-\r
-\r
-import java.io.*;\r
-import java.util.HashMap;\r
-import java.util.HashSet;\r
-import java.util.Hashtable;\r
-import java.util.IdentityHashMap;\r
-import java.util.Vector;\r
-import java.util.jar.*;\r
-import org.exolab.castor.xml.*;\r
-import org.exolab.castor.mapping.Mapping;\r
-\r
-/*\r
- * \r
- * static {\r
- * org.exolab.castor.util.LocalConfiguration.getInstance().getProperties().setProperty(\r
- * "org.exolab.castor.serializer", "org.apache.xml.serialize.XMLSerilazizer"); }\r
- * \r
- */\r
-\r
-public class VamsasDatastore {\r
- org.apache.commons.logging.Log log=org.apache.commons.logging.LogFactory.getLog(VamsasDatastore.class);\r
- Entry provEntry = null;\r
-\r
-\r
- org.exolab.castor.types.Date date = new org.exolab.castor.types.Date(\r
- new java.util.Date());\r
-\r
- ClientDoc cdoc;\r
-\r
- Hashtable vobj2jv;\r
-\r
- IdentityHashMap jv2vobj;\r
-\r
- public VamsasDatastore(ClientDoc cdoc, Hashtable vobj2jv,\r
- IdentityHashMap jv2vobj, Entry provEntry) {\r
- this.cdoc = cdoc;\r
- this.vobj2jv = vobj2jv;\r
- this.jv2vobj = jv2vobj;\r
- this.provEntry = provEntry;\r
- }\r
-\r
- /*\r
- * public void storeJalview(String file, AlignFrame af) { try { // 1. Load the\r
- * mapping information from the file Mapping map = new\r
- * Mapping(getClass().getClassLoader()); java.net.URL url =\r
- * getClass().getResource("/jalview_mapping.xml"); map.loadMapping(url); // 2.\r
- * Unmarshal the data // Unmarshaller unmar = new Unmarshaller();\r
- * //unmar.setIgnoreExtraElements(true); //unmar.setMapping(map); // uni =\r
- * (UniprotFile) unmar.unmarshal(new FileReader(file)); // 3. marshal the data\r
- * with the total price back and print the XML in the console Marshaller\r
- * marshaller = new Marshaller( new FileWriter(file) );\r
- * \r
- * marshaller.setMapping(map); marshaller.marshal(af); } catch (Exception e) {\r
- * e.printStackTrace(); } }\r
- * \r
- * \r
- */\r
- /**\r
- * @return the Vobject bound to Jalview datamodel object\r
- */\r
- protected Vobject getjv2vObj(Object jvobj) {\r
- if (jv2vobj.containsKey(jvobj))\r
- return cdoc.getObject((VorbaId) jv2vobj.get(jvobj));\r
- return null;\r
- }\r
-\r
- /**\r
- * \r
- * @param vobj\r
- * @return Jalview datamodel object bound to the vamsas document object\r
- */\r
- protected Object getvObj2jv(org.vamsas.client.Vobject vobj) {\r
- VorbaId id = vobj.getVorbaId();\r
- if (id == null)\r
- {\r
- id = cdoc.registerObject(vobj);\r
- log\r
- .debug("Registering new object and returning null for getvObj2jv");\r
- return null;\r
- }\r
- if (vobj2jv.containsKey(vobj.getVorbaId()))\r
- return vobj2jv.get(vobj.getVorbaId());\r
- return null;\r
- }\r
-\r
- protected void bindjvvobj(Object jvobj, org.vamsas.client.Vobject vobj) {\r
- VorbaId id = vobj.getVorbaId();\r
- if (id == null)\r
- {\r
- id = cdoc.registerObject(vobj);\r
- if (id==null || vobj.getVorbaId()==null)\r
- log.error("Failed to get id for "+(vobj.isRegisterable() ? "registerable" : "unregisterable") +" object "+vobj);\r
- }\r
- if (vobj2jv.containsKey(vobj.getVorbaId()) || jv2vobj.containsKey(jvobj))\r
- {\r
- log.error("Duplicate object binding! "+vobj+" id " +vobj.getVorbaId().getId()+" to "+jvobj);\r
- }\r
- else\r
- {\r
- vobj2jv.put(vobj.getVorbaId(), jvobj);// JBPNote - better implementing a\r
- // hybrid invertible hash.\r
- jv2vobj.put(jvobj, vobj.getVorbaId());\r
- }\r
- }\r
-\r
- /**\r
- * put the alignment viewed by AlignViewport into cdoc.\r
- * \r
- * @param av\r
- */\r
- public void storeVAMSAS(Object fromAppsDatamodel) {\r
- boolean nw = false;\r
- VAMSAS root = null; // will be resolved based on Dataset Parent.\r
- DataSet dataset = (DataSet) getjv2vObj(fromAppsDatamodel);\r
- if (dataset == null)\r
- {\r
- root = cdoc.getVamsasRoots()[0]; // default vamsas root for modifying.\r
- dataset = new DataSet();\r
- root.addDataSet(dataset);\r
- bindjvvobj(fromAppsDatamodel, dataset);\r
- dataset.setProvenance(dummyProvenance());\r
- dataset.getProvenance().addEntry(provEntry);\r
- nw = true;\r
- } else {\r
- root = (VAMSAS) dataset.getV_parent();\r
- }\r
- // etc...\r
- }\r
-\r
- private Property newProperty(String name, String type, String content) {\r
- Property vProperty=new Property();\r
- vProperty.setName(name);\r
- if (type!=null)\r
- vProperty.setType(type);\r
- vProperty.setContent(content);\r
- return vProperty;\r
- }\r
-\r
- /**\r
- * get start<end range of segment, adjusting for inclusivity flag and\r
- * polarity.\r
- * \r
- * @param visSeg\r
- * @param ensureDirection when true - always ensure start is less than end.\r
- * @return int[] { start, end, direction} where direction==1 for range running from end to start.\r
- */\r
- private int[] getSegRange(Seg visSeg, boolean ensureDirection) {\r
- boolean incl = visSeg.getInclusive();\r
- // adjust for inclusive flag.\r
- int pol = (visSeg.getStart() <= visSeg.getEnd()) ? 1 : -1; // polarity of\r
- // region.\r
- int start = visSeg.getStart() + (incl ? 0 : pol);\r
- int end = visSeg.getEnd() + (incl ? 0 : -pol);\r
- if (ensureDirection && pol==-1)\r
- {\r
- // jalview doesn't deal with inverted ranges, yet.\r
- int t = end;\r
- end = start;\r
- start = t;\r
- }\r
- return new int[] { start, end, pol<0 ? 1 : 0 };\r
- }\r
-\r
- public void updateToJalview() {\r
- VAMSAS _roots[] = cdoc.getVamsasRoots();\r
-\r
- for (int _root = 0; _root<_roots.length; _root++) {\r
- VAMSAS root = _roots[_root];\r
- boolean newds=false;\r
- for (int _ds=0,_nds=root.getDataSetCount(); _ds<_nds; _ds++) {\r
- // ///////////////////////////////////\r
- // ///LOAD DATASET\r
- DataSet dataset = root.getDataSet(_ds);\r
- int i, iSize = dataset.getSequenceCount();\r
- Vector dsseqs;\r
- Object appsdataset = (Object) getvObj2jv(dataset);\r
- int jremain=0;\r
- if (appsdataset==null) {\r
- log.debug("Initialising new dataset fields");\r
- newds=true;\r
- dsseqs=new Vector();\r
- } else {\r
- log.debug("Update dataset from vamsas dataset.");\r
- }\r
- // etc for annotations, alignments, trees, etc. \r
- }\r
- }\r
- }\r
- /**\r
- * get real bounds of a RangeType's specification. start and end are an\r
- * inclusive range within which all segments and positions lie.\r
- * TODO: refactor to vamsas utils\r
- * @param dseta\r
- * @return int[] { start, end}\r
- */\r
- private int[] getBounds(RangeType dseta) {\r
- if (dseta != null)\r
- {\r
- int[] se = null;\r
- if (dseta.getSegCount()>0 && dseta.getPosCount()>0)\r
- throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");\r
- if (dseta.getSegCount() > 0)\r
- {\r
- se = getSegRange(dseta.getSeg(0),true);\r
- for (int s = 1, sSize = dseta.getSegCount(); s < sSize; s++)\r
- {\r
- int nse[] = getSegRange(dseta.getSeg(s), true);\r
- if (se[0] > nse[0])\r
- se[0] = nse[0];\r
- if (se[1] < nse[1])\r
- se[1] = nse[1];\r
- }\r
- }\r
- if (dseta.getPosCount() > 0)\r
- {\r
- // could do a polarity for pos range too. and pass back indication of discontinuities.\r
- int pos = dseta.getPos(0).getI();\r
- se = new int[] { pos, pos };\r
- for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)\r
- {\r
- pos = dseta.getPos(p).getI();\r
- if (se[0] > pos)\r
- se[0] = pos;\r
- if (se[1] < pos)\r
- se[1] = pos;\r
- }\r
- }\r
- return se;\r
- }\r
- return null;\r
- }\r
- /**\r
- * map from a rangeType's internal frame to the referenced object's coordinate frame.\r
- * @param dseta\r
- * @return int [] { ref(pos)...} for all pos in rangeType's frame.\r
- */\r
- private int[] getMapping(RangeType dseta) {\r
- Vector posList=new Vector();\r
- if (dseta != null)\r
- {\r
- int[] se = null;\r
- if (dseta.getSegCount()>0 && dseta.getPosCount()>0)\r
- throw new Error("Invalid vamsas RangeType - cannot resolve both lists of Pos and Seg from choice!");\r
- if (dseta.getSegCount() > 0)\r
- {\r
- for (int s = 0, sSize = dseta.getSegCount(); s < sSize; s++)\r
- {\r
- se = getSegRange(dseta.getSeg(s), false);\r
- int se_end=se[1-se[2]]+(se[2]==0 ? 1 : -1);\r
- for (int p=se[se[2]]; p!=se_end; p+=se[2]==0 ? 1 : -1 ) {\r
- posList.add(Integer.valueOf(p));\r
- }\r
- }\r
- } \r
- else if (dseta.getPosCount() > 0)\r
- {\r
- int pos = dseta.getPos(0).getI();\r
-\r
- for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)\r
- {\r
- pos = dseta.getPos(p).getI();\r
- posList.add(Integer.valueOf(pos));\r
- }\r
- }\r
- }\r
- if (posList!=null && posList.size()>0) {\r
- int[] range=new int[posList.size()];\r
- for (int i=0; i<range.length; i++)\r
- range[i] = ((Integer)posList.elementAt(i)).intValue();\r
- posList.clear();\r
- return range;\r
- }\r
- return null;\r
- }\r
- /**\r
- * \r
- * @return default initial provenance list for a VamsasDatastore created vamsas\r
- * object.\r
- */\r
- Provenance dummyProvenance() {\r
- return dummyProvenance(null);\r
- }\r
-\r
- Entry dummyPEntry(String action) {\r
- Entry entry = new Entry();\r
- entry.setApp(this.provEntry.getApp());\r
- if (action != null)\r
- entry.setAction(action);\r
- else\r
- entry.setAction("created.");\r
- entry.setDate(new org.exolab.castor.types.Date(new java.util.Date()));\r
- entry.setUser(this.provEntry.getUser());\r
- return entry;\r
- }\r
-\r
- Provenance dummyProvenance(String action) {\r
- Provenance prov = new Provenance();\r
- prov.addEntry(dummyPEntry(action));\r
- return prov;\r
- }\r
-\r
- void addProvenance(Provenance p, String action) {\r
- p.addEntry(dummyPEntry(action));\r
- }\r
-\r
-}\r
git://source.jalview.org / vamsas.git / commitdiff