X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fobjects%2Fcore%2FEntry.java;h=7cf695ff6984b70d91a651670828fc80017203af;hb=1eea4b639911330e7cd65e17c5421cc584f0d22e;hp=350443c1c9defd7c9daf837076753fe0df6d4754;hpb=a06295cc0912455e0bc53b26cb4e0134e6759d0f;p=vamsas.git

diff --git a/src/uk/ac/vamsas/objects/core/Entry.java b/src/uk/ac/vamsas/objects/core/Entry.java
index 350443c..7cf695f 100644
--- a/src/uk/ac/vamsas/objects/core/Entry.java
+++ b/src/uk/ac/vamsas/objects/core/Entry.java
@@ -1,803 +1,1135 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id:Entry.java 264 2006-12-14 17:42:54Z JimP $
+ * This file is part of the Vamsas Client version 0.2. 
+ * Copyright 2010 by Jim Procter, Iain Milne, Pierre Marguerite, 
+ *  Andrew Waterhouse and Dominik Lindner.
+ * 
+ * Earlier versions have also been incorporated into Jalview version 2.4 
+ * since 2008, and TOPALi version 2 since 2007.
+ * 
+ * The Vamsas Client is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *  
+ * The Vamsas Client is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with the Vamsas Client.  If not, see <http://www.gnu.org/licenses/>.
  */
-
 package uk.ac.vamsas.objects.core;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- 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:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
+ * @version $Revision$ $Date: 2007-06-28 14:51:44 +0100 (Thu, 28 Jun 2007)
+ *          $
  */
-public class Entry extends uk.ac.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();
-    } //-- uk.ac.vamsas.objects.core.Entry()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method addInput
-     * 
-     * 
-     * 
-     * @param vInput
-     */
-    public void addInput(uk.ac.vamsas.objects.core.Input vInput)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _inputList.addElement(vInput);
-    } //-- void addInput(uk.ac.vamsas.objects.core.Input) 
-
-    /**
-     * Method addInput
-     * 
-     * 
-     * 
-     * @param index
-     * @param vInput
-     */
-    public void addInput(int index, uk.ac.vamsas.objects.core.Input vInput)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _inputList.insertElementAt(vInput, index);
-    } //-- void addInput(int, uk.ac.vamsas.objects.core.Input) 
-
-    /**
-     * Method addParam
-     * 
-     * 
-     * 
-     * @param vParam
-     */
-    public void addParam(uk.ac.vamsas.objects.core.Param vParam)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _paramList.addElement(vParam);
-    } //-- void addParam(uk.ac.vamsas.objects.core.Param) 
-
-    /**
-     * Method addParam
-     * 
-     * 
-     * 
-     * @param index
-     * @param vParam
-     */
-    public void addParam(int index, uk.ac.vamsas.objects.core.Param vParam)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _paramList.insertElementAt(vParam, index);
-    } //-- void addParam(int, uk.ac.vamsas.objects.core.Param) 
-
-    /**
-     * Method addProperty
-     * 
-     * 
-     * 
-     * @param vProperty
-     */
-    public void addProperty(uk.ac.vamsas.objects.core.Property vProperty)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _propertyList.addElement(vProperty);
-    } //-- void addProperty(uk.ac.vamsas.objects.core.Property) 
-
-    /**
-     * Method addProperty
-     * 
-     * 
-     * 
-     * @param index
-     * @param vProperty
-     */
-    public void addProperty(int index, uk.ac.vamsas.objects.core.Property vProperty)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _propertyList.insertElementAt(vProperty, index);
-    } //-- void addProperty(int, uk.ac.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;
+public class Entry extends uk.ac.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 java.util.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();
+    this._propertyList = new java.util.Vector();
+    this._paramList = new java.util.Vector();
+    this._inputList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vInput
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addInput(final uk.ac.vamsas.objects.core.Input vInput)
+      throws java.lang.IndexOutOfBoundsException {
+    this._inputList.addElement(vInput);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vInput
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addInput(final int index,
+      final uk.ac.vamsas.objects.core.Input vInput)
+      throws java.lang.IndexOutOfBoundsException {
+    this._inputList.add(index, vInput);
+  }
+
+  /**
+   * 
+   * 
+   * @param vParam
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addParam(final uk.ac.vamsas.objects.core.Param vParam)
+      throws java.lang.IndexOutOfBoundsException {
+    this._paramList.addElement(vParam);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vParam
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addParam(final int index,
+      final uk.ac.vamsas.objects.core.Param vParam)
+      throws java.lang.IndexOutOfBoundsException {
+    this._paramList.add(index, vParam);
+  }
+
+  /**
+   * 
+   * 
+   * @param vProperty
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addProperty(final uk.ac.vamsas.objects.core.Property vProperty)
+      throws java.lang.IndexOutOfBoundsException {
+    this._propertyList.addElement(vProperty);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vProperty
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addProperty(final int index,
+      final uk.ac.vamsas.objects.core.Property vProperty)
+      throws java.lang.IndexOutOfBoundsException {
+    this._propertyList.add(index, vProperty);
+  }
+
+  /**
+   * Method enumerateInput.
+   * 
+   * @return an Enumeration over all uk.ac.vamsas.objects.core.Input elements
+   */
+  public java.util.Enumeration enumerateInput() {
+    return this._inputList.elements();
+  }
+
+  /**
+   * Method enumerateParam.
+   * 
+   * @return an Enumeration over all uk.ac.vamsas.objects.core.Param elements
+   */
+  public java.util.Enumeration enumerateParam() {
+    return this._paramList.elements();
+  }
+
+  /**
+   * Method enumerateProperty.
+   * 
+   * @return an Enumeration over all uk.ac.vamsas.objects.core.Property elements
+   */
+  public java.util.Enumeration enumerateProperty() {
+    return this._propertyList.elements();
+  }
+
+  /**
+   * Overrides the java.lang.Object.equals method.
+   * 
+   * @param obj
+   * @return true if the objects are equal.
+   */
+  public boolean equals(final java.lang.Object obj) {
+    if (this == obj)
+      return true;
+
+    if (super.equals(obj) == false)
+      return false;
+
+    if (obj instanceof Entry) {
+
+      Entry temp = (Entry) obj;
+      boolean thcycle;
+      boolean tmcycle;
+      if (this._id != null) {
+        if (temp._id == null)
+          return false;
+        if (this._id != temp._id) {
+          thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id);
+          tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id);
+          if (thcycle != tmcycle) {
+            if (!thcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
             }
-            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;
+            ;
+            if (!tmcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
             }
-            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;
+            ;
+            return false;
+          }
+          if (!thcycle) {
+            if (!this._id.equals(temp._id)) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
+              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;
+            org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+            org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
+          }
+        }
+      } else if (temp._id != null)
+        return false;
+      if (this._user != null) {
+        if (temp._user == null)
+          return false;
+        if (this._user != temp._user) {
+          thcycle = org.castor.util.CycleBreaker.startingToCycle(this._user);
+          tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._user);
+          if (thcycle != tmcycle) {
+            if (!thcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._user);
             }
-            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;
+            ;
+            if (!tmcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._user);
             }
-            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;
+            ;
+            return false;
+          }
+          if (!thcycle) {
+            if (!this._user.equals(temp._user)) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._user);
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._user);
+              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;
+            org.castor.util.CycleBreaker.releaseCycleHandle(this._user);
+            org.castor.util.CycleBreaker.releaseCycleHandle(temp._user);
+          }
+        }
+      } else if (temp._user != null)
+        return false;
+      if (this._app != null) {
+        if (temp._app == null)
+          return false;
+        if (this._app != temp._app) {
+          thcycle = org.castor.util.CycleBreaker.startingToCycle(this._app);
+          tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._app);
+          if (thcycle != tmcycle) {
+            if (!thcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._app);
             }
-            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;
+            ;
+            if (!tmcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._app);
+            }
+            ;
+            return false;
+          }
+          if (!thcycle) {
+            if (!this._app.equals(temp._app)) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._app);
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._app);
+              return false;
             }
-            else if (temp._inputList != null)
-                return false;
-            return true;
+            org.castor.util.CycleBreaker.releaseCycleHandle(this._app);
+            org.castor.util.CycleBreaker.releaseCycleHandle(temp._app);
+          }
         }
+      } else if (temp._app != null)
         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 uk.ac.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 (uk.ac.vamsas.objects.core.Input) _inputList.elementAt(index);
-    } //-- uk.ac.vamsas.objects.core.Input getInput(int) 
-
-    /**
-     * Method getInput
-     * 
-     * 
-     * 
-     * @return Input
-     */
-    public uk.ac.vamsas.objects.core.Input[] getInput()
-    {
-        int size = _inputList.size();
-        uk.ac.vamsas.objects.core.Input[] mArray = new uk.ac.vamsas.objects.core.Input[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (uk.ac.vamsas.objects.core.Input) _inputList.elementAt(index);
-        }
-        return mArray;
-    } //-- uk.ac.vamsas.objects.core.Input[] getInput() 
-
-    /**
-     * Method getInputCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getInputCount()
-    {
-        return _inputList.size();
-    } //-- int getInputCount() 
-
-    /**
-     * Method getParam
-     * 
-     * 
-     * 
-     * @param index
-     * @return Param
-     */
-    public uk.ac.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 (uk.ac.vamsas.objects.core.Param) _paramList.elementAt(index);
-    } //-- uk.ac.vamsas.objects.core.Param getParam(int) 
-
-    /**
-     * Method getParam
-     * 
-     * 
-     * 
-     * @return Param
-     */
-    public uk.ac.vamsas.objects.core.Param[] getParam()
-    {
-        int size = _paramList.size();
-        uk.ac.vamsas.objects.core.Param[] mArray = new uk.ac.vamsas.objects.core.Param[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (uk.ac.vamsas.objects.core.Param) _paramList.elementAt(index);
-        }
-        return mArray;
-    } //-- uk.ac.vamsas.objects.core.Param[] getParam() 
-
-    /**
-     * Method getParamCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getParamCount()
-    {
-        return _paramList.size();
-    } //-- int getParamCount() 
-
-    /**
-     * Method getProperty
-     * 
-     * 
-     * 
-     * @param index
-     * @return Property
-     */
-    public uk.ac.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 (uk.ac.vamsas.objects.core.Property) _propertyList.elementAt(index);
-    } //-- uk.ac.vamsas.objects.core.Property getProperty(int) 
-
-    /**
-     * Method getProperty
-     * 
-     * 
-     * 
-     * @return Property
-     */
-    public uk.ac.vamsas.objects.core.Property[] getProperty()
-    {
-        int size = _propertyList.size();
-        uk.ac.vamsas.objects.core.Property[] mArray = new uk.ac.vamsas.objects.core.Property[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (uk.ac.vamsas.objects.core.Property) _propertyList.elementAt(index);
-        }
-        return mArray;
-    } //-- uk.ac.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) {
+      if (this._action != null) {
+        if (temp._action == null)
+          return false;
+        if (this._action != temp._action) {
+          thcycle = org.castor.util.CycleBreaker.startingToCycle(this._action);
+          tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._action);
+          if (thcycle != tmcycle) {
+            if (!thcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._action);
+            }
+            ;
+            if (!tmcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._action);
+            }
+            ;
             return false;
+          }
+          if (!thcycle) {
+            if (!this._action.equals(temp._action)) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._action);
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._action);
+              return false;
+            }
+            org.castor.util.CycleBreaker.releaseCycleHandle(this._action);
+            org.castor.util.CycleBreaker.releaseCycleHandle(temp._action);
+          }
         }
-        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 uk.ac.vamsas.objects.core.Input removeInput(int index)
-    {
-        java.lang.Object obj = _inputList.elementAt(index);
-        _inputList.removeElementAt(index);
-        return (uk.ac.vamsas.objects.core.Input) obj;
-    } //-- uk.ac.vamsas.objects.core.Input removeInput(int) 
-
-    /**
-     * Method removeParam
-     * 
-     * 
-     * 
-     * @param index
-     * @return Param
-     */
-    public uk.ac.vamsas.objects.core.Param removeParam(int index)
-    {
-        java.lang.Object obj = _paramList.elementAt(index);
-        _paramList.removeElementAt(index);
-        return (uk.ac.vamsas.objects.core.Param) obj;
-    } //-- uk.ac.vamsas.objects.core.Param removeParam(int) 
-
-    /**
-     * Method removeProperty
-     * 
-     * 
-     * 
-     * @param index
-     * @return Property
-     */
-    public uk.ac.vamsas.objects.core.Property removeProperty(int index)
-    {
-        java.lang.Object obj = _propertyList.elementAt(index);
-        _propertyList.removeElementAt(index);
-        return (uk.ac.vamsas.objects.core.Property) obj;
-    } //-- uk.ac.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, uk.ac.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, uk.ac.vamsas.objects.core.Input) 
-
-    /**
-     * Method setInput
-     * 
-     * 
-     * 
-     * @param inputArray
-     */
-    public void setInput(uk.ac.vamsas.objects.core.Input[] inputArray)
-    {
-        //-- copy array
-        _inputList.removeAllElements();
-        for (int i = 0; i < inputArray.length; i++) {
-            _inputList.addElement(inputArray[i]);
+      } else if (temp._action != null)
+        return false;
+      if (this._date != null) {
+        if (temp._date == null)
+          return false;
+        if (this._date != temp._date) {
+          thcycle = org.castor.util.CycleBreaker.startingToCycle(this._date);
+          tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._date);
+          if (thcycle != tmcycle) {
+            if (!thcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._date);
+            }
+            ;
+            if (!tmcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._date);
+            }
+            ;
+            return false;
+          }
+          if (!thcycle) {
+            if (!this._date.equals(temp._date)) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._date);
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._date);
+              return false;
+            }
+            org.castor.util.CycleBreaker.releaseCycleHandle(this._date);
+            org.castor.util.CycleBreaker.releaseCycleHandle(temp._date);
+          }
         }
-    } //-- void setInput(uk.ac.vamsas.objects.core.Input) 
-
-    /**
-     * Method setParam
-     * 
-     * 
-     * 
-     * @param index
-     * @param vParam
-     */
-    public void setParam(int index, uk.ac.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()+ "]");
+      } else if (temp._date != null)
+        return false;
+      if (this._propertyList != null) {
+        if (temp._propertyList == null)
+          return false;
+        if (this._propertyList != temp._propertyList) {
+          thcycle = org.castor.util.CycleBreaker
+              .startingToCycle(this._propertyList);
+          tmcycle = org.castor.util.CycleBreaker
+              .startingToCycle(temp._propertyList);
+          if (thcycle != tmcycle) {
+            if (!thcycle) {
+              org.castor.util.CycleBreaker
+                  .releaseCycleHandle(this._propertyList);
+            }
+            ;
+            if (!tmcycle) {
+              org.castor.util.CycleBreaker
+                  .releaseCycleHandle(temp._propertyList);
+            }
+            ;
+            return false;
+          }
+          if (!thcycle) {
+            if (!this._propertyList.equals(temp._propertyList)) {
+              org.castor.util.CycleBreaker
+                  .releaseCycleHandle(this._propertyList);
+              org.castor.util.CycleBreaker
+                  .releaseCycleHandle(temp._propertyList);
+              return false;
+            }
+            org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList);
+            org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
+          }
         }
-        _paramList.setElementAt(vParam, index);
-    } //-- void setParam(int, uk.ac.vamsas.objects.core.Param) 
-
-    /**
-     * Method setParam
-     * 
-     * 
-     * 
-     * @param paramArray
-     */
-    public void setParam(uk.ac.vamsas.objects.core.Param[] paramArray)
-    {
-        //-- copy array
-        _paramList.removeAllElements();
-        for (int i = 0; i < paramArray.length; i++) {
-            _paramList.addElement(paramArray[i]);
+      } else if (temp._propertyList != null)
+        return false;
+      if (this._paramList != null) {
+        if (temp._paramList == null)
+          return false;
+        if (this._paramList != temp._paramList) {
+          thcycle = org.castor.util.CycleBreaker
+              .startingToCycle(this._paramList);
+          tmcycle = org.castor.util.CycleBreaker
+              .startingToCycle(temp._paramList);
+          if (thcycle != tmcycle) {
+            if (!thcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._paramList);
+            }
+            ;
+            if (!tmcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._paramList);
+            }
+            ;
+            return false;
+          }
+          if (!thcycle) {
+            if (!this._paramList.equals(temp._paramList)) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._paramList);
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._paramList);
+              return false;
+            }
+            org.castor.util.CycleBreaker.releaseCycleHandle(this._paramList);
+            org.castor.util.CycleBreaker.releaseCycleHandle(temp._paramList);
+          }
         }
-    } //-- void setParam(uk.ac.vamsas.objects.core.Param) 
-
-    /**
-     * Method setProperty
-     * 
-     * 
-     * 
-     * @param index
-     * @param vProperty
-     */
-    public void setProperty(int index, uk.ac.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()+ "]");
+      } else if (temp._paramList != null)
+        return false;
+      if (this._inputList != null) {
+        if (temp._inputList == null)
+          return false;
+        if (this._inputList != temp._inputList) {
+          thcycle = org.castor.util.CycleBreaker
+              .startingToCycle(this._inputList);
+          tmcycle = org.castor.util.CycleBreaker
+              .startingToCycle(temp._inputList);
+          if (thcycle != tmcycle) {
+            if (!thcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._inputList);
+            }
+            ;
+            if (!tmcycle) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._inputList);
+            }
+            ;
+            return false;
+          }
+          if (!thcycle) {
+            if (!this._inputList.equals(temp._inputList)) {
+              org.castor.util.CycleBreaker.releaseCycleHandle(this._inputList);
+              org.castor.util.CycleBreaker.releaseCycleHandle(temp._inputList);
+              return false;
+            }
+            org.castor.util.CycleBreaker.releaseCycleHandle(this._inputList);
+            org.castor.util.CycleBreaker.releaseCycleHandle(temp._inputList);
+          }
         }
-        _propertyList.setElementAt(vProperty, index);
-    } //-- void setProperty(int, uk.ac.vamsas.objects.core.Property) 
-
-    /**
-     * Method setProperty
-     * 
-     * 
-     * 
-     * @param propertyArray
+      } else if (temp._inputList != null)
+        return false;
+      return true;
+    }
+    return false;
+  }
+
+  /**
+   * Returns the value of field 'action'. The field 'action' has the following
+   * description: Did what
+   * 
+   * @return the value of field 'Action'.
+   */
+  public java.lang.String getAction() {
+    return this._action;
+  }
+
+  /**
+   * Returns the value of field 'app'. The field 'app' has the following
+   * description: With which application
+   * 
+   * @return the value of field 'App'.
+   */
+  public java.lang.String getApp() {
+    return this._app;
+  }
+
+  /**
+   * Returns the value of field 'date'. The field 'date' has the following
+   * description: When
+   * 
+   * @return the value of field 'Date'.
+   */
+  public java.util.Date getDate() {
+    return this._date;
+  }
+
+  /**
+   * Returns the value of field 'id'. The field 'id' has the following
+   * description: Primary Key for vamsas object referencing
+   * 
+   * 
+   * @return the value of field 'Id'.
+   */
+  public java.lang.String getId() {
+    return this._id;
+  }
+
+  /**
+   * Method getInput.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the uk.ac.vamsas.objects.core.Input at the given index
+   */
+  public uk.ac.vamsas.objects.core.Input getInput(final int index)
+      throws java.lang.IndexOutOfBoundsException {
+    // check bounds for index
+    if (index < 0 || index >= this._inputList.size()) {
+      throw new IndexOutOfBoundsException("getInput: Index value '" + index
+          + "' not in range [0.." + (this._inputList.size() - 1) + "]");
+    }
+
+    return (uk.ac.vamsas.objects.core.Input) _inputList.get(index);
+  }
+
+  /**
+   * Method getInput.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public uk.ac.vamsas.objects.core.Input[] getInput() {
+    uk.ac.vamsas.objects.core.Input[] array = new uk.ac.vamsas.objects.core.Input[0];
+    return (uk.ac.vamsas.objects.core.Input[]) this._inputList.toArray(array);
+  }
+
+  /**
+   * Method getInputAsReference.Returns a reference to '_inputList'. No type
+   * checking is performed on any modifications to the Vector.
+   * 
+   * @return a reference to the Vector backing this class
+   */
+  public java.util.Vector getInputAsReference() {
+    return this._inputList;
+  }
+
+  /**
+   * Method getInputCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getInputCount() {
+    return this._inputList.size();
+  }
+
+  /**
+   * Method getParam.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the uk.ac.vamsas.objects.core.Param at the given index
+   */
+  public uk.ac.vamsas.objects.core.Param getParam(final int index)
+      throws java.lang.IndexOutOfBoundsException {
+    // check bounds for index
+    if (index < 0 || index >= this._paramList.size()) {
+      throw new IndexOutOfBoundsException("getParam: Index value '" + index
+          + "' not in range [0.." + (this._paramList.size() - 1) + "]");
+    }
+
+    return (uk.ac.vamsas.objects.core.Param) _paramList.get(index);
+  }
+
+  /**
+   * Method getParam.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public uk.ac.vamsas.objects.core.Param[] getParam() {
+    uk.ac.vamsas.objects.core.Param[] array = new uk.ac.vamsas.objects.core.Param[0];
+    return (uk.ac.vamsas.objects.core.Param[]) this._paramList.toArray(array);
+  }
+
+  /**
+   * Method getParamAsReference.Returns a reference to '_paramList'. No type
+   * checking is performed on any modifications to the Vector.
+   * 
+   * @return a reference to the Vector backing this class
+   */
+  public java.util.Vector getParamAsReference() {
+    return this._paramList;
+  }
+
+  /**
+   * Method getParamCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getParamCount() {
+    return this._paramList.size();
+  }
+
+  /**
+   * Method getProperty.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the uk.ac.vamsas.objects.core.Property at the given
+   *         index
+   */
+  public uk.ac.vamsas.objects.core.Property getProperty(final int index)
+      throws java.lang.IndexOutOfBoundsException {
+    // check bounds for index
+    if (index < 0 || index >= this._propertyList.size()) {
+      throw new IndexOutOfBoundsException("getProperty: Index value '" + index
+          + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
+    }
+
+    return (uk.ac.vamsas.objects.core.Property) _propertyList.get(index);
+  }
+
+  /**
+   * Method getProperty.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public uk.ac.vamsas.objects.core.Property[] getProperty() {
+    uk.ac.vamsas.objects.core.Property[] array = new uk.ac.vamsas.objects.core.Property[0];
+    return (uk.ac.vamsas.objects.core.Property[]) this._propertyList
+        .toArray(array);
+  }
+
+  /**
+   * Method getPropertyAsReference.Returns a reference to '_propertyList'. No
+   * type checking is performed on any modifications to the Vector.
+   * 
+   * @return a reference to the Vector backing this class
+   */
+  public java.util.Vector getPropertyAsReference() {
+    return this._propertyList;
+  }
+
+  /**
+   * Method getPropertyCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getPropertyCount() {
+    return this._propertyList.size();
+  }
+
+  /**
+   * Returns the value of field 'user'. The field 'user' has the following
+   * description: Who
+   * 
+   * @return the value of field 'User'.
+   */
+  public java.lang.String getUser() {
+    return this._user;
+  }
+
+  /**
+   * Overrides the java.lang.Object.hashCode method.
+   * <p>
+   * The following steps came from <b>Effective Java Programming Language
+   * Guide</b> by Joshua Bloch, Chapter 3
+   * 
+   * @return a hash code value for the object.
+   */
+  public int hashCode() {
+    int result = super.hashCode();
+
+    long tmp;
+    if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
+      result = 37 * result + _id.hashCode();
+      org.castor.util.CycleBreaker.releaseCycleHandle(_id);
+    }
+    if (_user != null && !org.castor.util.CycleBreaker.startingToCycle(_user)) {
+      result = 37 * result + _user.hashCode();
+      org.castor.util.CycleBreaker.releaseCycleHandle(_user);
+    }
+    if (_app != null && !org.castor.util.CycleBreaker.startingToCycle(_app)) {
+      result = 37 * result + _app.hashCode();
+      org.castor.util.CycleBreaker.releaseCycleHandle(_app);
+    }
+    if (_action != null
+        && !org.castor.util.CycleBreaker.startingToCycle(_action)) {
+      result = 37 * result + _action.hashCode();
+      org.castor.util.CycleBreaker.releaseCycleHandle(_action);
+    }
+    if (_date != null && !org.castor.util.CycleBreaker.startingToCycle(_date)) {
+      result = 37 * result + _date.hashCode();
+      org.castor.util.CycleBreaker.releaseCycleHandle(_date);
+    }
+    if (_propertyList != null
+        && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) {
+      result = 37 * result + _propertyList.hashCode();
+      org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList);
+    }
+    if (_paramList != null
+        && !org.castor.util.CycleBreaker.startingToCycle(_paramList)) {
+      result = 37 * result + _paramList.hashCode();
+      org.castor.util.CycleBreaker.releaseCycleHandle(_paramList);
+    }
+    if (_inputList != null
+        && !org.castor.util.CycleBreaker.startingToCycle(_inputList)) {
+      result = 37 * result + _inputList.hashCode();
+      org.castor.util.CycleBreaker.releaseCycleHandle(_inputList);
+    }
+
+    return result;
+  }
+
+  /**
+   * Method isValid.
+   * 
+   * @return true if this object is valid according to the schema
+   */
+  public boolean isValid() {
+    try {
+      validate();
+    } catch (org.exolab.castor.xml.ValidationException vex) {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * 
+   * 
+   * @param out
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void marshal(final java.io.Writer out)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException {
+    Marshaller.marshal(this, out);
+  }
+
+  /**
+   * 
+   * 
+   * @param handler
+   * @throws java.io.IOException
+   *           if an IOException occurs during marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   */
+  public void marshal(final org.xml.sax.ContentHandler handler)
+      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException {
+    Marshaller.marshal(this, handler);
+  }
+
+  /**
      */
-    public void setProperty(uk.ac.vamsas.objects.core.Property[] propertyArray)
-    {
-        //-- copy array
-        _propertyList.removeAllElements();
-        for (int i = 0; i < propertyArray.length; i++) {
-            _propertyList.addElement(propertyArray[i]);
-        }
-    } //-- void setProperty(uk.ac.vamsas.objects.core.Property) 
+  public void removeAllInput() {
+    this._inputList.clear();
+  }
 
-    /**
-     * 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 uk.ac.vamsas.objects.core.Entry unmarshal(java.io.Reader reader)
-        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
-    {
-        return (uk.ac.vamsas.objects.core.Entry) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Entry.class, reader);
-    } //-- uk.ac.vamsas.objects.core.Entry unmarshal(java.io.Reader) 
-
-    /**
-     * Method validate
-     * 
+  public void removeAllParam() {
+    this._paramList.clear();
+  }
+
+  /**
      */
-    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() 
+  public void removeAllProperty() {
+    this._propertyList.clear();
+  }
+
+  /**
+   * Method removeInput.
+   * 
+   * @param vInput
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeInput(final uk.ac.vamsas.objects.core.Input vInput) {
+    boolean removed = _inputList.remove(vInput);
+    return removed;
+  }
+
+  /**
+   * Method removeInputAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public uk.ac.vamsas.objects.core.Input removeInputAt(final int index) {
+    java.lang.Object obj = this._inputList.remove(index);
+    return (uk.ac.vamsas.objects.core.Input) obj;
+  }
+
+  /**
+   * Method removeParam.
+   * 
+   * @param vParam
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeParam(final uk.ac.vamsas.objects.core.Param vParam) {
+    boolean removed = _paramList.remove(vParam);
+    return removed;
+  }
+
+  /**
+   * Method removeParamAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public uk.ac.vamsas.objects.core.Param removeParamAt(final int index) {
+    java.lang.Object obj = this._paramList.remove(index);
+    return (uk.ac.vamsas.objects.core.Param) obj;
+  }
+
+  /**
+   * Method removeProperty.
+   * 
+   * @param vProperty
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeProperty(
+      final uk.ac.vamsas.objects.core.Property vProperty) {
+    boolean removed = _propertyList.remove(vProperty);
+    return removed;
+  }
+
+  /**
+   * Method removePropertyAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public uk.ac.vamsas.objects.core.Property removePropertyAt(final int index) {
+    java.lang.Object obj = this._propertyList.remove(index);
+    return (uk.ac.vamsas.objects.core.Property) obj;
+  }
+
+  /**
+   * 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(final java.lang.String action) {
+    this._action = action;
+  }
+
+  /**
+   * 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(final java.lang.String app) {
+    this._app = app;
+  }
+
+  /**
+   * Sets the value of field 'date'. The field 'date' has the following
+   * description: When
+   * 
+   * @param date
+   *          the value of field 'date'.
+   */
+  public void setDate(final java.util.Date date) {
+    this._date = 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(final java.lang.String id) {
+    this._id = id;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vInput
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setInput(final int index,
+      final uk.ac.vamsas.objects.core.Input vInput)
+      throws java.lang.IndexOutOfBoundsException {
+    // check bounds for index
+    if (index < 0 || index >= this._inputList.size()) {
+      throw new IndexOutOfBoundsException("setInput: Index value '" + index
+          + "' not in range [0.." + (this._inputList.size() - 1) + "]");
+    }
+
+    this._inputList.set(index, vInput);
+  }
+
+  /**
+   * 
+   * 
+   * @param vInputArray
+   */
+  public void setInput(final uk.ac.vamsas.objects.core.Input[] vInputArray) {
+    // -- copy array
+    _inputList.clear();
+
+    for (int i = 0; i < vInputArray.length; i++) {
+      this._inputList.add(vInputArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of '_inputList' by copying the given Vector. All elements
+   * will be checked for type safety.
+   * 
+   * @param vInputList
+   *          the Vector to copy.
+   */
+  public void setInput(final java.util.Vector vInputList) {
+    // copy vector
+    this._inputList.clear();
+
+    this._inputList.addAll(vInputList);
+  }
+
+  /**
+   * Sets the value of '_inputList' by setting it to the given Vector. No type
+   * checking is performed.
+   * 
+   * @deprecated
+   * 
+   * @param inputVector
+   *          the Vector to set.
+   */
+  public void setInputAsReference(final java.util.Vector inputVector) {
+    this._inputList = inputVector;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vParam
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setParam(final int index,
+      final uk.ac.vamsas.objects.core.Param vParam)
+      throws java.lang.IndexOutOfBoundsException {
+    // check bounds for index
+    if (index < 0 || index >= this._paramList.size()) {
+      throw new IndexOutOfBoundsException("setParam: Index value '" + index
+          + "' not in range [0.." + (this._paramList.size() - 1) + "]");
+    }
+
+    this._paramList.set(index, vParam);
+  }
+
+  /**
+   * 
+   * 
+   * @param vParamArray
+   */
+  public void setParam(final uk.ac.vamsas.objects.core.Param[] vParamArray) {
+    // -- copy array
+    _paramList.clear();
+
+    for (int i = 0; i < vParamArray.length; i++) {
+      this._paramList.add(vParamArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of '_paramList' by copying the given Vector. All elements
+   * will be checked for type safety.
+   * 
+   * @param vParamList
+   *          the Vector to copy.
+   */
+  public void setParam(final java.util.Vector vParamList) {
+    // copy vector
+    this._paramList.clear();
+
+    this._paramList.addAll(vParamList);
+  }
+
+  /**
+   * Sets the value of '_paramList' by setting it to the given Vector. No type
+   * checking is performed.
+   * 
+   * @deprecated
+   * 
+   * @param paramVector
+   *          the Vector to set.
+   */
+  public void setParamAsReference(final java.util.Vector paramVector) {
+    this._paramList = paramVector;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vProperty
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setProperty(final int index,
+      final uk.ac.vamsas.objects.core.Property vProperty)
+      throws java.lang.IndexOutOfBoundsException {
+    // check bounds for index
+    if (index < 0 || index >= this._propertyList.size()) {
+      throw new IndexOutOfBoundsException("setProperty: Index value '" + index
+          + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
+    }
+
+    this._propertyList.set(index, vProperty);
+  }
+
+  /**
+   * 
+   * 
+   * @param vPropertyArray
+   */
+  public void setProperty(
+      final uk.ac.vamsas.objects.core.Property[] vPropertyArray) {
+    // -- copy array
+    _propertyList.clear();
+
+    for (int i = 0; i < vPropertyArray.length; i++) {
+      this._propertyList.add(vPropertyArray[i]);
+    }
+  }
+
+  /**
+   * Sets the value of '_propertyList' by copying the given Vector. All elements
+   * will be checked for type safety.
+   * 
+   * @param vPropertyList
+   *          the Vector to copy.
+   */
+  public void setProperty(final java.util.Vector vPropertyList) {
+    // copy vector
+    this._propertyList.clear();
+
+    this._propertyList.addAll(vPropertyList);
+  }
+
+  /**
+   * Sets the value of '_propertyList' by setting it to the given Vector. No
+   * type checking is performed.
+   * 
+   * @deprecated
+   * 
+   * @param propertyVector
+   *          the Vector to set.
+   */
+  public void setPropertyAsReference(final java.util.Vector propertyVector) {
+    this._propertyList = propertyVector;
+  }
+
+  /**
+   * Sets the value of field 'user'. The field 'user' has the following
+   * description: Who
+   * 
+   * @param user
+   *          the value of field 'user'.
+   */
+  public void setUser(final java.lang.String user) {
+    this._user = user;
+  }
+
+  /**
+   * Method unmarshal.
+   * 
+   * @param reader
+   * @throws org.exolab.castor.xml.MarshalException
+   *           if object is null or if any SAXException is thrown during
+   *           marshaling
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   * @return the unmarshaled uk.ac.vamsas.objects.core.Entry
+   */
+  public static uk.ac.vamsas.objects.core.Entry unmarshal(
+      final java.io.Reader reader)
+      throws org.exolab.castor.xml.MarshalException,
+      org.exolab.castor.xml.ValidationException {
+    return (uk.ac.vamsas.objects.core.Entry) Unmarshaller.unmarshal(
+        uk.ac.vamsas.objects.core.Entry.class, reader);
+  }
+
+  /**
+   * 
+   * 
+   * @throws org.exolab.castor.xml.ValidationException
+   *           if this object is an invalid instance according to the schema
+   */
+  public void validate() throws org.exolab.castor.xml.ValidationException {
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+    validator.validate(this);
+  }
 
 }