X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FJalviewModelSequence.java;h=8d5cda16591297585891ef8f0611ad313f6bc4e5;hb=506d60f0e188723ddc91c26824b41ac7034df3fe;hp=ba0c4c8adbc2e0d93c28e0d19db1c30b11acad3e;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/JalviewModelSequence.java b/src/jalview/schemabinding/version2/JalviewModelSequence.java
index ba0c4c8..8d5cda1 100755
--- a/src/jalview/schemabinding/version2/JalviewModelSequence.java
+++ b/src/jalview/schemabinding/version2/JalviewModelSequence.java
@@ -1,948 +1,1001 @@
 /*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemabinding.version2;
 
-//---------------------------------/
-//- Imported classes and packages -/
-//---------------------------------/
-
-import java.util.*;
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
-import org.exolab.castor.xml.*;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
 
 /**
  * Class JalviewModelSequence.
- *
+ * 
  * @version $Revision$ $Date$
  */
-public class JalviewModelSequence
-    implements java.io.Serializable
+public class JalviewModelSequence implements java.io.Serializable
 {
 
-  //--------------------------/
-  //- Class/Member Variables -/
-  //--------------------------/
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
 
   /**
-   * Field _JSeqList
+   * Field _JSeqList.
    */
   private java.util.Vector _JSeqList;
 
   /**
-   * Field _JGroupList
+   * Field _JGroupList.
    */
   private java.util.Vector _JGroupList;
 
   /**
-   * Field _viewportList
+   * Field _viewportList.
    */
   private java.util.Vector _viewportList;
 
   /**
-   * Field _userColoursList
+   * Field _userColoursList.
    */
   private java.util.Vector _userColoursList;
 
   /**
-   * Field _treeList
+   * Field _treeList.
    */
   private java.util.Vector _treeList;
 
   /**
-   * Field _featureSettings
+   * Field _featureSettings.
    */
   private jalview.schemabinding.version2.FeatureSettings _featureSettings;
 
-  //----------------/
-  //- Constructors -/
-  //----------------/
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
   public JalviewModelSequence()
   {
     super();
-    _JSeqList = new Vector();
-    _JGroupList = new Vector();
-    _viewportList = new Vector();
-    _userColoursList = new Vector();
-    _treeList = new Vector();
-  } //-- jalview.schemabinding.version2.JalviewModelSequence()
-
-  //-----------/
-  //- Methods -/
-  //-----------/
-
-  /**
-   * Method addJGroup
-   *
-   *
-   *
+    this._JSeqList = new java.util.Vector();
+    this._JGroupList = new java.util.Vector();
+    this._viewportList = new java.util.Vector();
+    this._userColoursList = new java.util.Vector();
+    this._treeList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
    * @param vJGroup
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
    */
-  public void addJGroup(jalview.schemabinding.version2.JGroup vJGroup)
-      throws java.lang.IndexOutOfBoundsException
+  public void addJGroup(final jalview.schemabinding.version2.JGroup vJGroup)
+          throws java.lang.IndexOutOfBoundsException
   {
-    _JGroupList.addElement(vJGroup);
-  } //-- void addJGroup(jalview.schemabinding.version2.JGroup)
+    this._JGroupList.addElement(vJGroup);
+  }
 
   /**
-   * Method addJGroup
-   *
-   *
-   *
+   * 
+   * 
    * @param index
    * @param vJGroup
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
    */
-  public void addJGroup(int index,
-                        jalview.schemabinding.version2.JGroup vJGroup)
-      throws java.lang.IndexOutOfBoundsException
+  public void addJGroup(final int index,
+          final jalview.schemabinding.version2.JGroup vJGroup)
+          throws java.lang.IndexOutOfBoundsException
   {
-    _JGroupList.insertElementAt(vJGroup, index);
-  } //-- void addJGroup(int, jalview.schemabinding.version2.JGroup)
+    this._JGroupList.add(index, vJGroup);
+  }
 
   /**
-   * Method addJSeq
-   *
-   *
-   *
+   * 
+   * 
    * @param vJSeq
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
    */
-  public void addJSeq(jalview.schemabinding.version2.JSeq vJSeq)
-      throws java.lang.IndexOutOfBoundsException
+  public void addJSeq(final jalview.schemabinding.version2.JSeq vJSeq)
+          throws java.lang.IndexOutOfBoundsException
   {
-    _JSeqList.addElement(vJSeq);
-  } //-- void addJSeq(jalview.schemabinding.version2.JSeq)
+    this._JSeqList.addElement(vJSeq);
+  }
 
   /**
-   * Method addJSeq
-   *
-   *
-   *
+   * 
+   * 
    * @param index
    * @param vJSeq
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
    */
-  public void addJSeq(int index, jalview.schemabinding.version2.JSeq vJSeq)
-      throws java.lang.IndexOutOfBoundsException
+  public void addJSeq(final int index,
+          final jalview.schemabinding.version2.JSeq vJSeq)
+          throws java.lang.IndexOutOfBoundsException
   {
-    _JSeqList.insertElementAt(vJSeq, index);
-  } //-- void addJSeq(int, jalview.schemabinding.version2.JSeq)
+    this._JSeqList.add(index, vJSeq);
+  }
 
   /**
-   * Method addTree
-   *
-   *
-   *
+   * 
+   * 
    * @param vTree
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
    */
-  public void addTree(jalview.schemabinding.version2.Tree vTree)
-      throws java.lang.IndexOutOfBoundsException
+  public void addTree(final jalview.schemabinding.version2.Tree vTree)
+          throws java.lang.IndexOutOfBoundsException
   {
-    _treeList.addElement(vTree);
-  } //-- void addTree(jalview.schemabinding.version2.Tree)
+    this._treeList.addElement(vTree);
+  }
 
   /**
-   * Method addTree
-   *
-   *
-   *
+   * 
+   * 
    * @param index
    * @param vTree
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
    */
-  public void addTree(int index, jalview.schemabinding.version2.Tree vTree)
-      throws java.lang.IndexOutOfBoundsException
+  public void addTree(final int index,
+          final jalview.schemabinding.version2.Tree vTree)
+          throws java.lang.IndexOutOfBoundsException
   {
-    _treeList.insertElementAt(vTree, index);
-  } //-- void addTree(int, jalview.schemabinding.version2.Tree)
+    this._treeList.add(index, vTree);
+  }
 
   /**
-   * Method addUserColours
-   *
-   *
-   *
+   * 
+   * 
    * @param vUserColours
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
    */
-  public void addUserColours(jalview.schemabinding.version2.UserColours
-                             vUserColours)
-      throws java.lang.IndexOutOfBoundsException
+  public void addUserColours(
+          final jalview.schemabinding.version2.UserColours vUserColours)
+          throws java.lang.IndexOutOfBoundsException
   {
-    _userColoursList.addElement(vUserColours);
-  } //-- void addUserColours(jalview.schemabinding.version2.UserColours)
+    this._userColoursList.addElement(vUserColours);
+  }
 
   /**
-   * Method addUserColours
-   *
-   *
-   *
+   * 
+   * 
    * @param index
    * @param vUserColours
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
    */
-  public void addUserColours(int index,
-                             jalview.schemabinding.version2.UserColours
-                             vUserColours)
-      throws java.lang.IndexOutOfBoundsException
+  public void addUserColours(final int index,
+          final jalview.schemabinding.version2.UserColours vUserColours)
+          throws java.lang.IndexOutOfBoundsException
   {
-    _userColoursList.insertElementAt(vUserColours, index);
-  } //-- void addUserColours(int, jalview.schemabinding.version2.UserColours)
+    this._userColoursList.add(index, vUserColours);
+  }
 
   /**
-   * Method addViewport
-   *
-   *
-   *
+   * 
+   * 
    * @param vViewport
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
    */
-  public void addViewport(jalview.schemabinding.version2.Viewport vViewport)
-      throws java.lang.IndexOutOfBoundsException
+  public void addViewport(
+          final jalview.schemabinding.version2.Viewport vViewport)
+          throws java.lang.IndexOutOfBoundsException
   {
-    _viewportList.addElement(vViewport);
-  } //-- void addViewport(jalview.schemabinding.version2.Viewport)
+    this._viewportList.addElement(vViewport);
+  }
 
   /**
-   * Method addViewport
-   *
-   *
-   *
+   * 
+   * 
    * @param index
    * @param vViewport
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
    */
-  public void addViewport(int index,
-                          jalview.schemabinding.version2.Viewport vViewport)
-      throws java.lang.IndexOutOfBoundsException
+  public void addViewport(final int index,
+          final jalview.schemabinding.version2.Viewport vViewport)
+          throws java.lang.IndexOutOfBoundsException
   {
-    _viewportList.insertElementAt(vViewport, index);
-  } //-- void addViewport(int, jalview.schemabinding.version2.Viewport)
+    this._viewportList.add(index, vViewport);
+  }
 
   /**
-   * Method enumerateJGroup
-   *
-   *
-   *
-   * @return Enumeration
+   * Method enumerateJGroup.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.JGroup
+   *         elements
    */
   public java.util.Enumeration enumerateJGroup()
   {
-    return _JGroupList.elements();
-  } //-- java.util.Enumeration enumerateJGroup()
+    return this._JGroupList.elements();
+  }
 
   /**
-   * Method enumerateJSeq
-   *
-   *
-   *
-   * @return Enumeration
+   * Method enumerateJSeq.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.JSeq
+   *         elements
    */
   public java.util.Enumeration enumerateJSeq()
   {
-    return _JSeqList.elements();
-  } //-- java.util.Enumeration enumerateJSeq()
+    return this._JSeqList.elements();
+  }
 
   /**
-   * Method enumerateTree
-   *
-   *
-   *
-   * @return Enumeration
+   * Method enumerateTree.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.Tree
+   *         elements
    */
   public java.util.Enumeration enumerateTree()
   {
-    return _treeList.elements();
-  } //-- java.util.Enumeration enumerateTree()
+    return this._treeList.elements();
+  }
 
   /**
-   * Method enumerateUserColours
-   *
-   *
-   *
-   * @return Enumeration
+   * Method enumerateUserColours.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.UserColours
+   *         elements
    */
   public java.util.Enumeration enumerateUserColours()
   {
-    return _userColoursList.elements();
-  } //-- java.util.Enumeration enumerateUserColours()
+    return this._userColoursList.elements();
+  }
 
   /**
-   * Method enumerateViewport
-   *
-   *
-   *
-   * @return Enumeration
+   * Method enumerateViewport.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.Viewport
+   *         elements
    */
   public java.util.Enumeration enumerateViewport()
   {
-    return _viewportList.elements();
-  } //-- java.util.Enumeration enumerateViewport()
+    return this._viewportList.elements();
+  }
 
   /**
    * Returns the value of field 'featureSettings'.
-   *
-   * @return FeatureSettings
-   * @return the value of field 'featureSettings'.
+   * 
+   * @return the value of field 'FeatureSettings'.
    */
   public jalview.schemabinding.version2.FeatureSettings getFeatureSettings()
   {
     return this._featureSettings;
-  } //-- jalview.schemabinding.version2.FeatureSettings getFeatureSettings()
+  }
 
   /**
-   * Method getJGroup
-   *
-   *
-   *
+   * Method getJGroup.
+   * 
    * @param index
-   * @return JGroup
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.JGroup at the given
+   *         index
    */
-  public jalview.schemabinding.version2.JGroup getJGroup(int index)
-      throws java.lang.IndexOutOfBoundsException
+  public jalview.schemabinding.version2.JGroup getJGroup(final int index)
+          throws java.lang.IndexOutOfBoundsException
   {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _JGroupList.size()))
+    // check bounds for index
+    if (index < 0 || index >= this._JGroupList.size())
     {
-      throw new IndexOutOfBoundsException();
+      throw new IndexOutOfBoundsException("getJGroup: Index value '"
+              + index + "' not in range [0.."
+              + (this._JGroupList.size() - 1) + "]");
     }
 
-    return (jalview.schemabinding.version2.JGroup) _JGroupList.elementAt(index);
-  } //-- jalview.schemabinding.version2.JGroup getJGroup(int)
+    return (jalview.schemabinding.version2.JGroup) _JGroupList.get(index);
+  }
 
   /**
-   * Method getJGroup
-   *
-   *
-   *
-   * @return JGroup
+   * Method getJGroup.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 jalview.schemabinding.version2.JGroup[] getJGroup()
   {
-    int size = _JGroupList.size();
-    jalview.schemabinding.version2.JGroup[] mArray = new jalview.schemabinding.
-        version2.JGroup[size];
-    for (int index = 0; index < size; index++)
-    {
-      mArray[index] = (jalview.schemabinding.version2.JGroup) _JGroupList.
-          elementAt(index);
-    }
-    return mArray;
-  } //-- jalview.schemabinding.version2.JGroup[] getJGroup()
+    jalview.schemabinding.version2.JGroup[] array = new jalview.schemabinding.version2.JGroup[0];
+    return (jalview.schemabinding.version2.JGroup[]) this._JGroupList
+            .toArray(array);
+  }
 
   /**
-   * Method getJGroupCount
-   *
-   *
-   *
-   * @return int
+   * Method getJGroupCount.
+   * 
+   * @return the size of this collection
    */
   public int getJGroupCount()
   {
-    return _JGroupList.size();
-  } //-- int getJGroupCount()
+    return this._JGroupList.size();
+  }
 
   /**
-   * Method getJSeq
-   *
-   *
-   *
+   * Method getJSeq.
+   * 
    * @param index
-   * @return JSeq
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.JSeq at the given
+   *         index
    */
-  public jalview.schemabinding.version2.JSeq getJSeq(int index)
-      throws java.lang.IndexOutOfBoundsException
+  public jalview.schemabinding.version2.JSeq getJSeq(final int index)
+          throws java.lang.IndexOutOfBoundsException
   {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _JSeqList.size()))
+    // check bounds for index
+    if (index < 0 || index >= this._JSeqList.size())
     {
-      throw new IndexOutOfBoundsException();
+      throw new IndexOutOfBoundsException("getJSeq: Index value '" + index
+              + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
     }
 
-    return (jalview.schemabinding.version2.JSeq) _JSeqList.elementAt(index);
-  } //-- jalview.schemabinding.version2.JSeq getJSeq(int)
+    return (jalview.schemabinding.version2.JSeq) _JSeqList.get(index);
+  }
 
   /**
-   * Method getJSeq
-   *
-   *
-   *
-   * @return JSeq
+   * Method getJSeq.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 jalview.schemabinding.version2.JSeq[] getJSeq()
   {
-    int size = _JSeqList.size();
-    jalview.schemabinding.version2.JSeq[] mArray = new jalview.schemabinding.
-        version2.JSeq[size];
-    for (int index = 0; index < size; index++)
-    {
-      mArray[index] = (jalview.schemabinding.version2.JSeq) _JSeqList.elementAt(
-          index);
-    }
-    return mArray;
-  } //-- jalview.schemabinding.version2.JSeq[] getJSeq()
+    jalview.schemabinding.version2.JSeq[] array = new jalview.schemabinding.version2.JSeq[0];
+    return (jalview.schemabinding.version2.JSeq[]) this._JSeqList
+            .toArray(array);
+  }
 
   /**
-   * Method getJSeqCount
-   *
-   *
-   *
-   * @return int
+   * Method getJSeqCount.
+   * 
+   * @return the size of this collection
    */
   public int getJSeqCount()
   {
-    return _JSeqList.size();
-  } //-- int getJSeqCount()
+    return this._JSeqList.size();
+  }
 
   /**
-   * Method getTree
-   *
-   *
-   *
+   * Method getTree.
+   * 
    * @param index
-   * @return Tree
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.Tree at the given
+   *         index
    */
-  public jalview.schemabinding.version2.Tree getTree(int index)
-      throws java.lang.IndexOutOfBoundsException
+  public jalview.schemabinding.version2.Tree getTree(final int index)
+          throws java.lang.IndexOutOfBoundsException
   {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _treeList.size()))
+    // check bounds for index
+    if (index < 0 || index >= this._treeList.size())
     {
-      throw new IndexOutOfBoundsException();
+      throw new IndexOutOfBoundsException("getTree: Index value '" + index
+              + "' not in range [0.." + (this._treeList.size() - 1) + "]");
     }
 
-    return (jalview.schemabinding.version2.Tree) _treeList.elementAt(index);
-  } //-- jalview.schemabinding.version2.Tree getTree(int)
+    return (jalview.schemabinding.version2.Tree) _treeList.get(index);
+  }
 
   /**
-   * Method getTree
-   *
-   *
-   *
-   * @return Tree
+   * Method getTree.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 jalview.schemabinding.version2.Tree[] getTree()
   {
-    int size = _treeList.size();
-    jalview.schemabinding.version2.Tree[] mArray = new jalview.schemabinding.
-        version2.Tree[size];
-    for (int index = 0; index < size; index++)
-    {
-      mArray[index] = (jalview.schemabinding.version2.Tree) _treeList.elementAt(
-          index);
-    }
-    return mArray;
-  } //-- jalview.schemabinding.version2.Tree[] getTree()
+    jalview.schemabinding.version2.Tree[] array = new jalview.schemabinding.version2.Tree[0];
+    return (jalview.schemabinding.version2.Tree[]) this._treeList
+            .toArray(array);
+  }
 
   /**
-   * Method getTreeCount
-   *
-   *
-   *
-   * @return int
+   * Method getTreeCount.
+   * 
+   * @return the size of this collection
    */
   public int getTreeCount()
   {
-    return _treeList.size();
-  } //-- int getTreeCount()
+    return this._treeList.size();
+  }
 
   /**
-   * Method getUserColours
-   *
-   *
-   *
+   * Method getUserColours.
+   * 
    * @param index
-   * @return UserColours
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.UserColours at the
+   *         given index
    */
-  public jalview.schemabinding.version2.UserColours getUserColours(int index)
-      throws java.lang.IndexOutOfBoundsException
+  public jalview.schemabinding.version2.UserColours getUserColours(
+          final int index) throws java.lang.IndexOutOfBoundsException
   {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _userColoursList.size()))
+    // check bounds for index
+    if (index < 0 || index >= this._userColoursList.size())
     {
-      throw new IndexOutOfBoundsException();
+      throw new IndexOutOfBoundsException("getUserColours: Index value '"
+              + index + "' not in range [0.."
+              + (this._userColoursList.size() - 1) + "]");
     }
 
-    return (jalview.schemabinding.version2.UserColours) _userColoursList.
-        elementAt(index);
-  } //-- jalview.schemabinding.version2.UserColours getUserColours(int)
+    return (jalview.schemabinding.version2.UserColours) _userColoursList
+            .get(index);
+  }
 
   /**
-   * Method getUserColours
-   *
-   *
-   *
-   * @return UserColours
+   * Method getUserColours.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 jalview.schemabinding.version2.UserColours[] getUserColours()
   {
-    int size = _userColoursList.size();
-    jalview.schemabinding.version2.UserColours[] mArray = new jalview.
-        schemabinding.version2.UserColours[size];
-    for (int index = 0; index < size; index++)
-    {
-      mArray[index] = (jalview.schemabinding.version2.UserColours)
-          _userColoursList.elementAt(index);
-    }
-    return mArray;
-  } //-- jalview.schemabinding.version2.UserColours[] getUserColours()
+    jalview.schemabinding.version2.UserColours[] array = new jalview.schemabinding.version2.UserColours[0];
+    return (jalview.schemabinding.version2.UserColours[]) this._userColoursList
+            .toArray(array);
+  }
 
   /**
-   * Method getUserColoursCount
-   *
-   *
-   *
-   * @return int
+   * Method getUserColoursCount.
+   * 
+   * @return the size of this collection
    */
   public int getUserColoursCount()
   {
-    return _userColoursList.size();
-  } //-- int getUserColoursCount()
+    return this._userColoursList.size();
+  }
 
   /**
-   * Method getViewport
-   *
-   *
-   *
+   * Method getViewport.
+   * 
    * @param index
-   * @return Viewport
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.Viewport at the
+   *         given index
    */
-  public jalview.schemabinding.version2.Viewport getViewport(int index)
-      throws java.lang.IndexOutOfBoundsException
+  public jalview.schemabinding.version2.Viewport getViewport(final int index)
+          throws java.lang.IndexOutOfBoundsException
   {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _viewportList.size()))
+    // check bounds for index
+    if (index < 0 || index >= this._viewportList.size())
     {
-      throw new IndexOutOfBoundsException();
+      throw new IndexOutOfBoundsException("getViewport: Index value '"
+              + index + "' not in range [0.."
+              + (this._viewportList.size() - 1) + "]");
     }
 
-    return (jalview.schemabinding.version2.Viewport) _viewportList.elementAt(
-        index);
-  } //-- jalview.schemabinding.version2.Viewport getViewport(int)
+    return (jalview.schemabinding.version2.Viewport) _viewportList
+            .get(index);
+  }
 
   /**
-   * Method getViewport
-   *
-   *
-   *
-   * @return Viewport
+   * Method getViewport.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 jalview.schemabinding.version2.Viewport[] getViewport()
   {
-    int size = _viewportList.size();
-    jalview.schemabinding.version2.Viewport[] mArray = new jalview.
-        schemabinding.version2.Viewport[size];
-    for (int index = 0; index < size; index++)
-    {
-      mArray[index] = (jalview.schemabinding.version2.Viewport) _viewportList.
-          elementAt(index);
-    }
-    return mArray;
-  } //-- jalview.schemabinding.version2.Viewport[] getViewport()
+    jalview.schemabinding.version2.Viewport[] array = new jalview.schemabinding.version2.Viewport[0];
+    return (jalview.schemabinding.version2.Viewport[]) this._viewportList
+            .toArray(array);
+  }
 
   /**
-   * Method getViewportCount
-   *
-   *
-   *
-   * @return int
+   * Method getViewportCount.
+   * 
+   * @return the size of this collection
    */
   public int getViewportCount()
   {
-    return _viewportList.size();
-  } //-- int getViewportCount()
+    return this._viewportList.size();
+  }
 
   /**
-   * Method isValid
-   *
-   *
-   *
-   * @return boolean
+   * 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)
+    } catch (org.exolab.castor.xml.ValidationException vex)
     {
       return false;
     }
     return true;
-  } //-- boolean isValid()
+  }
 
   /**
-   * Method marshal
-   *
-   *
-   *
+   * 
+   * 
    * @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(java.io.Writer out)
-      throws org.exolab.castor.xml.MarshalException,
-      org.exolab.castor.xml.ValidationException
+  public void marshal(final 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
+   * @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);
-  } //-- void marshal(org.xml.sax.ContentHandler)
+  }
 
   /**
-   * Method removeAllJGroup
-   *
    */
   public void removeAllJGroup()
   {
-    _JGroupList.removeAllElements();
-  } //-- void removeAllJGroup()
+    this._JGroupList.clear();
+  }
 
   /**
-   * Method removeAllJSeq
-   *
    */
   public void removeAllJSeq()
   {
-    _JSeqList.removeAllElements();
-  } //-- void removeAllJSeq()
+    this._JSeqList.clear();
+  }
 
   /**
-   * Method removeAllTree
-   *
    */
   public void removeAllTree()
   {
-    _treeList.removeAllElements();
-  } //-- void removeAllTree()
+    this._treeList.clear();
+  }
 
   /**
-   * Method removeAllUserColours
-   *
    */
   public void removeAllUserColours()
   {
-    _userColoursList.removeAllElements();
-  } //-- void removeAllUserColours()
+    this._userColoursList.clear();
+  }
 
   /**
-   * Method removeAllViewport
-   *
    */
   public void removeAllViewport()
   {
-    _viewportList.removeAllElements();
-  } //-- void removeAllViewport()
+    this._viewportList.clear();
+  }
 
   /**
-   * Method removeJGroup
-   *
-   *
-   *
+   * Method removeJGroup.
+   * 
+   * @param vJGroup
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeJGroup(
+          final jalview.schemabinding.version2.JGroup vJGroup)
+  {
+    boolean removed = _JGroupList.remove(vJGroup);
+    return removed;
+  }
+
+  /**
+   * Method removeJGroupAt.
+   * 
    * @param index
-   * @return JGroup
+   * @return the element removed from the collection
    */
-  public jalview.schemabinding.version2.JGroup removeJGroup(int index)
+  public jalview.schemabinding.version2.JGroup removeJGroupAt(
+          final int index)
   {
-    java.lang.Object obj = _JGroupList.elementAt(index);
-    _JGroupList.removeElementAt(index);
+    java.lang.Object obj = this._JGroupList.remove(index);
     return (jalview.schemabinding.version2.JGroup) obj;
-  } //-- jalview.schemabinding.version2.JGroup removeJGroup(int)
+  }
 
   /**
-   * Method removeJSeq
-   *
-   *
-   *
+   * Method removeJSeq.
+   * 
+   * @param vJSeq
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeJSeq(final jalview.schemabinding.version2.JSeq vJSeq)
+  {
+    boolean removed = _JSeqList.remove(vJSeq);
+    return removed;
+  }
+
+  /**
+   * Method removeJSeqAt.
+   * 
    * @param index
-   * @return JSeq
+   * @return the element removed from the collection
    */
-  public jalview.schemabinding.version2.JSeq removeJSeq(int index)
+  public jalview.schemabinding.version2.JSeq removeJSeqAt(final int index)
   {
-    java.lang.Object obj = _JSeqList.elementAt(index);
-    _JSeqList.removeElementAt(index);
+    java.lang.Object obj = this._JSeqList.remove(index);
     return (jalview.schemabinding.version2.JSeq) obj;
-  } //-- jalview.schemabinding.version2.JSeq removeJSeq(int)
+  }
+
+  /**
+   * Method removeTree.
+   * 
+   * @param vTree
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeTree(final jalview.schemabinding.version2.Tree vTree)
+  {
+    boolean removed = _treeList.remove(vTree);
+    return removed;
+  }
 
   /**
-   * Method removeTree
-   *
-   *
-   *
+   * Method removeTreeAt.
+   * 
    * @param index
-   * @return Tree
+   * @return the element removed from the collection
    */
-  public jalview.schemabinding.version2.Tree removeTree(int index)
+  public jalview.schemabinding.version2.Tree removeTreeAt(final int index)
   {
-    java.lang.Object obj = _treeList.elementAt(index);
-    _treeList.removeElementAt(index);
+    java.lang.Object obj = this._treeList.remove(index);
     return (jalview.schemabinding.version2.Tree) obj;
-  } //-- jalview.schemabinding.version2.Tree removeTree(int)
+  }
 
   /**
-   * Method removeUserColours
-   *
-   *
-   *
+   * Method removeUserColours.
+   * 
+   * @param vUserColours
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeUserColours(
+          final jalview.schemabinding.version2.UserColours vUserColours)
+  {
+    boolean removed = _userColoursList.remove(vUserColours);
+    return removed;
+  }
+
+  /**
+   * Method removeUserColoursAt.
+   * 
    * @param index
-   * @return UserColours
+   * @return the element removed from the collection
    */
-  public jalview.schemabinding.version2.UserColours removeUserColours(int index)
+  public jalview.schemabinding.version2.UserColours removeUserColoursAt(
+          final int index)
   {
-    java.lang.Object obj = _userColoursList.elementAt(index);
-    _userColoursList.removeElementAt(index);
+    java.lang.Object obj = this._userColoursList.remove(index);
     return (jalview.schemabinding.version2.UserColours) obj;
-  } //-- jalview.schemabinding.version2.UserColours removeUserColours(int)
+  }
 
   /**
-   * Method removeViewport
-   *
-   *
-   *
+   * Method removeViewport.
+   * 
+   * @param vViewport
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeViewport(
+          final jalview.schemabinding.version2.Viewport vViewport)
+  {
+    boolean removed = _viewportList.remove(vViewport);
+    return removed;
+  }
+
+  /**
+   * Method removeViewportAt.
+   * 
    * @param index
-   * @return Viewport
+   * @return the element removed from the collection
    */
-  public jalview.schemabinding.version2.Viewport removeViewport(int index)
+  public jalview.schemabinding.version2.Viewport removeViewportAt(
+          final int index)
   {
-    java.lang.Object obj = _viewportList.elementAt(index);
-    _viewportList.removeElementAt(index);
+    java.lang.Object obj = this._viewportList.remove(index);
     return (jalview.schemabinding.version2.Viewport) obj;
-  } //-- jalview.schemabinding.version2.Viewport removeViewport(int)
+  }
 
   /**
    * Sets the value of field 'featureSettings'.
-   *
-   * @param featureSettings the value of field 'featureSettings'.
+   * 
+   * @param featureSettings
+   *                the value of field 'featureSettings'.
    */
-  public void setFeatureSettings(jalview.schemabinding.version2.FeatureSettings
-                                 featureSettings)
+  public void setFeatureSettings(
+          final jalview.schemabinding.version2.FeatureSettings featureSettings)
   {
     this._featureSettings = featureSettings;
-  } //-- void setFeatureSettings(jalview.schemabinding.version2.FeatureSettings)
+  }
 
   /**
-   * Method setJGroup
-   *
-   *
-   *
+   * 
+   * 
    * @param index
    * @param vJGroup
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
    */
-  public void setJGroup(int index,
-                        jalview.schemabinding.version2.JGroup vJGroup)
-      throws java.lang.IndexOutOfBoundsException
+  public void setJGroup(final int index,
+          final jalview.schemabinding.version2.JGroup vJGroup)
+          throws java.lang.IndexOutOfBoundsException
   {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _JGroupList.size()))
+    // check bounds for index
+    if (index < 0 || index >= this._JGroupList.size())
     {
-      throw new IndexOutOfBoundsException();
+      throw new IndexOutOfBoundsException("setJGroup: Index value '"
+              + index + "' not in range [0.."
+              + (this._JGroupList.size() - 1) + "]");
     }
-    _JGroupList.setElementAt(vJGroup, index);
-  } //-- void setJGroup(int, jalview.schemabinding.version2.JGroup)
+
+    this._JGroupList.set(index, vJGroup);
+  }
 
   /**
-   * Method setJGroup
-   *
-   *
-   *
-   * @param JGroupArray
+   * 
+   * 
+   * @param vJGroupArray
    */
-  public void setJGroup(jalview.schemabinding.version2.JGroup[] JGroupArray)
+  public void setJGroup(
+          final jalview.schemabinding.version2.JGroup[] vJGroupArray)
   {
-    //-- copy array
-    _JGroupList.removeAllElements();
-    for (int i = 0; i < JGroupArray.length; i++)
+    // -- copy array
+    _JGroupList.clear();
+
+    for (int i = 0; i < vJGroupArray.length; i++)
     {
-      _JGroupList.addElement(JGroupArray[i]);
+      this._JGroupList.add(vJGroupArray[i]);
     }
-  } //-- void setJGroup(jalview.schemabinding.version2.JGroup)
+  }
 
   /**
-   * Method setJSeq
-   *
-   *
-   *
+   * 
+   * 
    * @param index
    * @param vJSeq
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
    */
-  public void setJSeq(int index, jalview.schemabinding.version2.JSeq vJSeq)
-      throws java.lang.IndexOutOfBoundsException
+  public void setJSeq(final int index,
+          final jalview.schemabinding.version2.JSeq vJSeq)
+          throws java.lang.IndexOutOfBoundsException
   {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _JSeqList.size()))
+    // check bounds for index
+    if (index < 0 || index >= this._JSeqList.size())
     {
-      throw new IndexOutOfBoundsException();
+      throw new IndexOutOfBoundsException("setJSeq: Index value '" + index
+              + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
     }
-    _JSeqList.setElementAt(vJSeq, index);
-  } //-- void setJSeq(int, jalview.schemabinding.version2.JSeq)
+
+    this._JSeqList.set(index, vJSeq);
+  }
 
   /**
-   * Method setJSeq
-   *
-   *
-   *
-   * @param JSeqArray
+   * 
+   * 
+   * @param vJSeqArray
    */
-  public void setJSeq(jalview.schemabinding.version2.JSeq[] JSeqArray)
+  public void setJSeq(final jalview.schemabinding.version2.JSeq[] vJSeqArray)
   {
-    //-- copy array
-    _JSeqList.removeAllElements();
-    for (int i = 0; i < JSeqArray.length; i++)
+    // -- copy array
+    _JSeqList.clear();
+
+    for (int i = 0; i < vJSeqArray.length; i++)
     {
-      _JSeqList.addElement(JSeqArray[i]);
+      this._JSeqList.add(vJSeqArray[i]);
     }
-  } //-- void setJSeq(jalview.schemabinding.version2.JSeq)
+  }
 
   /**
-   * Method setTree
-   *
-   *
-   *
+   * 
+   * 
    * @param index
    * @param vTree
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
    */
-  public void setTree(int index, jalview.schemabinding.version2.Tree vTree)
-      throws java.lang.IndexOutOfBoundsException
+  public void setTree(final int index,
+          final jalview.schemabinding.version2.Tree vTree)
+          throws java.lang.IndexOutOfBoundsException
   {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _treeList.size()))
+    // check bounds for index
+    if (index < 0 || index >= this._treeList.size())
     {
-      throw new IndexOutOfBoundsException();
+      throw new IndexOutOfBoundsException("setTree: Index value '" + index
+              + "' not in range [0.." + (this._treeList.size() - 1) + "]");
     }
-    _treeList.setElementAt(vTree, index);
-  } //-- void setTree(int, jalview.schemabinding.version2.Tree)
+
+    this._treeList.set(index, vTree);
+  }
 
   /**
-   * Method setTree
-   *
-   *
-   *
-   * @param treeArray
+   * 
+   * 
+   * @param vTreeArray
    */
-  public void setTree(jalview.schemabinding.version2.Tree[] treeArray)
+  public void setTree(final jalview.schemabinding.version2.Tree[] vTreeArray)
   {
-    //-- copy array
-    _treeList.removeAllElements();
-    for (int i = 0; i < treeArray.length; i++)
+    // -- copy array
+    _treeList.clear();
+
+    for (int i = 0; i < vTreeArray.length; i++)
     {
-      _treeList.addElement(treeArray[i]);
+      this._treeList.add(vTreeArray[i]);
     }
-  } //-- void setTree(jalview.schemabinding.version2.Tree)
+  }
 
   /**
-   * Method setUserColours
-   *
-   *
-   *
+   * 
+   * 
    * @param index
    * @param vUserColours
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
    */
-  public void setUserColours(int index,
-                             jalview.schemabinding.version2.UserColours
-                             vUserColours)
-      throws java.lang.IndexOutOfBoundsException
+  public void setUserColours(final int index,
+          final jalview.schemabinding.version2.UserColours vUserColours)
+          throws java.lang.IndexOutOfBoundsException
   {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _userColoursList.size()))
+    // check bounds for index
+    if (index < 0 || index >= this._userColoursList.size())
     {
-      throw new IndexOutOfBoundsException();
+      throw new IndexOutOfBoundsException("setUserColours: Index value '"
+              + index + "' not in range [0.."
+              + (this._userColoursList.size() - 1) + "]");
     }
-    _userColoursList.setElementAt(vUserColours, index);
-  } //-- void setUserColours(int, jalview.schemabinding.version2.UserColours)
+
+    this._userColoursList.set(index, vUserColours);
+  }
 
   /**
-   * Method setUserColours
-   *
-   *
-   *
-   * @param userColoursArray
+   * 
+   * 
+   * @param vUserColoursArray
    */
-  public void setUserColours(jalview.schemabinding.version2.UserColours[]
-                             userColoursArray)
+  public void setUserColours(
+          final jalview.schemabinding.version2.UserColours[] vUserColoursArray)
   {
-    //-- copy array
-    _userColoursList.removeAllElements();
-    for (int i = 0; i < userColoursArray.length; i++)
+    // -- copy array
+    _userColoursList.clear();
+
+    for (int i = 0; i < vUserColoursArray.length; i++)
     {
-      _userColoursList.addElement(userColoursArray[i]);
+      this._userColoursList.add(vUserColoursArray[i]);
     }
-  } //-- void setUserColours(jalview.schemabinding.version2.UserColours)
+  }
 
   /**
-   * Method setViewport
-   *
-   *
-   *
+   * 
+   * 
    * @param index
    * @param vViewport
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
    */
-  public void setViewport(int index,
-                          jalview.schemabinding.version2.Viewport vViewport)
-      throws java.lang.IndexOutOfBoundsException
+  public void setViewport(final int index,
+          final jalview.schemabinding.version2.Viewport vViewport)
+          throws java.lang.IndexOutOfBoundsException
   {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _viewportList.size()))
+    // check bounds for index
+    if (index < 0 || index >= this._viewportList.size())
     {
-      throw new IndexOutOfBoundsException();
+      throw new IndexOutOfBoundsException("setViewport: Index value '"
+              + index + "' not in range [0.."
+              + (this._viewportList.size() - 1) + "]");
     }
-    _viewportList.setElementAt(vViewport, index);
-  } //-- void setViewport(int, jalview.schemabinding.version2.Viewport)
+
+    this._viewportList.set(index, vViewport);
+  }
 
   /**
-   * Method setViewport
-   *
-   *
-   *
-   * @param viewportArray
+   * 
+   * 
+   * @param vViewportArray
    */
-  public void setViewport(jalview.schemabinding.version2.Viewport[]
-                          viewportArray)
+  public void setViewport(
+          final jalview.schemabinding.version2.Viewport[] vViewportArray)
   {
-    //-- copy array
-    _viewportList.removeAllElements();
-    for (int i = 0; i < viewportArray.length; i++)
+    // -- copy array
+    _viewportList.clear();
+
+    for (int i = 0; i < vViewportArray.length; i++)
     {
-      _viewportList.addElement(viewportArray[i]);
+      this._viewportList.add(vViewportArray[i]);
     }
-  } //-- void setViewport(jalview.schemabinding.version2.Viewport)
+  }
 
   /**
-   * Method unmarshal
-   *
-   *
-   *
+   * Method unmarshal.
+   * 
    * @param reader
-   * @return Object
-   */
-  public static java.lang.Object unmarshal(java.io.Reader reader)
-      throws org.exolab.castor.xml.MarshalException,
-      org.exolab.castor.xml.ValidationException
-  {
-    return (jalview.schemabinding.version2.JalviewModelSequence) Unmarshaller.
-        unmarshal(jalview.schemabinding.version2.JalviewModelSequence.class,
-                  reader);
-  } //-- java.lang.Object 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();
+   * @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 jalview.schemabinding.version2.JalviewModelSequence
+   */
+  public static jalview.schemabinding.version2.JalviewModelSequence unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.JalviewModelSequence) Unmarshaller
+            .unmarshal(
+                    jalview.schemabinding.version2.JalviewModelSequence.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);
-  } //-- void validate()
+  }
 
 }